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Structural Basis of Lipid Targeting and Destruction by the Type V Secretion System of Pseudomonas aeruginosa
Abstract
The type V secretion system (T5SS) is a macromolecular machine employed by a number of bacteria to secrete virulence factors into the environment. The human pathogen Pseudomonas aeruginosa employs the newly described type Vd secretion system to secrete a soluble variant of PlpD, a lipase of the patatin-like family synthesized as a single macromolecule that also carries a POTRA domain and a 16-stranded β-barrel. Here we report the crystal structure of the secreted form of PlpD in its biologically active state. PlpD displays a classical lipase α/β hydrolase fold with a catalytic site located within a highly hydrophobic channel that entraps a lipidic molecule. The active site is covered by a flexible lid, as in other lipases, indicating that this region in PlpD must modify its conformation in order for catalysis at the water-lipid interface to occur. PlpD displays phospholipase A1 activity and is able to recognize a number of phosphatidylinositols and other phosphatidyl analogs. PlpD is the first example of an active phospholipase secreted through the T5SS, for which there are more than 200 homologs, revealing details of the lipid destruction arsenal expressed by Pseudomonas aeruginosa in order to establish infection.
... The construction of all T5SS subtypes that we familiar with, were distinguished by the three-dimensional structure of AT, including passenger-protein in T5SS precursor polypeptides and the mutual organization of these domains (Dautin, 2021). The structure of T5SS has been thoroughly studied with obtaining relevant data except for the translocation domain of Vd and Vf (Oomen et al., 2004;da Mata Madeira et al., 2016;Hage et al., 2015). All subtypes share a common domain, which mainly includes three parts (Jose et al., 1995;Henderson et al., 1998: (1) Signal peptide sequence: Proteins can be targeted to the inner membrane of the bacteria to deliver them to cyto-periplasm. ...
... Some AT passenger domains in type Va, such as EstA (Brzuszkiewicz et al., 2009). have α/β hydrolase folding structures, which are similar to type Vd (da Mata Madeira et al., 2016;Emsley et al., 1996). Therefore, type Vd is equal to the heterozygotes of Va and Ve subtypes, PlpD in Pseudomonas aeruginosa and FplA in Fusobacterium are quintessential examples (Salacha et al., 2010;Casasanta et al., 2017). ...
... AT can participate in the pathogenic activities of bacteria through the functions of lipase esterase protease and other enzymes (da Mata Madeira et al., 2016;Casasanta et al., 2017;Ocampo et al., 2021). The representative AT EstA with lipase domain plays multiple roles in the pathogenic process of bacteria, primarily involving in the formation of bacterial biofilm (Davey et al., 2003;Tielen et al., 2010), motility of bacteria (Wilhelm et al., 2007) and lipid hydrolysis of bacteria (Carinato et al. 1998), as well as cell signal transduction (Riedel et al., 2003). ...
... The passenger and translocator can be part of the same polypeptide chain or produced as two separate proteins (T5bSS). The translocator was initially thought to be the only protein [17,21,24] are represented as pale green cylinders, while BamA-like β-barrels (16-stranded) [19,22] are colored dark green. Hops (Helicobacter outer membrane proteins) β-barrel (predicted to be 8stranded) is colored cyan [32]. ...
... This ensures that proteins are delivered to the correct translocon and kept in the appropriate conformation for export. Indeed, whereas the TAT [17,21,24] are represented as pale green cylinders, while BamA-like β-barrels (16stranded) [19,22] are colored dark green. Hops (Helicobacter outer membrane proteins) β-barrel (predicted to be 8-stranded) is colored cyan [32]. ...
... Passenger domains adopting β-rich conformations are depicted as red cylinders for β-helices [16,18], red cubes for β-prisms/β-rolls [20,29], and red ovals for immunoglobulin-like domains [23,28]. Passenger domains adopting α-helical conformation are purple [22,25]. The N and C-termini of each domains are indicated. ...
The type 5 secretion system (T5SS) is one of the more widespread secretion systems in Gram-negative bacteria. Proteins secreted by the T5SS are functionally diverse (toxins, adhesins, enzymes) and include numerous virulence factors. Mechanistically, the T5SS has long been considered the simplest of secretion systems, due to the paucity of proteins required for its functioning. Still, despite more than two decades of study, the exact process by which T5SS substrates attain their final destination and correct conformation is not totally deciphered. Moreover, the recent addition of new sub-families to the T5SS raises additional questions about this secretion mechanism. Central to the understanding of type 5 secretion is the question of protein folding, which needs to be carefully controlled in each of the bacterial cell compartments these proteins cross. Here, the biogenesis of proteins secreted by the Type 5 secretion system is discussed, with a focus on the various factors preventing or promoting protein folding during biogenesis.
... The Mtb genome contains a PLP that has been described based on the occurrence of four conserved sequence blocks, which is a hallmark of the α/β hydrolase-fold family (Kuhle and Flieger, 2014). We study here the rv3091 gene of Mtb H37Rv, which has been previously described as a putative patatin-like protein superfamily gene in National Center for Biotechnology Information (NCBI; Wijeyesakere et al., 2014;Madeira et al., 2016). It was analyzed via bioinformatics and comparative genomics in order to understand the important evolutionary characteristics of Rv3091. ...
... PDB 5fya.1; Madeira et al., 2016). The amino acid homology of Rv3091 and PlpD was 11.91%. ...
... The proteins that share consensus motifs are thought to be essential for patatin-like family of phospholipases (Vanrheenen et al., 2006;Wilson and Knoll, 2018), which include four conserved sequence blocks with four conserved residues, Gly186-Ser214-Gly377-Asp407, in blocks I, II, III, and IV ( Figure 1A). The proteins of this family are known as PLPs (Madeira et al., 2016). Rv3091 consists of a stretch Gly186 proximal to the N-terminus within block I, which includes an oxyanion hole (Gly-Gly-X-Lys/ Arg-Gly) that is a hallmark of PLPs. ...
Patatin-like phospholipases (PLPs) are important virulence factors of many pathogens. However, there are no prevailing studies regarding PLPs as a virulence factor of Mycobacterium tuberculosis (Mtb). Analysis of Rv3091, a putative protein of Mtb, shows that it belongs to the PLPs family. Here, we cloned and expressed the rv3091 gene in Mycobacterium smegmatis and, subsequently, conducted protein purification and characterization. We show that it possesses phospholipase A1, phospholipase A2, and lipase activity. We confirm the putative active site residues, namely, Ser214 and Asp407, using site directed mutagenesis. The Rv3091 is an extracellular protein that alters the colony morphology of M. smegmatis. The presence of Rv3091 enhances the intracellular survival capability of M. smegmatis in murine peritoneal macrophages. Additionally, it promotes M. smegmatis phagosomal escape from macrophages. Moreover, Rv3091 significantly increased the survival of M. smegmatis and aggravated lesions in C57BL/6 J murine lungs in vivo. Taken together, our results indicate that Rv3091 as an extracellular PLP that is critical to the pathogenicity of mycobacterium as it allows mycobacterium to utilize phospholipids for its growth and provides resistance to phagosome killing, resulting in its enhanced intracellular survival.
... However, type Vd ATs have only one POTRA domain, whereas TpsB proteins have two POTRA domains for binding their TpsA substrate for secretion . Whereas type Va ATs have a passenger that typically folds into a β-helical structure, the passenger domains of type Vd ATs, which have been found to harbor lipase activity, adopt an α/β-hydrolase fold (Emsley et al., 1996;Da Mata Madeira et al., 2016). Note though that there are also some type Va ATs with passengers that have an α/β hydrolase fold, e.g., EstA (Brzuszkiewicz et al., 2009). ...
... Note though that there are also some type Va ATs with passengers that have an α/β hydrolase fold, e.g., EstA (Brzuszkiewicz et al., 2009). A key difference between Va and type Vd passengers seems to be that type Va passengers have a multitude of different folds and functionalities, while type Vd passengers characterized so far only function as lipases/esterases (Da Mata Madeira et al., 2016;Casasanta et al., 2017). ...
... It has been proposed that these enzymes aid in niche establishment especially for intracellular bacteria, but also in alteration of host cell signaling by phosphoinositide (PI) cleavage (Casasanta et al., 2017). Though there are some ideas and models for the role that ATs with lipase and esterase function play in virulence, their exact function is not clear, and it is quite possible that AT lipases of different bacteria act on different targets in the host (Da Mata Madeira et al., 2016;Casasanta et al., 2017). ...
Bacteria secrete proteins for different purposes such as communication, virulence functions, adhesion to surfaces, nutrient acquisition, or growth inhibition of competing bacteria. For secretion of proteins, Gram-negative bacteria have evolved different secretion systems, classified as secretion systems I through IX to date. While some of these systems consist of multiple proteins building a complex spanning the cell envelope, the type V secretion system, the subject of this review, is rather minimal. Proteins of the Type V secretion system are often called autotransporters (ATs). In the simplest case, a type V secretion system consists of only one polypeptide chain with a β-barrel translocator domain in the membrane, and an extracellular passenger or effector region. Depending on the exact domain architecture of the protein, type V secretion systems can be further separated into sub-groups termed type Va through e, and possibly another recently identified subtype termed Vf. While this classification works well when it comes to the architecture of the proteins, this is not the case for the function(s) of the secreted passenger. In this review, we will give an overview of the functions of the passengers of the different AT classes, shedding more light on the variety of functions carried out by type V secretion systems.
... The recent biochemical and structural characterization of the type Vd autotransporter PlpD from Pseudomonas aeruginosa revealed a secreted N-terminal patatin-like protein (PFAM: PF01734) with an α-β hydrolase fold containing a catalytic dyad (Ser, Asp) conferring phospholipase A1 activity (EC 3.1. 1.32) through the hydrolysis of glycerophospholipid moieties at the sn -1 position to release a fatty acid 32,33 . In addition, PlpD contains a 16-strand C-terminal β-barrel domain of the bacterial surface antigen family (PFAM: PF01103) for outer membrane anchorage, and a (POTRA) domain potentially involved in protein folding and export of the phospholipase domain to the surface. ...
... We tested FplA for binding to lipids found in human cells and found that it preferentially binds to human phosphoinositides, as was previously seen when characterizing the homologous enzyme PlpD from P. aeruginosa 33 ( Fig. S5 ). Upon incubation with a more diverse and freshly-prepared library of PIs, FplA was found to preferentially bind to PI(4,5)p 2 , and with even stronger affinity to PI(3,5)p 2 , and PI(3,4,5)p 3 lipids ( Fig. 9 ). ...
... The same method was used to search multiple Fusobacterium genomes resulting in the identification of only one protein with this structure in each strain. A PSI-BLAST search using FplA returned a close match to the Pseudomonas aeruginosa protein PlpD, which was previously characterized as a class A1 phospholipase and labeled as the first in a new class of type Vd autotransporters 32,33 . Alignment of FplA proteins from seven strains of Fusobacterium shown in Fig. S4 was performed using Geneious version 9.0.2 60 . ...
Fusobacterium nucleatum is an oral pathogen that is linked to multiple human infections and colorectal cancer. Strikingly, F. nucleatum achieves virulence in the absence of large, multi-protein secretion systems (Type I, II, III, IV, and VI) which are widely used by Gram-negative bacteria for pathogenesis. By contrast, F. nucleatum strains contain genomic expansions of Type V secreted effectors (autotransporters) that are critical for host cell adherence, invasion, and biofilm formation. Here we present the first characterization of a F. nucleatum Type Vd phospholipase class A1 autotransporter (strain ATCC 25586, gene FN1704) that we hereby rename Fusobacterium phospholipase autotransporter (FplA). Biochemical analysis of multiple Fusobacterium strains revealed that FplA is expressed as a full-length 85 kDa outer membrane embedded protein, or as a truncated phospholipase domain that remains associated with the outer membrane. While the role of Type Vd secretion in bacteria remains unidentified, we show that FplA binds with high affinity to host phosphoinositide signaling lipids, revealing a potential role for this enzyme in establishing a F. nucleatum intracellular niche. To further analyze the role of FplA we developed an fplA gene knockout strain, which will guide future in vivo studies to determine its potential role in F. nucleatum pathogenesis. In summary, using recombinant FplA constructs we have identified a biochemical toolbox that includes lipid substrates for enzymatic assays, potent inhibitors, and chemical probes to detect, track, and characterize the role of Type Vd secreted phospholipases in Gram-negative bacteria.
... The type V secretion system (T5SS), also known as the autotransporter system [26], and it is a macromolecular machine secreting mainly virulence factors that target eukaryotic cells and also plays roles in biofilm formation and cellular adherence [26,29]. The T5SS includes auto- [29]. ...
... The type V secretion system (T5SS), also known as the autotransporter system [26], and it is a macromolecular machine secreting mainly virulence factors that target eukaryotic cells and also plays roles in biofilm formation and cellular adherence [26,29]. The T5SS includes auto- [29]. The T5SS also has antibacterial functions to target other bacteria by a contact-dependent growth inhibition (CDI) mechanism [29]. ...
... The T5SS includes auto- [29]. The T5SS also has antibacterial functions to target other bacteria by a contact-dependent growth inhibition (CDI) mechanism [29]. ...
Pseudomonas aeruginosa is an opportunistic pathogen that can cause several acute and chronic infections in humans, and it has become an important cause of nosocomial infections and antibiotic resistance. Biofilm represents an important virulence factor for these bacteria, plays a role in P. aeruginosa infections and avoidance of immune defence mechanisms, and has the ability to protect the bacteria from antibiotics. Alginate, Psl and Pel, three exopolysaccharides, are the main components in biofilm matrix, with many biological functions attributed to them, especially with respect to the protection of the bacterial cell from antibiotics and the immune system. Pseudomonas infections, biofilm formation and development of resistance to antibiotics all require better understanding to achieve the best results using alternative treatment with phage therapy. This review describes the P. aeruginosa pathogenicity and virulence factors with a special focus on the biofilm and its role in infection and resistance to antibiotics and summarizes phage therapy as an alternative approach in treatment of P. aeruginosa infections. Pseudomonas aeruginosa • virulence • phage • biofilm • extracellular polysaccharide • depolymerase • therapy
... Type V secretion system is a common secretion system found in petogenous bacteria and compared to other secretion systems, it is a secretory system whose existence has only recently been understood. As researches on this secretory system have intensified, it has been determined that different autotransports are transported through different subclasses of Type V secretion system (Chauhan et al. 2016, Da Mata Madeira et al. 2016, Chauhan et al. 2019. ...
... However, while Type Vb autotransporter proteins require two PORTRA domains for their functionality, a single PORTRA domain is sufficient for the functionality of Type Vb proteins. In type Vd proteins, the PORTRA is an intrinsic domain (Da Mata Madeira et al., 2016;Casasanta et al., 2017;Leo and Linkle 2018). The inclusion of these proteins, which have characteristic lipase and esterase activities in their passenger domains, in a different subsecretory class is still controversial, due to their high similarity to the Va and Vb-type autotransporters, apart from the minor differences mentioned above (Pokharel, et al. 2020). ...
... In the past decade, the exceptional roles of lipases were confirmed such as in cellular functions, including membrane maintenance, cellular turnover, and inflammatory response generation ( Salacha et al., 2010;Burke and Dennis, 2009). A new family of bacterial lipolytic enzymes, PlpD, has been proposed recently ( Salacha et al., 2010;Banerji and Flieger, 2004;da Mata Madeira et al., 2016). The lipolytic passenger domain of PlpD is cleaved auto-catalytically after completion of auto-transport and could be secreted into the extracellular medium ( Salacha et al., 2010). ...
... These facts assume that the selected sequence could be useful in stimulating strong immune responses against most of the P. aeruginosa strains. Based on a previous investigation, it was confirmed that the full-length heterologous PlpD molecules are produced in E. coli BL21 (DE3) (da Mata Madeira et al., 2016). In P. aeruginosa, lipases, alone or synergistically with other virulence factors, can cause cell death, severe tissue destruction, and necrosis in the human host (Tielen et al., 2013). ...
... Another type of patatin-like acyl hydrolases is present in the genomes of some pathogenic, commensal, and environmental bacteria of the phyla Proteobacteria, Bacteroidetes, Fusobacteria, and Chlorobi. This enzyme type is secreted fused to a transporter 16-stranded -barrel domain that is similar to those of TpsB transporters of type Vb secretion systems (172,173). The archetype of this acyl hydrolases type is PlpD from P. aeruginosa (PDB ID 5FYA), which acts as a PLA 1 on phosphatidylinositols, PS, phosphatidic acid, and phosphatidylglycerol (173), although its role in pathogenesis has not been determined. ...
... This enzyme type is secreted fused to a transporter 16-stranded -barrel domain that is similar to those of TpsB transporters of type Vb secretion systems (172,173). The archetype of this acyl hydrolases type is PlpD from P. aeruginosa (PDB ID 5FYA), which acts as a PLA 1 on phosphatidylinositols, PS, phosphatidic acid, and phosphatidylglycerol (173), although its role in pathogenesis has not been determined. ...
Bacterial sphingomyelinases and phospholipases are a heterogeneous group of esterases which are usually surface associated or secreted by a wide variety of Gram-positive and Gram-negative bacteria. These enzymes hydrolyze sphingomyelin and glycerophospholipids, respectively, generating products identical to the ones produced by eukaryotic enzymes which play crucial roles in distinct physiological processes, including membrane dynamics, cellular signaling, migration, growth, and death. Several bacterial sphingomyelinases and phospholipases are essential for virulence of extracellular, facultative, or obligate intracellular pathogens, as these enzymes contribute to phagosomal escape or phagosomal maturation avoidance, favoring tissue colonization, infection establishment and progression, or immune response evasion. This work presents a classification proposal for bacterial sphingomyelinases and phospholipases that considers not only their enzymatic activities but also their structural aspects. An overview of the main physiopathological activities is provided for each enzyme type, as are examples in which inactivation of a sphingomyelinase- or a phospholipase-encoding gene impairs the virulence of a pathogen. The identification of sphingomyelinases and phospholipases important for bacterial pathogenesis and the development of inhibitors for these enzymes could generate candidate vaccines and therapeutic agents, which will diminish the impacts of the associated human and animal diseases.
... PlpD, whose folding mechanism and structure differ from those of other secreted passenger proteins, is the first active lipase found to be secreted through T5SS. Recombinant PlpD extracted from E. coli showed lipase activity, indicating its ability to recognize and catabolize lipids [51]. The phospholipase A1 autotransporter FplA from Fusobacterium nucleatum was found in 2017 [22]. ...
Bacteria have existed on Earth for billions of years, exhibiting ubiquity and involvement in various biological activities. To ensure survival, bacteria usually release and secrete effector proteins to acquire nutrients and compete with other microorganisms for living space during long-term evolution. Consequently, bacteria have developed a range of secretion systems, which are complex macromolecular transport machines responsible for transporting proteins across the bacterial cell membranes. Among them, one particular secretion system that stands out from the rest is the type V secretion system (T5SS), known as the “autotransporter”. Bacterial activities mediated by T5SS include adherence to host cells or the extracellular matrix, invasion of host cells, immune evasion and serum resistance, contact-dependent growth inhibition, cytotoxicity, intracellular flow, protease activity, autoaggregation, and biofilm formation. In a bacterial body, it is not enough to rely on T5SS alone; in most cases, T5SS cooperates with other secretion systems to carry out bacterial life activities, but regardless of how good the relationship is, there is friction between the secretion systems. T5SS and T1SS/T2SS/T3SS/T6SS all play a synergistic role in the pathogenic processes of bacteria, such as nutrient acquisition, pathogenicity enhancement, and immune modulation, but T5SS indirectly inhibits the function of T4SS. This could be considered a love–hate relationship between secretion systems. This paper uses the systematic literature review methodology to review 117 journal articles published within the period from 1995 to 2024, which are all available from the PubMed, Web of Science, and Scopus databases and aim to elucidate the link between T5SS and other secretion systems, providing clues for future prevention and control of bacterial diseases.
... Phospholipases are also secreted by other bacterial secretion systems [32][33][34] . Four different classes of type VI-secreted lipases, Tle1-4, have been characterised and all share the G-X-S-X-G motif that is also found at the active site of TslA. ...
The type VII protein secretion system (T7SS) is found in many Gram-positive bacteria and in pathogenic mycobacteria. All T7SS substrate proteins described to date share a common helical domain architecture at the N-terminus that typically interacts with other helical partner proteins, forming a composite signal sequence for targeting to the T7SS. The C-terminal domains are functionally diverse and in Gram-positive bacteria such as Staphylococcus aureus often specify toxic anti-bacterial activity. Here we describe the first example of a class of T7 substrate, TslA, that has a reverse domain organisation. TslA is widely found across Bacillota including Staphylococcus, Enterococcus and Listeria. We show that the S. aureus TslA N-terminal domain is a phospholipase A with anti-staphylococcal activity that is neutralised by the immunity lipoprotein TilA. Two small helical partner proteins, TlaA1 and TlaA2 are essential for T7-dependent secretion of TslA and at least one of these interacts with the TslA C-terminal domain to form a helical stack. Cryo-EM analysis of purified TslA complexes indicate that they share structural similarity with canonical T7 substrates. Our findings suggest that the T7SS has the capacity to recognise a secretion signal present at either end of a substrate.
... Another important enzyme produced by P. aeruginosa and secreted by its type V secretion system is PlpD, which displays a phospholipase A 1 activity and has a catalytic domain that is quite similar to ExoU. PlpD is also able to bind mainly to phosphatidylinositol, but also to phosphatidic acid, phosphatidylserine, and phosphatidylglycerol (Da Mata Madeira et al., 2016). Despite the well-described binding of PlpD to phospholipids, the exact role of this enzyme in phospholipids' cleavage is not completely understood. ...
Lipids are a big family of molecules with a vast number of functions in the cell membranes, within the cytoplasm, and extracellularly. Lipid droplets (LDs) are the most common storage organelles and are present in almost every tissue type in the body. They also have structural functions serving as building blocks of cellular membranes and may be precursors of other molecules such as hormones, and lipoproteins, and as messengers in signal transduction. Fatty acids (FAs), such as sterol esters and triacylglycerols, are stored in LDs and are used in β-oxidation as fuel for tricarboxylic acid cycle (TCA) and adenosine triphosphate (ATP) generation. FA uptake and entrance in the cytoplasm are mediated by membrane receptors. After a cytoplasmic round of α- and β-oxidation, FAs are guided into the mitochondrial matrix by the L-carnitine shuttle system, where they are fully metabolized, and enter the TCA cycle. Pathogen infections may lead to impaired lipid metabolism, usage of membrane phospholipids, and LD accumulation in the cytoplasm of infected cells. Otherwise, bacterial pathogens may use lipid metabolism as a carbon source, thus altering the reactions and leading to cellular and organelles malfunctioning. This review aims to describe cellular lipid metabolism and alterations that occur upon infections.
... Similar to SopF, a T3SS1 effector of Salmonella enterica serovar typhimurium which binds to multiple PIs -PI(3)P, PI(3,5)P2 and PI(3,4,5)P3, (Lau et al., 2019) PlpD, a T5SS effector of Pseudomonas aeruginosa which binds to multiple PIs -PI, PI(4)P, PI(4,5)P2 and PI(3,4,5)P3 (da Mata Madeira et al., 2016) and FplA, another T5SS effector of Fusobacterium nucleatum which binds to multiple PIs -PI(3,5)P2, PI(4,5)P2 and PI(3,4,5)P3 (Casasanta et al., 2017) as revealed by protein lipid overlay assays, recombinant PemB also binds to multiple phosphoinositides PI, PI(5)P, PI(3,4,5)P3 and PI(3,5)P2 in vitro with stronger affinity as compared to the other phosphoinositides, delineated by our ITC experiments. On comparative analyses of binding affinities, revealed by different quantitative methods like isothermal titration calorimetry, surface plasmon resonance and biolayer interferometry, among other known effector-phosphoinositide complexes from previous literature reports, we find that SidM, SetA and LtpM, three T4SS effectors of Legionella pneumophila, bind to PI(4)P with K d of 56 nM (ITC), (Del Campo et al., 2014) PI(3)P with K d of 806 nM (SPR) (Jank et al., 2012) and PI(3)P with K d of 591 nM (SPR) (Levanova et al., 2019) respectively and OpiA, a T6SS ii effector of Francisella tularensis binds to PI(3)P with K d of 194 nM (BLI), (Ledvina et al., 2018) implying good agreement with our experimental results. ...
Type Three Secretion System (T3SS) is a sophisticated nano‐scale weapon utilized by several gram negative bacteria under stringent spatio‐temporal regulation to manipulate and evade host immune systems in order to cause infection. To the best of our knowledge, this present study is the first report where we embark upon characterizing inherent features of native type three secretion effector protein PemB through biophysical techniques. Herein, first, we demonstrate binding affinity of PemB for phosphoinositides through isothermal calorimetric titrations. Second, we shed light on its strong homo‐oligomerization propensity in aqueous solution through multiple biophysical methods. Third, we also employ several spectroscopic techniques to delineate its disordered and helical conformation. Lastly, we perform a phylogenetic analysis of this new effector to elucidate evolutionary relationship with other organisms. Taken together, our results shall surely contribute to our existing knowledge of Pseudomonas aeruginosa secretome.
... T5SS has two subtypes: autotransporters (AT) and two-partner secretion (TPS) [50]. P. aeruginosa possesses a type V system that secretes the autotransporter: patatin-like protein: PlpD [26]. PlpD functions as a lipolytic enzyme. ...
The emergence of Pseudomonas aeruginosa as a potential threat in persistent infections can be attributed to the plethora of virulence factors expressed by it. This review discusses the various virulence factors that help this pathogen to establish an infection and regulatory systems controlling these virulence factors. Cell-associated virulence factors such as flagella, type IV pili and non-pilus adhesins have been reviewed. Extracellular virulence factors have also been explained. Quorum-sensing systems present in P. aeruginosa play a cardinal role in regulating the expression of virulence factors. The identification of novel virulence factors in hypervirulent strains indicate that the expression of virulence is dynamic and constantly evolving. An understanding of this is critical for the better clinical management of infections.
... The structure of the putative hydrolase PA2151 was reliably modelled (Fig 4I and S7 Table) with the glycogen-degrading virulence factor SpuA from Streptococcus pneumoniae, which is involved in host-pathogen interactions [56]. The putative extracellular hydrolyse PA1640 was modelled (Fig 4J) with 100% confidence using the structure of type V secreted phospholipase PlpD, which is a putative virulence factor of P. aeruginosa [57,58]. PlpD and the P. aeruginosa type III secretory toxin ExoU [59] belong to the patatin-like family of phospholipases. ...
The efficacy of antibiotics to treat bacterial infections declines rapidly due to antibiotic resistance. This problem has stimulated the development of novel antibiotics, but most attempts have failed. Consequently, the idea of mining uncharacterized genes of pathogens to identify potential targets for entirely new classes of antibiotics was proposed. Without knowing the biochemical function of a protein, it is difficult to validate its potential for drug targeting; therefore, the functional characterization of bacterial proteins of unknown function must be accelerated. Here, we present a paradigm for comprehensively predicting the biochemical functions of a large set of proteins encoded by hypothetical genes in human pathogens to identify candidate drug targets. A high-throughput approach based on homology modelling with ten templates per target protein was applied to the set of 2103 P . aeruginosa proteins encoded by hypothetical genes. The >21000 homology modelling results obtained and available biological and biochemical information about several thousand templates were scrutinized to predict the function of reliably modelled proteins of unknown function. This approach resulted in assigning one or often multiple putative functions to hundreds of enzymes, ligand-binding proteins and transporters. New biochemical functions were predicted for 41 proteins whose essential or virulence-related roles in P . aeruginosa were already experimentally demonstrated. Eleven of them were shortlisted as promising drug targets that participate in essential pathways (maintaining genome and cell wall integrity), virulence-related processes (adhesion, cell motility, host recognition) or antibiotic resistance, which are general drug targets. These proteins are conserved in other WHO priority pathogens but not in humans; therefore, they represent high-potential targets for preclinical studies. These and many more biochemical functions assigned to uncharacterized proteins of P . aeruginosa , made available as PaPUF database, may guide the design of experimental screening of inhibitors, which is a crucial step towards the validation of the highest-potential targets for the development of novel drugs against P . aeruginosa and other high-priority pathogens.
... Yersinia enterocolitica [105]). Dans SST5d on retrouve des protéines comme PlpD de P. aeruginosa [106], [107]. entéropathogéniques [112]. ...
Pseudomonas aeruginosa est une bactérie responsable de sévères infections nosocomiales. Ces infections sont un réel problème pour la santé publique car P. aeruginosa fait partie des pathogènes ESKAPE qui ont développé des facteurs de résistance aux antibiotiques ce qui leur permet d’échapper aux traitements classiques. P. aeruginosa, en plus d’être résistante aux antibiotiques est capable d’exprimer de nombreux facteurs de virulences. Parmi ces facteurs on retrouve les systèmes de sécrétion de type V (SST5) sur lequel j’ai pu travailler durant ma thèse.Une nouvelle souche de P. aeruginosa a été découverte à Grenoble il y a quelques années. Cette souche n’exprime pas les mêmes facteurs de virulence que les souches communément étudiées mais en demeure bien plus toxique. La toxicité de cette souche est due à l’expression de deux protéines ExlB et ExlA faisant partie de la famille du SST5b et ayant un mécanisme d’action complètement nouveau car aucun homologue n’est connu. La toxine ExlA est capable de faire des pores dans les membranes des cellules eucaryotes entrainant leur mort. Le but de ma thèse était donc de comprendre à l’échelle moléculaire le fonctionnement de ExlA.Pour identifier le mécanisme d’action de cette toxine, nous l’avons divisée en deux domaines que nous avons étudiés séparément. En utilisant des techniques de RMN, de SEC-MALLS, de flottaison différentielle, de SAXS et d’AFM, nous avons pu définir que le domaine C-terminal de cette protéine était un « molten globule» en solution et était capable de faire des trous dans les membranes lipidiques reconstituées. Ce domaine semble être le domaine responsable de l’interaction d’ExlA avec les lipides. Ceci additionné à des études menées in vivo sur la toxine ExlA complète et comportant uniquement son domaine N-terminal nous a permis de définir un possible mécanisme d’action de la toxine ExlA. La somme de nos études fait l’objet d’un article en cours d’écriture.
... Notably, the TPS system mainly secretes virulence factors that target eukaryotic cells, but is also important for biofilm formation and cellular adherence [13][14][15]. In addition, the TPS system can also target other bacteria through a CDI (contact-dependent growth inhibition) mechanism where a stalled, partially secreted state ensures that TpsA is only secreted upon contact with the target bacterium, as is the case for the recently reported CdiA toxin from E. coli [16]. ...
Bacteria employ several mechanisms, and most notably secretion systems, to translocate effectors from the cytoplasm to the extracellular environment or the cell surface. Pseudomonas aeruginosa widely employs secretion machineries such as the Type III secretion system (T3SS) to support virulence and cytotoxicity. However, recently identified P. aeruginosa strains that do not express T3SS have been shown to express ExlA, an exolysin translocated through a Two Partner Secretion System (TPS), and are the causative agents of severe lung hemorrhage. Sequence predictions of ExlA indicate filamentous haemagglutinin (FHA-2) domains as the prevalent features, followed by a C-terminal domain with no known homologs. In this work we have addressed the mechanism employed by ExlA to target membrane bilayers by using NMR, small angle X-ray scattering, atomic force microscopy, and cellular infection techniques. We show that the C-terminal domain of ExlA displays a ‘molten globule-like’ fold that punctures small holes into membranes composed of negatively-charged lipids, while other domains could play a lesser role in target recognition. In addition, epithelial cells infected with P. aeruginosa strains expressing different ExlA variants allow localization of the toxin to lipid rafts. ExlA homologs have been identified in numerous bacterial strains, indicating that lipid bilayer destruction is an effective strategy employed by bacteria to establish interactions with multiple hosts.
... Our current computational work on the NTE catalytic domain has shown that a patatin-like protein, PlpD, is a better template than patatin itself for creating a homology model (RJR, unpublished observations). PlpD is a virulence factor with phospholipase A1 activity secreted by Pseudomonas aeroginosa, a bacterium commonly associated with opportunistic and hospital-acquired infections (da Mata Madeira et al., 2016;Foulkes et al., 2019). Similarly, replication of coronaviruses and flaviviruses have been shown to involve manipulation of host phospholipid homeostasis via activation of phospholipase A2 enzymes, and inhibition of these activities compromises viral replication (Liebscher et al., 2018;M€ uller et al., 2018). ...
Systemic inhibition of neuropathy target esterase (NTE) with certain organophosphorus (OP) compounds produces OP compound-induced delayed neurotoxicity (OPIDN), a distal degeneration of axons in the central nervous system (CNS) and peripheral nervous system (PNS), thereby providing a powerful model for studying a spectrum of neurodegenerative diseases. Axonopathies are important medical entities in their own right, but in addition, illnesses once considered primary neuronopathies are now thought to begin with axonal degeneration. These disorders include Alzheimer's disease, Parkinson's disease, and motor neuron diseases such as amyotrophic lateral sclerosis (ALS). Moreover, conditional knockout of NTE in the mouse CNS produces vacuolation and other degenerative changes in large neurons in the hippocampus, thalamus, and cerebellum, along with degeneration and swelling of axons in ascending and descending spinal cord tracts. In humans, NTE mutations cause a variety of neurodegenerative conditions resulting in a range of deficits including spastic paraplegia and blindness. Mutations in the Drosophila NTE orthologue SwissCheese (SWS) produce neurodegeneration characterized by vacuolization that can be partially rescued by expression of wild-type human NTE, suggesting a potential therapeutic approach for certain human neurological disorders. This chapter defines NTE and OPIDN, presents an overview of OP compounds, provides a rationale for NTE research, and traces the history of discovery of NTE and its relationship to OPIDN. It then briefly describes subsequent studies of NTE, including practical applications of the assay; aspects of its domain structure, subcellular localization, and tissue expression; abnormalities associated with NTE mutations, knockdown, and conventional or conditional knockout; and hypothetical models to help guide future research on elucidating the role of NTE in OPIDN.
... Un exemple de SST5d retrouvé chez PA est la protéine PlpD dont le domaine « passager » est libéré dans le milieu extracellulaire . La protéine PlpD présente une activité lipase (Banerji and Flieger, 2004;da Mata Madeira et al., 2016). ...
Pseudomonas aeruginosa (PA) est une bactérie Gram négatif, pathogène opportuniste, impliquée dans un grand nombre d’infections nosocomiales. Cette bactérie est aussi le principal micro-organisme responsable des surinfections broncho-pulmonaires chez les patients atteints de mucoviscidose. Cette prééminence est due en partie à la capacité de PA à former des biofilms, ce qui lui confèrent une résistance exceptionnelle aux antimicrobiens. Au sein de notre laboratoire, une analyse protéomique différentielle a permis de démontrer, en 2004, l’existence d’un protéome spécifique lorsque la bactérie se développe en mode biofilm. Parmi les protéines spécifiquement exprimées en mode biofilm, la protéine hypothétique PA3731 a été plus particulièrement étudiée. Cette protéine est impliquée dans la formation de biofilm, la production de rhamnolipides, la résistance à la tobramycine et la mobilité de type « swarming ». Des recherches bioinformatiques ont montré que le gène pA3731 appartient à un cluster de 4 gènes allant de pA3729 à pA3732 (système BAC), qui pourraient être impliqués dans l’élaboration et/ou la régulation d’un même système protéique. Cette hypothèse a constitué le point de départ de ce travail de thèse. La présente étude a permis de confirmer l’implication du système BAC dans la formation du biofilm, la résistance aux antibiotiques et la production de rhamnolipides chez PA. Les études protéomiques ont mis en évidence l’implication de ce système dans l’expression de la pompe MexEF-OprN, de la porine OprD, et dans la régulation du Quorum Sensing. Des études intéractomiques, menées en parallèle, ont montré une forte interaction entre la protéine PA3731 et PA3732. Ces études ont également permis de valider une forte interaction entre ces protéines et les rhamnolipides. L’ensemble de ces résultats nous permettent d’avancer une hypothèse quant à l’implication du système BAC dans le transport des rhamnolipides vers le milieu extracellulaire.
... PopB and PopD mediate membrane lysis following interaction with the eukaryotic lipids cholesterol and phosphatidylserine [51,52]. ExoU, a phospholipase A2 with affinity for phosphatidylinositol [53,54], is one of several identified phospholipases that may be involved in chronic pulmonary infection and during pathogenesis of the cystic fibrosis lung [55][56][57][58][59][60][61][62]. In addition, phosphatidylcholine is prevalent in the mammalian lung and is targeted by P. aeruginosa during infection [63]. ...
Background
Pseudomonas aeruginosa, a common opportunistic pathogen, is known to cause infections in a variety of compromised human tissues. An emerging mechanism for microbial survival is the incorporation of exogenous fatty acids to alter the cell’s membrane phospholipid profile. With these findings, we show that exogenous fatty acid exposure leads to changes in bacterial membrane phospholipid structure, membrane permeability, virulence phenotypes and consequent stress responses that may influence survival and persistence of Pseudomonas aeruginosa. ResultsThin-layer chromatography and ultra performance liquid chromatography / ESI-mass spectrometry indicated alteration of bacterial phospholipid profiles following growth in the presence of polyunsaturated fatty acids (PUFAs) (ranging in carbon length and unsaturation). The exogenously supplied fatty acids were incorporated into the major bacterial phospholipids phosphatidylethanolamine and phosphatidylglycerol. The incorporation of fatty acids increased membrane permeability as judged by both accumulation and exclusion of ethidium bromide. Individual fatty acids were identified as modifying resistance to the cyclic peptide antibiotics polymyxin B and colistin, but not the beta-lactam imipenem. Biofilm formation was increased by several PUFAs and significant fluctuations in swimming motility were observed. Conclusions
Our results emphasize the relevance and complexity of exogenous fatty acids in the membrane physiology and pathobiology of a medically important pathogen. P. aeruginosa exhibits versatility with regard to utilization of and response to exogenous fatty acids, perhaps revealing potential strategies for prevention and control of infection.
... Le « passenger » de la protéine est un domaine patatine qui est libéré dans le milieu extracellulaire. Ce domaine est doté d'une activité phospholipase envers les phosphatidylinositoles ainsi que d'autres lipides analogues da Mata Madeira et al., 2016). ...
Pseudomonas aeruginosa est un pathogène opportuniste responsable de maladies nosocomiales. Il provoque des infections aiguës ou chroniques en employant conjointement plusieurs facteurs de virulence. Les souches les plus agressives possèdent un système de sécrétion de type III (SST3), injectant des toxines directement dans le cytoplasme des cellules eucaryotes grâce à une nano-aiguille. Récemment, une souche clinique hyper-virulente, appelée CLJ1, a été isolée dans l'unité de soins intensifs de l'hôpital universitaire de Grenoble sur un patient souffrant d'une infection pulmonaire hémorragique. Cette souche ne possède pas les gènes codant pour le SST3 mais sécrète une pore-forming toxin, ExlA, non identifiée auparavant. ExlA est une protéine de 172 kDa, formant des pores de 1,6 nm dans la membrane plasmique de plusieurs types de cellules, à l'exception des érythrocytes. Le pore provoque la rétraction des cellules hôtes et finit par induire la mort de la cellule. Nous avons montré que CLJ1 appartenait à un nouveau clade très divergent des souches classiques de P. aeruginosa, dont les membres possèdent le gène exlA au lieu des gènes codant pour le SST3. Les souches exlA-positives que nous avons collectées dans le monde proviennent d'infections humaines et d'échantillons environnementaux. Leur cytotoxicité, sur diverses cellules humaines et sur un modèle murin d’infection pulmonaire, est corrélée avec les niveaux de sécrétion d'ExlA. En plus de la toxicité membranaire, les souches exlA-positives ont montré des activités protéolytiques élevées envers les VE et E-cadhérines, deux protéines adhésives des jonctions adhérentes requises pour l'intégrité de l'endothélium et de l'épithélium, respectivement. Nous avons démontré que la formation de pores par ExlA dans la membrane eucaryote induisait une entrée massive et rapide de calcium dans le cytosol. Cet afflux de calcium permet la maturation et l'activation d'ADAM10, une protéase eucaryote située à la membrane plasmique. L'activation d’ADAM10 induit le clivage de ses substrats naturels : les VE et E-cadhérines. ExlA fait partie de la même famille de pore forming toxin que ShlA de Serratia marcescens. Nous avons démontré que ShlA utilisait le même mécanisme qu’ExlA pour induire le clivage des cadhérines. En conclusion, les souches bactériennes produisant ExlA ou ShlA détournent un mécanisme naturel de l'hôte pour induire la perte d'intégrité tissulaire.
... Homologs of PlpD are restricted to specific lineages of Proteobacteria, Fusobacteria, Bacteroidetes, and Chlorobi, suggesting that they may have been acquired by horizontal transfer (Salacha et al., 2010). The passenger protein carries the four sequence blocks typical of patatin-like proteins (PLP) (da Mata Madeira et al., 2016) and has lipolytic activity. It is released into the milieu from the precursor by proteolytic cleavage. ...
Initially identified in pathogenic Gram-negative bacteria, the two-partner secretion (TPS) pathway, also known as Type Vb secretion, mediates the translocation across the outer membrane of large effector proteins involved in interactions between these pathogens and their hosts. More recently, distinct TPS systems have been shown to secrete toxic effector domains that participate in inter-bacterial competition or cooperation. The effects of these systems are based on kin vs. non-kin molecular recognition mediated by specific immunity proteins. With these new toxin-antitoxin systems, the range of TPS effector functions has thus been extended from cytolysis, adhesion, and iron acquisition, to genome maintenance, inter-bacterial killing and inter-bacterial signaling. Basically, a TPS system is made up of two proteins, the secreted TpsA effector protein and its TpsB partner transporter, with possible additional factors such as immunity proteins for protection against cognate toxic effectors. Structural studies have indicated that TpsA proteins mainly form elongated β helices that may be followed by specific functional domains. TpsB proteins belong to the Omp85 superfamily. Open questions remain on the mechanism of protein secretion in the absence of ATP or an electrochemical gradient across the outer membrane. The remarkable dynamics of the TpsB transporters and the progressive folding of their TpsA partners at the bacterial surface in the course of translocation are thought to be key elements driving the secretion process.
Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote critical OMP assembly and/or protein translocation reactions. Pseudomonas aeruginosa PlpD is the prototype of an Omp85 protein family that contains an N-terminal patatin-like (PL) domain that is thought to be translocated across the OM by a C-terminal β-barrel domain. Challenging the current dogma, we find that the PlpD PL-domain resides exclusively in the periplasm and, unlike previously studied Omp85 proteins, PlpD forms a homodimer. Remarkably, the PL-domain contains a segment that exhibits unprecedented dynamicity by undergoing transient strand-swapping with the neighboring β-barrel domain. Our results show that the Omp85 superfamily is more structurally diverse than currently believed and suggest that the Omp85 scaffold was utilized during evolution to generate novel functions.
Mycobacterium tuberculosis (Mtb) is a bacterial pathogen that can endure for long periods in an infected patient, without causing disease. There are a number of virulence factors that increase its ability to invade the host. One of these factors is lipolytic enzymes, which play an important role in the pathogenic mechanism of Mtb. Bacterial lipolytic enzymes hydrolyze lipids in host cells, thereby releasing free fatty acids that are used as energy sources and building blocks for the synthesis of cell envelopes, in addition to regulating host immune responses. This review summarizes the relevant recent studies that used in vitro and in vivo models of infection, with particular emphasis on the virulence profile of lipolytic enzymes in Mtb. A better understanding of these enzymes will aid the development of new treatment strategies for TB. The recent work done that explored mycobacterial lipolytic enzymes and their involvement in virulence and pathogenicity was highlighted in this study. Lipolytic enzymes are expected to control Mtb and other intracellular pathogenic bacteria by targeting lipid metabolism. They are also potential candidates for the development of novel therapeutic agents.
Pseudomonas aeruginosa requires a significant breach in the host defense to cause an infection. While its virulence factors are well studied, its tropism cannot be explained only by studying its interaction with the host. Why are P. aeruginosa infections so rare in the intestine compared with the lung and skin? There is not enough evidence to claim specificity in virulence factors deployed by P. aeruginosa in each anatomical site, and host physiology differences between the lung and the intestine cannot easily explain the observed differences in virulence. This perspective highlights a relatively overlooked parameter in P. aeruginosa virulence, namely, potential synergies with bacteria found in the human skin and lung, as well as antagonisms with bacteria of the human intestine.
Despite its genome sequencing more than two decades ago, the majority of the genes of Mycobacterium tuberculosis remain functionally uncharacterized. Patatins are one such class of proteins that, despite undergoing an expansion in this pathogenic species compared to their non-pathogenic cousins, remain largely unstudied. Recent advances in protein structure prediction using machine learning tools such as AlphaFold2 have provided high-confidence predicted structures for all M. tuberculosis proteins. Here we present detailed analyses of the patatin family of M. tuberculosis using AlphaFold-predicted structures, providing insights into likely modes of regulation, membrane interaction and substrate binding. Regulatory domains within this family of proteins include cyclic nucleotide binding, lid-like domains and other helical domains. Using structural homologues, we identified the likely membrane localization mechanisms and substrate-binding sites. These analyses reveal diversity in their regulatory capacity, mechanisms of membrane binding and likely length of fatty acid substrates. Together, this analysis suggests unique roles for the eight predicted patatins of M. tuberculosis .
Many pseudomonads are non‐pathogenic, but P. aeruginosa is an important opportunistic pathogen. Injury, trauma, surgery, burns, or indwelling devices such as intravenous lines or urinary catheters make the host susceptible to P. aeruginosa colonization. Growth and multiplication of Pseudomonas involves genetic regulatory systems upregulating the expression of virulence factors including extracellular products, type‐III secretion system, change to the biofilm mode of growth, all in the presence of intrinsic multidrug resistance conferred by low outer‐membrane permeability and numerous efflux pumps. P. aeruginosa exhibits broad antibiotic resistance, including to commonly used biocides like triclosan. This multifactorial resistance frequently makes infections difficult to manage, and careful selection of therapeutic agent is necessary. Careful surveillance of treatment outcomes is wise, with repeated culture susceptibility testing if the infection is not resolved.
The Omp85 protein superfamily is found in the outer membrane (OM) of all gram-negative bacteria and eukaryotic organelles of bacterial origin. Members of the family catalyze both the membrane insertion of β-barrel proteins and the translocation of proteins across the OM. Although the mechanism(s) by which these proteins function is unclear, striking new insights have emerged from recent biochemical and structural studies. In this review we discuss the entire Omp85 superfamily but focus on the function of the best-studied member, BamA, which is an essential and highly conserved component of the bacterial barrel assembly machinery (BAM). Because BamA has multiple functions that overlap with those of other Omp85 proteins, it is likely the prototypical member of the Omp85 superfamily. Furthermore, BamA has become a protein of great interest because of the recent discovery of small-molecule inhibitors that potentially represent an important new class of antibiotics.
Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Cells steadily adapt their membrane glycerophospholipid (GPL) composition to changing environmental and developmental conditions. While the regulation of membrane homeostasis via GPL synthesis in bacteria has been studied in detail, the mechanisms underlying the controlled degradation of endogenous GPLs remain unknown. Thus far, the function of intracellular phospholipases A (PLAs) in GPL remodeling (Lands cycle) in bacteria is not clearly established. Here, we identified the first cytoplasmic membrane-bound phospholipase A1 (PlaF) from Pseudomonas aeruginosa, which might be involved in the Lands cycle. PlaF is an important virulence factor, as the P. aeruginosa ΔplaF mutant showed strongly attenuated virulence in Galleria mellonella and macrophages. We present a 2.0-Å-resolution crystal structure of PlaF, the first structure that reveals homodimerization of a single-pass transmembrane (TM) full-length protein. PlaF dimerization, mediated solely through the intermolecular interactions of TM and juxtamembrane regions, inhibits its activity. The dimerization site and the catalytic sites are linked by an intricate ligand-mediated interaction network, which might explain the product (fatty acid) feedback inhibition observed with the purified PlaF protein. We used molecular dynamics simulations and configurational free energy computations to suggest a model of PlaF activation through a coupled monomerization and tilting of the monomer in the membrane, which constrains the active site cavity into contact with the GPL substrates. Thus, these data show the importance of the PlaF mediated GPL remodeling pathway for virulence and could pave the way for the development of novel therapeutics targeting PlaF.
PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates have remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free-energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid (FA) products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by FA-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
Microalgae as an alternative renewable resource for biofuel production have captured much significance. Nonetheless, its economic viability is a field of major concern for researchers. Unraveling the lipid catabolic pathway and gaining insights into the sequence-structural features of its primary functioning enzyme, Triacylglycerol lipase, will impart valuable information to target microalgae for augmented lipid content. In the present study, a genome-wide comparative study on putative Triacylglycerol lipase (TAGL) enzyme from algal species belonging to varied phylogenetic lineages was performed. The comprehensive sequence analysis revealed that TAGL comprises of three distinct conserved domains, such as, Patatin, Class III Lipase, and Abhydro_lipase, and also confirmed the ubiquitous presence of GXSXG motif in the sequences analyzed. In the absence of a crystal structure of algal TAGL till date, we developed the first 3D model of patatin domain of TAGL from an oleaginous microalga, Phaedactylum tricornutum, employing homology modeling, docking and molecular dynamic simulations methods. The domain-substrate complex having the low-ranking docking score revealed the binding of palmitic acid to the TAGL patatin domain surface with strong hydrogen bond interactions. The simulation results implied that the substrate-complexed patatin domain and the free enzyme adopted a more stable conformation after 40 ns. This is the first ever attempt to provide in-silico insights into the structural and dynamical insights on catalytic mechanism of the TAGL patatin domain. Subsequently, these findings aided our understanding on their structural stability, folding mechanism and protein-substrate interactions, which could be further utilized to design site-specific mutagenic experiments for engineering microalgal strains.
Communicated by Ramaswamy H. Sarma
PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates has remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by fatty acid-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
Inoculation of selected microbial species into the soils is one of the most effective means of bioremediation of soils polluted by persistent organic pollutants as well as of biocontrol of plant pests. However, this procedure turns out frequently to be ineffective due to the membrane-destructive enzymes secreted to the soil by the autochthonous microorganisms. Especial role play here phospholipases and among them phospholipase A1 (PLA1), Therefore, to explain the interactions of microbial membranes and PLA1 at molecular level and to find the correlation between the composition of the membrane and its resistance to PLA1 action we applied phospholipid Langmuir monolayers as model microbial membranes. As a representative soil extracellular PLA1 we applied Lecitase ultra which is a commercially available hybrid enzyme of PLA1 activity. With the application of specific sn1-ether-sn2-ester phospholipids we proved that Lecitase ultra has solely PLA1 activity; thus, can be applied as an effective model of soil PLA1s. Our studies proved that this enzyme has vast substrate specificity and can hydrolyze structural phospholipids regardless the structure of their polar headgroup. It turned out that the hydrolysis rate was controlled by the condensation of the model membranes. These built of the phospholipids with long saturated fatty acid chains were especially resistant to the action of this enzyme, whereas these formed by the 1-saturated-2-unsaturated-sn-glycero-3-phospholipids were readily degraded. Regarding the polar headgroup we proposed the following row of substrate preference of Lecitase ultra: phosphatidylglycerols > phosphatidylcholines > phosphatidylethanolamines > cardiolipins.
Characterization and inhibition of Pseudomonas aeruginosa Type III Secretion SystemPseudomonas aeruginosa is a Gram-negative opportunistic pathogen that causes nosocomial diseases and infects cystic fibrosis patients. The Type III Secretion System (T3SS) is one of its most important virulence factors, allowing the direct injection of four exotoxins into the target eukaryotic cells. An important protein of T3SS is the conserved ATPase, named PscN that is involved in the assembly and functioning of this system. In this work, we demonstrated the interaction of PscN with T3SS secreted cargo proteins and with their chaperons in complex or alone using ELISA, HTRF and MST assays. Of important, MST (Microscale Thermophoresis) allowed us to determine the dissociation constants (Kd) of these proteins and PscN, showing the interaction preference of this enzyme for the cargo or complex proteins rather than for the corresponding chaperons alone. This confirm the hypothesis that the chaperons are released in the bacterial cytoplasm after the complex dissociation. Otherwise, we assess the Kd between the effector, translocator or needle complexes and PscN bound or not to the gate-keeper complex which is described as a regulator of substrate sorting for the secretion. The results showed that the binding of the gate-keeper to PscN dramatically increases its relative affinity for the needle complex, thus revealing a new role of the gate-keeper in the loading of the needle complex to the ATPase for the control of substrate hierarchical secretion in P. aeruginosa.In parallel, committed to the anti-virulence strategy, we take the opportunity to characterize the ex vivo and in vivo effects of compounds identified by a previous in vitro screening to inhibit the interaction of PscE and PscG. These proteins are the two cognate chaperons of the T3SS needle protein PscF in the bacterial cytoplasm. This interaction had been shown to be a valid anti-virulence target because single or double point mutations introduced within the binding site between PscE and PscG lead to a decrease of P. aeruginosa virulence. This work points out two best leads which belong to the structural hybrid cluster combining hits from two different chemical libraries. The two compounds inhibit the cell damages caused by T3SS positive P. aeruginosa strains, are non-toxic for eukaryotic cell and have minimal effect on bacterial fitness. They were also shown to be specific for T3SS and could protect Galleria mellonnela against P. aeruginosa infection.Key words: Pseudomonas aeruginosa, Type III Secretion System, ATPase, Anti-virulence
The genome of Mycobacterium tuberculosis encode for several hypothetical proteins that needed to be characterized. Rv2037c, a hypothetical protein, was 25 and 4 folds upregulated under acidic and nutritive stress, respectively in M. tuberculosis H37Ra. The protein demonstrated lipolytic activity with pNP-decanoate with optimum pH 8.0 and temperature 40 °C. In addition, the protein demonstrated phospholipase activity. To understand the effect of rv2037c on mycobacterium physiology, the gene was cloned and expressed in M. smegmatis. The protein was found in membrane and extracellular fraction. The expression of rv2037c in M. smegmatis (MS_Rv2037c) altered colony morphology and cell surface features like enhanced biofilm and pellicle formation. MS_Rv2037c decreased cell-wall permeability, enhanced TDM content, resistance against various stresses and antibiotics. MS_Rv2037c demonstrated better infection and intracellular survival capability in infected THP-1 macrophage. Macrophages treated with Rv2037c demonstrated irregular cell membrane. Mice infected with MS_Rv2037c had higher bacterial load in lung, liver and spleen compared to control. Rv2037c induced the production of pro-inflammatory cytokines TNFα and IL12, suggesting its role in immune-modulation. Recombinant protein also generated humoral response in EPTB and MDR-TB patients. The results pointed towards the crucial role of this enzyme in cell-wall modulation, infection and intracellular survival of mycobacterium.
Autotransporters, or type 5 secretion systems, are widespread surface proteins of Gram-negative bacteria often associated with virulence functions. Autotransporters consist of an outer membrane β-barrel domain and an exported passenger. In the poorly studied type 5d subclass, the passenger is a patatin-like lipase. The prototype of this secretion pathway is PlpD of Pseudomonas aeruginosa, an opportunistic human pathogen. The PlpD passenger is a homodimer with phospholipase A1 (PLA1) activity. Based on sequencing data, PlpD-like proteins are present in many bacterial species. We characterized the enzymatic activity, specific lipid binding and oligomeric status of PlpD homologs from Aeromonas hydrophila (a fish pathogen), Burkholderia pseudomallei (a human pathogen) and Ralstonia solanacearum (a plant pathogen) and compared these with PlpD. We demonstrate that recombinant type 5d-secreted patatin domains have lipase activity and form dimers or higher-order oligomers. However, dimerization is not necessary for lipase activity; in fact, by making monomeric variants of PlpD, we show that enzymatic activity slightly increases while protein stability decreases. The lipases from the intracellular pathogens A. hydrophila and B. pseudomallei display PLA2 activity in addition to PLA1 activity. Although the type 5d-secreted lipases from the animal pathogens bound to intracellular lipid targets, phosphatidylserine and phosphatidylinositol phosphates, hydrolysis of these lipids could only be observed for FplA of Fusobacterium nucleatum Yet, we noted a correlation between high lipase activity in type 5d autotransporters and intracellular lifestyle. We hypothesize that type 5d phospholipases are intracellularly active and function in modulation of host cell signaling events.
Type V Secretion in Gram-Negative Bacteria, Page 1 of 2
Abstract
Type V, or “autotransporter,” secretion is an umbrella term that is often used to refer to a group of distinct but conceptually related protein export pathways that are widely distributed in Gram-negative bacteria. Autotransporters are generally single polypeptides that contain a signal peptide that promotes translocation across the inner membrane (IM) via the Sec pathway, an extracellular (“passenger”) domain, and a domain that anchors the protein to the outer membrane (OM). Passenger domains have a wide variety of functions, but they often promote virulence ( 1 ). In the archetypical, or “classical” (type Va), autotransporter pathway, which was discovered in 1987, the passenger domain is located at the N terminus of the protein adjacent to the signal peptide ( 2 ). Although passenger domains range in size from ∼20 to 300 kDa and are highly diverse in sequence ( 3 ), X-ray crystallographic and in silico studies predict that they usually fold into a repetitive structure known as a β helix ( 4 – 8 ) ( Fig. 1 ). The membrane anchor domains are ∼30 kDa and are also highly diverse in sequence but contain short conserved sequence motifs ( 3 , 9 ). Like most membrane-spanning segments associated with OM proteins (OMPs), these domains fold into a closed, amphipathic β sheet or “β barrel” structure. The C-terminal domains that have been crystallized to date all form nearly superimposable 12-stranded β barrels ( 10 – 15 ). The two domains are connected by a short α-helical “linker” that is embedded inside the β barrel domain ( 10 , 12 , 13 , 16 ). Many passenger domains are released from the cell surface by a proteolytic cleavage following their secretion ( 17 ).
Bacterial phospholipases act as intracellular and extracellular enzymes promoting the destruction of phospholipid barriers and inflammation during infections. Identifying enzymes with a common mechanism of activation is an initial step in understanding structural and functional properties. These properties serve as critical information for the design of specific inhibitors to reduce enzymatic activity and ameliorate host cell death. In this study, we identify and verify cytotoxic PLA 2 enzymes from several bacterial pathogens. Similar to the founding member of the group, ExoU, these enzymes share the property of ubiquitin-mediated activation. The identification and validation of potential toxins from multiple bacterial species provide additional proteins from which to derive structural insights that could lead to paninhibitors useful for treating a variety of infections.
The versatile and ubiquitous Pseudomonas aeruginosa is an opportunistic pathogen causing acute and chronic infections in predisposed human subjects. Here we review recent progress in understanding P. aeruginosa population biology and virulence, its cyclic di-GMP-mediated switches of lifestyle, and its interaction with the mammalian host as well as the role of the type III and type VI secretion systems in P. aeruginosa infection.
Most bacteria produce adhesion molecules to facilitate the interaction with host cells and establish successful infections. An important group of bacterial adhesins belong to the autotransporter (AT) superfamily, the largest group of secreted and outer membrane proteins in Gram-negative bacteria. AT adhesins possess diverse functions that facilitate bacterial colonisation, survival and persistence, and as such are often associated with increased bacterial fitness and pathogenic potential. In this review, we will describe AIDA-I type AT adhesins, which comprise the biggest and most diverse group in the AT family. We will focus on Escherichia coli proteins and define general aspects of their biogenesis, distribution, structural properties and key roles in infection. This article is protected by copyright. All rights reserved.
Bacteria have evolved a remarkable array of sophisticated nanomachines to export various virulence factors across the bacterial cell envelope. In recent years, considerable progress has been made towards elucidating the structural and molecular mechanisms of the six secretion systems (types I-VI) of Gram-negative bacteria, the unique mycobacterial type VII secretion system, the chaperone-usher pathway and the curli secretion machinery. These advances have greatly enhanced our understanding of the complex mechanisms that these macromolecular structures use to deliver proteins and DNA into the extracellular environment or into target cells. In this Review, we explore the structural and mechanistic relationships between these single- and double-membrane-embedded systems, and we briefly discuss how this knowledge can be exploited for the development of new antimicrobial strategies.
Bacterial toxins require localization to specific intracellular compartments following injection into host cells. In this study, we examine the membrane targeting of a broad family of bacterial proteins, the patatin-like phospholipases. The best-characterized member of this family is ExoU, an effector of the Pseudomonas aeruginosa type III secretion system. Upon injection into host cells, ExoU localizes to the plasma membrane, where it uses its phospholipase A2 activity to lyse infected cells. The targeting mechanism of ExoU is poorly characterized, but it was recently found to bind to the phospholipid phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a marker for the plasma membrane of eukaryotic cells. We confirmed that the membrane localization domain (MLD) of ExoU had direct affinity for PI(4,5)P2 and determined that this binding was required for ExoU localization. Previously uncharacterized ExoU homologs from Pseudomonas fluorescens and Photorhabdus asymbiotica also localized to the plasma membrane and required PI(4,5)P2 for this localization. A conserved arginine within the MLD was critical for interaction of each protein with PI(4,5)P2 and for localization. Further, we determined the crystal structure of the full-length P. fluorescens ExoU and found that it was similar to that of P. aeruginosa ExoU. Each MLD contains a four-helical bundle, with the conserved arginine exposed at its cap to allow for interaction with the negatively charged PI(4,5)P2. Overall, these findings provide a structural explanation for the targeting of patatin-like phospholipases to the plasma membrane and define the MLD of ExoU as a member of a new class of PI(4,5)P2 binding domains.
Copyright © 2014, The American Society for Biochemistry and Molecular Biology.
Significance
A long-standing question in the field of microbial pathogenesis is how virulence factors are regulated within host cells and how their activity is specifically directed toward a particular host cell compartment. Legionella pneumophila resolves this dilemma by tightly coupling the phospholipase A1 activity of one of its effectors, vacuolar protein sorting inhibitor protein D (VipD), to this protein’s interaction with endosomal host GTPases. We now present the crystal structure of VipD in complex with host cell Rab5c, providing a detailed look into the ingenious molecular mechanisms underlying the allosteric activation of a virulence factor by a host protein and its spatiotemporal regulation. These results open the path for the development of novel therapeutics aimed at blocking the VipD activation process rather than the enzyme’s active site.
Pseudomonas aeruginosa is an opportunistic pathogen that is associated with hospital-acquired infections, ventilator-associated pneumonia, and morbidity of immunocompromised individuals. A subpopulation of P. aeruginosa encodes a protein, ExoU, which exhibits acute cytotoxicity. Toxicity is directly related to the phospholipase A2 activity of the protein after injection into the host cytoplasm via a type III secretion system. ExoU enzymatic activity requires eukaryotic cofactors, ubiquitin or ubiquitin-modified proteins. When administered extracellularly, ExoU is unable to intoxicate epithelial cells in culture, even in the presence of the cofactor. Injection or transfection of ExoU is necessary to observe the acute cytotoxic response. Biochemical approaches indicate that ExoU possesses high affinity to a multifunctional phosphoinositide, phosphatidylinositol 4,5-bisphosphate or PI(4,5)P2 and that it is capable of utilizing this phospholipid as a substrate. In eukaryotic cells, PI(4,5)P2 is mainly located in the cytoplasmic side of the plasma membrane and anchors adaptor proteins that are involved in cytoskeletal structures, focal adhesions, and plasma membranes. Time-lapse fluorescent microscopy analyses of infected live cells demonstrate that ExoU intoxication correlates with intracellular damage in the early phases of infection, such as disruption of focal adhesions, cytoskeletal collapse, actin depolymerization, and cell rounding. At later time points, a membrane blebbing phenotype was prominent prior to the loss of the plasma membrane integrity and barrier function. Membrane blebbing appears to accelerate membrane rupture and the release of intracellular markers. Our data suggest that in eukaryotic host cells, intracellular ExoU targets and hydrolyzes PI(4,5)P2 on the plasma membrane, causing a subsequent disruption of cellular structures and membrane integrity.
Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins.
XDSAPP is a Tcl/Tk‐based graphical user interface for the easy and convenient processing of diffraction data sets using XDS. It provides easy access to all XDS functionalities, automates the data processing and generates graphical plots of various data set statistics provided by XDS. By incorporating additional software, further information on certain features of the data set, such as radiation decay during data collection or the presence of pseudo‐translational symmetry and/or twinning, can be obtained. Intensity files suitable for CCP4, CNS and SHELX are generated.
The two membranes of Gram-negative bacteria contain protein machines that have a general function in their assembly. To interact with the extra-cellular milieu, Gram-negatives target proteins to their cell surface and beyond. Many specialized secretion systems have evolved with dedicated translocation machines that either span the entire cell envelope or localize to the outer membrane. The latter act in concert with inner-membrane transport systems (i.e. Sec or Tat). Secretion via the Type V secretion system follows a two-step mechanism that appears relatively simple. Proteins secreted via this pathway are important for the Gram-negative life-style, either as virulence factors for pathogens or by contributing to the survival of non-invasive environmental species. Furthermore, this system appears well suited for the secretion of biotechnologically relevant proteins. In this review we focus on the biogenesis and application of two Type V subtypes, the autotransporters and two-partner secretion (TPS) systems. For translocation across the outer membrane the autotransporters require the assistance of the Bam complex that also plays a generic role in the assembly of outer membrane proteins. The TPS systems do use a dedicated translocator, but this protein shows resemblance to BamA, the major component of the Bam complex. Interestingly, both the mechanistic and more applied studies on these systems have provided a better understanding of the secretion mechanism and the biogenesis of outer membrane proteins. This article is part of a Special Issue entitled: Protein Trafficking & Secretion.
Monoacylglycerol lipases (MGLs) play an important role in lipid catabolism across all kingdoms of life by catalyzing the release of free fatty acids from monoacylglycerols. The three-dimensional structures of human and a bacterial MGL were determined only recently as the first members of this lipase family. In addition to the α/β-hydrolase core, they showed unexpected structural similarities even in the cap region. Nevertheless, the structural basis for substrate binding and conformational changes of MGLs is poorly understood. Here, we present a comprehensive study of five crystal structures of MGL from Bacillus sp. H257 in its free form and in complex with different substrate analogs and the natural substrate 1-lauroylglycerol. The occurrence of different conformations reveals a high degree of conformational plasticity of the cap region. We identify a specific residue, Ile-145, that might act as a gatekeeper restricting access to the binding site. Site-directed mutagenesis of Ile-145 leads to significantly reduced hydrolase activity. Bacterial MGLs in complex with 1-lauroylglycerol, myristoyl, palmitoyl, and stearoyl substrate analogs enable identification of the binding sites for the alkyl chain and the glycerol moiety of the natural ligand. They also provide snapshots of the hydrolytic reaction of a bacterial MGL at different stages. The alkyl chains are buried in a hydrophobic tunnel in an extended conformation. Binding of the glycerol moiety is mediated via Glu-156 and water molecules. Analysis of the structural features responsible for cap plasticity and the binding modes of the ligands suggests conservation of these features also in human MGL.
Autotransporters are widely distributed among Gram-negative bacteria. They can have a large variety of functions and many of them have a role in virulence. They are synthesized as large precursors with an N-terminal signal sequence that mediates transport across the inner membrane via the Sec machinery and a translocator domain that mediates the transport of the connected passenger domain across the outer membrane to the bacterial cell surface. Like integral outer membrane proteins, the translocator domain folds in a β-barrel structure and requires the Bam machinery for its insertion into the outer membrane. After transport across the outer membrane, the passenger may stay connected via the translocator domain to the bacterial cell surface or it is proteolytically released into the extracellular milieu. Based on the size of the translocator domain and its position relative to the passenger in the precursor, autotransporters are divided into four sub-categories. We review here the current knowledge of the biogenesis, structure and function of various autotransporters.
Author Summary
Legionella pneumophila is a pathogen bacterium that causes Legionnaires' disease accompanied by severe pneumonia. Surprisingly, this pathogen invades and replicates inside macrophages, whose major function is to detect and destroy invading microorganisms. How L. pneumophila can be “immune” to this primary immune cell has been a focus of intensive research. Upon being engulfed by a macrophage cell, L. pneumophila translocates hundreds of bacterial proteins into this host cell. These proteins, called bacterial effectors, are thought to manipulate normal host cellular processes. However, which host molecules and how they are targeted by the bacterial effectors are largely unknown. In this study, we determined the three-dimensional structure of L. pneumophila effector protein VipD, whose function in macrophage was unknown. Ensuing analyses revealed that VipD selectively and tightly binds two host signaling proteins Rab5 and Rab22, which are key regulators of early endosomal vesicle trafficking. These interactions prevent the activated form of Rab5 and Rab22 from binding their downstream signaling proteins, resulting in the blockade of endosomal trafficking in macrophages. The presented work shows that L. pneumophila targets endosomal Rab proteins and delineates the underlying molecular mechanism, providing a new insight into the pathogen's strategies to dysregulate normal intracellular processes.
Disease causing bacteria often manipulate host cells in a way that facilitates the infectious process. Many pathogenic gram-negative bacteria accomplish this by using type III secretion systems. In these complex secretion pathways, bacterial chaperones direct effector proteins to a needle-like secretion apparatus, which then delivers the effector protein into the host cell cytosol. The effector protein ExoU and its chaperone SpcU are components of the Pseudomonas aeruginosa type III secretion system. Secretion of ExoU has been associated with more severe infections in both humans and animal models. Here we describe the 1.92 Å X-ray structure of the ExoU-SpcU complex, a full-length type III effector in complex with its full-length cognate chaperone. Our crystallographic data allow a better understanding of the mechanism by which ExoU kills host cells and provides a foundation for future studies aimed at designing inhibitors of this potent toxin.
The type III secretion system (T3SS) is a complex macromolecular machinery employed by a number of Gram-negative pathogens to inject effectors directly into the cytoplasm of eukaryotic cells. ExoU from the opportunistic pathogen Pseudomonas aeruginosa is one of the most aggressive toxins injected by a T3SS, leading to rapid cell necrosis. Here we report the crystal structure of ExoU in complex with its chaperone, SpcU. ExoU folds into membrane-binding, bridging, and phospholipase domains. SpcU maintains the N-terminus of ExoU in an unfolded state, required for secretion. The phospholipase domain carries an embedded catalytic site whose position within ExoU does not permit direct interaction with the bilayer, which suggests that ExoU must undergo a conformational rearrangement in order to access lipids within the target membrane. The bridging domain connects catalytic domain and membrane-binding domains, the latter of which displays specificity to PI(4,5)P₂. Both transfection experiments and infection of eukaryotic cells with ExoU-secreting bacteria show that ExoU ubiquitination results in its co-localization with endosomal markers. This could reflect an attempt of the infected cell to target ExoU for degradation in order to protect itself from its aggressive cytotoxic action.
Autotransport in Gram-negative bacteria denotes the ability of surface-localized proteins to cross the outer membrane (OM) autonomously. Autotransporters perform this task with the help of a β-barrel transmembrane domain localized in the OM. Different classes of autotransporters have been investigated in detail in recent years; classical monomeric but also trimeric autotransporters comprise many important bacterial virulence factors. So do the two-partner secretion systems, which are a special case as the transported protein resides on a different polypeptide chain than the transporter. Despite the great interest in these proteins, the exact mechanism of the transport process remains elusive. Moreover, different periplasmic and OM factors have been identified that play a role in the translocation, making the term 'autotransport' debatable. In this review, we compile the wealth of details known on the mechanism of single autotransporters from different classes and organisms, and put them into a bigger perspective. We also discuss recently discovered or rediscovered classes of autotransporters.
Phospholipases represent one of the earliest enzyme activities to be identified and studied, and the phospholipase A 2 superfamily traces its roots to the identification of lytic actions of snake venom at the end of the 19th century. Both electrostatic and hydrophobic interactions contribute to the interfacial binding of sPLA 2 to anionic phospholipid membranes. The interaction between basic residues on the binding surface with anionic vesicles plays an important role in interfacial binding. The major functions will be summarized below and include the ability to kill Gram-positive and Gram-negative bacteria, thereby affecting host defense against bacterial infections. sPLA 2 may be involved in the pathogensis of inflammatory bowel disease including Crohn's disease and ulcerative colitis. GIIA sPLA2 protein and mRNA were detected in Paneth cells of the small intestinal mucosa in the intestine in Crohn's disease patients.
Bacteria have developed remarkable systems that sense neighboring target cells upon contact and initiate a series of events that enhance their survival and growth at the expense of the target cells. Four main classes of bacterial cell surface structures have been identified that interact with prokaryotic or eukaryotic target cells to deliver DNA or protein effectors. Type III secretion systems (T3SS) use a flagellum-like tube to deliver protein effectors into eukaryotic host cells, whereas Type IV systems use a pilus-based system to mediate DNA or protein transfer into recipient cells. The contact-dependent growth inhibition system (CDI) is a Type V system, using a long β-helical cell surface protein to contact receptors in target cells and deliver a growth inhibitory signal. Type VI systems utilize a phage-like tube and cell puncturing device to secrete effector proteins into both eukaryotic and prokaryotic target cells.
ExoU is a potent effector protein that causes rapid host cell death upon injection by the type III secretion system of Pseudomonas aeruginosa. The N-terminal half of ExoU contains a patatin-like phospholipase A2 (PLA2) domain that requires the host cell cofactor superoxide dismutase 1 (SOD1) for activation, while the C-terminal 137 amino
acids constitute a membrane localization domain (MLD). Previous studies had utilized insertion and deletion mutations to show
that portions of the MLD are required for membrane localization and catalytic activity. Here we further characterize this
domain by identifying six residues that are essential for ExoU activity. Substitutions at each of these positions resulted
in abrogation of membrane targeting, decreased ExoU-mediated cytotoxicity, and reductions in PLA2 activity. Likewise, each of the six MLD residues was necessary for full virulence in cell culture and murine models of acute
pneumonia. Purified recombinant ExoU proteins with substitutions at five of the six residues were not activated by SOD1, suggesting
that these five residues are critical for activation by this cofactor. Interestingly, these same five ExoU proteins were partially
activated by HeLa cell extracts, suggesting that a host cell cofactor other than SOD1 is capable of modulating the activity
of ExoU. These findings add to our understanding of the role of the MLD in ExoU-mediated virulence.
Classical density-modification techniques (as opposed to statistical approaches) offer a computationally cheap method for improving phase estimates in order to provide a good electron-density map for model building. The rise of statistical methods has lead to a shift in focus away from the classical approaches; as a result, some recent developments have not made their way into classical density-modification software. This paper describes the application of some recent techniques, including most importantly the use of prior phase information in the likelihood estimation of phase errors within a classical density-modification framework. The resulting software gives significantly better results than comparable classical methods, while remaining nearly two orders of magnitude faster than statistical methods.
We discovered a novel secreted protein by Pseudomonas aeruginosa, PlpD, as a member of the bacterial lipolytic enzyme family of patatin-like proteins (PLPs). PlpD is synthesized as a single molecule consisting of a secreted domain fused to a transporter domain. The N-terminus of PlpD includes a classical signal peptide followed by the four PLP conserved blocks that account for its lipase activity. The C-terminus consists of a POTRA (polypeptide transport-associated) motif preceding a putative 16-stranded beta-barrel similar to those of TpsB transporters of Type Vb secretion system. We showed that the C-terminus remains inserted into the outer membrane while the patatin moiety is secreted. The association between a TpsB component and a passenger protein is a unique hybrid organization that we propose to classify as Type Vd. More than 200 PlpD orthologues exist among pathogenic and environmental bacteria, which suggests that bacteria secrete numerous PLPs using this newly defined mechanism.
Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
Porphyromonas gingivalis secretes strong proteases called gingipains that are implicated in periodontal pathogenesis. Protein secretion systems common to other Gram-negative bacteria are lacking in P. gingivalis, but several proteins, including PorT, have been linked to gingipain secretion. Comparative genome analysis and genetic experiments revealed 11 additional proteins involved in gingipain secretion. Six of these (PorK, PorL, PorM, PorN, PorW, and Sov) were similar in sequence to Flavobacterium johnsoniae gliding motility proteins, and two others (PorX and PorY) were putative two-component system regulatory proteins. Real-time RT-PCR analysis revealed that porK, porL, porM, porN, porP, porT, and sov were down-regulated in P. gingivalis porX and porY mutants. Disruption of the F. johnsoniae porT ortholog resulted in defects in motility, chitinase secretion, and translocation of a gliding motility protein, SprB adhesin, to the cell surface, providing a link between a unique protein translocation system and a motility apparatus in members of the Bacteroidetes phylum.
Pseudomonas aeruginosa delivers the toxin ExoU to eukaryotic cells via a type III secretion system. Intoxication with ExoU is associated with lung injury, bacterial dissemination and sepsis in animal model and human infections. To search for ExoU targets in a genetically tractable system, we used controlled expression of the toxin in Saccharomyces cerevisiae. ExoU was cytotoxic for yeast and caused a vacuolar fragmentation phenotype. Inhibitors of human calcium-independent (iPLA(2)) and cytosolic phospholipase A(2) (cPLA(2)) lipase activity reduce the cytotoxicity of ExoU. The catalytic domains of patatin, iPLA(2) and cPLA(2) align or are similar to ExoU sequences. Site-specific mutagenesis of predicted catalytic residues (ExoUS142A or ExoUD344A) eliminated toxicity. ExoU expression in yeast resulted in an accumulation of free palmitic acid, changes in the phospholipid profiles and reduction of radiolabeled neutral lipids. ExoUS142A and ExoUD344A expressed in yeast failed to release palmitic acid. Recombinant ExoU demonstrated lipase activity in vitro, but only in the presence of a yeast extract. From these data we conclude that ExoU is a lipase that requires activation or modification by eukaryotic factors.
A number of clinical isolates of Pseudomonas aeruginosa are cytotoxic to mammalian cells due to the action of the 74-kDa protein ExoU, which is secreted into host cells by the type III secretion system and whose function is unknown. Here we report that the swift and profound cytotoxicity induced by purified ExoU or by an ExoU-expressing strain of P. aeruginosa is blocked by various inhibitors of cytosolic (cPLA2) and Ca2+ -independent (iPLA2) phospholipase A2 enzymes. In contrast, no cytoprotection is offered by inhibitors of secreted phospholipase A2 enzymes or by a number of inhibitors of signal transduction pathways. This suggests that phospholipase A2 inhibitors may represent a novel mode of treatment for acute P. aeruginosa infections. We find that 300-600 molecules of ExoU/cell are required to achieve half-maximal cell killing and that ExoU localizes to the host cell plasma membrane in punctate fashion. We also show that ExoU interacts in vitro with an inhibitor of cPLA2 and iPLA2 enzymes and contains a putative serine-aspartate catalytic dyad homologous to those found in cPLA2 and iPLA2 enzymes. Mutation of either the serine or the aspartate renders ExoU non-cytotoxic. Although no phospholipase or esterase activity is detected in vitro, significant phospholipase activity is detected in vivo, suggesting that ExoU requires one or more host cell factors for activation as a membrane-lytic and cytotoxic phospholipase.
BUSTER-TNT is a maximum-likelihood macromolecular refinement package. BUSTER assembles the structural model, scales observed and calculated structure-factor amplitudes and computes the model likelihood, whilst TNT handles the stereochemistry and NCS restraints/constraints and shifts the atomic coordinates, B factors and occupancies. In real space, in addition to the traditional atomic and bulk-solvent models, BUSTER models the parts of the structure for which an atomic model is not yet available ('missing structure') as low-resolution probability distributions for the random positions of the missing atoms. In reciprocal space, the BUSTER structure-factor distribution in the complex plane is a two-dimensional Gaussian centred around the structure factor calculated from the atomic, bulk-solvent and missing-structure models. The errors associated with these three structural components are added to compute the overall spread of the Gaussian. When the atomic model is very incomplete, modelling of the missing structure and the consistency of the BUSTER statistical model help structure building and completion because (i) the accuracy of the overall scale factors is increased, (ii) the bias affecting atomic model refinement is reduced by accounting for some of the scattering from the missing structure, (iii) the addition of a spatial definition to the source of incompleteness improves on traditional Luzzati and sigmaA-based error models and (iv) the program can perform selective density modification in the regions of unbuilt structure alone.
CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.
Gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. To overcome this barrier, bacteria have developed several systems for protein secretion. The type V secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type Vc or AT-2 family of proteins. Since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the advent of the genomic age, to become the largest group of secreted proteins in gram-negative bacteria. Several of these proteins play essential roles in the pathogenesis of bacterial infections and have been characterized in detail, demonstrating a diverse array of function including the ability to condense host cell actin and to modulate apoptosis. However, most of the autotransporter proteins remain to be characterized. In light of new discoveries and controversies in this research field, this review considers the autotransporter secretion process in the context of the more general field of bacterial protein translocation and exoprotein function.
Bacteria have developed mechanisms to communicate and compete with each other for limited environmental resources. We found that certain Escherichia coli, including uropathogenic strains, contained a bacterial growth-inhibition system that uses direct cell-to-cell contact. Inhibition was conditional, dependent upon the growth state of the inhibitory cell and the pili expression state of the target cell. Both a large cell-surface protein designated Contact-dependent inhibitor A (CdiA) and two-partner secretion family member CdiB were required for growth inhibition. The CdiAB system may function to regulate the growth of specific cells within a differentiated bacterial population.
Phospholipase A (PLA) is one of the few enzymes present in the outer membrane of Gram-negative bacteria, and is likely to be involved in the membrane disruption processes that occur during host cell invasion. Both secreted and membrane-bound phospholipase A(2) activities have been described in bacteria, fungi and protozoa. Recently there have been increasing reports on the involvement of PLA in bacterial invasion and pathogenesis. This review highlights the latest findings on PLA as a virulence factor in Gram-negative bacteria.
We present here the automated structure solution pipeline "autoSHARP." It is built around the heavy-atom refinement and phasing program SHARP, the density modification program SOLOMON, and the ARP/wARP package for automated model building and refinement (using REFMAC). It allows fully automated structure solution, from merged reflection data to an initial model, without any user intervention. We describe and discuss the preparation of the user input, the data flow through the pipeline, and the various results obtained throughout the procedure.
The two-partner secretion (TPS) pathway is a branch of type V secretion. TPS systems are dedicated to the secretion across the outer membrane of long proteins that form extended β-helices. They are composed of a 'TpsA' cargo protein and a 'TpsB' transporter, which belongs to the Omp85 superfamily. This basic design can be supplemented by additional components in some TPS systems. X-ray structures are available for the conserved TPS domain of several TpsA proteins and for one TpsB transporter. However, the molecular mechanisms of two-partner secretion remain to be deciphered, and in particular, the specific role(s) of the TPS domain and the conformational dynamics of the TpsB transporter. Deciphering the TPS pathway may reveal functional features of other transporters of the Omp85 superfamily.
This chapter discusses the maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement (MIR) and multiwavelength anomalous diffraction (MAD). The chapter describes its extension to probability distributions incorporating anomalous diffraction effects, as well as measurement error and nonisomorphism. Integrating these distributions in a whole complex plane leads to likelihood functions that can be used for heavy-atom detection and refinement and for producing phase-probability distributions. The current implementation of this formalism in the computer program statistical heavy-atom refinement and phasing (SHARP) is also described in the chapter. Likelihood functions can be used for the final phasing and calculation of Hendrickson–Lattman coefficients. Numerical tests have been performed for three types of common refinements—namely, single isomorphous replacement, multiple isomorphous replacement with anomalous scattering (MIRAS), and MAD—and the results are summarized in the chapter. A key feature of SHARP is its ability to refine lack-of-isomorphism parameters along with all the others.
On the one-step hydroxylation of benzene to phenol over a Pd membrane reactor, the bifunctional effects between Pd membrane and metal particles were investigated. In this reaction system, the active oxygen species are formed by the reaction with the permeated hydrogen and adsorbed oxygen over Pd membrane. The active oxygen species are reacted with benzene and directly converts into phenol. For improving this system, various active metals were loaded on the α-Al2O3 porous tube which was the substrate of the thin Pd membrane. The loading of noble metals resulted in the enhancement of the activity of side reactions, i.e., complete oxidation and hydrogenation, and a decrease in the hydroxylation activity. The negative effect on hydroxylation was due to the imbalance between the catalytic activities of highly dispersed noble metal particles and the Pd membrane, which has a relatively small surface area. In contrast, the loading of Cu suppressed complete oxidation and enhanced the hydroxylation activity. This effect was mainly due to the increase in the hydrogenation activity without significant acceleration of oxidation. In addition, the potential for the selective conversion of benzene to cyclohexanone by this reactor was discussed.
The lipase from Malassezia globosa (SMG1) was identified to be strictly specific for mono- and diacylglycerol but not triacylglycerol. The crystal structures of SMG1 were solved in the closed conformation, but they failed to provide direct evidence of factors responsible for this unique selectivity. To address this problem, we constructed a structure in the open, active conformation and modeled a diacylglycerol analogue into the active site. Molecular dynamics simulations were performed on this enzyme-analogue complex to relax steric clashes. This bound diacylglycerol analogue unambiguously identified the position of two pockets which accommodated two alkyl chains of substrate. The structure of SMG1-analogue complex revealed that Leu103 and Phe278 divided the catalytic pocket into two separated moieties, an exposed groove and a narrow tunnel. Analysis of the binding model suggested that the unique selectivity of this lipase mainly resulted from the shape and size of this narrow tunnel, in which there was no space for the settlement of the third chain of triacylglycerol. These results expand our understanding on the mechanism underlying substrate selectivity of enzyme, and could pave the way for site-directed mutagenesis experiments to improve the enzyme for application.
Phospholipase activity is important in bacterial pathogenicity and could contribute to the pathogenic role of Helicobacter pylori by degradation of the gastric mucus, and in maintaining long-term colonisation. Our aim was to determine the degree of variation in the phospholipase A gene (pldA) of H. pylori from different geographic locations, and to investigate links between pldA genotype and clinical disease severity, as well as with variation in cagA status and vacA genotypes. PCR-restriction fragment length polymorphism (RFLP) analysis with Mbo I and Hae III was used to study 124 isolates from 10 countries that included the two genome-sequenced strains (26695 and J99), as well as Tx30a and NCTC 11637 (type strain). The 925-bp pldA fragment was amplified with a frequency of 90%. The presence of pldA was confirmed in the other strains using an alternative forward primer. Isolates were distinguished by PCR-RFLP analysis with 10 Mbo I and four Hae III restriction patterns that combined to give 25 distinct pldA RFLP types. The pldA M2H2 strain genotype was most common (20%) in the UK but similar strains came from several other countries. Microdiversity was evident in pldA sequences of strains representing different RFLP types, and five M2H2 strains each had a distinct pldA sequence type. Intragenic variation was independent of gastric disease severity as well as strain cagA status and vacA genotype, with the exception of eight geographically diverse strains all with the pldA M4H3/cagA+/vacA s1m1 genotype predominantly from peptic ulcer patients. The study indicated a spectrum of genotypic variants and was supportive of a pldA function in H. pylori colonisation and persistence rather than in chronicity of infection.
Most lipases contain a lid domain to shield the hydrophobic binding site from the water environment. The lid, mostly in helical form, can undergo a conformational change to expose the active cleft during the interfacial activation. Here we report the crystal structures of Malassezia globosa LIP1 (SMG1) at 1.45 and 2.60 Å resolution in two crystal forms. The structures present SMG1 in its closed form, with a novel lid in loop conformation. SMG1 is one of the few members in the fungal lipase family that has been found to be strictly specific for mono- and diacylglycerol. To date, the mechanism for this substrate specificity remains largely unknown. To investigate the substrate binding properties, we built a model of SMG1 in open conformation. Based on this model, we found that the two bulky hydrophobic residues adjacent to the catalytic site and the N-terminal hinge region of the lid both may act as steric hindrances for triacylglycerols binding. These unique structural features of SMG1 will provide a better understanding on the substrate specificity of mono- and diacylglycerol lipases and a platform for further functional study of this enzyme.
Autotransporters are large proteins produced and secreted by Gram-negative bacteria. They consist of an N-terminal passenger domain, which typically harbours enzymatic activity and exerts a virulence function, and a C-terminal membrane anchor domain. Somehow, the membrane domain facilitates the transport of the passenger domain into the extracellular space. Several autotransporters possess hydrolase passenger domains that belong to the GDSL family of lipolytic enzymes. GDSL autotransporters represent a functionally distinct family and are characterized by several features of their passenger domains; these include 1) the absence of a conserved right-handed parallel β-helix, 2) lipolytic activity, and thus the capability to hydrolyse membranes, and 3) covalent attachment to the respective C-terminal β-domain, with the hydrolase domain exposed to the exterior. The esterase EstA of Pseudomonas aeruginosa is a typical enzyme of this type. Its physiological role was studied, its potential biotechnological application has been demonstrated, and its crystal structure was solved recently. Furthermore, it is capable of displaying different classes of enzymes in a range of Gram-negative bacteria including Escherichia coli, and FACS-based high-throughput screening for enantioselective esterases could be achieved using EstA.
The type III secretion system (T3SS) is employed by a number of Gram-negative bacterial pathogens to inject toxins into eukaryotic cells. The biogenesis of this complex machinery requires the regulated interaction between over 20 cytosolic, periplasmic, and membrane-imbedded proteins, many of which undergo processes such as polymerization, partner recognition, and partial unfolding. Elements of this intricate macromolecular system have been characterized through electron microscopy, crystallography, and NMR techniques, allowing for an initial understanding of the spatiotemporal regulation of T3SS-related events. Here, we report recent advances in the structural characterization of T3SS proteins from a number of bacteria, and provide an overview of recently identified small molecule T3SS inhibitors that could potentially be explored for novel antibacterial development.
A high-resolution structure of a ligand-bound, soluble form of human monoglyceride lipase (MGL) is presented. The structure highlights a novel conformation of the regulatory lid-domain present in the lipase family as well as the binding mode of a pharmaceutically relevant reversible inhibitor. Analysis of the structure lacking the inhibitor indicates that the closed conformation can accommodate the native substrate 2-arachidonoyl glycerol. A model is proposed in which MGL undergoes conformational and electrostatic changes during the catalytic cycle ultimately resulting in its dissociation from the membrane upon completion of the cycle. In addition, the study outlines a successful approach to transform membrane associated proteins, which tend to aggregate upon purification, into a monomeric and soluble form.
The bacterial injectisome is a specialized protein-export system utilized by many pathogenic Gram-negative bacteria for the delivery of virulence proteins into the hosts they infect. This needle-like molecular nanomachine comprises >20 proteins creating a continuous passage from bacterial to host cytoplasm. The last few years have witnessed significant progress in our understanding of the structure of the injectisome with important contributions from X-ray crystallography, NMR and EM. This review will present the current state of the structure of the injectisome with particular focus on the molecular structures of individual components and how these assemble together in a functioning T3SS.
Pathogenic microorganisms have to face hostile environments while colonizing and infecting their hosts. Unfortunately, they can cope with it and have evolved a number of complex secretion systems, which direct virulence factors either at the bacterial cell surface into the environmental extracellular milieu or into the host cell cytosol. Six different classes of secretion systems have been described so far, currently identified as type I secretion system (T1SS) up to type VI secretion system (T6SS). The Gram-negative opportunistic human pathogen Pseudomonas aeruginosa possesses a broad panel of secretion systems. Five of the six secretion machines characterized in Gram-negative bacteria are at P. aeruginosa disposal, sometimes in several copies. All these machines are dedicated to the specific secretion of exoproteins, which display various activities useful for bacterial adaptation to the environment or for bacterial pathogenicity. This review will summarize the functional organization of these different secretion systems, which could constitute potential targets for therapeutic treatment of patients infected by one of the most potent nosocomial pathogens identified nowadays.
We previously identified Legionella pneumophila PlaB as the major cell-associated phospholipase A/lysophospholipase A with contact-dependent hemolytic activity. In this study, we further characterized this protein and found it to be involved in the virulence of L. pneumophila. PlaB was mainly expressed and active during exponential growth. Active PlaB was outer membrane-associated and at least in parts surface-exposed. Transport to the outer membrane was not dependent on the type I (T1SS), II (T2SS), IVB (T4BSS) or Tat secretion pathways. Furthermore, PlaB activity was not dependent on the presence of the macrophage infectivity potentiator (Mip) or the major secreted zinc metalloproteinase A (MspA). Despite the fact that PlaB is not essential for replication in protozoa or macrophage cell lines, we found that plaB mutants were impaired for replication in the lungs and dissemination to the spleen in the guinea pig infection model. Histological sections monitored less inflammation and destruction of the lung tissue after infection with the plaB mutants compared to L. pneumophila wild type. Taken together, PlaB is the first phospholipase A/lysophospholipase A with a confirmed role in the establishment of Legionnaires' disease.
The usage and control of recent modifications of the program package XDS for the processing of rotation images are described in the context of previous versions. New features include automatic determination of spot size and reflecting range and recognition and assignment of crystal symmetry. Moreover, the limitations of earlier package versions on the number of correction/scaling factors and the representation of pixel contents have been removed. Large program parts have been restructured for parallel processing so that the quality and completeness of collected data can be assessed soon after measurement.
The autotransporter (AT) secretion mechanism is the most common mechanism for the secretion of virulence factors across the outer membrane (OM) from pathogenic Gram-negative bacteria. In addition, ATs have attracted biotechnological and biomedical interest for protein display on bacterial cell surfaces. Despite their importance, the mechanism by which passenger domains of ATs pass the OM is still unclear. The classical view is that the beta-barrel domain provides the conduit through which the unfolded passenger moves, with the energy provided by vectorial folding of the beta-strand-rich passenger on the extracellular side of the OM. We present here the first structure of a full-length AT, the esterase EstA from Pseudomonas aeruginosa, at a resolution of 2.5 A. EstA has a relatively narrow, 12-stranded beta-barrel that is covalently attached to the passenger domain via a long, curved helix that occupies the lumen of the beta-barrel. The passenger has a structure that is dramatically different from that of other known passengers, with a globular fold that is dominated by alpha-helices and loops. The arrangement of secondary-structure elements suggests that the passenger can fold sequentially, providing the driving force for passenger translocation. The esterase active-site residues are located at the apical surface of the passenger, at the entrance of a large hydrophobic pocket that contains a bound detergent molecule that likely mimics substrate. The EstA structure provides insight into AT mechanism and will facilitate the design of fusion proteins for cell surface display.
Cytosolic phospholipase A2 initiates the biosynthesis of prostaglandins, leukotrienes, and platelet-activating factor (PAF), mediators of the pathophysiology of asthma and arthritis. Here, we report the X-ray crystal structure of human cPLA2 at 2.5 A. cPLA2 consists of an N-terminal calcium-dependent lipid-binding/C2 domain and a catalytic unit whose topology is distinct from that of other lipases. An unusual Ser-Asp dyad located in a deep cleft at the center of a predominantly hydrophobic funnel selectively cleaves arachidonyl phospholipids. The structure reveals a flexible lid that must move to allow substrate access to the active site, thus explaining the interfacial activation of this important lipase.
A new method for the size-distribution analysis of polymers by sedimentation velocity analytical ultracentrifugation is described. It exploits the ability of Lamm equation modeling to discriminate between the spreading of the sedimentation boundary arising from sample heterogeneity and from diffusion. Finite element solutions of the Lamm equation for a large number of discrete noninteracting species are combined with maximum entropy regularization to represent a continuous size-distribution. As in the program CONTIN, the parameter governing the regularization constraint is adjusted by variance analysis to a predefined confidence level. Estimates of the partial specific volume and the frictional ratio of the macromolecules are used to calculate the diffusion coefficients, resulting in relatively high-resolution sedimentation coefficient distributions c(s) or molar mass distributions c(M). It can be applied to interference optical data that exhibit systematic noise components, and it does not require solution or solvent plateaus to be established. More details on the size-distribution can be obtained than from van Holde-Weischet analysis. The sensitivity to the values of the regularization parameter and to the shape parameters is explored with the help of simulated sedimentation data of discrete and continuous model size distributions, and by applications to experimental data of continuous and discrete protein mixtures.
Patatin is the major protein constituent of potato tubers and displays broad esterase activity. The native enzyme actually belongs to a highly homologous multigene family of vacuolar glycoproteins. From these, the patB2 patatin gene was selected and cloned into pUC19 without its signal sequence but with an N-terminal histidine-tag. This patatin was overexpressed under the control of the lac promotor in Escherichia coli strain DH5α. The protein was recovered as inclusion bodies, folded into its native state by solubilization in urea and purified to homogeneity. Starting with one gram of inclusion bodies, 19 mg of pure and active recombinant patatin was isolated, with even higher specific activity than the glycosylated wild-type patatin purified from potato tubers. The purified enzyme showed esterolytic activity with p-nitrophenylesters dissolved in Triton X-100 micelles. The activity of patatin on p-nitrophenylesters with different carbon chain lengths showed an optimum for p-nitrophenylesters with 10 carbon atoms. Besides general esterolytic activity, the pure enzyme was found to display high phospholipase A activity in particular with the substrates 1,2-dioctanoyl-sn-glycero-3-phosphocholine (diC8PCho) (127 U·mg−1) and 1,2-dinonanoyl-sn-glycero-3-phosphocholine (diC9PCho) (109 U·mg−1).
Recently, the structure of human cytosolic PLA2 (cPLA2) was solved, showing a novel Ser-Asp active site dyad [1]. Based on a partial sequence alignment of patatin with human cPLA2, we propose that patatin contains a similar active site dyad. To verify this assumption, conserved Ser, Asp and His residues in the family of patatins have been modified in patatin B2. Identification of active site residues was based on the observation of correctly folded but inactive variants. This led to the assignment of Ser54 and Asp192 as the active site serine and aspartate residues in patatin B2, respectively.
Phospholipase activity is important in bacterial pathogenicity and could contribute to the pathogenic role of Helicobacter pylori by degradation of the gastric mucus, and in maintaining long-term colonisation. Our aim was to determine the degree of variation in the phospholipase A gene (pldA) of H. pylori from different geographic locations, and to investigate links between pldA genotype and clinical disease severity, as well as with variation in cagA status and vacA genotypes. PCR-restriction fragment length polymorphism (RFLP) analysis with MboI and HaeIII was used to study 124 isolates from 10 countries that included the two genome-sequenced strains (26695 and J99), as well as Tx30a and NCTC 11637 (type strain). The 925-bp pldA fragment was amplified with a frequency of 90%. The presence of pldA was confirmed in the other strains using an alternative forward primer. Isolates were distinguished by PCR-RFLP analysis with 10 MboI and four HaeIII restriction patterns that combined to give 25 distinct pldA RFLP types. The pldA M2H2 strain genotype was most common (20%) in the UK but similar strains came from several other countries. Microdiversity was evident in pldA sequences of strains representing different RFLP types, and five M2H2 strains each had a distinct pldA sequence type. Intragenic variation was independent of gastric disease severity as well as strain cagA status and vacA genotype, with the exception of eight geographically diverse strains all with the pldA M4H3/cagA+/vacA s1m1 genotype predominantly from peptic ulcer patients. The study indicated a spectrum of genotypic variants and was supportive of a pldA function in H. pylori colonisation and persistence rather than in chronicity of infection.
The combination of a large genome encoding metabolic versatility and conserved secreted virulence determinants makes Pseudomonas aeruginosa a model pathogen that can be used to study host-parasite interactions in many eukaryotic hosts. One of the virulence regulons that likely plays a role in the ability of P. aeruginosa to avoid innate immune clearance in mammals is a type III secretion system (TTSS). Upon cellular contact, the P. aeruginosa TTSS is capable of delivering a combination of at least four different effector proteins, exoenzyme S (ExoS), ExoT, ExoU, and ExoY. Two of the four translocated proteins, ExoS and ExoU, are cytotoxic to cells during infection and transfection. The mechanism of cytotoxicity of ExoS is unclear. ExoU, however, has recently been characterized as a member of the phospholipase A family of enzymes, possessing at least phospholipase A2 activity. Similar to ExoS, ExoT and ExoY, ExoU requires either a eukaryotic-specific modification or cofactor for its activity in vitro. The biologic effects of minimal expression of ExoU in yeast can be visualized by membrane damage to different organelles and fragmentation of the vacuole. In mammalian cells, the direct injection of ExoU causes irreversible damage to cellular membranes and rapid necrotic death. ExoU likely represents a unique enzyme and is the first identified phopholipase virulence factor that is translocated into the cytosol by TTSS.
Type III secretion/translocation systems are essential actors in the pathogenicity of Gram-negative bacteria. The injection of bacterial toxins across the host cell plasma membranes is presumably accomplished by a proteinaceous structure, the translocon. In vitro, Pseudomonas aeruginosa translocators PopB and PopD form ringlike structures observed by electron microscopy. We demonstrate here that PopB and PopD are functionally active and sufficient to form pores in lipid vesicles. Furthermore, the two translocators act in synergy to promote membrane permeabilization. The size-based selectivity observed for the passage of solutes indicates that the membrane permeabilization is due to the formation of size-defined pores. Our results provide also new insights into the mechanism of translocon pore formation that may occur during the passage of toxins from the bacterium into the cell. While proteins bind to lipid vesicles equally at any pH, the kinetics of membrane permeabilization accelerate progressively with decreasing pH values. Electrostatic interactions and the presence of anionic lipids were found to be crucial for pore formation whereas cholesterol did not appear to play a significant role in functional translocon formation.
The superfamily of phospholipase A(2) (PLA(2)) enzymes currently consists of 15 Groups and many subgroups and includes five distinct types of enzymes, namely the secreted PLA(2)s (sPLA(2)), the cytosolic PLA(2)s (cPLA(2)), the Ca(2+) independent PLA(2)s (iPLA(2)), the platelet-activating factor acetylhydrolases (PAF-AH), and the lysosomal PLA(2)s. In 1994, we established the systematic Group numbering system for these enzymes. Since then, the PLA(2) superfamily has grown continuously and over the intervening years has required several updates of this Group numbering system. Since our last update, a number of new PLA(2)s have been discovered and are now included. Additionally, tools for the investigation of PLA(2)s and approaches for distinguishing between the different Groups are described.