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| Schematic representation of various functions of Gram-negative bacterial capsular polysaccharide. From clockwise direction: Offering physical barrier to antibiotics, preventing bacterial cell desiccation due to hydrated nature, facilitating the bacteria to adhere onto host cell surface, helping the bacteria to escape from host immune response by inhibiting complement cascade, preventing antibody opsonization, precluding the recognition by macrophage, mimicking host molecules and inhibiting the penetration of cationic antibiotics by binding with it.
Source publication
Bacteria evolving resistance against the action of multiple drugs and its ability to disseminate the multidrug resistance trait(s) across various strains of the same bacteria or different bacterial species impose serious threat to public health. Evolution of such multidrug resistance is due to the fact that, most of the antibiotics target bacterial...
Contexts in source publication
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... being anionic binds these peptides and prevents the cell lysis ( Band and Weiss, 2015). Figure 3 illustrates all the above-discussed mechanisms. ...
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... can be blocked using carbohydrate blockers such as γ-cyclodextrin ( Kong et al., 2013). However, the membrane spanning alpha helical barrel of Wza sequence is highly diverse at the extracellular side even among E. coli strains (Figure 13A). This poses a major challenge in developing a universal drug molecule against Gram- negative bacteria that uses Wzy-dependent CPS exportation pathway, as the residues exposed to extracellular side are crucial in dictating the binding specificity with drug molecules. ...
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... poses a major challenge in developing a universal drug molecule against Gram- negative bacteria that uses Wzy-dependent CPS exportation pathway, as the residues exposed to extracellular side are crucial in dictating the binding specificity with drug molecules. This is true despite the fact that Wza blocker like γ-cyclodextrin can easily fit into the Wza channel: ∼13Å diameter (former) versus 21 Å (latter) (Figures 13B,C). It is possible that chemical modification of γ-cyclodextrin molecule would help to solve the issue, at least to treat pathogenic E. coli. ...
Citations
... Several genes that were shown to be involved in antibiotic resistance in other bacterial species were induced in A153 in response to IAA (Table 1; Tables S1 and S2), including those encoding the OmpC porin (50), the multidrug transporter permeases SanA (51) and MdtB (52), the multidrug transporter MacB (53), a multidrug resistance protein (AWY96_RS15045) (54), capsular polysaccharide (CPS) biosynthesis proteins (55), and a β-lactamase (AWY96_RS20405) (56). To investigate the effect of IAA on antibiotic resistance in A153, we determined the MIC values of various antibiotics that operate with different mechanisms of action, namely, ampicillin, chloramphenicol, gentamicin, kanamycin, nalidixic acid, streptomycin, rifampicin, and tetracycline. ...
The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.
IMPORTANCE
Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.
... The permeation path of the molecule(s) may not always be a single file. One such example is given in Figure 1A, which is a waterconducting [25,26] outer membrane channel of E. coli, Wzi [27]. Besides, this protein channel has multiple entries and exits located at both periplasmic and extracellular sides. ...
Background and Objective
Molecular dynamics (MD) simulations are indispensable and versatile in capturing the time-dependent conformational changes of biomolecules to shed light on the concomitant biological processes. MD is used to provide critical mechanistic insights into the transportation of solvent/solute/drug molecules across protein channels embedded in a membrane bilayer. The huge size and volume of the MD trajectories of a membrane-embedded system provide challenges in the analyses of membrane permeation events. Thus, a software, Molecular Dynamics Trajectory Analysis of Permeation (MDTAP), is presented here to analyze the permeation events across membrane-embedded proteins and nucleic acids automatically.
Methods
A software is developed here to automatically detect the permeation events across the channels irrespective of their shape and size and the type of solute molecules from the MD trajectories. MDTAP employs bash scripts to fetch information about the permeation, residence time, and diffusion of the molecules of interest in a Linux/Mac-based environment. The source code of MDTAP is freely available to the public, along with installation and usage information on GitHub ( attached as supplementary for the review process and will be made accessible to the public through the following link upon acceptance for publication: https://github.com/MBL-lab/MDTAP ).
Results
The efficiency of MDTAP is demonstrated here by considering the MD trajectories of 2 water-conducting channels as test cases: E. coli outer membrane protein Wzi and E. coli Aquaporin Z. The dimensions of the channels and their capacity to accommodate and conduct water, the number of permeating water molecules along with the path traced and time taken to cross the channel is validated.
Conclusion
In summary, the graphical representation of the time-dependent behavior of the solute/solvent permeation events corresponding to an MD trajectory in MDTAP allows the user to easily visualize the mechanism of permeation, including the localization of the permeating molecule (if any) and permeating path. Thus, MDTAP immensely reduces the difficult task of manually analyzing solute/solvent permeations from the bulk MD trajectories. Such a simplistic representation of permeation events across the protein transporters helps in the design of drug molecules to treat the associated diseases. Further, MDTAP is also designed to characterize the permeation events across artificial nucleic acid channels, considering their importance in recent times.
... Within this cluster are a number of genes (wza, wzb, and wzc) that are conserved across a range of genera, including, but not restricted to, E. coli, Vibrio vulnificus, and Klebsiella species (57-59). In this system, newly synthesized CPS is exported through Wza, an outer membrane translocon, aided by Wzc, a tyrosine autokinase, and Wzb, a tyrosine phosphatase, located on the inner membrane (60). Wza exhibits limited specificity for the translocated sugar and can therefore export CPS with significant structural diversity (61), suggesting an explanation for conservation of this system across bacteria producing diverse polysaccharides. ...
The intrinsic resistance of B. pseudomallei to many antibiotics complicates treatment. This opportunistic pathogen possesses a wide range of virulence factors, resulting in severe and potentially fatal disease.
... Since the CPS (or K-antigen) (Campos et al., 2004;Llobet et al., 2008;Sachdeva et al., 2017) and LPS (lipopolysaccharide or O-antigen) (Yethon and Whitfield, 2001;Matsuura, 2013;Zhang et al., 2013;Maldonado et al., 2016) surface antigens of Gramnegative bacteria play vital roles in therapeutic treatment, vaccine development, phage therapy, and understanding host-pathogen interactions, the knowledge about their three-dimensional structures is of major importance. Realization of this aspect has led to several time-to-time reviews on K-and O-antigen structures of Gram-negative bacteria such as E. coli (Stenutz et al., 2006;Liu et al., 2020), Salmonella (Liu et al., 2014), and Shigella (Liu et al., 2008). ...
Acinetobacter baumannii is an emerging opportunistic pathogen. It exhibits multi-, extreme-, and pan-drug resistance against several classes of antibiotics. Capsular polysaccharide (CPS or K-antigen) is one of the major virulence factors which aids A. baumannii in evading the host immune system. K-antigens of A. baumannii exploit the Wzx/Wzy-dependent pathway that involves 13 different proteins for its assembly and transport onto the outer membrane. A total of 64 (out of 237 K-locus(KL) types) known K-antigen sugar repeating structures are discussed here and are classified into seven groups based on their initial sugars, QuiNAc4NAc, GalNAc, GlcNAc, Gal, QuiNAc/FucNAc, FucNAc, and GlcNAc along with Leg5Ac7Ac/Leg5Ac7R. Thus, the corresponding seven initializing glycosyltransferases (ItrA1, ItrA2, ItrA3, ItrA4, ItrB1, ItrB3, and ItrA3 along with ItrB2) exhibit serotype specificity. The modeled 3D-structural repository of the 64 K-antigens can be accessed at https://project.iith.ac.in/ABSD/k_antigen.html . The topology of K-antigens further reveals the presence of 2-6 and 0-4 sugar monomers in the main and side chains, respectively. The presence of negatively (predominant) or neutrally charged K-antigens is observed in A. baumannii . Such diversity in the K-antigen sugar composition provides the K-typing specificity ( viz ., 18–69% in terms of reliability) for Wza, Wzb, Wzc, Wzx, and Wzy proteins involved in the Wzx/Wzy-dependent pathway. Interestingly, the degree of uniqueness of these proteins among different K-types is estimated to be 76.79%, considering the 237 reference sequences. This article summarizes the A. baumannii K-antigen structural diversity and creation of a K-antigen digital repository and provides a systematic analysis of the K-antigen assembly and transportation marker proteins.
... Antibiotic resistant bacteria (ARB) can develop of chromosomal DNA mutation (3). This bacteria product varies types of antibiotic resistance genes (ARGs) that can transfer from type of bacteria to other types, pathogen or non-pathogen, by horizontal gene transfer (HGT) via conjunction, transformation, and transduction, ARGs transferred by mobile genetic elements (MGE) integrons, plasmids, and transposon (4). Livestock manure contains many types of (ARGs) that used in soil fertilization, which lead to separation of these genes in the environment e.g. ...
... Human and animals that exposure to ARB via varies routes like inhalation and ingestion (10). According to the WHO in 2017, ARB is the highest danger on the human health, it annually causes about 23 000 deaths in USA deaths and 25 000 in the Europe (4).In this review we highlighted on possibility of treat this problem by some technologies that used to inactivate of ARGs in livestock wastes. many conventional methods are used to degrade ARB and eliminate ARGs from contaminate soil and waste water, like membrane filtration, chlorination, ozone, ultraviolet irradiation (UV), Non-thermal atmospheric pressure plasmas (NTAPPs) and pulsed electric field (PEF) (3,(11)(12)(13)(14)(15) Livestock waste is contaminating soil with ARB and ARGs when addition to it, therefore, this problem has been treated with some methods that inactivate or decrease the number of these bacteria and genes (16), one of these methods is field treatment system by decreasing nitrogen with Wood chips denitrifying bioreactors, but in this method, manure can retain 70-90% of manure borne antibiotics (17). ...
The manure of cattle is containing more than 60 different ARGs with varying resistome different from heard to another. ARGs are associated with bacteria and their prophages and phages, and can be found extracellular on transposable elements and plasmids. Antibiotic resistance Genes in one species of bacteria can be horizontally transferred to another species by one of three defined mechanisms such as conjugation, transformation and transduction. The rapid dissemination of antibiotic resistance genes in this method is becoming medically confrontation to deal with. Animal livestock wastes consider as hotspot for dissemination of ARGs to natural environment. Therefore, treatment of ARGs in environmental elements including livestock waste can decrease abundance and diversity of these genes and protect human protecting human and animal health. However, there no single treatment method has ability to completely inactivation of resistant bacteria or gene in the animal wastes. In this review, we evaluate some technologies that used to inactivate of ARGs in livestock wastes.
... The island's rich content of A+T could be evidence of its recent acquisition since over time, the G+C content increases, and the sequence composition of the island becomes comparable to that of the core genome [7]. The secretion of capsular polysaccharide (CPS or K-antigen) allocates a negative charge on the bacterial surfaces, thus rendering the bacteria hydrophilic and shielded from mucus entrapment [32]. In addition, these exopolysaccharides block the activation of the complement pathway in the host, thus providing the producing bacteria additional protection from phagocytosis and serum killing processes [33]. ...
Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). The pathogenesis of UTIs relies upon UPEC’s acquisition of virulence determinants that are commonly inserted into large chromosomal blocks which are termed ‘pathogenicity islands’ (PAIs). In this study, we investigated the virulence-associated genes embedded in the chromosome of a UPEC Egyptian strain, EC14142. Additionally, we present a detailed characterization of the PAIs in the EGY_EC14142 chromosome. The isolate displayed a multidrug-resistant phenotype, and whole genome sequencing indicated that it belonged to the globally disseminated O25:H4-ST131 pandemic lineage and the H30-Rx clade. EGY_EC14142 carried genes that are responsible for resistance to aminoglycosides, fluoroquinolones, extended-spectrum β-lactams, macrolides, folate pathway antagonists, and tetracyclines. It encoded five PAIs with a high similarity to PAI II536, PAI IV536, PAI V536, PAI-536-icd, and PAIusp. The genome analysis of EGY_EC14142 with other closely related UPEC strains revealed that they have a high nucleotide sequence identity. The constructed maximum-likelihood phylogenetic tree showed the close clonality of EGY_EC14142 with the previously published ST131 UPEC international isolates, thus endorsing the broad geographical distribution of this clone. This is the first report characterizing PAIs in a UPEC Egyptian strain belonging to the globally disseminated pandemic clone O25:H4-ST131.
... In 2017, the WHO announced that antibiotic-resistant bacteria pose the highest risk to human health. Antimicrobial resistance causes 25,000 deaths in Europe and 23,000 deaths in the United States annually [3]. ...
Bacterial resistance to antibiotics has become a major public health problem in recent years. The occurrence of antibiotics in the environment, especially in wastewater treatment plants, has contributed to the development of antibiotic-resistant bacteria (ARB) and the spread of antibiotic resistance genes (ARGs). Despite the potential of some conventional processes used in wastewater treatment plants, the removal of ARB and ARGs remains a challenge that requires further research and development of new technologies to avoid the release of emerging contaminants into aquatic environments. Non-thermal atmospheric pressure plasmas (NTAPPs) have gained a significant amount of interest for wastewater treatment due to their oxidizing potential. They have shown their effectiveness in the inactivation of a wide range of bacteria in several fields. In this review, we discuss the application of NTAPPs for the degradation of antibiotic resistance genes in wastewater treatment.
... Also known as K-antigen, is a high molecular weight polysaccharide which has a negative charge, it helps bacteria to prevent distraction by phagocytosis and increase the resistance of the bacterial outer membrane to the final complement complex (serum resistance) this facilitated bacterial survival and extraintestinal infection (Scott et al., 2013). The capsule also services as antimicrobial, reacts with microbicidal cationic antimicrobial peptides by binding to these peptides and stop cell lysis (Band and Weiss, 2015;Fleitas and Franco, 2016;Sachdeva et al., 2017). Capsule is classified according to genetic and biochemical properties into four groups 1, 2, 3, and 4. ...
... The degree of virulence depends on the size and composition of the capsule (Kunduru et al., 2016;Sachdeva et al., 2017). ...
The current study was done in the period extended from 1/9/2019 to 1/10/2021 in both Mosul and Basrah governorate, the study aimed to investigate the immune responses induced by LPS extracted from local isolate and study the lipopolysaccharide immunomodulating effects in an animal model.
One objective of this research is to extract LPS from a local isolate of E. coli. The results of the existing study showed that using the modified hot phenol method for extraction can give a high yield of LPS extraction from Shigatoxigenic E. coli isolate and reach 242.3 mg. The purity of LPS was high when treated specially with Proteinase K, DNase, and RNase. The agarose gel electrophoresis revealed no DNA or RNA in extracted LPS (ELPS). While the SDS-PAGE gel stained with Coomassie blue uncovered the ELPS without protein contamination. The SDS-PAGE stained with silver nitrate showed that the ELPS has several bands with molecular weights ranging between 32-40 kDa; these bands represent the rough LPS and lower two bands with molecular weight range between15- 20 kDa (lipid A). Further analysis of ELPS using HPLC showed that ELPS has one peak with a retention time reach of 1.650 min.
The biological activity of ELPS was detected using the rabbit pyrogen test. The test was considered positive when the temperature raised to 39.9 ℃ after injection of LPS intravenously.
The results of indirect hemagglutination test revealed the elevation of antibodies against LPS, and the titer reached 1/640 when used ELPS in dose 5 mg/kg compared to control animals after 28 days of LPS subcutaneous injection in rats.
Both ELPS and SLPS were able to increase the phagocytic index (62.86 ±12.84) and respiratory burst (59.88 ± 3.82) after 28 days of subcutaneous injection at 5mg/kg dose.
Furthermore, the respiratory bursts (RB) examination showed elevation of response when using intraperitoneal or intravenous routes of injection. However,
Summary
II
low LPS dose (100 μg/kg) gave significant RB elevation rather than high LPS dose. SLPS exhibited a high response on the phagocytic index compared to those in rats injected with ELPS of the same dose and routes. The route of injection revealed that no difference occurs when using the intraperitoneal or intravenous routes on the phagocytic index, whereas, low LPS dose gave a significant increase in the phagocytic index after 6, 12, and 24 h of LPS injection. These results provide information about the ability of the ELPS to stimulate the phagocytic index and the respiratory burst of the peripheral white blood cells.
The effect of both ELPS and SLPS on hematological parameters showed transient leukopenia, lymphocytopenia, granulocytopenia, followed by an increasing number of leukocytes, lymphocyte, polymorphonuclear leukocyte after injection of LPS at 24 h. in different doses and routes of injection used, also significant elevation of WBCs count was occured in intraperitoneal route groups at P ≤ 0.05; while low dose had a significant rise in WBCs count than the high dose in rats. Both types of LPS showed variable effects on circulating cells (midocytes), and meaningful alteration in midocytes count was recorded after the intraperitoneal route of injection.
The current study showed an increase in the expression of CD14 mRNA in the liver after using different LPS types injected with different routes and reaches to 200.02 fold change after 24h of ELPS high dose (5mg/kg) with a significant difference from other groups, but overall ELPS cause a lower elevation in CD14 mRNA gene expression comparing with SLPS regardless of the dose and route of administration.
The gene expression analysis of TLR4 mRNA revealed upregulation caused by both LPS types. Yet, a high dose of LPS injected by intraperitoneal route recorded the 0.96 fold change after 6h which was the lowest point of TLR4 mRNA gene expression. However, the higher elevation of TLR4 mRNA gene expression (151.27) was recorded at 24h when used ELPS intravenously. The
Summary
III
SLPS had appears to have a more rising effect on the expression of the TLR4 gene of the rat’s model rather than ELPS, which exhibits a less elevation effect on the same model. While different routes and doses appeared to have little effect on TLR4 mRNA expression and recorded similar expression in different experimental times.
Both LPS types showed the variable effect on TNFα mRNA gene expression, but TNFα mRNA expression showed time response with a significant increase in the first 6h followed by a decrease in TNFα mRNA gene expression. ELPS has a lower effect on the TNFα mRNA gene expression compared with SLPS. Regardless of the routes of injection in all experimental animals, the low LPS doses induced more upregulation rather than the high dose.
Both LPS used in this study caused upregulation of IL1 expression in all animals' groups, the time response of IL1 expression showed no relationship with the dose, route of injection of LPS and gave similar expression at all times. The ELPS showed a lower influence on IL1 gene expression compared with SLPS regardless of the route of injection. The higher LPS dose used caused a lowest effect on IL1α mRNA gene expression compared with the low LPS dose.
This study concluded that ELPS was able to induce liver immune responses with the different routes of injection and this mediated by an increase in CD14 /TLR4 gene expression and activation downstream signaling result to increase TNFα, IL1 α expression to produce either inflammation or regeneration of liver tissue
... Therefore, CPS is considered as a potential target for therapeutic intervention against klebsiella. Reports suggest that biosynthesis of CPS or K-antigen occurring via the Wzx/Wzy-dependent pathway that facilitates the surface expression of CPS can also be a good vaccine/drug target [12,13]. As in this study, the two genes play a vital role in the Wzx/Wzy-dependent pathway hence is highly antigenic for inclusion in vaccine construct. ...
Background
: Klebsiella pneumoniae is an emerging human pathogen causing neonatal lung disease, catheter-associated infections, and nosocomial outbreaks with high fatality rates. Capsular polysaccharide (CPS) protein plays a major determinant in virulence and is considered as a promising target for vaccine development.
Research design and methods
: In this study, we used immunoinformatic approaches to design a multi-peptide vaccine against K. pneumonia. The epitopes were selected through several immune filters, such as antigenicity, conservancy, non-toxicity, non-allergenicity, binding affinity to HLA alleles, overlapping epitopes, and peptides having common epitopes.
Results
: Finally, a construct comprising 2 B-Cell, 8 CTL, 2 HTL epitopes, along with adjuvant, linkers was designed. Peptide-HLA interaction analysis showed strong binding of these epitopes with several common HLA molecules. The in silico immune simulation and population coverage analysis of the vaccine showed its potential to evoke strong immune responses and to cover up a worldwide population of 99.11%. Further, the interaction between vaccine and immune was evaluated by docking and simulation, revealing high affinity and complex stability. Codon adaptation and in silico cloning revealed higher expression of vaccine in E. coli K12 expression system.
Conclusions
: Conclusively, the findings of the present study suggest that the designed novel multi-epitopic vaccine holds potential for further experimental validation against the pathogen.
... Therefore, CPS is considered as a potential target for therapeutic intervention against klebsiella. Reports suggest that biosynthesis of CPS or K-antigen occurring via the Wzx/Wzy-dependent pathway that facilitates the surface expression of CPS can also be a good vaccine/drug target [12,13]. As in this study, the two genes play a vital role in the Wzx/Wzy-dependent pathway hence is highly antigenic for inclusion in vaccine construct. ...
Pneumonia is a major endemic disease around the world, and an effective vaccine is the need of the hour to fight against the disease. When there are no appropriate antiviral and associated therapies available, vaccine development becomes even more essential. Therefore, in the present study, a variety of immunoinformatics techniques was utilized to develop a novel multi-epitope vaccine that targets the highly immunodominant type 3 fimbrial protein of Klebsiella pneumoniae, the causal organism for pneumonia. The putative B and T cell epitopes were predicted from the protein and screened for antigenicity, toxicity, allergenicity, and cross-reactivity with human proteomes. Subsequently, the selected epitopes were joined with the help of linkers to form a robust vaccine construct. In addition, an adjuvant was applied to the N-terminal of the construct to improve the immunogenicity of the vaccine. The physicochemical properties, solubility, the secondary and tertiary structure of the final vaccine were also established. MD simulations for 100 ns were employed to assess the stability of the vaccine-TLR-2 docked complex. The final vaccine was optimized and cloned in pET28a (+) vector with His-tag to achieve maximum vaccine protein expression for ease of purification. Immune simulation results indicated the potency of this vaccine candidate as a probable therapeutic agent. In conclusion, the overall results of various immunoinformatics tools and methods employed revealed that the constructed multi-epitope vaccine exhibits a high potential for stimulating both B and T-cells immune responses against pneumonia infection. However, experimental immunological studies are required to corroborate the viability of the novel multi-epitope construct as a commercial vaccine.
