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Schematic model for the possible role of type IV secretion systems in DNA transfer events of the gastric pathogen Helicobacter pylori. Each potential DNA transfer mechanism is indicated with the corresponding name and red arrows, which includes the proposed direction of DNA delivery. H. pylori is coloured in green, C. jejuni in brown, and the mammalian host cell in grey
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The gastric pathogen Helicobacter pylori is one of the most genetically diverse bacteria. Recombination and DNA transfer contribute to its genetic variability and enhance host adaptation. Among the strategies described to increase genetic diversity in bacteria, DNA transfer by conjugation is one of the best characterized. Using this mechanism, a fr...
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Context 1
... analyses suggest the occurrence of frequent recombination events and other important changes at the genetic level, which help to explain the organism's evolution in the stomach and certain adaptation events during transmission [16]. Here we review the dif- ferent known and proposed mechanisms used by H. pylori to acquire and transfer exogenous DNA, and thus, increase its genetic variability and adaptation to the host ( Figure 1). We also provide an overview of the various DNA transfer machineries employed by H. pylori to deliver genetic material to other bacterial species and possibly even to organisms in different kingdoms. ...
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... occurred within the various H. pylori strains during this long time of co-existence with humans, which helped it to adapt perfectly to its colonization niche. This high genetic variability stimulated the scientific community to investigate how DNA can be gained and lost during bacterial evolution, and several mechanisms have been proposed (Fig. 1). One of the molecular mechanisms that H. pylori used to gain exogenous DNA is by natural transformation using the ComB system. Nevertheless, an increasing number of reports on natural plasmids in H. pylori strains, together with the presence of putative con- jugative genes, encouraged researchers to propose that active DNA transfer ...
Citations
... Additionally, the use of phage therapy may raise questions about the regulation and oversight of such treatments, particularly in countries where phage therapy is not yet widely used or regulated. It is important for researchers and healthcare providers to carefully consider these ethical considerations and ensure that patients are fully informed about the potential risks and benefits of phage therapy before undergoing treatment [22][23] [24]. ...
Helicobacter pylori is a bacterium that can cause a range of gastrointestinal diseases, including gastritis, peptic ulcers, and stomach cancer. Traditional treatments for H. pylori infections involve the use of antibiotics, but the increasing prevalence of antibiotic resistance has led to the exploration of alternative therapies, including phage therapy. Phage therapy is a treatment approach that involves the use of bacteriophages, viruses that infect and kill bacteria, to target specific strains of bacteria. In this paper, we review the current understanding of the use of phage therapy in the treatment of H. pylori infections. We discuss the methods used for identifying and isolating phages that target H. pylori and the testing and validation of phages for their effectiveness in vitro. Although phage therapy shows promise as a potential treatment for H. pylori infections, further research is needed to evaluate the safety and efficacy of this approach.)
... In unusual cases, T4SS-dependent mechanisms facilitate interbacterial killing via toxin delivery (17,18) or the contact-independent secretion of multisubunit protein toxins into the extracellular environment (2,19). The third T4SS subfamily comprised of "DNA uptake and release" systems function in a contact-independent manner to import exogenous DNA or to secrete DNA into the extracellular milieu (1,2,5,14,(20)(21)(22)(23). Thus, these dedicated genetic exchange systems expand the molecular arsenal employed by Gram-negative bacteria to acquire survival elements during infection (14,20,24). ...
The versatile type IV secretion system (T4SS) nanomachine plays a pivotal role in bacterial pathogenesis and the propagation of antibiotic resistance determinants throughout microbial populations. In addition to paradigmatic DNA conjugation machineries, diverse T4SSs enable the delivery of multifarious effector proteins to target prokaryotic and eukaryotic cells, mediate DNA export and uptake from the extracellular milieu, and in rare examples, facilitate transkingdom DNA translocation. Recent advances have identified new mechanisms underlying unilateral nucleic acid transport through the T4SS apparatus, highlighting both functional plasticity and evolutionary adaptations that enable novel capabilities. In this review, we describe the molecular mechanisms underscoring DNA translocation through diverse T4SS machineries, emphasizing the architectural features that implement DNA exchange across the bacterial membrane and license transverse DNA release across kingdom boundaries. We further detail how recent studies have addressed outstanding questions surrounding the mechanisms by which nanomachine architectures and substrate recruitment strategies contribute to T4SS functional diversity.
... Infectious symptoms of existence of H. pylori are diagnosed with gastric along with duodenal pathology which includes the chronic gastritis, peptic ulcers, and even gastric cancer in the population which also depends on the variation of virulence of bacteria, genetic attributes of the host, and environmental factors (Nr and Muller 2013;Cover and Blaser 2009). H. pylori possess more genetic diversity in the class of bacteria which pathogenic in nature (Fischer et al. 2010;Fernandez-Gonzalez and Backert 2014) and also more often takes part in the horizontal gene transfer (HGT) and adapts accordingly with the host environment via recombination processes (Covacci et al. 1993). The mutational abilities of DNA polymerase I help in recombination of genes according to the selected host (Fernandez-Gonzalez and Backert 2014). ...
... Identification of gene clusters which are co-occurring Determination of gene sequences whiceh are mobile H. pylori strains are classified into two different wide-ranging families temporarily addressed as types I and II, which are known as the bases of expression of vacuolating cytotoxin (VacA) and the CagA antigen (cytotoxin-associated gene A) (Fischer et al. 2010). Type I strain infections are seen in patients who are diagnosed with duodenal ulcers, tumors and duodenitis which with CagA and the cytotoxin which expresses together with other genes play a role in its virulence (Fischer et al. 2010;Fernandez-Gonzalez and Backert 2014;Covacci et al. 1993). The epidemiological studies are assisted by experiments in the mouse models. ...
Genomic Islands (GI) of Klebsiella pneumoniae include integrative and conjugative elements (ICEs), prophages, integrons, and transposons belonging to a group of genetic elements transferred horizontally and have integrated into the genome of K. pneumoniae. Integrative and conjugative elements of K. pneumoniae (ICEKp) are flanked by direct repeats, encode the yersiniabactin (ybt) locus, a mobilization locus-type 4 secretion system (T4SS), and other variable regions based on which they are classified into 14 types (ICEKp1–14). Their sizes range from 75–200 kb and their chromosomal insertion site is mostly one of the four tRNA-Asn sites. Each K. pneumoniae genome can harbor one to six prophages; accounting for 0.1–8% of the genome. The site of phage integration could be either the tRNA or ABC transporter permease SapC. Class I integrons are the most commonly found integrons in K. pneumoniae. They contain three essential components for the capture of external genes: an integrase, attI site, and an outwardly oriented promoter (Pc) that controls transcription of the captured genes. Conjugative transposons (CTn) in K. pneumoniae are associated with resistance (Tn916 and Tn6009) and hypervirulence (Tn6497).KeywordsIntegrative and conjugative elementsProphagesIntegronsTransposons
K. pneumoniae
... Infectious symptoms of existence of H. pylori are diagnosed with gastric along with duodenal pathology which includes the chronic gastritis, peptic ulcers, and even gastric cancer in the population which also depends on the variation of virulence of bacteria, genetic attributes of the host, and environmental factors (Nr and Muller 2013;Cover and Blaser 2009). H. pylori possess more genetic diversity in the class of bacteria which pathogenic in nature (Fischer et al. 2010;Fernandez-Gonzalez and Backert 2014) and also more often takes part in the horizontal gene transfer (HGT) and adapts accordingly with the host environment via recombination processes (Covacci et al. 1993). The mutational abilities of DNA polymerase I help in recombination of genes according to the selected host (Fernandez-Gonzalez and Backert 2014). ...
... Identification of gene clusters which are co-occurring Determination of gene sequences whiceh are mobile H. pylori strains are classified into two different wide-ranging families temporarily addressed as types I and II, which are known as the bases of expression of vacuolating cytotoxin (VacA) and the CagA antigen (cytotoxin-associated gene A) (Fischer et al. 2010). Type I strain infections are seen in patients who are diagnosed with duodenal ulcers, tumors and duodenitis which with CagA and the cytotoxin which expresses together with other genes play a role in its virulence (Fischer et al. 2010;Fernandez-Gonzalez and Backert 2014;Covacci et al. 1993). The epidemiological studies are assisted by experiments in the mouse models. ...
Iron is an important element for all life forms. In microbial life, it plays a significant bearing either as an important growth factor and/or cofactor for various metabolic processes in case of environmental bacteria or as a virulence determinant for many pathogenic microorganisms to affect their disease-causing ability. Microorganisms have developed a variety of modes to acquire iron from local environment. In iron scarcity conditions, many bacteria adopt specific strategies to fulfill their iron requisite and survive. Distinct genetic machinery targeted for iron uptake and utilization have been documented and have been extensively studied. Different microorganisms harbor distinct genomic islands specifically intended to accomplish the iron uptake and few have been described in detail to provide insights into this important area. The current chapter provides an update on the various microbial mechanisms of iron uptake, general aspects of bacterial genomic islands and the details of the genomic islands involved in the microbial iron uptake mechanisms.KeywordsIron uptakeGenomic islandsFerric ionSiderophoresHemeYersiniabactin
... Several 6 factors, such as translational and transcriptional phase variation, as well as mutation, contribute to nucleotide diversity. (Kuipers et al., 2000;Falush et al., 2003 andFernandez-Gonzalez andBackert, 2014) ...
... Several 6 factors, such as translational and transcriptional phase variation, as well as mutation, contribute to nucleotide diversity. (Kuipers et al., 2000;Falush et al., 2003 andFernandez-Gonzalez andBackert, 2014) ...
Helicobacter pylori is a gram-negative bacteria that infects a majority of the world's population. It causes various diseases such as chronic gastritis, peptic ulcer and gastric cancer. While a majority of the people infected with H.pylori is asymptomatic. The main factors, which determine the development of H. pylori-related diseases might be bacterial virulence, host genetic and environmental factors.
The present study was carried out to determine the frequency of H. pylori infection in patients attending the endoscopic unit at Al-Sadr Teaching Hospital in Basrah who are suffering from gastrointestinal symptoms and were diagnosed by a specialist doctor.
During November 2020 to May 2021, three types of clinical samples were collected from 120 patients ( 53 male and 67 female), the age range was ( 11-76 years), including tissue, saliva and stool. To investigate H.pylori three biopsies of gastric mucosal tissue were taken for rapid urease test (RUT), bacterial culture and polymerase chain reaction (PCR) technique. Stool antigen detection. saliva swabs were taken and cultured.
The incidence of H. pylori infection among these patients was 48 by using four diagnostic methods, including rapid urease test( RUT), stool antigen test and PCR. While 20 H.pylori were isolated by culturing method on selective and modified media ( Modified Columbia Urea Agar, Modified Brain Heart Infusion Agar and H. pylori special peptone medium (HPSP )agar, and identified through biochemical tests ( Oxidase, Catalase, and Urease ) as well as Gram stain.
There was no significant difference (P>0.05) between males and females in the rate of H. pylori infection, the percentage of males was 54.2% and 45.8% . The highest percentage of infection was in the age group ≥ 60, which amounted to 55.6%, and there were no significant differences (P>0.05) between age groups of H.pylori infection.
An antibiotic sensitivity test was conducted on the isolates using six types of antibiotics. Multiple resistance to most antibiotics was recorded. Amoxicillin 60%, Doxycycline 70%, Metronidazole 100%, Ciprofloxacin 55%, Clarithromycin is the most used antibiotic 70%, while the most effective antibiotic according to the result of this study was Levofloxacin, which recorded a higher sensitivity 85%.
The results of 16S rRNA ( PCR) showed that 48 of H. pylori infection by using 138 base pairs gene-specific primer. The virulence factors were evaluated by using a gene-specific primer. Cag A gene was detected in 27 and Vac A gene was detected in 29 of the samples from both isolates and biopsies directly.
Helicobacter pylori crude supernatant production were performed through inoculated brain heart infusion broth by the bacteria isolates and incubated in a rotary-shaker incubator, respective supernatants were then carefully separated and poured into new vials and stored at room temperature after which the supernatant was freeze-drying the effective were the appearance of 10 chemical compounds that at the same time in with different percentages, when analysis GC-MS device.
The toxicity of H.pylori was examined by using experimental animals ( Balb/c) mice. Two mice from six were injected intraperitoneally ( I.P.) with 155 mg/ml H.pylori crude supernatant died after 48 hours of injection, while six mice that were administered H.pylori crude supernatant orally were survived and compared to the control group. For the interpretation of the toxin effect, the abdomen was opened and the complete stomach, intestine, kidney, and liver for all groups were removed and promptly fixed in 10% formalin overnight. The macroscopic results revealed the differences between normal ( control ) and H. pylori crude supernatant injected mice, such as hypertrophied liver, degenerated stomach characteristics, and infiltration of inflammatory cells in the lamina propria, when compared to normal mice.
To study the effect of H. pylori crude supernatant, three types of cell lines were used HBL-100 (normal breast), SKG (esophageal cancer), and HCAM (liver cancer).
The results indicated that H. pylori crude supernatant has an effect on the viability of the HBL-100 cell line. The viability of cells is dependent on concentrations, from selected five isolates only one affected the viability of the HBL-100 cell line concentration 1000 ìg /ml, while the effect of H. pylori crude supernatant on Esophagus Cancer and Liver Cancer can be inhibited DNA synthesis and stop the proliferation of the cells. The viability decreased from 30 %,40 %, and 50% when the SKG (Esophagus Cancer) and HCAM(Liver Cancer) cells were treated with H. pylori crude supernatant.
... Its diversity is due to a higher level of spontaneous mutations occurring within the restricted gastric niche, a higher frequency of horizontal gene transfer, and natural competence (Israel et al., 2001). Impaired DNA repair, integration of acquired DNA into the "plasticity zones, " and higher intraspecific recombination also contributed to diverse genetic forms (Fernandez-Gonzalez and Backert, 2014). H. pylori remains a very successful human pathogen for centuries with a considerably lower proportion of terminal clinical outcomes and higher self-propagation across generations with a plethora of virulence factors that facilitate chronic colonization in the human stomach, where the pH is nearly 2. H. pylori virulence factors include urease, flagella, adhesins, and several effector proteins that lead to pathogenesis. ...
It is increasingly being recognized that severe gastroduodenal diseases such as peptic ulcer and gastric cancer are not just the outcomes of Helicobacter pylori infection in the stomach. Rather, both diseases develop and progress due to the perfect storms created by a combination of multiple factors such as the expression of different H. pylori virulence proteins, consequent human immune responses, and dysbiosis in gastrointestinal microbiomes. In this mini review, we have discussed how the genomes of H. pylori and other gastrointestinal microbes as well as the genomes of different human populations encode complex and variable virulome–immunome interplay, which influences gastroduodenal health. The heterogeneities that are encrypted in the genomes of different human populations and in the genomes of their respective resident microbes partly explain the inconsistencies in clinical outcomes among the H. pylori-infected people.
... Worldwide H. pylori strains from different continents are genetically highly diverse [5]. During the long co-evolution with its human host, which lasted for over 100,000 years [6], various type-IV secretion systems (T4SSs) were acquired and/or evolved, each of which with specific functions (reviewed by [7,8]). These T4SSs are molecular transport systems that assemble in the inner and outer membranes of many bacteria and are frequently associated with a protruding pilus [9]. ...
... Conjugation in bacteria represents T4SS-mediated transfer of DNA between many bacterial species, and also facilitates delivery of DNA from bacteria into eukaryotic target cells upon infection [9,10]. Canonical T4SSs involved in this conjugational DNA transfer typically consist of two major elements, the DNA transfer and replication system (called Dtr) and the mating pair formation system (named Mpf), following the characteristic "replication and secretion" scheme (reviewed in [7,9,10,55,56]). The Mpf system is basically composed of the above described 11 membrane-spanning VirB or Tra proteins, which translocate substrates across the membranes and form an extracellular pilus [9,10]. ...
The genomes of the gastric bacterial pathogen Helicobacter pylori harbor multiple type-IV secretion systems (T4SSs). Here we analyzed components of three T4SSs, the cytotoxin-associated genes ( cag ) T4SS, TFS3 and TFS4. The cag T4SS delivers the effector protein CagA and the LPS-metabolite ADP-heptose into gastric epithelial cells, which plays a pivotal role in chronic infection and development of gastric disease. In addition, the cag T4SS was reported to facilitate conjugative transport of chromosomal bacterial DNA into the host cell cytoplasm, where injected DNA activates intracellular toll-like receptor 9 (TLR9) and triggers anti-inflammatory signaling. Canonical DNA-delivering T4SSs in a variety of bacteria are composed of 11 VirB proteins (VirB1-11) which assemble and engage VirD2 relaxase and VirD4 coupling proteins that mediate DNA processing and guiding of the covalently bound DNA through the T4SS channel. Nevertheless, the role of the latter components in H. pylori is unclear. Here, we utilized isogenic knockout mutants of various virB ( virB9 and virB10 , corresponding to cagX and cagY ), virD2 ( rlx1 and rlx2 ) , virD4 ( cag5, traG1/2 ) and xerD recombinase genes in H. pylori laboratory strain P12 and studied their role in TLR9 activation by reporter assays. While inactivation of the structural cag T4SS genes cagX and cagY abolished TLR9 activation, the deletion of rlx1 , rlx2, cag5 , traG or xerD genes had no effect. The latter mutants activated TLR9 similar to wild-type bacteria, suggesting the presence of a unique non-canonical T4SS-dependent mechanism of TLR9 stimulation by H. pylori that is not mediated by VirD2, VirD4 and XerD proteins. These findings were confirmed by the analysis of TLR9 activation by H. pylori strains of worldwide origin that possess different sets of T4SS genes. The exact mechanism of TLR9 activation should be explored in future studies.
... The function of the T4SS encoded by tfs3 remains unclear. A possible role of Tfs3 has been suggested in DNA transfer, but the actual function of Tfs3 still remains widely unclear (Fernandez-Gonzalez and Backert, 2014). Some studies have suggested that this system constitutes a complete set of putative T4SS channels with other homologous genes (Mcclelland et al., 2007). ...
... Alandiyjany et al. indicated a role for the tfs3 T4SS in CtkA-mediated proinflammatory signalling by H. pylori (Alandiyjany et al., 2017a). In addition, in the tfs3 system of strain PeCan18B, homologs VirB4, VirB11, and VirD4 jointly form an enzyme complex related to the hydrolysis of adenosine triphosphate in the cytoplasmic membrane, providing sufficient energy for the transmembrane transport of macromolecular substrates (Fernandez-Gonzalez and Backert, 2014). ...
The gene of Helicobacter pylori can encode three to four type IV secretory systems, of which a new gene region has been found in the H. pylori plasticity region. The coding products of this region can form a new T4SS named tfs3, but its function is unclear. This study investigated the effect of VirD4 recombinant protein in the tfs3 secretory system of the H. pylori clinical strain SBK on GES-1 cells. We observed changes in cell morphology after VirD4 treatment. Further analysis indicated that VirD4 increased inflammation by increasing the activation of NF-κB. VirD4 can also inhibited proliferation, and induced migration of cells. Moreover, VirD4 caused apoptosis in GES-1 cells in caspase and ERK1/2/Ras dependent signaling events. Our study laid a foundation for further research on the biological function of VirD4 and the detection and treatment of H. pylori-related diseases.
... Interestingly, unidirectional DNaseI-resistant conjugation-like transfer of a chromosomal resistance gene was observed from H. pylori to C. jejuni (Oyarzabal et al. 2007), demonstrating the potential of bacteria of the class Campylobacterales for genetic exchange (Fernandez-Gonzalez et al. 2014). ...
Thermophilic Campylobacter , in particular Campylobacter jejuni , C. coli and C. lari are the main relevant Campylobacter species for human infections. Due to their high capacity of genetic exchange by horizontal gene transfer (HGT), rapid adaptation to changing environmental and host conditions contribute to successful spreading and persistence of these foodborne pathogens. However, extensive HGT can exert dangerous side effects for the bacterium, such as the incorporation of gene fragments leading to disturbed gene functions. Here we discuss mechanisms of HGT, notably natural transformation, conjugation and bacteriophage transduction and limiting regulatory strategies of gene transfer. In particular, we summarize the current knowledge on how the DNA macromolecule is exchanged between single cells. Mechanisms to stimulate and to limit HGT obviously coevolved and maintained an optimal balance. Chromosomal rearrangements and incorporation of harmful mutations are risk factors for survival and can result in drastic loss of fitness. In Campylobacter , the restricted recognition and preferential uptake of free DNA from relatives are mediated by a short methylated DNA pattern and not by a classical DNA uptake sequence as found in other bacteria. A class two CRISPR-Cas system is present but also other DNases and restriction–modification systems appear to be important for Campylobacter genome integrity. Several lytic and integrated bacteriophages have been identified, which contribute to genome diversity. Furthermore, we focus on the impact of gene transfer on the spread of antibiotic resistance genes (resistome) and persistence factors. We discuss remaining open questions in the HGT field, supposed to be answered in the future by current technologies like whole-genome sequencing and single-cell approaches.
... The uptake apparatus is encoded by two distinct operons, comB2-B4 and comB6-B10, as well as the comEC and comH genes ( Table 2). All components except ComB7 are essential for transformation but they are not all fully functionally characterized (Hofreuter, Odenbreit and Haas 2001;Karnholz et al. 2006;Stingl et al. 2010;Fernandez-Gonzalez & Backert 2014;Damke et al. 2019). ...
Helicobacter pylori is a Gram-negative, spiral shaped bacterium, that selectively and chronically infects the gastric mucosa of humans. The clinical course of this infection can range from lifelong asymptomatic infection to severe disease, including peptic ulcers, or gastric cancer. The high mutation rate and natural competence typical of this species are responsible for massive inter-strain genetic variation exceeding that observed in all other bacterial human pathogens. The adaptive value of such a plastic genome is thought to derive from a rapid exploration of the fitness landscape resulting in fast adaptation to the changing conditions of the gastric environment. Nevertheless, diversity is also lost through recurrent bottlenecks and H. pylori’s lifestyle is thus a perpetual race to maintain an appropriate pool of standing genetic variation able to withstand selection events. Another aspect of H. pylori’s diversity is a large and variable repertoire of restriction-modification systems. While not yet completely understood, methylome evolution could generate enough transcriptomic variation to provide another intricate layer of adaptive potential. This review provides an up to date synopsis of this rapidly emerging area of H. pylori research that has been enabled by the ever-increasing throughput of Omics technologies and a multitude of other technological advances.
