Cooperation of two distinct coupling proteins creates chemosensory network connections

Helicobacter pylori cheV1 mutants recover semisolid agar migration due to loss of a previously uncharacterized Type IV filament membrane alignment complex homolog

The bacterial chemotaxis system is a well-understood signaling pathway that promotes bacterial success. Chemotaxis systems comprise chemoreceptors and the CheA kinase, linked by CheW or CheV scaffold proteins. Scaffold proteins provide connections between chemoreceptors and CheA and also between chemoreceptors to create macromolecular arrays. Chemotaxis is required for host colonization by many microbes, including the stomach pathogen Helicobacter pylori. This bacterium builds chemoreceptor-CheA contacts with two distinct scaffold proteins, CheW and CheV1. H. pylori cheW or cheV1 deletion mutants both lose chemoreceptor array formation, but show differing semisolid agar chemotaxis assay behaviors: ∆cheW mutants exhibit total migration failure, whereas ∆cheV1::cat mutants display a 50% reduction. On investigating these varied responses, we found that both mutants initially struggle with migration. However, over time, ∆cheV1::cat mutants develop a stable, enhanced migration capability, termed "migration-able" (Mig+). Whole-genome sequencing analysis of four distinct ∆cheV1::cat Mig+ strains identified single-nucleotide polymorphisms (SNPs) in hpg27_252 (hp0273) that were predicted to truncate the encoded protein. Computational analysis of the hpg27_252-encoded protein revealed it encoded a hypothetical protein that was a remote homolog of the PilO Type IV filament membrane alignment complex protein. Although H. pylori lacks Type IV filaments, our analysis showed it retains an operon of genes for homologs of PilO, PilN, and PilM. Deleting hpg27_252 in the ∆cheV1::cat or wild type strain resulted in enhanced migration in semisolid agar. Our study thus reveals that while cheV1 mutants initially have significant migration defects, they can recover the migration ability through genetic suppressors, highlighting a complex regulatory mechanism in bacterial migration.

IMPORTANCE

Chemotactic motility, present in over half of bacteria, depends on chemotaxis signaling systems comprising receptors, kinases, and scaffold proteins. In Helicobacter pylori, a stomach pathogen, chemotaxis is crucial for colonization, with CheV1 and CheW as key scaffold proteins. While both scaffolds are essential for building chemoreceptor complexes, their roles vary in other assays. Our research reexamines cheV1 mutants' behavior in semisolid agar, a standard chemotaxis test. Initially, cheV1 mutants exhibited defects similar to those of cheW mutants, but they evolved genetic suppressors that enhanced migration. These suppressors involve mutations in a previously uncharacterized gene, unknown in motility behavior. Our findings highlight the significant chemotaxis defects in cheV1 mutants and identify new elements influencing bacterial motility.

The involvement of the T6SS vgrG gene in the pathogenicity of Pseudomonas plecoglossicida

Pseudomonas plecoglossicida, the causative agent of white spot disease of large yellow croaker, has caused serious economic losses to the aquaculture industry. The type VI secretion system (T6SS) is a significant virulence system widely distributed among Gram-negative bacteria. VgrG, a structural and core component of T6SS, is crucial to the function of T6SS. To explore the biological profiles mediated by vgrG gene and its effects on the pathogenicity of P. plecoglossicida, the vgrG gene deletion (ΔvgrG) strain and complementary (C-ΔvgrG) strain were constructed and the differences in pathogenicity and virulence-related characteristics between different strains were analysed. The results showed that vgrG gene deletion significantly affected the virulence-related characteristics of P. plecoglossicida, including chemotaxis, adhesion, and biofilm formation. In addition, the LD50 of ΔvgrG strain was nearly 50-fold higher than that of the NZBD9 strain. Transcriptome data analysis suggested that the vgrG gene may affect the virulence of P. plecoglossicida by regulating the quorum sensing pathway to inhibit the secretion of virulence factors and affect biofilm formation. Besides, deletion of the vgrG gene may reduce bacterial pathogenicity by affecting bacterial signal transduction processes and the ability to adapt to chemotactic substances.

The mechanisms of metronidazole resistance of Helicobacter pylori: A transcriptomic and biochemical study

Helicobacter pylori (H. pylori) is a bacterial pathogen in the stomach, causing gastritis, gastric ulcer, duodenal ulcer and even gastric cancer. The triple therapy containing one bismuth-containing compound or a proton-pump inhibitor with two antibiotics was the cornerstone of the treatment of H. pylori infections. However the drug resistance of Helicobacter pylori is more and more common, which leads to the continued decline in the radical cure rate. The purpose of this study was to investigate the mechanism of metronidazole resistance of H. pylori through transcriptomics and biochemical characterizations. In this study, a 128-time-higher metronidazole-resistant H. pylori strain compared to the sensitive strain was domesticated, and 374 significantly differential genes were identified by transcriptomic sequencing as compared to the metronidazole-sensitive strain. Through GO and KEGG enrichment analysis, antibiotic-resistance pathways were found to be mainly involved in redox, biofilm formation and ABC transportation, and the results were verified by qRT-PCR. The subsequent biochemical analysis found that the urease activity of the drug-resistant strain decreased, and whereas the capabilities of bacterial energy production, membrane production and diffusion ability increased. The work here will drop hints for the mechanisms of antibiotic-resistance of H. pylori and provide promising biomarkers for the further development of new-kind drugs to treat metronidazole-resistant H. pylori.

Helicobacter pylori intragastric colonization and migration: Endoscopic manifestations and potential mechanisms

After being ingested and entering the human stomach, Helicobacter pylori (H. pylori) adopts several effective strategies to adhere to and colonize the gastric mucosa and move to different regions of the stomach to obtain more nutrients and escape from the harsher environments of the stomach, leading to acute infection and chronic gastritis, which is the basis of malignant gastric tumors. The endoscopic manifestations and pathological features of H. pylori infection are diverse and vary with the duration of infection. In this review, we describe the endoscopic manifestations of each stage of H. pylori gastritis and then reveal the potential mechanisms of bacterial intragastric colonization and migration from the perspective of endoscopists to provide direction for future research on the effective therapy and management of H. pylori infection.

Molecular characterization and in-depth genome analysis of Enterobacter sp. S-16

Enterobacter species are considered to be an opportunistic human pathogen owing to the existence of antibiotic-resistant strains and drug resides; however, the detailed analysis of the antibiotic resistance and virulence features in environmental isolates is poorly characterized. Here, in the study, we characterized the biochemical characteristics, and genome, pan-genome, and comparative genome analyses of an environmental isolate Enterobacter sp. S-16. The strain was identified as Enterobacter spp. by using 16S rRNA gene sequencing. To unravel genomic features, whole genome of Enterobacter sp. S-16 was sequenced using a hybrid assembly approach and genome assembly was performed using the Unicycler tool. The assembled genome contained the single conting size 5.3 Mbp, GC content 55.43%, and 4500 protein-coding genes. The genome analysis revealed the various gene clusters associated with virulence, antibiotic resistance, type VI secretion system (T6SS), and many stress tolerant genes, which may provide important insight for adapting to changing environment conditions. Moreover, different metabolic pathways were identified that potentially contribute to environmental survival. Various hydrolytic enzymes and motility functions equipped the strain S-16 as an active colonizer. The genome analysis confirms the presence of carbohydrate-active enzymes (CAZymes), and non-enzymatic carbohydrate-binding modules (CBMs) involved in the hydrolysis of complex carbohydrate polymers. Moreover, the pan-genome analysis provides detailed information about the core genes and shared genes with the closest related Enterobacter species. The present study is the first report showing the presence of YdhE/NorM in Enterobacter spp. Thus, the elucidation of genome sequencing will increase our understanding of the pathogenic nature of environmental isolate, supporting the One Health Concept.

Strategies adopted by gastric pathogen Helicobacter pylori for a mature biofilm formation: Antimicrobial peptides as a visionary treatment

Enormous efforts in recent past two decades to eradicate the pathogen that has been prevalent in half of the world's population have been problematic. The biofilm formed by Helicobacter pylori provides resistance towards innate immune cells, various combinatorial antibiotics, and human antimicrobial peptides, despite the fact that these all are potent enough to eradicate it in vitro. Biofilm provides the opportunity to secrete various virulence factors that strengthen the interaction between host and pathogen helping in evading the innate immune system and ultimately leading to persistence. To our knowledge, this review is the first of its kind to explain briefly the journey of H. pylori starting with the chemotaxis, the mechanism for selecting the site for colonization, the stress faced by the pathogen, and various adaptations to evade these stress conditions by forming biofilm and the morphological changes acquired by the pathogen in mature biofilm. Furthermore, we have explained the human GI tract antimicrobial peptides and the reason behind the failure of these AMPs, and how encapsulation of Pexiganan-A(MSI-78A) in a chitosan microsphere increases the efficiency of eradication.

Discovery of Type IV filament membrane alignment complex homologs in H. pylori that promote soft-agar migration

The stomach pathogen Helicobacter pylori utilizes two scaffold proteins, CheW and CheV1, to build critical chemotaxis arrays. Chemotaxis helps bacteria establish and maintain infection. Mutants lacking either of these chemotaxis proteins have different soft agar phenotypes: deletion of cheW creates non-chemotactic strains, while deletion of cheV1 results in 50% loss of chemotaxis. In this work, we characterized the cheV1 deletion mutant phenotype in detail. cheV1 deletion mutants had poor soft-agar migration initially, but regained migration ability over time. This improved bacterial migration was stable, suggesting a genetic suppressor phenotype, termed Che+. Whole-genome sequencing analysis of four distinct cheV1 Che+ strains revealed single nucleotide polymorphisms (SNPs) in a common gene, HPG27_252 (HP0273). These SNPs were predicted to truncate the encoded protein. To confirm the role of HPG27_252 in the cheV1 phenotype, we created a targeted deletion of HPG27_252 and found that loss of HPG27_252 enhanced soft-agar migration. HPG27_252 and CheV1 appear to interact directly, based on bacterial two-hybrid analysis. HPG27_252 is predicted to encode a 179 amino acid, 21 kDa protein annotated as a hypothetical protein. Computational analysis revealed this protein to be a remote homolog of the PilO Type IV filament membrane alignment complex protein. Although H. pylori is not known to possess Type IV filaments, our analysis showed it retains an operon of genes for homologs of PilO, PilN, and PilM, but does not possess other Type IV pili genes. Our data suggest the PilO homolog plays a role in regulating H. pylori chemotaxis and motility, suggesting new ideas about evolutionary steps for controlling migration through semi-solid media.

Influence of Helicobacter pylori oncoprotein CagA in gastric cancer: A critical-reflective analysis

Gastric cancer is the fifth most common malignancy and third leading cancer-related cause of death worldwide. Helicobacter pylori is a Gram-negative bacterium that inhabits the gastric environment of 60.3% of the world’s population and represents the main risk factor for the onset of gastric neoplasms. CagA is the most important virulence factor in H. pylori, and is a translocated oncoprotein that induces morphofunctional modifications in gastric epithelial cells and a chronic inflammatory response that increases the risk of developing precancerous lesions. Upon translocation and tyrosine phosphorylation, CagA moves to the cell membrane and acts as a pathological scaffold protein that simultaneously interacts with multiple intracellular signaling pathways, thereby disrupting cell proliferation, differentiation and apoptosis. All these alterations in cell biology increase the risk of damaged cells acquiring pro-oncogenic genetic changes. In this sense, once gastric cancer sets in, its perpetuation is independent of the presence of the oncoprotein, characterizing a “hit-and-run” carcinogenic mechanism. Therefore, this review aims to describe H. pylori- and CagA-related oncogenic mechanisms, to update readers and discuss the novelties and perspectives in this field.

Polar localization of CheO under hypoxia promotes Campylobacter jejuni chemotactic behavior within host

Campylobacter jejuni is a food-borne zoonotic pathogen of worldwide concern and the leading cause of bacterial diarrheal disease. In contrast to other enteric pathogens, C. jejuni has strict growth and nutritional requirements but lacks many virulence factors that have evolved for pathogenesis or interactions with the host. It is unclear how this bacterium has adapted to an enteric lifestyle. Here, we discovered that the CheO protein (CJJ81176_1265) is required for C. jejuni colonization of mice gut through its role in chemotactic control of flagellar rotation in oxygen-limiting environments. CheO interacts with the chemotaxis signaling proteins CheA and CheZ, and also with the flagellar rotor components FliM and FliY. Under microaerobic conditions, CheO localizes at the cellular poles where the chemosensory array and flagellar machinery are located in C. jejuni and its polar localization depends on chemosensory array formation. Several chemoreceptors that mediate energy taxis coordinately determine the bipolar distribution of CheO. Suppressor screening for a ΔcheO mutant identified that a single residue variation in FliM can alleviate the phenotype caused by the absence of CheO, confirming its regulatory role in the flagellar rotor switch. CheO homologs are only found in species of the Campylobacterota phylum, mostly species of host-associated genera Campylobacter, Helicobacter and Wolinella. The CheO results provide insights into the complexity of chemotaxis signal transduction in C. jejuni and closely related species. Importantly, the recruitment of CheO into chemosensory array to promote chemotactic behavior under hypoxia represents a new adaptation strategy of C. jejuni to human and animal intestines.

Bacteria use chemotaxis to navigate their flagellar motility towards or away from a variety of environmental stimuli. For many pathogens, chemotactic motility plays an important role in infection and disease. Understanding the mechanism of chemotaxis behavior in pathogens can help the development of therapeutic strategies by interfering with chemotactic signal transduction. In this study, we identified a novel chemotaxis protein CheO in Campylobacter jejuni, a leading cause of human gastroenteritis worldwide. We demonstrated that CheO is directly involved in chemotactic control of the flagellar motor switch, the reason that it is required for colonization of different animal models. We also provide evidences that CheO is responsive to environmental oxygen variation, with a more prominent role in energy taxis under low oxygen levels. Therefore, CheO presents a novel mechanism for C. jejuni adaptation to hypoxia conditions such as those existing in human and animal intestines. Targeting CheO and other chemotaxis regulators could reduce the survival of C. jejuni within hosts and in the food chain.

Generalizable strategy to analyze domains in the context of parent protein architecture: A CheW case study

Domains are the three-dimensional building blocks of proteins. An individual domain can occur in a variety of domain architectures that perform unique functions and are subject to different evolutionary selective pressures. We describe an approach to evaluate the variability in amino acid sequences of a single domain across architectural contexts. The ability to distinguish different evolutionary outcomes of one protein domain can help determine whether existing knowledge about a specific domain will apply to an uncharacterized protein, lead to insights and hypotheses about function, and guide experimental priorities. We developed and tested our approach on CheW-like domains (PF01584), which mediate protein/protein interactions and are difficult to compare experimentally. CheW-like domains occur in CheW scaffolding proteins, CheA kinases, and CheV proteins that regulate bacterial chemotaxis. We analyzed 16 domain architectures that included 94% of all CheW-like domains found in nature. We identified six Classes of CheW-like domains with presumed functional differences. CheV and most CheW proteins contained Class 1 domains, whereas some CheW proteins contained Class 6 (~20%) or Class 2 (~1%) domains instead. Most CheA proteins contained Class 3 domains. CheA proteins with multiple Hpt domains contained Class 4 domains. CheA proteins with two CheW-like domains contained one Class 3 and one Class 5. We also created SimpLogo, an innovative method for visualizing amino acid composition across large sets of multiple sequence alignments of arbitrary length. SimpLogo offers substantial advantages over standard sequence logos for comparison and analysis of related protein sequences. The R package for SimpLogo is freely available.

The evolutionary path of chemosensory and flagellar macromolecular machines in Campylobacterota

The evolution of macromolecular complex is a fundamental biological question, which is related to the origin of life and also guides our practice in synthetic biology. The chemosensory system is one of the complex structures that evolved very early in bacteria and displays enormous diversity and complexity in terms of composition and array structure in modern species. However, how the diversity and complexity of the chemosensory system evolved remains unclear. Here, using the Campylobacterota phylum with a robust “eco-evo” framework, we investigated the co-evolution of the chemosensory system and one of its important signaling outputs, flagellar machinery. Our analyses show that substantial flagellar gene alterations will lead to switch of its primary chemosensory class from one to another, or result in a hybrid of two classes. Unexpectedly, we discovered that the high-torque generating flagellar motor structure of Campylobacter jejuni and Helicobacter pylori likely evolved in the last common ancestor of the Campylobacterota phylum. Later lineages that experienced significant flagellar alterations lost some key components of complex scaffolding structures, thus derived simpler structures than their ancestor. Overall, this study revealed the co-evolutionary path of the chemosensory system and flagellar system, and highlights that the evolution of flagellar structural complexity requires more investigation in the Bacteria domain based on a resolved phylogenetic framework, with no assumptions on the evolutionary direction.

Chemosensory system is the most complicated signal transduction system in bacteria with great diversity in both composition and structural organization across species. One of its important signaling output is flagellar motility driven by a propeller, which is made of dozens of proteins and shows considerable variation and complexity surrounding the core motor structure in different species. The evolution of both chemosensory system and flagellum are important biological questions but remain obscure. Here, we carefully examined the evolutionary paths of chemosensory system and flagellar structure in a bacterial phylum, providing detailed molecular evidences for their co-evolution. Our study provides a paradigm to study the evolution of macromolecular complexes based on robust bacterial phylogeny and co-evolved systems/components in genome context.

Asymmetric random walks reveal that the chemotaxis network modulates flagellar rotational bias in Helicobacter pylori

The canonical chemotaxis network modulates the bias for a particular direction of rotation in the bacterial flagellar motor to help the cell migrate toward favorable chemical environments. How the chemotaxis network in Helicobacter pylori modulates flagellar functions is unknown, which limits our understanding of chemotaxis in this species. Here, we determined that H. pylori swim faster (slower) whenever their flagella rotate counterclockwise (clockwise) by analyzing their hydrodynamic interactions with bounding surfaces. This asymmetry in swimming helped quantify the rotational bias. Upon exposure to a chemo-attractant, the bias decreased and the cells tended to swim exclusively in the faster mode. In the absence of a key chemotaxis protein, CheY, the bias was zero. The relationship between the reversal frequency and the rotational bias was unimodal. Thus, H. pylori’s chemotaxis network appears to modulate the probability of clockwise rotation in otherwise counterclockwise-rotating flagella, similar to the canonical network.

Bioengineering of Bordetella pertussis Adenylate Cyclase Toxin for Vaccine Development and Other Biotechnological Purposes

The adenylate cyclase toxin, CyaA, is one of the key virulent factors produced by Bordetella pertussis, the causative agent of whooping cough. This toxin primarily targets innate immunity to facilitate bacterial colonization of the respiratory tract. CyaA exhibits several remarkable characteristics that have been exploited for various applications in vaccinology and other biotechnological purposes. CyaA has been engineered as a potent vaccine vehicle to deliver antigens into antigen-presenting cells, while the adenylate cyclase catalytic domain has been used to design a robust genetic assay for monitoring protein-protein interactions in bacteria. These two biotechnological applications are briefly summarized in this chapter.

Helicobacter pylori senses bleach (HOCl) as a chemoattractant using a cytosolic chemoreceptor

The gastric pathogen Helicobacter pylori requires a noncanonical cytosolic chemoreceptor transducer-like protein D (TlpD) for efficient colonization of the mammalian stomach. Here, we reconstituted a complete chemotransduction signaling complex in vitro with TlpD and the chemotaxis (Che) proteins CheW and CheA, enabling quantitative assays for potential chemotaxis ligands. We found that TlpD is selectively sensitive at micromolar concentrations to bleach (hypochlorous acid, HOCl), a potent antimicrobial produced by neutrophil myeloperoxidase during inflammation. HOCl acts as a chemoattractant by reversibly oxidizing a conserved cysteine within a 3His/1Cys Zn-binding motif in TlpD that inactivates the chemotransduction signaling complex. We found that H. pylori is resistant to killing by millimolar concentrations of HOCl and responds to HOCl in the micromolar range by increasing its smooth-swimming behavior, leading to chemoattraction to HOCl sources. We show related protein domains from Salmonella enterica and Escherichia coli possess similar reactivity toward HOCl. We propose that this family of proteins enables host-associated bacteria to sense sites of tissue inflammation, a strategy that H. pylori uses to aid in colonizing and persisting in inflamed gastric tissue.

Pathogenesis of Helicobacter pylori infection

In this review, we highlight progress in the last year in characterizing known virulence factors like flagella and the Cag type IV secretion system with sophisticated structural and biochemical approaches to yield new insight on the assembly and functions of these critical virulence determinants. Several aspects of Helicobacter pylori physiology were newly explored this year and evaluated for their functions during stomach colonization, including a fascinating role for the essential protease HtrA in allowing access of H. pylori to the basolateral side of the gastric epithelium through cleavage of the tight junction protein E-cadherin to facilitate CagA delivery. Molecular biology tools standard in model bacteria, including regulated gene expression during animal infection and fluorescent reporter gene fusions, were newly applied to H. pylori to explore functions for urease beyond initial colonization and establish high salt consumption as a mediator of gene expression changes. New sequencing technologies enabled validation of long postulated roles for DNA methylation in regulating H. pylori gene expression. On the cell biology side, elegant work using lineage tracing in the murine model and organoid primary cell culture systems has provided new insights into how H. pylori manipulates gastric tissue functions, locally and at a distance, to promote its survival in the stomach and induce pathologic changes. Finally, new work has bolstered the case for genomic variation as an important mechanism to generate phenotypic diversity during changing environmental conditions in the context of diet manipulation in animal infection models and during human experimental infection after vaccination.

Two Agrobacterium tumefaciens CheW Proteins Are Incorporated into One Chemosensory Pathway with Different Efficiencies

Agrobacterium tumefaciens is the agent that causes crown gall tumor disease on more than 140 species of dicotyledonous plants. Chemotaxis of A. tumefaciens toward the wound sites of the host plant is the first step to recognize the host. CheW is a coupling protein that bridges the histidine kinase CheA and the chemoreceptors to form the chemotaxis core signaling complex and plays a crucial role in the assembly and function of the large chemosensory array. Unlike all previously reported chemotaxis systems, A. tumefaciens has only one major che operon but two cheW homologs (atu2075 as cheW₁ and atu2617 as cheW₂) on unlinked loci. The in-frame deletion of either cheW gene significantly affects A. tumefaciens chemotaxis but does not abolish the chemotaxis, unless both cheW genes were deleted. The effect of cheW₂ deletion on the chemotaxis is more severe than that of cheW₁ deletion. Either CheW can interact with CheA and couple it to the cell poles. The promoter activity of cheW₂ is always higher than that of cheW₁ under all of the tested conditions. When two cheW genes were adjusted to the same expression level by using the identical promoter, the difference between the effects of two CheW proteins on the chemotaxis still existed. Therefore, we envision that both the different molecular ratio of two CheW proteins in cell and the different affinities of two CheW proteins with CheA and chemoreceptors result in the efficiency difference of two CheW proteins in functioning in the large chemosensory array.

Colonization, localization, and inflammation: the roles of H. pylori chemotaxis in vivo

Helicobacter pylori is a Gram-negative bacterium that infects half of the world's population, causing gastritis, peptic ulcers, and gastric cancer. To establish chronic stomach infection, H. pylori utilizes chemotaxis, driven by a conserved signal transduction system. Chemotaxis allows H. pylori to sense an array of environmental and bacterial signals within the stomach, guiding its motility towards its preferred niche within the gastric mucosa and glands. Fine-tuned localization, regulated by the chemotaxis system, enables robust colonization during the acute stage of infection. During chronic infection, chemotaxis helps maintain bacterial populations and modulates the host immune response. Given its importance in host colonization and disease, chemotaxis is an attractive target for future treatments against H. pylori infections.

Pathogenesis of Helicobacter pylori infection

Helicobacter pylori is responsible for the most commonly found infection in the world's population. It is the major risk factor for gastric cancer development. Numerous studies published over the last year provide new insights into the strategies employed by H. pylori to adapt to the extreme acidic conditions of the gastric environment, to establish persistent infection and to deregulate host functions, leading to gastric pathogenesis and cancer. In this review, we report recent data on the mechanisms involved in chemotaxis, on the essential role of nickel in acid resistance and gastric colonization, on the importance of adhesins and Hop proteins and on the role of CagPAI-components and CagA. Among the host functions, a special focus has been made on the escape from immune response, the ability of bacteria to induce genetic instability and modulate telomeres, the mechanism of autophagy and the deregulation of micro RNAs.