Structural analysis of the flagellar capping protein FliD from Helicobacter pylori

How Long Will It Take to Launch an Effective Helicobacter pylori Vaccine for Humans?

Helicobacter pylori infection often occurs in early childhood, and can last a lifetime if not treated with medication. H. pylori infection can also cause a variety of stomach diseases, which can only be treated with a combination of antibiotics. Combinations of antibiotics can cure H. pylori infection, but it is easy to relapse and develop drug resistance. Therefore, a vaccine is a promising strategy for prevention and therapy for the infection of H. pylori. After decades of research and development, there has been no appearance of any H. pylori vaccine reaching the market, unfortunately. This review summarizes the aspects of candidate antigens, immunoadjuvants, and delivery systems in the long journey of H. pylori vaccine research, and also introduces some clinical trials that have displayed encouraging or depressing results. Possible reasons for the inability of an H. pylori vaccine to be available over the counter are cautiously discussed and some propositions for the future of H. pylori vaccines are outlined.

Contribution of flagellar cap gene in virulence and pathogenicity of Aeromonas veronii

Aeromonas veronii is an important zoonotic and aquatic pathogen that causes a number of illnesses in both humans and animals. It is related to gastroenteritis, skin and soft tissue infections and bacteremia in humans, as well as causing significant economic losses in aquaculture owing to fish sepsis. Here, we constructed the flagellar cap gene (fliD) mutant strain of A. veronii by suicide plasmid-mediated homologous recombination system and analysed its characteristics. It was found that the deletion of fliD had no effect on growth and biochemical properties and could be inherited stably. However, the motility of A. veronii ΔfliD was significantly reduced, the flagellum was defective and the biofilm formation was attenuated compared with that of A. veronii wild-type strain. In vivo experiments revealed that the colonization capacity of ΔfliD was significantly lower than that of the wild-type strain in the period of first 24 h, and the median lethal dose (LD₅₀ ) was 56 times higher than that of the wild-type strain. The Cyprinus carpio infected with the wild-type strain indicated faster death speed and more severe clinical signs compared to ΔfliD strain. These results suggest that fliD is closely related to the virulence of A. veronii and plays an important role in pathogenicity, providing the foundation for pathogenic mechanism studies of A. veronii.

A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor

Genome minimization is an effective way for industrial chassis development. In this study, Zymomonas mobilis ZMNP, a plasmid-free mutant strain of Z. mobilis ZM4 with four native plasmids deleted, was constructed using native type I-F CRISPR-Cas system. Cell growth of ZMNP under different temperatures and industrial effluent of xylose mother liquor were examined to investigate the impact of native plasmid removal. Despite ZMNP grew similarly as ZM4 under different temperatures, ZMNP had better xylose mother liquor utilization than ZM4. In addition, genomic, transcriptomic, and proteomic analyses were applied to unravel the molecular changes between ZM4 and ZMNP. Whole-genome resequencing result indicated that an S267P mutation in the C-terminal of OxyR, a peroxide-sensing transcriptional regulator, probably alters the transcription initiation of antioxidant genes for stress responses. Transcriptomic and proteomic studies illustrated that the reason that ZMNP utilized the toxic xylose mother liquor better than ZM4 was probably due to the upregulation of genes in ZMNP involving in stress responses as well as cysteine biosynthesis to accelerate the intracellular ROS detoxification and nucleic acid damage repair. This was further confirmed by lower ROS levels in ZMNP compared to ZM4 in different media supplemented with furfural or ethanol. The upregulation of stress response genes due to the OxyR mutation to accelerate ROS detoxification and DNA/RNA repair not only illustrates the underlying mechanism of the robustness of ZMNP in the toxic xylose mother liquor, but also provides an idea for the rational design of synthetic inhibitor-tolerant microorganisms for economic lignocellulosic biochemical production.

Comparing Diagnostic Accuracy of the fliD Gene and the glmM Gene in Helicobacter pylori

Background: Helicobacter pylori (H. pylori) is one of the most common human bacterial infections, accounting for the infection of half of the world's population. The polymerase chain reaction (PCR) has high specificity and sensitivity in diagnosing this bacterial infection. Objectives: The present study aimed to compare the sensitivity and specificity of the fliD gene and the most widely used glmM gene in the PCR technique. Methods: The research population encompassed patients with indications for upper endoscopy. This cross-sectional study compared the sensitivity and specificity of a proposed gene (fliD) with the most widely used glmM gene to detect the H. pylori infection in tissue samples. Results: The participants encompassed ninety-nine participants aged above 18 years. Their median age was 45.92 ± 13.63 years. The most common complaints of the patients were epigastric pain and heartburn. Our described gold standard detected 61.6% and 38.4% as positive and negative, respectively. The sensitivity and specificity were 72.1% and 100.0% for the routine PCR (glmM gene) and 80.3% and 94.7% for the proposed PCR (fliD gene). Conclusions: Different genes have been used to detect H. pylori in PCR. The glmM gene is easily used to diagnose the H. pylori infection; however, according to the present findings, the fliD gene has higher sensitivity than the glmM gene. Accordingly, the former can be used as a screening gene for the H. pylori infection in the PCR technique.

Molecular Determinants of Filament Capping Proteins Required for the Formation of Functional Flagella in Gram-Negative Bacteria

Bacterial flagella are cell surface protein appendages that are critical for motility and pathogenesis. Flagellar filaments are tubular structures constructed from thousands of copies of the protein flagellin, or FliC, arranged in helical fashion. Individual unfolded FliC subunits traverse the filament pore and are folded and sorted into place with the assistance of the flagellar capping protein complex, an oligomer of the FliD protein. The FliD filament cap is a stool-like structure, with its D2 and D3 domains forming a flat head region, and its D1 domain leg-like structures extending perpendicularly from the head towards the inner core of the filament. Here, using an approach combining bacterial genetics, motility assays, electron microscopy and molecular modeling, we define, in numerous Gram-negative bacteria, which regions of FliD are critical for interaction with FliC subunits and result in the formation of functional flagella. Our data indicate that the D1 domain of FliD is its sole functionally important domain, and that its flexible coiled coil region comprised of helices at its extreme N- and C-termini controls compatibility with the FliC filament. FliD sequences from different bacterial species in the head region are well tolerated. Additionally, head domains can be replaced by small peptides and larger head domains from different species and still produce functional flagella.

Bacterial Flagellar Filament: A Supramolecular Multifunctional Nanostructure

The bacterial flagellum is a complex and dynamic nanomachine that propels bacteria through liquids. It consists of a basal body, a hook, and a long filament. The flagellar filament is composed of thousands of copies of the protein flagellin (FliC) arranged helically and ending with a filament cap composed of an oligomer of the protein FliD. The overall structure of the filament core is preserved across bacterial species, while the outer domains exhibit high variability, and in some cases are even completely absent. Flagellar assembly is a complex and energetically costly process triggered by environmental stimuli and, accordingly, highly regulated on transcriptional, translational and post-translational levels. Apart from its role in locomotion, the filament is critically important in several other aspects of bacterial survival, reproduction and pathogenicity, such as adhesion to surfaces, secretion of virulence factors and formation of biofilms. Additionally, due to its ability to provoke potent immune responses, flagellins have a role as adjuvants in vaccine development. In this review, we summarize the latest knowledge on the structure of flagellins, capping proteins and filaments, as well as their regulation and role during the colonization and infection of the host.

Structural Conservation and Adaptation of the Bacterial Flagella Motor

Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.

Review - Helicobacter, inflammation, immunology and vaccines

Understanding the mechanisms involved in induction and regulation of the immune and inflammatory response to Helicobacter pylori is extremely important in determining disease outcomes. H pylori expresses a plethora of factors that influence the host response. Vaccines against H pylori are desperately needed for the prevention of gastric carcinogenesis, especially with the increasing trends in antimicrobial resistance. This review summarizes some important findings, published between 1 April 2019 and 31 March 2020, in the areas of H pylori-mediated inflammation, immunity and vaccines.

Atomic structure of the Campylobacter jejuni flagellar filament reveals how ε Proteobacteria escaped Toll-like receptor 5 surveillance

Vertebrates, from zebra fish to humans, have an innate immune recognition of many bacterial flagellins. This involves a conserved eight-amino acid epitope in flagellin recognized by the Toll-like receptor 5 (TLR5). Several important human pathogens, such as Helicobacter pylori and Campylobacter jejuni, have escaped TLR5 activation by mutations in this epitope. When such mutations were introduced into Salmonella flagellin, motility was abolished. It was previously argued, using very low-resolution cryoelectron microscopy (cryo-EM), that C. jejuni accommodated these mutations by forming filaments with 7 protofilaments, rather than the 11 found in other bacteria. We have now determined the atomic structure of the C. jejuni G508A flagellar filament from a 3.5-Å-resolution cryo-EM reconstruction, and show that it has 11 protofilaments. The residues in the C. jejuni TLR5 epitope have reduced contacts with the adjacent subunit compared to other bacterial flagellar filament structures. The weakening of the subunit-subunit interface introduced by the mutations in the TLR5 epitope is compensated for by extensive interactions between the outer domains of the flagellin subunits. In other bacteria, these outer domains can be nearly absent or removed without affecting motility. Furthermore, we provide evidence for the stabilization of these outer domain interactions through glycosylation of key residues. These results explain the essential role of glycosylation in C. jejuni motility, and show how the outer domains have evolved to play a role not previously found in other bacteria.

The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation

The bacterial flagellum is a remarkable molecular motor, whose primary function in bacteria is to facilitate motility through the rotation of a filament protruding from the bacterial cell. A cap complex, consisting of an oligomer of the protein FliD, is localized at the tip of the flagellum, and is essential for filament assembly, as well as adherence to surfaces in some bacteria. However, the structure of the intact cap complex, and the molecular basis for its interaction with the filament, remains elusive. Here we report the cryo-EM structure of the Campylobacter jejuni cap complex, which reveals that FliD is pentameric, with the N-terminal region of the protomer forming an extensive set of contacts across several subunits, that contribute to FliD oligomerization. We also demonstrate that the native C. jejuni flagellum filament is 11-stranded, contrary to a previously published cryo-EM structure, and propose a molecular model for the filament-cap interaction.

FliD forms a cap complex at the tip of bacterial flagella and is essential for flagellum filament assembly. Here, the authors present the cryo-EM structure of the Campylobacter jejuni cap complex, revealing a pentameric assembly of FliD and further show that the C. jejuni flagellum filament is 11-stranded.

Crystal structure of the flagellar cap protein FliD from Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus is a predator bacterial species of the Deltaproteobacteria class that requires flagellum-mediated motility to initiate the parasitization of other gram-negative bacteria. The flagellum is capped by FliD, which polymerizes flagellin into a flagellar filament. FliD has been reported to function as a species-specific oligomer, such as a tetramer, a pentamer, or a hexamer, in members of the Gammaproteobacteria class. However, the oligomeric state and structural features of FliD from bacterial species outside the Gammaproteobacteria class are unknown. Based on structural and biochemical analyses, we report here that B. bacteriovorus FliD (bbFliD) forms a tetramer. bbFliD tetramerizes in a circular head-to-tail arrangement by inserting the D2 domain of one subunit into the concave surface of the second subunit generated between the D2 and D3 domains as observed in Serratia marcescens FliD. However, bbFliD adopts a more compact and flat oligomeric structure, which exhibits a more extended tetramerization interface flanked by two additional surfaces due to different intersubunit and interdomain organizations as well as an elongated loop. In conclusion, FliD from B. bacteriovorus, which belongs to the Deltaproteobacteria class, also produces a tetramer similar to FliD from Gammaproteobacterial species but adopts a unique species-specific oligomeric structure.