scholarly journals Structural basis for the recognition of muramyltripeptide byHelicobacter pyloriCsd4, aD,L-carboxypeptidase controlling the helical cell shape

2014 ◽  
Vol 70 (11) ◽  
pp. 2800-2812 ◽  
Author(s):  
Hyoun Sook Kim ◽  
Jieun Kim ◽  
Ha Na Im ◽  
Doo Ri An ◽  
Mijoon Lee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cell Shape ◽  
Gastrointestinal Diseases ◽  
Human Stomach ◽  
Structural Basis ◽  
Cross Linking ◽  
Peptic Ulcers ◽  
Significant Structural Change ◽  
Peptidoglycan Hydrolases ◽  
H Pylori

Helicobacter pyloriinfection causes a variety of gastrointestinal diseases, including peptic ulcers and gastric cancer. Its colonization of the gastric mucosa of the human stomach is a prerequisite for survival in the stomach. Colonization depends on its motility, which is facilitated by the helical shape of the bacterium. InH. pylori, cross-linking relaxation or trimming of peptidoglycan muropeptides affects the helical cell shape. Csd4 has been identified as one of the cell shape-determining peptidoglycan hydrolases inH. pylori. It is a Zn2+-dependent D,L-carboxypeptidase that cleaves the bond between the γ-D-Glu and themDAP of the non-cross-linked muramyltripeptide (muramyl-L-Ala-γ-D-Glu-mDAP) of the peptidoglycan to produce the muramyldipeptide (muramyl-L-Ala-γ-D-Glu) andmDAP. Here, the crystal structure ofH. pyloriCsd4 (HP1075 in strain 26695) is reported in three different states: the ligand-unbound form, the substrate-bound form and the product-bound form.H. pyloriCsd4 consists of three domains: an N-terminal D,L-carboxypeptidase domain with a typical carboxypeptidase fold, a central β-barrel domain with a novel fold and a C-terminal immunoglobulin-like domain. The D,L-carboxypeptidase domain recognizes the substrate by interacting primarily with the terminalmDAP moiety of the muramyltripeptide. It undergoes a significant structural change upon binding eithermDAP or themDAP-containing muramyltripeptide. It it also shown that Csd5, another cell-shape determinant inH. pylori, is capable of interacting not only withH. pyloriCsd4 but also with the dipeptide product of the reaction catalyzed by Csd4.

scholarly journals Structural basis for the peptidoglycan recognition by Helicobacter pylori Csd4

2014 ◽  
Vol 70 (a1) ◽  
pp. C817-C817
Author(s):  
Hyoun Sook Kim ◽  
Byung Woo Han ◽  
Byung Il Lee ◽  
Se Won Suh
Keyword(s):  
Helicobacter Pylori ◽  
Gastric Mucosa ◽  
Cell Shape ◽  
Gastrointestinal Diseases ◽  
Structural Basis ◽  
Free Form ◽  
Peptic Ulcers ◽  
Carboxypeptidase H ◽  
Ligand Free ◽  
H Pylori

Helicobacter pylori infection causes a variety of gastrointestinal diseases including peptic ulcers and gastric cancer. The colonization of this bacterium in the gastric mucosa is required for the survival in the stomach. Its colonization of the gastric mucosa of human stomach depends on its motility, which is facilitated by the helical cell shape. In H. pylori, crosslinking relaxation or trimming of peptidoglycan muropeptide affects the helical shape. Among several cell shape-determining peptidoglycan hydrolases identified in H. pylori, Csd4 is a Zn2+-dependent D,L-carboxypeptidase that cleaves the bond between the γ-D-Glu and mDAP bond of the uncrosslinked tripeptide of peptidoglycan (L-Ala-γ-D-Glu-mDAP) to produce L-Ala-γ-D-Glu dipeptide and mDAP, promoting the helical cell shape. Inhibition of D,L-carboxypeptidase activity of Csd4 may represent a novel therapeutic approach. We report here the crystal structures of H. pylori Csd4 in three different states: the ligand-free form, the substrate-bound form, and the product-bound form. H. pylori Csd4 consists of three domains: an N-terminal D,L-carboxypeptidase domain, a novel β-barrel domain, and a C-terminal immunoglobulin-like domain. Our ligand-bound structures provide structural basis of peptidoglycan recognition by D,L-carboxypeptidase. H. pylori Csd4 recognizes primarily the terminal mDAP of the tripeptide substrate and undergoes a significant structural change upon binding either mDAP or mDAP-containing tripeptide.

scholarly journals A Genome-WideHelicobacter pyloriMorphology Screen Uncovers a Membrane-Spanning Helical Cell Shape Complex

2019 ◽  
Vol 201 (14) ◽  
Author(s):  
Desirée C. Yang ◽  
Kris M. Blair ◽  
Jennifer A. Taylor ◽  
Timothy W. Petersen ◽  
Tate Sessler ◽  
...  
Keyword(s):  
Cell Wall ◽  
Helicobacter Pylori ◽  
Light Scattering ◽  
Protein Interactions ◽  
Cell Morphology ◽  
Cell Shape ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
Content Type ◽  
H Pylori

ABSTRACTEvident in its name, the gastric pathogenHelicobacter pylorihas a helical cell morphology which facilitates efficient colonization of the human stomach. An improved light-focusing strategy allowed us to robustly distinguish even subtle perturbations ofH. pyloricell morphology by deviations in light-scattering properties measured by flow cytometry. Profiling of an arrayed genome-wide deletion library identified 28 genes that influence different aspects of cell shape, including properties of the helix, cell length or width, cell filament formation, cell shape heterogeneity, and cell branching. Included in this mutant collection were two that failed to form any helical cells, a soluble lytic transglycosylase and a previously uncharacterized putative multipass inner membrane protein HPG27_0728, renamed Csd7. A combination of cell fractionation, mutational, and immunoprecipitation experiments show that Csd7 and Csd2 collaborate to stabilize the Csd1 peptidoglycan (PG) endopeptidase. Thus, bothcsd2andcsd7mutants show the same enhancement of PG tetra-pentapeptide cross-linking ascsd1mutants. Csd7 also links Csd1 with the bactofilin CcmA via protein-protein interactions. Although Csd1 is stable inccmAmutants, these mutants show altered PG tetra-pentapeptide cross-linking, suggesting that Csd7 may directly or indirectly activate as well as stabilize Csd1. These data begin to illuminate a highly orchestrated program to regulate PG modifications that promote helical shape, which includes nine nonessential nonredundant genes required for helical shape and 26 additional genes that further modifyH. pylori’s cell morphology.IMPORTANCEThe stomach ulcer and cancer-causing pathogenHelicobacter pylorihas a helical cell shape which facilitates stomach infection. Using light scattering to measure perturbations of cell morphology, we identified 28 genes that influence different aspects of cell shape. A mutant in a previously uncharacterized protein renamed Csd7 failed to form any helical cells. Biochemical analyses showed that Csd7 collaborates with other proteins to stabilize the cell wall-degrading enzyme Csd1. Csd7 also links Csd1 with a putative filament-forming protein via protein-protein interactions. These data suggest that helical cell shape arises from a highly orchestrated program to regulate cell wall modifications. Targeting of this helical cell shape-promoting program could offer new ways to block infectivity of this important human pathogen.

scholarly journals Structural basis of sialidase in complex with geranylated flavonoids as potent natural inhibitors

2014 ◽  
Vol 70 (5) ◽  
pp. 1357-1365 ◽  
Author(s):  
Youngjin Lee ◽  
Young Bae Ryu ◽  
Hyung-Seop Youn ◽  
Jung Keun Cho ◽  
Young Min Kim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Domain ◽  
Enzyme Inhibitor ◽  
Gastrointestinal Diseases ◽  
Structural Basis ◽  
Cellular Interactions ◽  
Inhibitory Effects ◽  
Inhibitor Complex ◽  
Structural Framework ◽  
Natural Inhibitors

Sialidase catalyzes the removal of a terminal sialic acid from glycoconjugates and plays a pivotal role in nutrition, cellular interactions and pathogenesis mediating various infectious diseases including cholera, influenza and sepsis. An array of antiviral sialidase agents have been developed and are commercially available, such as zanamivir and oseltamivir for treating influenza. However, the development of bacterial sialidase inhibitors has been much less successful. Here, natural polyphenolic geranylated flavonoids which show significant inhibitory effects againstCp-NanI, a sialidase fromClostridium perfringens, are reported. This bacterium causes various gastrointestinal diseases. The crystal structure of theCp-NanI catalytic domain in complex with the best inhibitor, diplacone, is also presented. This structure explains how diplacone generates a stable enzyme–inhibitor complex. These results provide a structural framework for understanding the interaction between sialidase and natural flavonoids, which are promising scaffolds on which to discover new anti-sialidase agents.

scholarly journals Helicobacter pyloriin First Nations and Recent Immigrant Populations in Canada

2012 ◽  
Vol 26 (2) ◽  
pp. 97-103 ◽  
Author(s):  
Nicola L Jones ◽  
Naoki Chiba ◽  
Carlo Fallone ◽  
Alan Thomson ◽  
Richard Hunt ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
First Nations ◽  
Cost Effective ◽  
Gastrointestinal Diseases ◽  
Population Based ◽  
Peptic Ulcers ◽  
Canadian Population ◽  
High Prevalence ◽  
H Pylori ◽  
Low Prevalence

The diminishing prevalence ofHelicobacter pyloriinfection among most segments of the Canadian population has led to changes in the etiologies and patterns of associated upper gastrointestinal diseases, including fewer peptic ulcers and their complications. Canadian Aboriginals and recent immigrants are among populations in which the prevalence ofH pyloriinfection remains high and, therefore, the health risks imposed byH pyloriremain a significant concern. Population-based strategies forH pylorieradication in groups with a low prevalence of infection are unlikely to be cost effective, but such measures are attractive in groups in which the prevalence rates of infection remain substantial. In addition to a lower prevalence of peptic ulcers and dyspepsia, the public health value of eradication may be particularly important if this leads to a reduction in the prevalence of gastric cancer in high prevalence groups. Therefore The Canadian Helicobacter Study Group held a conference that brought together experts in the field to address these issues, the results of which are reviewed in the present article. Canadians with the highest prevalence ofH pyloriinfection are an appropriate focus for considering the health advantages of eradicating persistent infection. In Canadian communities with a high prevalence of bothH pyloriand gastric cancer, there remains an opportunity to test the hypothesis thatH pyloriinfection is a treatable risk factor for malignancy.

scholarly journals Structure of α-carbonic anhydrase from the human pathogenHelicobacter pylori

2015 ◽  
Vol 71 (8) ◽  
pp. 1005-1011 ◽  
Author(s):  
Maria Elena Compostella ◽  
Paola Berto ◽  
Francesca Vallese ◽  
Giuseppe Zanotti
Keyword(s):  
Crystal Structure ◽  
Carbonic Anhydrase ◽  
Bacterial Colonization ◽  
Human Stomach ◽  
Negative Ion ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Antibiotic Drugs ◽  
H Pylori ◽  
Definition Of

The crystal structure of α-carbonic anhydrase, an enzyme present in the periplasm ofHelicobacter pylori, a bacterium that affects humans and that is responsible for several gastric pathologies, is described. Two enzyme monomers are present in the asymmetric unit of the monoclinic space groupP21, forming a dimer in the crystal. Despite the similarity of the enzyme structure to those of orthologues from other species, theH. pyloriprotein has adopted peculiar features in order to allow the bacterium to survive in the difficult environment of the human stomach. In particular, the crystal structure shows how the bacterium has corrected for the mutation of an essential amino acid important for catalysis using a negative ion from the medium and how it localizes close to the inner membrane in the periplasm. Since carbonic anhydrase is essential for the bacterial colonization of the host, it is a potential target for antibiotic drugs. The definition of the shape of the active-site entrance and cavity constitutes a basis for the design of specific inhibitors.

scholarly journals Structure of Csd3 fromHelicobacter pylori, a cell shape-determining metallopeptidase

2015 ◽  
Vol 71 (3) ◽  
pp. 675-686 ◽  
Author(s):  
Doo Ri An ◽  
Hyoun Sook Kim ◽  
Jieun Kim ◽  
Ha Na Im ◽  
Hye Jin Yoon ◽  
...  
Keyword(s):  
Cell Shape ◽  
Peptide Bond ◽  
Gastrointestinal Diseases ◽  
Human Gastric Mucosa ◽  
Tail Region ◽  
The Core ◽  
Sequence Identity ◽  
Endopeptidase Activity ◽  
A Cell ◽  
H Pylori

Helicobacter pyloriis associated with various gastrointestinal diseases such as gastritis, ulcers and gastric cancer. Its colonization of the human gastric mucosa requires high motility, which depends on its helical cell shape. Seven cell shape-determining genes (csd1,csd2,csd3/hdpA,ccmA,csd4,csd5andcsd6) have been identified inH. pylori. Their proteins play key roles in determining the cell shape through modifications of the cell-wall peptidoglycan by the alteration of cross-linking or by the trimming of peptidoglycan muropeptides. Among them, Csd3 (also known as HdpA) is a bifunctional enzyme. Its D,D-endopeptidase activity cleaves the D-Ala4-mDAP3peptide bond between cross-linked muramyl tetrapeptides and pentapeptides. It is also a D,D-carboxypeptidase that cleaves off the terminal D-Ala5from the muramyl pentapeptide. Here, the crystal structure of this protein has been determined, revealing the organization of its three domains in a latent and inactive state. The N-terminal domain 1 and the core of domain 2 share the same fold despite a very low level of sequence identity, and their surface-charge distributions are different. The C-terminal LytM domain contains the catalytic site with a Zn2+ion, like the similar domains of other M23 metallopeptidases. Domain 1 occludes the active site of the LytM domain. The core of domain 2 is held against the LytM domain by the C-terminal tail region that protrudes from the LytM domain.

scholarly journals Cost-effectiveness Analysis Comparing Vonoprazanbased Triple Therapy with Proton Pump Inhibitorbased Therapy in the Treatment of Helicobacter pylori Infection in Thailand

2021 ◽  
Vol 73 (12) ◽  
pp. 823-831
Author(s):  
Jadesada Lertsirimunkong ◽  
Wiwat Thavornwattanayong ◽  
Yosita Napuk ◽  
Watcharapong Ajcharoen ◽  
Vipavee Chaisitsanguan ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Cost Effectiveness ◽  
Triple Therapy ◽  
Gastrointestinal Diseases ◽  
Dominant Strategy ◽  
Peptic Ulcers ◽  
Life Years ◽  
First Choice ◽  
H Pylori ◽  
The Cost

Objective: Helicobacter pylori (H. pylori) infection is one of the leading causes of gastrointestinal diseases such as dyspepsia, peptic ulcers. Thailand has a 45.9% prevalence of the infection and an increasing rate of resistance to clarithromycin, leading to standard treatments being less successful. Vonoprazan represents a novel drug offering a new treatment regimen. Although vonoprazan has been available in Thailand since 2019, its cost-effectiveness has not been studied previously.Materials and Methods: This study analysed the cost-effectiveness of vonoprazan-based triple therapy compared with PPI-based therapy, in treating clarithromycin resistant H. pylori, by using the markov model from a societal perspective.Results: The total cost of vonoprazan-based triple therapy, levofloxacin-PPI based triple therapy and concomitant-PPI therapy were 784,932.08 baht, 783,863.65 baht and 783,874.55 baht respectively. The quality-adjusted life years (QALYs) of vonoprazan-based triple therapy, levofloxacin-PPI based triple therapy and concomitant-PPI therapy were 25.1118 years, 25.1147 years and 25.1054 years respectively. The cost-effectiveness ratio (CER) of vonoprazanbased triple therapy, levofloxacin-PPI based triple therapy and concomitant-PPI therapy were 31,257.50 baht/ QALYs, 31,211.35 baht/QALYs and 31,223.34 baht per QALYs respectively.Conclusion: Therefore, levofloxacin-PPI based triple therapy was found to be the most cost-effective regimen and the dominant strategy compared with concomitant-PPI or vonoprazan-based triple therapy. It provided higher QALYs and lower treatment costs. Levofloxacin-PPI based triple therapy should be the first choice of an alternative strategy in treating clarithromycin-resistant H. pylori. The results of this study can be used by policymakers to help inform their decisions.

scholarly journals Crystal structure of the Csd3 protein from Helicobacter pylori

2014 ◽  
Vol 70 (a1) ◽  
pp. C1630-C1630
Author(s):  
Doo Ri An ◽  
Se Won Suh
Keyword(s):  
Crystal Structure ◽  
Helicobacter Pylori ◽  
Active Site ◽  
Cell Shape ◽  
Proteolytic Processing ◽  
Anomalous Scattering ◽  
Gastric Mucus ◽  
Peptide Hydrolysis ◽  
Substrate Peptide ◽  
H Pylori

The helical cell shape of Helicobacter pylori facilitates the penetration of thick gastric mucus and promotes virulence. The peptidoglycan plays a structural role in the bacterial cell wall and its controlled modification is essential for determining the helical shape. Several H. pylori genes were identified to contribute to its helical cell shape through alterations in peptidoglycan crosslinking and trimming of the peptide (Sycuro et al., 2010; Sycuro et al., 2012). One of them is the hp0506 gene that encodes a putative periplasmic peptidase belonging to the M23-family of zinc-metallopeptidase (Sycuro et al., 2010). The HP0506 protein carries out not only a D,D-endopeptidase activity but also a D,D-carboxypeptidase activity. Hence, it has been named Helicobacter D,D-peptidase A (HdpA) and cell shape determinant 3 (Csd3). Csd3 is the first enzyme belonging to the M23-peptidase family that can perform the D,D-carboxypeptidation to regulate the cell shape (Mathilde et al., 2010). To gain structural and functional insights at the molecular level, we have determined the crystal structure of Csd3 at 2.1 Å resolution by using the Pt SAD data. H. pylori Csd3 consists of three domains including a LytM domain, which contains the highly conserved active site motif among the M23 metallopeptidase family. An anomalous scattering experiment with Zn2+ confirmed the metal-binding site in the active site. The Zn2+ ion is tetrahedrally coordinated and a catalytic water for peptide hydrolysis is absent in the active site of Csd3. Furthermore, domain 1 blocks the active site, thus prohibiting the substrate peptide binding. Our mass analysis shows that the full-length Csd3 is inactive as the D,D-carboxypeptidase. These results suggest that proteolytic processing may be necessary for the activation of Csd3.

scholarly journals Effects of Infections of Helicobacter Pylori With Different Virulent Factors on Severity of Gastrointestinal Diseases

2021 ◽  
Author(s):  
Yan Zhang ◽  
Xiang-ming Fang ◽  
Kui Tian
Keyword(s):  
Helicobacter Pylori ◽  
Bacterial Infections ◽  
Gastrointestinal Diseases ◽  
Ulcer Bleeding ◽  
Type I ◽  
Peptic Ulcers ◽  
Type Ii ◽  
Type Iii ◽  
Significant Difference ◽  
H Pylori

Abstract Background: Helicobacter Pylori (H. pylori) infection, one of the most common chronic bacterial infections, has been considered as a major cause of diseases such as lymphoma, gastritis, peptic ulcers, and stomach cancer. Here, we aimed to determine whether H. pylori strains with different virulence contribute to the gastrointestinal diseases differentially in clinical settings, which may provide future direction for eradication of H. pylori infection. Methods: We recruited 501 patients with gastrointestinal disorders for analysis of antibody types of H. pylori infection. Correlation analysis was done to determine the association of different virulence of H. pylori with patients’ baseline parameters and personal disease history. Next, subjects with each type of anti- H. pylori infection antibody were subjected to esophagogastro duodenoscopy（EGD) and colonoscopy examinations. The pathological diagnosis was also conducted in endoscopic samples. Chi-squared test was employed to compare the differences in endoscopic assessments and pathological findings among three types of H. pylori infection determined by the presence of antibodies to virulent factors. Results: There were 296 cases with Type I H. pylori infection, 120 cases with Type II H. pylori infection, and 85 cases without H. pylori infection (negative, Type III). No correlation was found between different virulence of H. pylori and participants’ baseline data (P > 0.05). EGD results showed that the incidences of peptic ulcer, bleeding and malignant lesions in Type I group were significantly higher than that in Type II and Type III (P＜0.05). Despite of increased trends of incidences of precancerous alterations and the malignance in Type I group compared with type II and III groups, there was no significant difference (P > 0.05). In addition, coloscopic features were similar among three groups. On the other hand, infections of H. pylori with cytotoxin-associated gene A (CagA) and/or vacuolating cytotoxin A (VacA) virulent factors resulted in more severe histopathological diseases than that with only Ure A/B factor and without infection (P < 0.05). Conclusions: Infections of H. pylori strains with CagA/VacA are likely to cause development of severe gastrointestinal diseases. These results are helpful to treat for H. pylori infection clinically.

scholarly journals High prevalence of cytotoxin positive Helicobacter pylori in patients unrelated to the presence of peptic ulcers in Japan

Gut ◽  
1997 ◽  
Vol 41 (4) ◽  
pp. 463-468 ◽  
Author(s):  
K Ogura ◽  
F Kanai ◽  
S Maeda ◽  
H Yoshida ◽  
M Ogura ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Western Blot ◽  
Gastrointestinal Diseases ◽  
Normal Mucosa ◽  
Peptic Ulcers ◽  
Western Blot Assay ◽  
Vacuolating Cytotoxin ◽  
Western Blot Method ◽  
High Prevalence ◽  
H Pylori

Background—It has been reported that infection with vacuolating cytotoxin positive Helicobacter pyloristrains is associated with gastroduodenal disease in Western countries.Aims—To evaluate the prevalence of cytotoxin producing strains among patients with H pyloriinfection in relation to gastrointestinal diseases in Japan.Patients—Ninety seven patients undergoing endoscopy.Methods—A Western blot assay was conducted to detect serum antibodies against the cytotoxin using recombinant cytotoxin (VacA protein) as an antigen. To obtain a purified recombinant cytotoxin, the vacA gene (2233 nucleotides) was cloned into an expression vector to produce the protein (744 amino acids), which was expressed in Escherichia coli.Results—Serum IgG antibodies to the cytotoxin were present in 85%, 95%, 95%, and 100% of infected patients with gastric ulcer (n=26), duodenal ulcer (n=21), chronic gastritis (n=19), and endoscopically normal mucosa (n=14), respectively.Conclusion—The western blot method using recombinant VacA protein is simple and useful for detecting antibody to vacuolating cytotoxin. This method showed antibodies against cytotoxin were highly prevalent, even in subjects with endoscopically normal mucosa in Japan, indicating that the cytotoxin may not be an independent cause of gastrointestinal diseases induced by H pylori infection.

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