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 Crystal structure of JHP933 from Helicobacter pylori J99

2014 ◽  
Vol 70 (a1) ◽  
pp. C823-C823
Author(s):  
Sang Jae Lee ◽  
Ji Young Yoon ◽  
Bong-Jin Lee ◽  
Se Won Suh
Keyword(s):  
Crystal Structure ◽  
Helicobacter Pylori ◽  
Peptic Ulcer ◽  
Functional Characterization ◽  
Domain Architecture ◽  
Structural Similarity ◽  
Terminal Domain ◽  
Plasticity Region ◽  
H Pylori ◽  
And Function

Helicobacter pylori infection is the main cause of chronic gastritis, gastric mucosal atrophy, peptic ulcer, and some forms of gastric cancer. There has been considerable interest in strain-specific genes found outside of the cag pathogenicity island, especially genes in the plasticity regions of H. pylori. In H. pylori strain J99, the plasticity region contains 48 genes ranging from jhp0914 to jhp0961. Because little is known about many of these genes in the plasticity region, further studies are necessary to elucidate their roles in H. pylori-associated pathogenesis. The JHP933 protein, encoded by the jhp0933 gene in the plasticity region of H. pylori J99, is one of the prevalently expressed proteins in some gastritis and peptic ulcer patients. However, its structure and function remain unknown. Here, we have determined the crystal structure of JHP933, revealing the first two-domain architecture of DUF1814 family. The N-terminal domain has the nucleotidyltransferase fold and the C-terminal domain is a helix bundle. Structural similarity of JHP933 to known nucleotidyltransferases is very remote, suggesting that it may function as a novel nucleotidyltransferase. It is expected that this study will facilitate functional characterization of JHP933 to obtain an insight into its role in pathogenesis by the H. pylori plasticity region.

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 Helicobacter pylori in vivo causes structural changes in the adherent gastric mucus layer but barrier thickness is not compromised

Gut ◽  
1998 ◽  
Vol 43 (4) ◽  
pp. 470-475 ◽  
Author(s):  
J L Newton ◽  
N Jordan ◽  
L Oliver ◽  
V Strugala ◽  
J Pearson ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Structural Changes ◽  
Endoscopic Biopsy ◽  
Gastric Atrophy ◽  
Mucus Layer ◽  
Gastric Mucus ◽  
Mucus Gel ◽  
Mucus Barrier ◽  
H Pylori

Background—It has been proposed that a pathogenic effect of Helicobacter pylori is a weakening of the protective mucus barrier; however, this remains controversial.Aims—To clarify the effects of H pylori infection on the mucus gel barrier in vivo.Methods—Mucus gel polymeric structure and the thickness of the adherent mucus barrier were measured in endoscopic biopsy samples in subjects with and without H pyloriinfection.Results—There was a significant 18% reduction in the proportion of polymeric gel forming mucin in the adherent mucus layer in H pylori positive compared with negative subjects. There was no change in the adherent mucus thickness betweenH pylori positive and negative subjects without gastric atrophy (mean (SD): 104 (26) μm, 106 (30) μm respectively). There was however a significant reduction in mucus thickness in those H pylori positive subjects with underlying gastric atrophy (84 (13) μm, p=0.03) compared with those without atrophy.Conclusions—A partial breakdown in gel forming structure of the gastric mucus barrier does occur in H pylori infection per se but this is insufficient to cause a collapse of the mucus barrier.

scholarly journals The Interaction of Helicobacter pylori with TFF1 and Its Role in Mediating the Tropism of the Bacteria Within the Stomach

2019 ◽  
Vol 20 (18) ◽  
pp. 4400 ◽  
Author(s):  
Marguerite Clyne ◽  
Felicity E. B. May
Keyword(s):  
Helicobacter Pylori ◽  
Gastric Mucin ◽  
Carbohydrate Binding ◽  
Mucus Layer ◽  
Gastric Mucus ◽  
Core Oligosaccharide ◽  
Epithelial Surface ◽  
Hydrophobic Residues ◽  
H Pylori ◽  
Trefoil Factor 1

Helicobacter pylori colonises the human stomach and has tropism for the gastric mucin, MUC5AC. The majority of organisms live in the adherent mucus layer within their preferred location, close to the epithelial surface where the pH is near neutral. Trefoil factor 1 (TFF1) is a small trefoil protein co-expressed with the gastric mucin MUC5AC in surface foveolar cells and co-secreted with MUC5AC into gastric mucus. Helicobacter pylori binds with greater avidity to TFF1 dimer, which is present in gastric mucus, than to TFF1 monomer. Binding of H. pylori to TFF1 is mediated by the core oligosaccharide subunit of H. pylori lipopolysaccharide at pH 5.0–6.0. Treatment of H. pylori lipopolysaccharide with mannosidase or glucosidase inhibits its interaction with TFF1. Both TFF1 and H. pylori have a propensity for binding to mucins with terminal non-reducing α- or β-linked N-acetyl-d-glucosamine or α-(2,3) linked sialic acid or Gal-3-SO42−. These findings are strong evidence that TFF1 has carbohydrate-binding properties that may involve a conserved patch of aromatic hydrophobic residues on the surface of its trefoil domain. The pH-dependent lectin properties of TFF1 may serve to locate H. pylori deep in the gastric mucus layer close to the epithelium rather than at the epithelial surface. This restricted localisation could limit the interaction of H. pylori with epithelial cells and the subsequent host signalling events that promote inflammation.

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 Newly Discovered Cell Shape Promoting Protein Complex Involved in the Maintenance of Distinct Helical Shape of Helicobacter Pylori

2019 ◽  
pp. 28-30
Author(s):  
Freeman Paczkowski
Keyword(s):  
Cell Wall ◽  
Helicobacter Pylori ◽  
Cell Shape ◽  
Drug Target ◽  
Clinical Implications ◽  
Potential Drug Target ◽  
Potential Drug ◽  
Multiple Cell ◽  
H Pylori ◽  
Cell Shape Formation

The distinct helical shape of the bacterium Helicobacter Pylori (H. pylori) assists this organism in colonizing the digestive organs of its target host. It has been discovered that a key determinant of helical cell shape formation in H. pylori is the Csd5 protein, which engages in multiple cell shape promoting interactions with the cell wall and other various proteins. This finding has significant clinical implications, as it outlines Csd5 as a potential drug target for treating H. pylori infection in the future.

scholarly journals Non-helical Helicobacter pylori show altered gland colonization and elicit less gastric pathology during chronic infection

2018 ◽  
Author(s):  
Laura E Martinez ◽  
Valerie P O'Brien ◽  
Christina Leverich ◽  
Sue E Knoblaugh ◽  
Nina R Salama
Keyword(s):  
Helicobacter Pylori ◽  
Post Infection ◽  
Chronic Infection ◽  
Cell Shape ◽  
Quantitative Imaging ◽  
Acute Infection ◽  
Wild Type ◽  
Tissue Interactions ◽  
Colony Forming Units ◽  
H Pylori

Half of all humans harbor Helicobacter pylori in their stomachs. Helical cell shape is thought to facilitate H. pylori's ability to bore into the protective mucus layer in a corkscrew-like motion, thus enhancing colonization of the stomach. H. pylori cell shape mutants show impaired colonization of the mouse stomach, highlighting the importance of cell shape in infection. To gain a deeper understanding of how helical cell morphology promotes host colonization by H. pylori, we used 3D-confocal microscopy to visualize the clinical isolate PMSS1 and an isogenic straight rod mutant (Dcsd6) within thick longitudinal mouse stomach sections and performed volumetric image analysis to quantify the number of bacteria residing within corpus and antral glands in addition to measuring total colony forming units (CFU). We found that straight rods show attenuation during acute colonization of the stomach (one day or one week post-infection) as measured by total CFU. Our quantitative imaging revealed that wild-type bacteria extensively colonized antral glands at one week post-infection, while csd6 mutants showed variable colonization of the antrum at this timepoint. During chronic infection (one or three months post-infection), total CFU were highly variable, but similar for wild-type and straight rods. Both wild-type and straight rods persisted and expanded in corpus glands during chronic infection. However, the straight rods showed reduced inflammation and disease progression. Thus, helical cell shape contributes to tissue interactions that promote inflammation during chronic infection, in addition to facilitating niche acquisition during acute infection.

scholarly journals Acetylation regulates the oligomerization state and activity of RNase J, the major ribonuclease of Helicobacter pylori

2021 ◽  
Author(s):  
alejandro Tejada-Arranz ◽  
Maxime Bouilloux-Lafont ◽  
Xue-Yuan PEI ◽  
Thibaut Douche ◽  
Mariette Matondo ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Active Site ◽  
Protein Complex ◽  
In Vitro Activity ◽  
Post Translational Modifications ◽  
Dead Box ◽  
Rna Degradosome ◽  
H Pylori ◽  
Post Transcriptional Regulation

In the pathogenic bacterium Helicobacter pylori, post-transcriptional regulation is dominated by the activity of a protein complex, known as the RNA degradosome, composed of the essential ribonuclease RNase J and the DEAD-box RNA helicase RhpA. Here, we describe post-translational modifications of this protein complex that affect its activity. Cell-extracted RNase J is acetylated on multiple residues, one of which, K649, impacts strongly on RNase J oligomerization, which in turn influences recruitment into the degradosome and ribonuclease activity. Corroborating the link between oligomerization and activity, mutations targeting K649 and other residues affect the dimerization and in vitro activity of RNase J. Our crystal structure of RNase J reveals loops that gate access to the active site and rationalizes how oligomerization state influences activity. We show that the acetylated residues of RNase J are important for H. pylori morphology, highlighting that the modifications affect the cellular function of RNase J. We propose acetylation as a regulatory level controlling the activity of RNase J and the H. pylori RNA degradosome.

Crystal structure of Helicobacter pylori spermidine synthase: A Rossmann-like fold with a distinct active site

2007 ◽  
Vol 67 (3) ◽  
pp. 743-754 ◽  
Author(s):  
Po Kai Lu ◽  
Jia-Yin Tsai ◽  
Hsiang Yi Chien ◽  
Haimei Huang ◽  
Chen-Hsi Chu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Helicobacter Pylori ◽  
Active Site ◽  
Spermidine Synthase
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