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Gut Pathogens
Published in: Gut Pathogens 1/2017

Open Access 01-12-2017 | Research

Outer membrane phospholipase A’s roles in Helicobacter pylori acid adaptation

Authors: Hilde S. Vollan, Tone Tannæs, Dominique A. Caugant, Gert Vriend, Geir Bukholm

Published in: Gut Pathogens | Issue 1/2017

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Abstract

Background

The pH of the human gastric mucosa varies around 2.5 so that only bacteria with strong acidic stress tolerance can colonize it. The ulcer causing Helicobacter pylori thrives in the gastric mucosa. We analyse the roles of the key outer membrane protein OMPLA in its roles in acid tolerance.

Results

The homology model of Helicobacter pylori outer membrane phospholipase A (OMPLA) reveals a twelve stranded β-barrel with a pore that allows molecules to pass with a diameter up to 4 Å. Structure based multiple sequence alignments revealed the functional roles of many amino acids, and led to the suggestion that OMPLA has multiple functions. Besides its role as phospholipase it lets urea enter and ammonium exit the periplasm. Combined with an extensive literature study, our work leads to a comprehensive model for H. pylori’s acid tolerance. This model is based on the conversion of urea into ammonium, and it includes multiple roles for OMPLA and involves two hitherto little studied membrane channels in the OMPLA operon.

Conclusion

The three-dimensional model of OMPLA predicts a transmembrane pore that can aid H. pylori’s acid tolerance through urea influx and ammonium efflux. After urea passes through OMPLA into the periplasm, it passes through the pH-gated inner membrane channel UreI into the cytoplasm where urease hydrolyses it into NH3 and CO2. Most of the NH3 becomes NH4 + that is likely to need an inner membrane channel to reach the periplasm. Two genes that are co-regulated with OMPLA in gastric Helicobacter operons could aid this transport. The NH4 + that might leave the cell through the OMPLA pore has been implicated in H. pylor’s pathogenesis.
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Literature
1.
Lund P, Tramonti A, De Biase D. Coping with low pH: molecular strategies in neutralophilic bacteria. FEMS Microbiol Rev. 2014;38:1091–125.CrossRefPubMed
2.
Koebnik R, Locher KP, Van Gelder P. Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol Microbiol. 2000;37:239–53.CrossRefPubMed
3.
4.
Menard A, Pere-Vedrenne C, Haesebrouck F, Flahou B. Gastric and enterohepatic Helicobacters other than Helicobacter pylori. Helicobacter. 2014;19(Suppl 1):59–67.CrossRefPubMed
5.
Mikkonen TP, Karenlampi RI, Hanninen ML. Phylogenetic analysis of gastric and enterohepatic Helicobacter species based on partial HSP60 gene sequences. Int J Syst Evol Microbiol. 2004;54:753–8.CrossRefPubMed
6.
Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS, Kim JF. Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods. Helicobacter. 2014;19:407–16.CrossRefPubMed
7.
Scott DR, Marcus EA, Wen Y, Oh J, Sachs G. Gene expression in vivo shows that Helicobacter pylori colonizes an acidic niche on the gastric surface. Proc Natl Acad Sci USA. 2007;104:7235–40.CrossRefPubMedPubMedCentral
8.
Pflock M, Kennard S, Delany I, Scarlato V, Beier D. Acid-induced activation of the urease promoters is mediated directly by the ArsRS two-component system of Helicobacter pylori. Infect Immun. 2005;73:6437–45.CrossRefPubMedPubMedCentral
9.
Bishop RE. Structural biology of membrane-intrinsic β-barrel enzymes: sentinels of the bacterial outer membrane. Biochim Biophys Acta. 2008;1778:1881–96.CrossRefPubMed
10.
Dorrell N, Martino MC, Stabler RA, Ward SJ, Zhang ZW, McColm AA, Farthing MJ, Wren BW. Characterization of Helicobacter pylori PldA, a phospholipase with a role in colonization of the gastric mucosa. Gastroenterology. 1999;117:1098–104.CrossRefPubMed
11.
Istivan TS, Coloe PJ. Phospholipase A in Gram-negative bacteria and its role in pathogenesis. Microbiology. 2006;152:1263–74.CrossRefPubMed
12.
Tannaes T, Dekker N, Bukholm G, Bijlsma JJ, Appelmelk BJ. Phase variation in the Helicobacter pylori phospholipase A gene and its role in acid adaptation. Infect Immun. 2001;69:7334–40.CrossRefPubMedPubMedCentral
13.
14.
Vollan HS, Tannaes T, Yamaoka Y, Bukholm G. In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA). BMC Microbiol. 2012;12:206.CrossRefPubMedPubMedCentral
15.
Snijder HJ, Ubarretxena-Belandia I, Blaauw M, Kalk KH, Verheij HM, Egmond MR, Dekker N, Dijkstra BW. Structural evidence for dimerization-regulated activation of an integral membrane phospholipase. Nature. 1999;401:717–21.CrossRefPubMed
16.
Vollan HS, Tannæs T, Vriend G, Bukholm G. In silico structure and sequence analysis of bacterial porins and specific diffusion channels for hydrophilic molecules: conservation, multimericity and multifunctionality. IJMS. 2016;17:599.CrossRefPubMedCentral
17.
Tannæs T, Dekker N, Bukholm G, Bijlsma JJE, Appelmelk BJ. Phase variation in the Helicobacter pylori phospholipase A gene and its role in acid adaptation. Infect Immun. 2001;69:7334–40.CrossRefPubMedPubMedCentral
18.
Kuipers RK, Joosten HJ, Van Berkel WJ, Leferink NG, Rooijen E, Ittmann E, Van Zimmeren F, Jochens H, Bornscheuer U, Vriend G, et al. 3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities. Proteins. 2010;78:2101–13.PubMed
19.
Oliveira L, Paiva PB, Paiva AC, Vriend G. Identification of functionally conserved residues with the use of entropy-variability plots. Proteins. 2003;52:544–52.CrossRefPubMed
20.
Marti-Renom MA, Madhusudhan MS, Eswar N, Pieper U, Shen M, Sali A, Fiser A, Mirkovic N, John B, Stuart A. Modeling protein structure from its sequence. In: current protocols in bioinformatics. New York: Wiley; 2002.
21.
22.
O’Toole PW, Snelling WJ, Canchaya C, Forde BM, Hardie KR, Josenhans C, Graham R, McMullan G, Parkhill J, Belda E, Bentley SD. Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen. BMC Genom. 2010;11:164.CrossRef
23.
Flahou B, Haesebrouck F, Smet A, Yonezawa H, Osaki T, Kamiya S. Gastric and enterohepatic non-Helicobacter pylori Helicobacters. Helicobacter. 2013;18(Suppl 1):66–72.CrossRefPubMed
24.
Cáceres-Delpiano J, Teneb J, Mansilla R, García A, Salas-Burgos A. Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study. BMC Struct Biol. 2015;15:11.CrossRefPubMedPubMedCentral
25.
Mari SA, Koster S, Bippes CA, Yildiz O, Kuhlbrandt W, Muller DJ. pH-induced conformational change of the β-barrel-forming protein OmpG reconstituted into native E. coli lipids. J Mol Biol. 2010;396:610–6.CrossRefPubMed
26.
Basle A, Qutub R, Mehrazin M, Wibbenmeyer J, Delcour AH, Bayley H. Deletions of single extracellular loops affect pH sensitivity, but not voltage dependence, of the Escherichia coli porin OmpF. Protein Eng Des Sel. 2004;17:665–72.CrossRefPubMed
27.
Li CC, Ho TY, Kao CH, Wu SL, Liang JA, Hsiang CY. Conserved charged amino acid residues in the extracellular region of sodium/iodide symporter are critical for iodide transport activity. J Biomed Sci. 2010;17:89.CrossRefPubMedPubMedCentral
28.
Liu N, Delcour AH. Inhibitory effect of acidic pH on OmpC porin: wild-type and mutant studies. FEBS Lett. 1998;434:160–4.CrossRefPubMed
29.
Kadurin I, Huber S, Grunder S. A single conserved proline residue determines the membrane topology of stomatin. Biochem J. 2009;418:587–94.CrossRefPubMed
30.
Deber CM, Therien AG. Putting the β-breaks on membrane protein misfolding. Nat Struct Biol. 2002;9:318–9.CrossRefPubMed
31.
Dutton RJ, Boyd D, Berkmen M, Beckwith J. Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation. Proc Natl Acad Sci USA. 2008;105:11933–8.CrossRefPubMedPubMedCentral
32.
Tie JK, Jin DY, Stafford DW. Conserved loop cysteines of vitamin K epoxide reductase complex subunit 1-like 1 (VKORC1L1) are involved in its active site regeneration. J Biol Chem. 2014;289:9396–407.CrossRefPubMedPubMedCentral
33.
Wang X, Jiang F, Zheng J, Chen L, Dong J, Sun L, Zhu Y, Liu B, Yang J, Yang G, Jin Q. The outer membrane phospholipase A is essential for membrane integrity and type III secretion in Shigella flexneri. Open Biol. 2016;6(9):160073.CrossRefPubMedPubMedCentral
34.
Wheatley M, Wootten D, Conner MT, Simms J, Kendrick R, Logan RT, Poyner DR, Barwell J. Lifting the lid on GPCRs: the role of extracellular loops. Br J Pharmacol. 2012;165:1688–703.CrossRefPubMedPubMedCentral
35.
36.
Taboada B, Ciria R, Martinez-Guerrero CE, Merino E. ProOpDB: prokaryotic operon database. Nucleic Acids Res. 2012;40:D627–31.CrossRefPubMed
37.
Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:33–6.CrossRefPubMedPubMedCentral
38.
Bala PA, Foster J, Carvelli L, Henry LK. SLC6 transporters: structure, function, regulation, disease association and therapeutics. Mol Asp Med. 2013;34:197–219.CrossRef
39.
Malinauskaite L, Quick M, Reinhard L, Lyons JA, Yano H, Javitch JA, Nissen P. A mechanism for intracellular release of Na+ by neurotransmitter/sodium symporters. Nat Struct Mol Biol. 2014;21:1006–12.CrossRefPubMedPubMedCentral
40.
Singh SK, Pal A. Biophysical approaches to the study of LeuT, a prokaryotic homolog of neurotransmitter sodium symporters. Methods Enzymol. 2015;557:167–98.CrossRefPubMedPubMedCentral
41.
42.
Scott DR, Marcus EA, Wen Y, Singh S, Feng J, Sachs G. Cytoplasmic histidine kinase (HP0244)-regulated assembly of urease with UreI, a channel for urea and its metabolites, CO2, NH3, and NH4 +, is necessary for acid survival of Helicobacter pylori. J Bacteriol. 2010;192:94–103.CrossRefPubMed
43.
Stingl K, Uhlemann EM, Schmid R, Altendorf K, Bakker EP. Energetics of Helicobacter pylori and its implications for the mechanism of urease-dependent acid tolerance at pH 1. J Bacteriol. 2002;184:3053–60.CrossRefPubMedPubMedCentral
44.
Fischer F, De Reuse H. Adaptation of Helicobacter pylori metabolism to persistent gastric colonization. In: Backert S, Yamaoka Y, editors. Helicobacter pylori research: from bench to bedside. Tokyo: Springer; 2016. p. 29–56.
45.
Huang JY, Goers Sweeney E, Guillemin K, Amieva MR. Multiple acid sensors control Helicobacter pylori colonization of the stomach. PLoS Pathog. 2017;13:e1006118.CrossRefPubMedPubMedCentral
46.
Marcus EA, Scott DR. Gastric colonization by H. pylori. In: Kim N, editor. Helicobacter pylori. Singapore: Springer; 2016. p. 23–34 (Part II).CrossRef
47.
Tannaes T, Bukholm G. Cholesteryl-6-O-acyl-alpha-D-glucopyranoside of Helicobacter pylori relate to relative lysophospholipid content. FEMS Microbiol Lett. 2005;244:117–20.CrossRefPubMed
48.
49.
Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph. 1990;8(52–56):29.
50.
Krieger E, Koraimann G, Vriend G. Increasing the precision of comparative models with YASARA NOVA–a self-parameterizing force field. Proteins. 2002;47:393–402.CrossRefPubMed
51.
Krieger E, Vriend G. New ways to boost molecular dynamics simulations. J Comput Chem. 2015;36:996–1007.CrossRefPubMed
52.
Rose PW, Prlic A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, et al. The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 2017;45:D271–81.CrossRefPubMed
53.
Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM. MUSTANG: a multiple structural alignment algorithm. Proteins. 2006;64:559–74.CrossRefPubMed
54.
Voorintholt R, Kosters MT, Vegter G, Vriend G, Hol WG. A very fast program for visualizing protein surfaces, channels and cavities. J Mol Graph. 1989;7:243–5.CrossRefPubMed
55.
Pellegrini-Calace M, Maiwald T, Thornton JM. PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure. PLoS Comput Biol. 2009;5:e1000440.CrossRefPubMedPubMedCentral
56.
Esbensen Y, Vollan HS, Tannaes TM. A functional Outer membrane phospholipase A (OMPLA) is required for survival of Helicobacter pylori at pH 3.5 [abstract]. Helicobacter. 2011;16(suppl 1):97–8.
57.
Vollan HS, Portella G, Tannaes T, de Groot BL, Vriend G, Bukholm G. A homology model of H. pylori OMPLA [abstract]. Helicobacter. 2008;13:423.
Metadata
Title
Outer membrane phospholipase A’s roles in Helicobacter pylori acid adaptation
Authors
Hilde S. Vollan
Tone Tannæs
Dominique A. Caugant
Gert Vriend
Geir Bukholm
Publication date
01-12-2017
Publisher
BioMed Central
Published in
Gut Pathogens / Issue 1/2017
Electronic ISSN: 1757-4749
DOI
https://doi.org/10.1186/s13099-017-0184-y

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