Identification of Type II Restriction and Modification Systems in Helicobacter Pylori Reveals Their Substantial Diversity Among Strains

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2000 Aug 16

PMID 10944229

Citations 57

Authors

Q Xu

R D Morgan

R J Roberts

M J Blaser

Affiliations

Soon will be listed here.

Abstract

A total of 22 type II restriction endonucleases with 18 distinct specificities have been identified in six Helicobacter pylori strains. Among these 18 specificities are three completely new endonucleases, Hpy178III, Hpy99I, and Hpy188I, that specifically cleave DNA at TCNNGA, CGWCG, and TCNGA sites, respectively. The set of endonucleases identified in each strain varies, but all have four- or five-base recognition sequences. Among 16 H. pylori strains, examination of the DNA modification status at the recognition sites of 15 restriction endonucleases reveals that each strain has a substantially different complement of type II modification systems. We conclude that the type II restriction-modification systems in H. pylori are highly diverse between strains, a unique characteristic of H. pylori. The diverse methylation status of H. pylori chromosomal DNA may serve as a new typing system to discriminate H. pylori isolates for epidemiological and clinical purposes. This study also demonstrates that H. pylori is a rich source of type II restriction endonucleases.

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References

Berg D, Logan R . Helicobacter pylori, individual host specificity and human disease. European Helicobacter Study Group Meeting, Copenhagen, October 16-19, 1996. Bioessays. 1997; 19(1):86-90. DOI: 10.1002/bies.950190114. View

Wayne J, Holden M, Xu S . The Tsp45I restriction-modification system is plasmid-borne within its thermophilic host. Gene. 1998; 202(1-2):83-8. DOI: 10.1016/s0378-1119(97)00457-5. View

Suerbaum S, Smith J, Bapumia K, Morelli G, Smith N, Kunstmann E . Free recombination within Helicobacter pylori. Proc Natl Acad Sci U S A. 1998; 95(21):12619-24. PMC: 22880. DOI: 10.1073/pnas.95.21.12619. View

Owen R, Fraser J, Costas M, Morgan D, Morgan D . Signature patterns of DNA restriction fragments of Helicobacter pylori before and after treatment. J Clin Pathol. 1990; 43(8):646-9. PMC: 502646. DOI: 10.1136/jcp.43.8.646. View

Braaten B, Nou X, Kaltenbach L, Low D . Methylation patterns in pap regulatory DNA control pyelonephritis-associated pili phase variation in E. coli. Cell. 1994; 76(3):577-88. DOI: 10.1016/0092-8674(94)90120-1. View

Roberts D, Hoopes B, McClure W, Kleckner N . IS10 transposition is regulated by DNA adenine methylation. Cell. 1985; 43(1):117-30. DOI: 10.1016/0092-8674(85)90017-0. View

Figueiredo C, Quint W, Sanna R, Sablon E, DONAHUE J, Xu Q . Genetic organization and heterogeneity of the iceA locus of Helicobacter pylori. Gene. 2000; 246(1-2):59-68. DOI: 10.1016/s0378-1119(00)00054-8. View

Norlander L, Davies J, Hagblom P, Normark S . Deoxyribonucleic acid modifications and restriction endonuclease production in Neisseria gonorrhoeae. J Bacteriol. 1981; 145(2):788-95. PMC: 217180. DOI: 10.1128/jb.145.2.788-795.1981. View

Arber W, DUSSOIX D . Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambda. J Mol Biol. 1962; 5:18-36. DOI: 10.1016/s0022-2836(62)80058-8. View

10.

Piekarowicz A, Stein D . Purification and characterization of a new DNA methyltransferase from Neisseria gonorrhoeae. Gene. 1995; 157(1-2):101-2. DOI: 10.1016/0378-1119(94)00531-v. View

11.

DUSSOIX D, Arber W . Host specificity of DNA produced by Escherichia coli. II. Control over acceptance of DNA from infecting phage lambda. J Mol Biol. 1962; 5:37-49. DOI: 10.1016/s0022-2836(62)80059-x. View

12.

Kansau I, Raymond J, Bingen E, Courcoux P, Kalach N, Bergeret M . Genotyping of Helicobacter pylori isolates by sequencing of PCR products and comparison with the RAPD technique. Res Microbiol. 1996; 147(8):661-9. DOI: 10.1016/0923-2508(96)84023-x. View

13.

Stein D, Gunn J, Radlinska M, Piekarowicz A . Restriction and modification systems of Neisseria gonorrhoeae. Gene. 1995; 157(1-2):19-22. DOI: 10.1016/0378-1119(94)00649-d. View

14.

Kuhnlein U, Arber W . Host specificity of DNA produced by Escherichia coli. XV. The role of nucleotide methylation in in vitro B-specific modification. J Mol Biol. 1972; 63(1):9-19. DOI: 10.1016/0022-2836(72)90518-9. View

15.

Korch C, Hagblom P, Normark S . Sequence-specific DNA modification in Neisseria gonorrhoeae. J Bacteriol. 1983; 155(3):1324-32. PMC: 217831. DOI: 10.1128/jb.155.3.1324-1332.1983. View

16.

Blaser M, Parsonnet J . Parasitism by the "slow" bacterium Helicobacter pylori leads to altered gastric homeostasis and neoplasia. J Clin Invest. 1994; 94(1):4-8. PMC: 296275. DOI: 10.1172/JCI117336. View

17.

Taylor N, Fox J, Akopyants N, Berg D, Thompson N, Shames B . Long-term colonization with single and multiple strains of Helicobacter pylori assessed by DNA fingerprinting. J Clin Microbiol. 1995; 33(4):918-23. PMC: 228068. DOI: 10.1128/jcm.33.4.918-923.1995. View

18.

Ivic A, Jakeman K, Penn C, Brown N . Type II restriction endonucleases from Helicobacter pylori include an enzyme with a novel recognition sequence. FEMS Microbiol Lett. 1999; 179(1):175-80. DOI: 10.1111/j.1574-6968.1999.tb08724.x. View

19.

Peek Jr R, Thompson S, DONAHUE J, Tham K, Atherton J, Blaser M . Adherence to gastric epithelial cells induces expression of a Helicobacter pylori gene, iceA, that is associated with clinical outcome. Proc Assoc Am Physicians. 1998; 110(6):531-44. View

20.

Repin V, Puchkova L, Ananko G, Reshetnikov O, Kurilovich S . [HpyNI--a novel restriction endonuclease isolated from the pathogenic microorganism Helicobacter pylori]. Mol Gen Mikrobiol Virusol. 1998; (3):37-8. View