Characterization of helicobacter pylori bacteriophage KHP30

Applied and Environmental Microbiology

Volumn 79, Issue 10, 2013, Pages 3176-3184

  Uchiyama, Jumpei ^a   Takeuchi, Hiroaki ^b   Kato, Shin Ichiro ^a   Gamoh, Keiji ^a   Takemura Uchiyama, Iyo ^a,b   Ujihara, Takako ^a   Daibata, Masanori ^a   Matsuzaki, Shigenobu ^a  

^a KOCHI UNIVERSITY   (Japan)

^b KOCHI MEDICAL SCHOOL   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDIC ENVIRONMENT; BACTERIAL EVOLUTION; BIOLOGICAL CHARACTERISTIC; CAUSATIVE AGENTS; GENOMIC ORGANIZATION; GENOMIC SEQUENCE; HELICOBACTER PYLORI; PROTEIN SEQUENCING;

BIOLOGY; DISEASES; GENE ENCODING; MASS SPECTROMETRY; PROTEINS; SPHERES;

BACTERIOPHAGES;

VIRUS DNA; VIRUS PROTEIN;

BACTERIOPHAGE; BACTERIUM; GENOMICS; LIPID; MUCUS; PATHOGENICITY; PH; PUBLIC HEALTH;

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE; GENETICS; HELICOBACTER PYLORI; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; OPEN READING FRAME; PH; PHYSIOLOGY; PLASMID; TRANSMISSION ELECTRON MICROSCOPY; ULTRASTRUCTURE; VIROLOGY; VIRUS CULTURE; VIRUS GENOME; VIRUS LATENCY;

AMINO ACID SEQUENCE; BACTERIOPHAGES; DNA, VIRAL; GENOME, VIRAL; HELICOBACTER PYLORI; HYDROGEN-ION CONCENTRATION; MICROSCOPY, ELECTRON, TRANSMISSION; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PLASMIDS; VIRAL PLAQUE ASSAY; VIRAL PROTEINS; VIRUS LATENCY;

EID: 84877106692     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03530-12     Document Type: Article

References (67)

1. Konturek PC, Konturek SJ, Brzozowski T. 2009. Helicobacter pylori infection in gastric cancerogenesis. J. Physiol. Pharmacol. 60:3-21.
2. Peek RM, Blaser MJ. 2002. Helicobacter pylori and gastrointestinal tract adenocarcinomas. Nat. Rev. Cancer 2:28 -37.
3. Atherton JC, Blaser MJ. 2009. Coadaptation of Helicobacter pylori and humans: ancient history, modern implications. J. Clin. Invest. 119:2475- 2487.
4. Suzuki R, Shiota S, Yamaoka Y. 2012. Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori. Infect. Genet. Evol. 12:203-213.
5. Canchaya C, Fournous G, Chibani-Chennoufi S, Dillmann ML, Brüssow H. 2003. Phage as agents of lateral gene transfer. Curr. Opin. Microbiol. 6:417- 424.
6. Kashiwagi A, Yomo T. 2011. Ongoing phenotypic and genomic changesin experimental coevolution of RNA bacteriophage Q._ and Escherichia coli. PLoS Genet. 7:e1002188. doi:10.1371/journal.pgen.1002188.
7. Krylov VN. 2003. Role of horizontal gene transfer by bacteriophages in the origin of pathogenic bacteria. Genetika 39:595- 620. (In Russian.)
8. Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson NR, Quail M, Smith F, Walker D, Libberton B, Fenton A, Hall N, Brockhurst MA. 2010. Antagonistic coevolution accelerates molecular evolution. Nature 464:275-278.
9. Heintschel von Heinegg E, Nalik HP, Schmid EN. 1993. Characterization of a Helicobacter pylori phage (HP1). J. Med. Microbiol. 38:245-249.
10. Lehours P, Vale FF, Bjursell MK, Melefors O, Advani R, Glavas S, Guegueniat J, Gontier E, Lacomme S, Alves Matos A, Menard A, Mégraud F, Engstrand L, Andersson AF. 2011. Genome sequencing reveals a phage in Helicobacter pylori. mBio 2(6):e00239 -11. doi:10.1128 /mBio.00239-11.
11. Luo CH, Chiou PY, Yang CY, Lin NT. 2012. Genome, integration, and transduction of a novel temperate phage of Helicobacter pylori. J. Virol. 86:8781- 8792.
12. Schmid EN, von Recklinghausen G, Ansorg R. 1990. Bacteriophages in Helicobacter (Campylobacter) pylori. J. Med. Microbiol. 32:101-104.
13. Wan XQ, Tang DS, Liu AP, Tan SY, Li WK, Kuang J, Li HM. 2011. Isolation of a wild-type virulent phage of Helicobacter pylori and its simulated treatments of gastrointestinal Hp in vitro. Nan Fang Yi Ke Da Xue Xue Bao 31:304 -307. (In Chinese.)
14. Arnold IC, Zigova Z, Holden M, Lawley TD, Rad R, Dougan G, Falkow S, Bentley SD, Müller A. 2011. Comparative whole genome sequence analysis of the carcinogenic bacterial model pathogen Helicobacter felis. Genome Biol. Evol. 3:302-308.
15. Eppinger M, Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M, Schuster SC. 2006. Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet. 2:e120. doi:10.1371/journal.pgen.0020120.
16. Uchiyama J, Takeuchi H, Kato S, Takemura-Uchiyama I, Ujihara T, Daibata M, Matsuzaki S. 2012. Complete genome sequences of two Helicobacter pylori bacteriophages isolated from Japanese patients. J. Virol. 86:11400 -11401.
17. Karita M, Kouchiyama T, Okita K, Nakazawa T. 1991. New small animalmodel for human gastric Helicobacter pylori infection: success in both nude and euthymic mice. Am. J. Gastroenterol. 86:1596 -1603.
18. Akopyants NS, Eaton KA, Berg DE. 1995. Adaptive mutation and cocolonization during Helicobacter pylori infection of gnotobiotic piglets. Infect. Immun. 63:116 -121.
19. Lee A, O'Rourke J, De Ungria MC, Robertson B, Daskalopoulos G, Dixon MF. 1997. A standardized mouse model of Helicobacter pylori infection: introducing the Sydney strain. Gastroenterology 112:1386- 1397.
20. Marshall BJ, Royce H, Annear DI, Goodwin CS, Pearman JW, Warren JR, Armstrong JA. 1984. Original isolation of Campylobacter pyloridis from human gastric mucosa. Microbios Lett. 25:83- 88.
21. Trang VT, Takeuchi H, Kudo H, Aoki A, Katsuno S, Shimamura T, Sugiura T, Ukeda H. 2009. Antimicrobial activity of aminoreductone against Helicobacter pylori. J. Agric. Food Chem. 57:11343-11348.
22. Yamaguchi H, Osaki T, Taguchi H, Sato N, Toyoda A, Takahashi M, Kai M, Nakata N, Komatsu A, Atomi Y, Kamiya S. 2003. Effect of bacterial flora on postimmunization gastritis following oral vaccination of mice with Helicobacter pylori heat shock protein 60. Clin. Diagn. Lab. Immunol. 10:808-812.
23. Bair MJ, Chen CL, Chiang CK, Huang MF, Hu CC, Chang HT. 2008. Capillary electropherograms for restriction fragment length polymorphism of Helicobacter pylori. Electrophoresis 29:3964 -3970.
24. Uchiyama J, Takemura I, Hayashi I, Matsuzaki S, Satoh M, Ujihara T, Murakami M, Imajoh M, Sugai M, Daibata M. 2011. Characterization of lytic enzyme open reading frame 9 (ORF9) derived from Enterococcus faecalis bacteriophage _EF24C. Appl. Environ. Microbiol. 77:580 -585.
25. Aalto AP, Bitto D, Ravantti JJ, Bamford DH, Huiskonen JT, Oksanen HM. 2012. Snapshot of virus evolution in hypersaline environments from the characterization of a membrane-containing Salisaeta icosahedral phage 1. Proc. Natl. Acad. Sci. U. S. A. 109:7079 -7084.
26. Bamford DH, Bamford JKH. 2005. Lipid-containing bacteriophage PM2, the type organism of Corticoviridae, p 171-174. In Calendar R, Abedon ST (ed), The bacteriophages, 2nd ed. Oxford University Press, New York, NY.
27. Dröge A, Santos MA, Stiege AC, Alonso JC, Lurz R, Trautner TA, Tavares P. 2000. Shape and DNA packaging activity of bacteriophage SPP1 procapsid: protein components and interactions during assembly. J. Mol. Biol. 296:117-132.
28. Fukuda K, Ishida W, Uchiyama J, Rashel M, Kato S, Morita T, Muraoka A, Sumi T, Matsuzaki S, Daibata M, Fukushima A. 2012. Pseudomonas aeruginosa keratitis in mice: effects of topical bacteriophage KPP12 administration. PLoS One 7:e47742. doi:10.1371/journal.pone.0047742.
29. Grahn AM, Butcher SJ, Bamford JKH, Bamford DH. 2005. PRD1: dissecting the genome, structure, and entry, p 161-170. In Calendar R, Abedon ST (ed), The bacteriophages, 2nd ed. Oxford University Press, New York, NY.
30. Hoshiba H, Uchiyama J, Kato S, Ujihara T, Muraoka A, Daibata M, Wakiguchi H, Matsuzaki S. 2010. Isolation and characterization of a novel Staphylococcus aureus bacteriophage, _MR25, and its therapeutic potential. Arch. Virol. 155:545-552.
31. Jaatinen ST, Happonen LJ, Laurinmäki P, Butcher SJ, Bamford DH. 2008. Biochemical and structural characterisation of membranecontaining icosahedral dsDNA bacteriophages infecting thermophilic Thermus thermophilus. Virology 379:10 -19.
32. Jalasvuori M, Jaatinen ST, Laurinavicius S, Ahola-Iivarinen E, Kalkkinen N, Bamford DH, Bamford JK. 2009. The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea. J. Virol. 83:9388 -9397.
33. Kazmierczak KM, Rothman-Denes LC. 2005. Bacteriophage N4, p 302- 314. In Calendar R, Abedon ST (ed), The bacteriophages, 2nd ed. Oxford University Press, New York, NY.
34. Kivelä HM, Kalkkinen N, Bamford DH. 2002. Bacteriophage PM2 has a protein capsid surrounding a spherical proteinaceous lipid core. J. Virol. 76:8169-8178.
35. Klumpp J, Dorscht J, Lurz R, Bielmann R, Wieland M, Zimmer M, Calendar R, Loessner MJ. 2008. The terminally redundant, nonpermuted genome of Listeria bacteriophage A511: a model for the SPO1-like myoviruses of gram-positive bacteria. J. Bacteriol. 190:5753-5765.
36. Lehnherr H. 2005. Bacteriophage P1, p 350-364. In Calendar R, Abedon ST (ed), The bacteriophages, 2nd ed. Oxford University Press, New York, NY.
37. Lickfeld KG, Menge B. 1976. Morphogenesis of bacteriophage lambda: electron microscopy of thin sections. J. Mol. Biol. 103:299 -318.
38. Matsuzaki S, Yasuda M, Nishikawa H, Kuroda M, Ujihara T, Shuin T, Shen Y, Jin Z, Fujimoto S, Nasimuzzaman MD, Wakiguchi H, Sugihara S, Sugiura T, Koda S, Muraoka A, Imai S. 2003. Experimental protection of mice against lethal Staphylococcus aureus infection by novel bacteriophage _MR11. J. Infect. Dis. 187:613- 624.
39. Nagy E, Prágai B, Ivánovics G. 1976. Characteristics of phage AP50, an RNA phage containing phospholipids. J. Gen. Virol. 32:129 -132.
40. Ravantti JJ, Gaidelyte A, Bamford DH, Bamford JK. 2003. Comparative analysis of bacterial viruses Bam35, infecting a gram-positive host, and PRD1, infecting gram-negative hosts, demonstrates a viral lineage. Virology 313:401- 414.
41. Smith MCM. 2005. Molecular genetics of Streptococcus phages, p 621- 635. In Calendar R, Abedon ST (ed), The bacteriophages, 2nd ed. Oxford University Press, New York, NY.
42. Son JS, Lee SJ, Jun SY, Yoon SJ, Kang SH, Paik HR, Kang JO, Choi YJ. 2010. Antibacterial and biofilm removal activity of a podoviridae Staphylococcus aureus bacteriophage SAP-2 and a derived recombinant cell-walldegrading enzyme. Appl. Microbiol. Biotechnol. 86:1439 -1449.
43. Uchiyama J, Rashel M, Maeda Y, Takemura I, Sugihara S, Akechi K, Muraoka A, Wakiguchi H, Matsuzaki S. 2008. Isolation and characterization of a novel Enterococcus faecalis bacteriophage _EF24C as a therapeutic candidate. FEMS Microbiol. Lett. 278:200 -206.
44. Uchiyama J, Rashel M, Takemura I, Kato S, Ujihara T, Muraoka A, Matsuzaki S, Daibata M. 2012. Genetic characterization of Pseudomonas aeruginosa bacteriophage KPP10. Arch. Virol. 157:733-738.
45. Verheust C, Fornelos N, Mahillon J. 2005. GIL16, a new gram-positive tectiviral phage related to the Bacillus thuringiensis GIL01 and the Bacillus cereus pBClin15 elements. J. Bacteriol. 187:1966 -1973.
46. Ackermann HW, DuBow MS. 1987. Viruses of prokaryotes, vol I. General properties of bacteriophages. CRC Press, Boca Raton, FL.
47. Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M. 2008. Genome-Matcher: a graphical user interface for DNA sequence comparison. BMC Bioinformatics 9:376. doi:10.1186/1471-2105-9-376.
48. Hosaka Y, Irinoda K, Nakano R, Tanabe S, Koizumi W, Saigenji K, Inoue M. 2005. Use of the restriction enzyme EcoRI for pulsed-field gel electrophoretic analysis of Helicobacter pylori. J. Clin. Microbiol. 43:931- 932.
49. Green MR, Sambrook J. 2012. Molecular cloning: a laboratory manual, 4th ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
50. Vincze T, Posfai J, Roberts RJ. 2003. NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res. 31:3688 -3691.
51. Uchiyama J, Takemura I, Satoh M, Kato S, Ujihara T, Akechi K, Matsuzaki S, Daibata M. 2011. Improved adsorption of an Enterococcus faecalis bacteriophage _EF24C with a spontaneous point mutation. PLoS One 6:e26648. doi:10.1371/journal.pone.0026648.
52. Shilov IV, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaeffer DA. 2007. The Paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol. Cell. Proteomics 6:1638 -1655.
53. Ackermann HW. 2009. Phage classification and characterization. Methods Mol. Biol. 501:127-140.
54. Lavigne R, Molineux IJ, Kropinski AM. 2012. Order Caudovirales, p 39-45. In King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (ed), Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Academic Press, Waltham, MA.
55. Oksanen HM, Bamford DH. 2012. Tectiviridae, p 317-321. In King AMQ, Lefkowitz E, Michael J, Adams MJ, Carstens EB (ed), Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Academic Press, Waltham, MA.
56. Prangishvili D. 2012. Corticoviridae, p 179-186. In King AMQ, Lefkowitz E, Michael J, Adams MJ, Carstens EB (ed), Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Academic Press, Waltham, MA.
57. Carlson K. 2005. Working with bacteriophages: common techniques and methodological approaches, p 437-487. In Kutter E, Sulakvelidze A (ed), Bacteriophages biology and applications. CRC Press, Boca Raton, FL.
58. Guttman B, Raya R, Kutter E. 2005. Basic phage biology, p 29-66. In Kutter E, Sulakvelidze A (ed), Bacteriophages biology and applications. CRC Press, Boca Raton, FL.
59. Comtois SL, Gidley MD, Kelly DJ. 2003. Role of the thioredoxin system and the thiol-peroxidases Tpx and Bcp in mediating resistance to oxida-tive and nitrosative stress in Helicobacter pylori. Microbiology 149:121- 129.
60. Sachs G, Scott DR, Wen Y. 2011. Gastric infection by Helicobacter pylori. Curr. Gastroenterol. Rep. 13:540 -546.
61. Golais F, Hollý J, Vítkovská J. 2012. Coevolution of bacteria and their viruses. Folia Microbiol. (Praha) doi:10.1007/s12223-012-0195-5.
62. Los M, Wegrzyn G. 2012. Pseudolysogeny. Adv. Virus Res. 82:333-343.
63. Black LW, Showe MK, Steven AC. 1994. Morphogenesis of the T4 head, p 218-258. In Karam JD, Drake JW, Kreuzer KN, Mosig G, Hall DH, Eiserling FA, Black LW, Spicer EK, Kutter E, Carlson K, Miller ES (ed), Molecular biology of bacteriophage T4. ASM Press, Washington, DC.
64. Uchiyama J, Rashel M, Matsumoto T, Sumiyama Y, Wakiguchi H, Matsuzaki S. 2009. Characteristics of a novel Pseudomonas aeruginosa bacteriophage, PAJU2, which is genetically related to bacteriophage D3. Virus Res. 139:131-134.
65. Uchiyama J, Rashel M, Takemura I, Wakiguchi H, Matsuzaki S. 2008. In silico and in vivo evaluation of bacteriophage _EF24C, a candidate for treatment of Enterococcus faecalis infections. Appl. Environ. Microbiol. 74:4149-4163.
66. Botstein D. 1980. A theory of modular evolution for bacteriophages. Ann. N. Y. Acad. Sci. 354:484-490.
67. Comeau AM, Bertrand C, Letarov A, Tetart F, Krisch HM. 2007. Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. Virology 362:384 -396.