Global analysis of Helicobacter pylori gene expression in human gastric mucosa

Gastroenterology

Volumn 123, Issue 5, 2002, Pages 1637-1648

  Graham, James E ^a   Peek, Richard M ^a   Krishna, Uma ^a   Cover, Timothy L ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; COMPLEMENTARY DNA; DNA FRAGMENT; RNA;

ADULT; AGED; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BACTERIAL GROWTH; CASE REPORT; CONTROLLED STUDY; DNA HYBRIDIZATION; GENE EXPRESSION; GENE ISOLATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOME; HELICOBACTER PYLORI; HUMAN; HUMAN TISSUE; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; RNA ANALYSIS; SEQUENCE ANALYSIS; STOMACH DISEASE; STOMACH MUCOSA; STRAIN DIFFERENCE;

EID: 0036828277     PISSN: 00165085     EISSN: None     Source Type: Journal    
DOI: 10.1053/gast.2002.36589     Document Type: Article

References (35)

1. Dunn BE, Cohen H, Blaser MJ. Helicobacter pylori, Clin Microbiol Rev 1997;10:720-741.
2. Cover TL, Berg DE, Blaser MJ, Mobley HLT. Helicobacter pylori pathogenesis. In: Groisman EA, ed. Principles of Bacterial Pathogenesis. San Diego, CA: Academic Press, 2001:509-558.
3. Lee SH, Hava DL, Waldor MK, Camilli A. Regulation and temporal expression patterns of Vibrio cholerae virulence genes during infection. Cell 1999;99:625-634.
4. Lucas RL, Lee CA. Unravelling the mysteries of virulence gene regulation in Salmonella typhimurium. Mol Microbiol 2000;36:1024-1033.
5. Mekalanos JJ. Environmental signals controlling expression of virulence determinants in bacteria, J Bacteriol 1992;174:1-7.
6. Handfield M, Levesque RC. Strategies for isolation of in vivo expressed genes from bacteria. FEMS Microbiol Rev 1999;23:69-91.
7. Slauch JM, Mahan MJ, Mekalanos JJ. In vivo expression technology for selection of bacterial genes specifically induced in host tissues. Methods Enzymol 1994;235:481-492.
8. Merrell DS, Camilli A. Detection and analysis of gene expression during infection by in vivo expression technology. Philos Trans R Soc Lond B Biol Sci 2000;355:587-599.
9. Valdivia RH, Falkow S. Probing bacterial gene expression within host cells. Trends Microbiol 1997;5:360-363.
10. Moxon R, Tang C. Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens. Philos Trans R Soc Lond B Biol Sci 2000;355:643-656.
11. Graham JE, Clark-Curtiss JE. Identification of Mycobacterium tuberculosis RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS). Proc Natl Acad Sci U S A 1999;96:11554-11559.
12. Peek RM Jr, Thompson SA, Donahue JP, Tham KT, Atherton JC, Blaser MJ, Miller GG. Adherence to gastric epithelial cells induces expression of a Helicobacter pylori gene, iceA, that is associated with clinical outcome. Proc Assoc Am Physicians 1998;110:531-544.
13. Atherton JC, Cao P, Peek RM Jr, Tummuru MK, Blaser MJ, Cover TL. Mosaicism in vacuolating cytotoxin alleles of Helicobacter pylori. Association of specific vacA types with cytotoxin production and peptic ulceration. J Biol Chem 1995;270:17771-17777.
14. Peek RM Jr, Moss SF, Tham KT, Perez-Perez GI, Wang S, Miller GG, Atherton JC, Holt PR, Blaser MJ. Helicobacter pylori cagA+ strains and dissociation of gastric epithelial cell proliferation from apoptosis. J Natl Cancer Inst 1997;89:863-868.
15. Israel DA, Salama N, Arnold CN, Moss SF, Ando T, Wirth HP, Tham KT, Camorlinga M, Blaser MJ, Falkow S, Peek RM Jr. Helicobacter pylori strain-specific differences in genetic content, identified by microarray, influence host inflammatory responses. J Clin Invest 2001;107:611-620.
16. Emory SA, Belasco JG. The ompA 5′ untranslated RNA segment functions in Escherichia coli as a growth-rate-regulated mRNA stabilizer whose activity is unrelated to translational efficiency. J Bacteriol 1990;172:4472-4481.
17. Atherton JC, Tham KT, Peek RM Jr, Cover TL, Blaser MJ. Density of Helicobacter pylori infection in vivo as assessed by quantitative culture and histology. J Infect Dis 1996;174:552-556.
18. Froussard P. A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA. Nucleic Acids Res 1992;20:2900.
19. Teng DH, Hsu F, Peterson I, Cardon KE, Caponigro G, Kamb A. Template selection during manipulation of complex mixtures by PCR. Biotechniques 2001;30:868-872, 874, 876-877.
20. Ko MS, Ko SB, Takahashi N, Nishiguchi K, Abe K. Unbiased amplification of a highly complex mixture of DNA fragments by 'lone linker'-tagged PCR. Nucleic Acids Res 1990;18:4293-4294.
21. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
22. Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci USA 2000;97:14668-14673.
23. Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge BL, Carmel G, Tummino PJ, Caruso A, Uria-Nickelsen M, Mills DM, Ives C, Gibson R, Merberg D, Mills SD, Jiang Q, Taylor DE, Vovis GF, Trust TJ. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 1999;397:176-180.
24. Fawcett P, Eichenberger P, Losick R, Youngman P. The transcriptional profile of early to middle sporulation in Bacillus subtilis. Proc Natl Acad Sci USA 2000;97:8063-8068.
25. Peek RM Jr, Miller GG, Tham KT, Perez-Perez Gl, Cover TL, Atherton JC, Dunn GD, Blaser MJ. Detection of Helicobacterpylori gene expression in human gastric mucosa. J Clin Microbiol 1995;33:28-32.
26. Jungblut PR, Bumann D, Haas G, Zimny-Arndt U, Holland P, Lamer S, Siejak F, Aebischer A, Meyer TF. Comparative proteome analysis of Helicobacter pylori. Mol Microbiol 2000;36:710-725.
27. Alm RA, Bina J, Andrews BM, Doig P, Hancock RE, Trust TJ. Comparative genomics of Helicobacter pylori: Analysis of the outer membrane protein families. Infect Immun 2000;68:4155-4168.
28. Iliopoulos I, Tsoka S, Andrade MA, Janssen P, Audit B, Tramontano A, Valencia A, Leroy C, Sander C, Ouzounis CA. Genome sequences and great expectations. Genome Biol 2001;2:1.1-1.3.
29. Wooff E, Michell SL, Gordon SV, Chambers MA, Bardarov S, Jacobs WR Jr, Hewinson RG, Wheeler PR. Functional genomics reveals the sole sulphate transporter of the Mycobacterium tuberculosis complex and its relevance to the acquisition of sulphur in vivo. Mol Microbiol 2002;43:653-663.
30. Donahue JP, Peek RM, Van Doorn, Thompson SA, Xu Q, Blaser MJ, Miller GG. Analysis of iceA1 transcription in Helicobacter pylori. Helicobacter 2000;5:1-12.
31. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 1997;388:539-547.
32. Huynen M, Dandekar T, Bork P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett 1998;426:1-5.
33. Daigle F, Graham JE, Curtiss R III. Identification of Salmonella typhi genes expressed within macrophages by selective capture of transcribed sequences (SCOTS). Mol Microbiol 2001;41:1211-1222.
34. Liu S, Graham JE, Bigelow L, Morse PD II, Wilkinson BJ. Identification of Listeria monocytogenes genes expressed in response to growth at low temperature. Appl Environ Microbiol 2002;68:1697-1705.
35. Hou JY, Graham JE, Clark-Curtiss JE. Mycobacterium avium genes expressed during growth in human macrophages detected by selective capture of transcribed sequences (SCOTS). Infect Immun 2002;70:3714-3726.