Gene expression diversity among Mycobacterium tuberculosis clinical isolates

Microbiology

Volumn 151, Issue 1, 2005, Pages 5-14

  Gao, Qian ^a,c   Kripke, Katharine E ^a   Saldanha, Alok J ^a   Yan, Weihong ^a,d   Holmes, Susan ^b   Small, Peter M ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY   (United States)

^c FUDAN UNIVERSITY   (China)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; T LYMPHOCYTE ANTIGEN;

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIOPHAGE; BACTERIUM CULTURE; BACTERIUM ISOLATE; CONTROLLED STUDY; ESSENTIAL GENE; GENE DELETION; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE INSERTION; GENE SEQUENCE; GENETIC VARIABILITY; LIPID METABOLISM; LIQUID CULTURE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; STRAIN DIFFERENCE;

BACTERIAL PROTEINS; GENE DELETION; GENE EXPRESSION; GENES, ESSENTIAL; HUMANS; MYCOBACTERIUM TUBERCULOSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RECEPTORS, ANTIGEN, T-CELL; TUBERCULOSIS, PULMONARY; VARIATION (GENETICS);

HELICOBACTER; INSERTION SEQUENCES; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; SALMONELLA;

EID: 13444269651     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.27539-0     Document Type: Article

References (38)

1. Azad, A. K., Sirakova, T. D., Fernandes, N. D. & Kolattukudy, P. E. (1997). Gene knockout reveals a novel gene cluster for the synthesis of a class of cell wall lipids unique to pathogenic mycobacteria. J Biol Chem 272, 16741-16745.
2. Banu, S., Honore, N., Saint-Joanis, B., Philpott, D., Prevost, M. C. & Cole, S. T. (2002). Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens? Mol Microbiol 44, 9-19.
3. Barry, C. E., 3rd (2001). Interpreting cell wall 'virulence factors' of Mycobacterium tuberculosis. Trends Microbiol 9, 237-241.
4. Behr, M. A., Wilson, M. A., Gill, W. P., Salamon, H., Schoolnik, G. K., Rane, S. & Small, P. M. (1999). Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284, 1520-1523.
5. Betts, J. C., Lukey, P. T., Robb, L. C., McAdam, R. A. & Duncan, K. (2002). Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol 43, 717-731.
6. Brennan, M. J. & Delogu, G. (2002). The PE multigene family: a 'molecular mantra' for mycobacteria. Trends Microbiol 10, 246-249.
7. Brennan, M. J., Delogu, G., Chen, Y., Bardarov, S., Kriakov, J., Alavi, M. & Jacobs, W. R., Jr (2001). Evidence that mycobacterial PE_PGRS proteins are cell surface constituents that influence interactions with other cells. Infect Immun 69, 7326-7333.
8. Chaicumpar, K., Fujiwara, N., Nishimura, O., Hotta, H., Pan, J. W., Takahashi, M., Abe, C. & Yano, I. (1997). Studies of polymorphic DNA fingerprinting and lipid pattern of Mycobacterium tuberculosis patient isolates in Japan. Microbiol Immunol 41 107-119.
9. Cole, S. T., Brosch, R., Parkhill, J. & 39 other authors (1998). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537-544.
10. Covert, B. A., Spencer, J. S., Orme, I. M. & Belisle, J. T. (2001). The application of proteomics in defining the T cell antigens of Mycobacterium tuberculosis. Proteomics 1, 574-586.
11. Cox, J. S., Chen, B., McNeil, M. & Jacobs, W. R., Jr (1999). Complex lipid determines tissue-specific replication of Mycobacterium tuberculosis in mice. Nature 402, 79-83.
12. Daffe, M. & Etienne, G. (1999). The capsule of Mycobacterium tuberculosis and its implications for pathogenicity. Tuber Lung Dis 79, 153-169.
13. Dudoit, S., Yang, Y. H., Callow, M. J. & Speed, T. P. (2002). Statistical methods for identifying differentially expressed genes in replicated microarray experiments. Statistica Sinica 12 111-139.
14. Dudoit, S., Shaffer, J. P. & Boldrick, J. C. (2003). Multiple hypothesis testing in microarray experiments. Stat Sci 18, 71-103.
15. Fellenberg, K., Hauser, N. C., Brors, B., Neutzner, A., Hoheisel, J. D. & Vingron, M. (2001). Correspondence analysis applied to microarray data. Proc Natl Acad Sci U S A 98, 10781-10786.
16. Fisher, M. A., Plikaytis, B. B. & Shinnick, T. M. (2002). Microarray analysis of the Mycobacterium tuberculosis transcriptional response to the acidic conditions found in phagosomes. J Bacteriol 184, 4025-4032.
17. Fleischmann, R. D., Alland, D., Eisen, J. A. & 23 other authors (2002). Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 184 5479-5490.
18. Girke, T., Todd, J., Ruuska, S., White, J., Benning, C. & Ohlrogge, J. (2000). Microarray analysis of developing Arabidopsis seeds. Plant Physiol 124, 1570-1581.
19. Greenacre, M. (1984). Theory and Applications of Correspondence Analysis. London: Academic Press.
20. Hiromatsu, K., Dascher, C. C., LeClair, K. P., Sugita, M., Furlong, S. T., Brenner, M. B. & Porcelli, S. A. (2002). Induction of CD1-restricted immune responses in guinea pigs by immunization with mycobacterial lipid antigens. J Immunol 169, 330-339.
21. Jasmer, R. M., Hahn, J. A., Small, P. M. & 7 other authors (1999). A molecular epidemiologic analysis of tuberculosis trends in San Francisco, 1991-1997. Ann Intern Med 130, 971-978.
22. Kana, B. D. & Mizrahi, V. (2004). Molecular genetics of Mycobacterium tuberculosis in relation to the discovery of novel drugs and vaccines. Tuberculosis (Edinb) 84, 63-75.
23. Kane, M. D., Jatkoe, T. A., Stumpf, C. R., Lu, J., Thomas, J. D. & Madore, S. J. (2000). Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28, 4552-4557.
24. Kato-Maeda, M., Rhee, J. T., Gingeras, T. R., Salamon, H., Drenkow, J., Smittipat, N. & Small, P. M. (2001). Comparing genomes within the species Mycobacterium tuberculosis. Genome Res 11, 547-554.
25. Kolattukudy, P. E., Fernandes, N. D., Azad, A. K., Fitzmaurice, A. M. & Sirakova, T. D. (1997). Biochemistry and molecular genetics of cell-wall lipid biosynthesis in mycobacteria. Mol Microbiol 24, 263-270.
26. Kuznetsov, V. A., Knott, G. D. & Bonner, R. F. (2002). General statistics of stochastic process of gene expression in eukaryotic cells. Genetics 161, 1321-1332.
27. Manganelli, R., Voskuil, M. I., Schoolnik, G. K., Dubnau, E., Gomez, M. & Smith, I. (2002). Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression. Mol Microbiol 45, 365-374.
28. Puzo, G. (1990). The carbohydrate- and lipid-containing cell wall of mycobacteria, phenolic glycolipids: structure and immunological properties. Crit Rev Microbiol 17, 305-327.
29. Rook, G. A. & Zumla, A. (2001). Advances in the immunopathogenesis of pulmonary tuberculosis. Curr Opin Pulm Med 7, 116-123.
30. Rosat, J. P., Grant, E. P., Beckman, E. M. & 7 other authors (1999). CD1-restricted microbial lipid antigen-specific recognition found in the CD8+ alpha beta T cell pool. J Immunol 162, 366-371.
31. Sampson, S. L., Lukey, P., Warren, R. M., van Helden, P. D., Richardson, M. & Everett, M. J. (2001). Expression, characterization and subcellular localization of the Mycobacterium tuberculosis PPE gene Rv1917c. Tuberculosis (Edinb) 81, 305-317.
32. Sassetti, C. M., Boyd, D. H. & Rubin, E. J. (2003). Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48, 77-84.
33. Smith, C. V., Sharma, V. & Sacchettini, J. C. (2004). TB drug discovery: addressing issues of persistence and resistance. Tuberculosis (Edinb) 84, 45-55.
34. Talaat, A. M., Howard, S. T., Hale, W. T., Lyons, R., Garner, H. & Johnston, S. A. (2002). Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis. Nucleic Acids Res 30, e104.
35. Tsolaki, A. G., Hirsh, A. E., DeRiemer, K. & 7 other authors (2004). Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc Natl Acad Sci U S A 101, 4865-4870.
36. Valway, S. E., Sanchez, M. P., Shinnick, T. F., Orme, I., Agerton, T., Hoy, D., Jones, J. S., Westmoreland, H. & Onorato, I. M. (1998). An outbreak involving extensive transmission of a virulent strain of Mycobacterium tuberculosis. N Engl J Med 338, 633-639.
37. Wilson, M., DeRisi, J., Kristensen, H. H., Imboden, P., Rane, S., Brown, P. O. & Schoolnik, G. K. (1999). Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc Natl Acad Sci U S A 96, 12833-12838.
38. Xu, W., Bak, S., Decker, A., Paquette, S. M., Feyereisen, R. & Galbraith, D. W. (2001). Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana. Gene 272, 61-74.