Mycobacterium smegmatis genomic characteristics associated with its saprophyte lifestyle

Journal of Cellular Biochemistry

Volumn 113, Issue 10, 2012, Pages 3051-3055

  Long, Quanxin ^a   Zhou, Qi ^b,c   Ji, Lei ^a   Wu, Jun ^a   Wang, Wen ^b   Xie, Jianping ^a  

^a SOUTHWEST UNIVERSITY   (China)

^b KUNMING INSTITUTE OF ZOOLOGY   (China)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

comparative genomics; mycobacterium smegmatis; mycobacterium tuberculosis; saprophyte

Indexed keywords

BACTERIAL GENOME; ECOLOGICAL NICHE; ENRICHMENT CULTURE; GENE ONTOLOGY ENRICHMENT ANALYSIS; GENETIC ANALYSIS; LIFESTYLE; MYCOBACTERIUM ABSCESSUS; MYCOBACTERIUM BOVIS; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM MARINUM; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM ULCERANS; NONHUMAN; PRIORITY JOURNAL; REVIEW; SALT TOLERANCE; SAPROTROPH;

ADAPTATION, PHYSIOLOGICAL; BACTERIAL PROTEINS; CARBOHYDRATE METABOLISM; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; MODELS, BIOLOGICAL; MYCOBACTERIUM SMEGMATIS; PQQ COFACTOR; SALT-TOLERANCE; TIME FACTORS; TRANSCRIPTION FACTORS;

EID: 84865043623     PISSN: 07302312     EISSN: 10974644     Source Type: Journal    
DOI: 10.1002/jcb.24199     Document Type: Review

References (27)

1. Alexeyenko A, Tamas I, Liu G, Sonnhammer EL,. 2006. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: e9-e15.
2. Ameyama M, Matsushita K, Shinagawa E, Hayashi M, Adachi O,. 1988. Pyrroloquinoline quinone: Excretion by methylotrophs and growth stimulation for microorganisms. Biofactors 1: 51-53.
3. Bange FC, Collins FM, Jacobs WR Jr., 1999. Survival of mice infected with Mycobacterium smegmatis containing large DNA fragments from Mycobacterium tuberculosis. Tuber Lung Dis 79: 171-180.
4. Bauer S, Grossmann S, Vingron M, Robinson PN,. 2008. Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24: 1650-1651.
5. Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA,. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417: 141-147.
6. Bercovier H, Vincent V,. 2001. Mycobacterial infections in domestic and wild animals due to Mycobacterium marinum, M. fortuitum, M. chelonae, M. porcinum, M. farcinogenes, M. smegmatis, M. scrofulaceum, M. xenopi, M. kansasii, M. simiae and M. genavense. Rev Sci Tech 20: 265-290.
7. Bursy J, Pierik AJ, Pica N, Bremer E,. 2007. Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase. J Biol Chem 282: 31147-31155.
8. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG,. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
9. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG,. 2001. Massive gene decay in the leprosy bacillus. Nature 409: 1007-1011.
10. Domenech P, Menendez MC, Garcia MJ,. 1994. Restriction fragment length polymorphisms of 16S rRNA genes in the differentiation of fast-growing mycobacterial species. FEMS Microbiol Lett 116: 19-24.
11. Duine JA, Jongejan JA,. 1989. Quinoproteins, enzymes with pyrrolo-quinoline quinone as cofactor. Annu Rev Biochem 58: 403-426.
12. Eschbach M, Mobitz H, Rompf A, Jahn D,. 2003. Members of the genus Arthrobacter grow anaerobically using nitrate ammonification and fermentative processes: Anaerobic adaptation of aerobic bacteria abundant in soil. FEMS Microbiol Lett 223: 227-230.
13. Kubica Vas GP, Kilburn JO, Smithwick RW, Beam RE, Jones WD JR, Stottmeier KD,. 1970. Differential identification of mycobacteria VI. Mycobacterium triviale Kubica sp. nov. Int J Syst Bacteriol 20: 161.
14. Jebbar M, Talibart R, Gloux K, Bernard T, Blanco C,. 1992. Osmoprotection of Escherichia coli by ectoine: Uptake and accumulation characteristics. J Bacteriol 174: 5027-5035.
15. Lagier B, Pelicic V, Lecossier D, Prod'hom G, Rauzier J, Guilhot C, Gicquel B, Hance AJ,. 1998. Identification of genetic loci implicated in the survival of Mycobacterium smegmatis in human mononuclear phagocytes. Mol Microbiol 29: 465-475.
16. Liesack W, Sela S, Bercovier H, Pitulle C, Stackebrandt E,. 1991. Complete nucleotide sequence of the Mycobacterium leprae 23 S and 5 S rRNA genes plus flanking regions and their potential in designing diagnostic oligonucleotide probes. FEBS Lett 281: 114-118.
17. Mauchline TH, Fowler JE, East AK, Sartor AL, Zaheer R, Hosie AH, Poole PS, Finan TM,. 2006. Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome. Proc Natl Acad Sci USA 103: 17933-17938.
18. Menendez MC, Garcia MJ, Navarro MC, Gonzalez-y-Merchand JA, Rivera-Gutierrez S, Garcia-Sanchez L, Cox RA,. 2002. Characterization of an rRNA operon (rrnB) of Mycobacterium fortuitum and other mycobacterial species: Implications for the classification of mycobacteria. J Bacteriol 184: 1078-1088.
19. O'Brien KP, Remm M, Sonnhammer EL,. 2005. Inparanoid: A comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33: D476-D480.
20. Pelicic V, Reyrat JM, Gicquel B,. 1998. Genetic advances for studying Mycobacterium tuberculosis pathogenicity. Mol Microbiol 28: 413-420.
21. Reitzer L,. 2003. Nitrogen assimilation and global regulation in Escherichia coli. Annu Rev Microbiol 57: 155-176.
22. Remm M, Storm CE, Sonnhammer EL,. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.
23. Reyrat JM, Kahn D,. 2001. Mycobacterium smegmatis: An absurd model for tuberculosis? Trends Microbiol 9: 472-474.
24. Sassetti CM, Rubin EJ,. 2003. Genetic requirements for mycobacterial survival during infection. Proc Natl Acad Sci USA 100: 12989-12994.
25. Sleator RD, Hill C,. 2002. Bacterial osmoadaptation: The role of osmolytes in bacterial stress and virulence. FEMS Microbiol Rev 26: 49-71.
26. Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, Garnier T, Meurice G, Simon D, Bouchier C, Ma L, Tichit M, Porter JL, Ryan J, Johnson PD, Davies JK, Jenkin GA, Small PL, Jones LM, Tekaia F, Laval F, Daffe M, Parkhill J, Cole ST,. 2007. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res 17: 192-200.
27. Tyagi JS, Sharma D,. 2002. Mycobacterium smegmatis and tuberculosis. Trends Microbiol 10: 68-69.