Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 89, Issue 1, 2006, Pages 135-146

  Wu, Gang ^a   Nie, Lei ^b   Zhang, Weiwen ^c  

^a UNIVERSITY OF MARYLAND   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

^c PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Codon adaptation index; Gene expression; Nocardia farcinica

Indexed keywords

BACTERIAL PROTEIN; CATALASE; FATTY ACID SYNTHASE; GLUTATHIONE PEROXIDASE; METHIONINE SULFOXIDE REDUCTASE; MYCOLIC ACID; POLYKETIDE SYNTHASE; PREDICTED HIGHLY EXPRESSED PROTEIN; REACTIVE OXYGEN METABOLITE; RIBOSOME PROTEIN; SIDEROPHORE; SUPEROXIDE DISMUTASE; THIOREDOXIN; THIOREDOXIN REDUCTASE; UNCLASSIFIED DRUG;

BACTERIUM; GENE; GENOME; METABOLISM; PATHOGEN;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL METABOLISM; BACTERIAL SURVIVAL; BACTERIAL VIRULENCE; CELL GROWTH; CELL WALL; CODON; FATTY ACID SYNTHESIS; GENE EXPRESSION REGULATION; GENE LOCATION; GENE REPLICATION; GENE SEQUENCE; GRAM POSITIVE BACTERIUM; HOST CELL; HOUSEKEEPING GENE; NOCARDIA FARCINICA; NONHUMAN; PHAGOCYTE; PLASMID; PREDICTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE;

ANIMALS; BACTERIAL PROTEINS; BASE COMPOSITION; CODON; DNA, BACTERIAL; ENERGY METABOLISM; GENE EXPRESSION; GENES, BACTERIAL; HUMANS; NOCARDIA; VIRULENCE;

BACTERIA (MICROORGANISMS); NOCARDIA; NOCARDIA FARCINICA; POSIBACTERIA; STREPTOMYCES;

EID: 33646063776     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10482-005-9016-z     Document Type: Article

References (53)

1. Beaman B.L., Beaman L. (1994). Nocardia species: Host-parasite relationships. Clin. Microbiol. Rev. 7:213-264
2. Bentley S.D., Chater K.F., Cerdeno-Tarraga A.M., et al. (2002). Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141-147
3. Birch A., Leiser A., Robinson J.A. (1993). Cloning, sequencing, and expression of the gene encoding methylmalonyl-coenzyme A mutase from Streptomyces cinnamonensis. J. Bacteriol. 175:3511-3519
4. Blanco G., Rodicio M.R., Puglia A.M., Mendez C., Thompson C.J., Salas J.A. (1994). Synthesis of ribosomal proteins during growth of Streptomyces coelicolor. Mol. Microbiol. 12:375-385
5. Chakraburtty R., Bibb M. (1997). The ppGpp synthetase gene (relA) of Streptomyces coelicolor A3(2) plays a conditional role in antibiotic production and morphological differentiation. J. Bacteriol. 179:5854-5861
6. Chitale S., Ehrt S., Kawamura I., Fujimura T., Shimono N., Anand N., Lu S., Cohen-Gould L., Riley L.W. (2001). Recombinant Mycobacterium tuberculosis protein associated with mammalian cell entry. Cell Microbiol. 3:247-254
7. Coghlan A., Wolfe K.H. (2000). Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16:1131-1145
8. Domingue G.J. Sr, Woody H.B. (1997). Bacterial persistence and expression of disease. Clin. Microbiol. Rev. 10:320-344
9. Dos Reis M., Wernisch L., Savva R. (2003). Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res. 31:6976-6985
10. S). J. Bacteriol. 181:572-576
11. S is positively regulated by ppGpp. J Bacteriol 175:7982-7989
12. Haile Y., Bjune G., Wiker H.G. (2002). Expression of the mceA, esat-6 and hspX genes in Mycobacterium tuberculosis and their responses to aerobic conditions and to restricted oxygen supply. Microbiology 148:3881-3886
13. Huang J., Lih C.J., Pan K.H., Cohen S.N. (2001). Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev. 15:3183-3192
14. Hopwood D.A., Sherman D.H. (1990). Molecular genetics of polyketides and its comparison to fatty acid biosynthesis. Annu. Rev. Genet. 24:37-66
15. Hubble J.P., Cao T., Kjelstrom J.A., Koller W.C., Beaman B.L. (1995). Nocardia species as an etiologic agent in Parkinson's disease: serological testing in a case-control study. J. Clin. Microbiol. 33:2768-2769
16. Ikeda H., Ishikawa J., Hanamoto K., et al. (2003). Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nature Biotech. 21:526-531
17. Ikemura T. (1981). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151:389-409
18. Ikemura T. (1982). Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J. Mol. Biol. 158:573-97
19. Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K., Shiba T., Hattori M. (2004). The complete genomic sequence of Nocardia farcinica IFM 10152. Proc. Natl. Acad. Sci. (USA) 101:14925-14930
20. Javaly K., Horowitz H.W., Wormser G.P. (1992). Nocardiosis in patients with human immunodeficiency virus infection. Medicine (Baltimore) 71:128-138
21. Kageyama A., Yazawa K., Ishikawa J., Hotta K., Nishimura K., Mikami Y. (2004). Nocardial infections in Japan from 1992 to 2001, including the first report of infection by Nocardia transvalensis. Eur. J. Epidemiol. 19:383-389
22. Karlin S., Mrazek J. (2000). Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182:5238-5250
23. Karlin S., Mrazek J., Campbell A., Kaiser D. (2001). Characterizations of highly expressed genes of four fast-growing bacteria. J. Bacteriol. 183:5025-5040
24. Karlin S., Brocchieri L., Campbell A., Cyert M., Mrazek J. (2005). Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes. Proc. Natl. Acad. Sci. USA 102:7309-7314
25. Knight R.D., Freeland S.J. and Landweber L.F. 2001. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol. 2: RESEARCH0010
26. Lafay B., Atherton J.C., Sharp P.M. (2000). Absence of translationally selected synonymous codon usage bias in Helicobacter pylori. Microbiology. 146:851-60
27. Li C., Florova G., Akopiants K., Reynolds K.A. (2004). Crotonyl-coenzyme A reductase provides methylmalonyl-CoA precursors for monensin biosynthesis by Streptomyces cinnamonensis in an oil-based extended fermentation. Microbiology 150:3463-3472
28. Liu H., Reynolds K.A. (1999). Role of crotonyl coenzyme A reductase in determining the ratio of polyketides monensin A and monensin B produced by Streptomyces cinnamonensis. J. Bacteriol. 181:6806-6813
29. Martin-Galiano A.J., Wells J.M., de la Campa A.G. (2004). Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae. Microbiology 150:2313-2325
30. Médigue C., Rouxel T., Vigier P., Hénaut A., Danchin A. (1991). Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222:851-856
31. Moskovitz J., Rahman M.A., Strassman J., Yancey S.O., Kushner S.R., Brot N., Weissbach H. (1995). Escherichia coli peptide methionine sulfoxide reductase gene: Regulation of expression and role in protecting against oxidative damage. J. Bacteriol. 177:502-507
32. Moskovitz J., Berlett B.S., Poston J.M., Stadtman E.R. (1997). The yeast peptide-methionine sulfoxide reductase functions as an antioxidant in vivo. Proc. Natl. Acad. Sci. USA 94:9585-9589
33. Mrazek J., Bhaya D., Grossman A.R., Karlin S. (2001). Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res. 29:1590-1601
34. Newton G.L., Arnold K., Price M.S., Sherrill C., Delcardayre S.B., Aharonowitz Y., Cohen G., Davies J., Fahey R.C., Davis C. (1996). Distribution of thiols in microorganisms: Mycothiol is a major thiol in most actinomycetes. J. Bacteriol. 178:1990-1995
35. Okamoto S., Lezhava A., Hosaka T., Okamoto-Hosoya Y., Ochi K. (2003). Enhanced expression of S-adenosylmethionine synthetase causes overproduction of actinorhodin in Streptomyces coelicolor A3(2). J. Bacteriol. 185:601-609
36. Pan A., Dutta C., Das J. (1998). Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: Translational selection versus mutational bias. Gene 215:405-413
37. Perriere G., Thioulouse J. (2002). Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res. 30:4548-4555
38. Portevin D., De Sousa-D'Auria C., Houssin C., Grimaldi C., Chami M., Daffe M., Guilhot C. (2004). A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms. Proc. Natl. Acad. Sci. USA 101:314-319
39. Quadri L.E.N., Sello J., Keating T.A., Weinreb P.H., Walsh C.T. (1998). Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin. Chem. Biol. 5:631-645
40. Rodionov D.A., Dubchak I., Arkin A., Alm E., Gelfand M.S. (2004). Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol. 5: R90
41. Rao V., Fujiwara N., Porcelli S.A., Glickman M.S. (2005). Mycobacterium tuberculosis controls host innate immune activation through cyclopropane modification of a glycolipid effector molecule. J. Exp. Med. 201:535-543
42. Scharf C., Riethdorf S., Ernst H., Engelmann S., Volker U., Hecker M. (1998). Thioredoxin is an essential protein induced by multiple stresses in Bacillus subtilis. J. Bacteriol. 180:1869-1877
43. Sharp P.M. and Li W.H. (1986). An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 24:28-38
44. Sharp P.M., Li W.H. (1987). The Codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295
45. Shigemori H., Komaki H., Yazawa K., Mikami Y., Nemoto A., Tanaka Y., Sasaki Y., Ishida T., Kobayashi J. (1998). Brasilicardin A A novel tricyclic metabolite with potent immunosuppressive activity from actinomycete Nocardia brasiliensis. J. Org. Chem. 63:6900-6904
46. Trotter E.W., Grant C.M. (2003). Non-reciprocal regulation of the redox state of the glutathione-glutaredoxin and thioredoxin systems. EMBO Rep. 4:184-188
47. Uziel O., Borovok I., Schreiber R., Cohen G., Aharonowitz Y. (2004). Transcriptional regulation of the Staphylococcus aureus thioredoxin and thioredoxin reductase genes in response to oxygen and disulfide stress. J. Bacteriol. 186:326-334 326-334
48. Venketaraman V., Dayaram Y.K., Talaue M.T., Connell N.D. (2005). Glutathione and nitrosoglutathione in macrophage defense against Mycobacterium tuberculosis. Infect. Immun. 73:1886-1889
49. Wayne L.G., Hayes L.G. (1998). Nitrate reduction as a marker for hypoxic shiftdown of Mycobacterium tuberculosis. Tuber. Lung. Dis. 79:127-132
50. Wu G., Culley D.E., Zhang W. (2005). Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism. Microbiology 151:2175-2187
51. Wright F. (1990). The effective number of codons used in a gene. Gene 87:23-29
52. Zerbe-Burkhardt K., Ratnatilleke A., Philippon N., Birch A., Leiser A., Vrijbloed J.W., Hess D., Hunziker P., Robinson J.A. (1998). Cloning, sequencing, expression, and insertional inactivation of the gene for the large subunit of the coenzyme B12-dependent isobutyryl-CoA mutase from Streptomyces cinnamonensis. J. Biol. Chem. 273:6508-6517
53. 12 -dependent mutase, provides methylmalonyl coenzyme A for monensin biosynthesis in Streptomyces cinnamonensis. J. Bacteriol. 183:2071-2080