Functionality of essential genes drives gene strand-bias in bacterial genomes

Biochemical and Biophysical Research Communications

Volumn 396, Issue 2, 2010, Pages 472-476

  Lin, Yan ^a   Gao, Feng ^a   Zhang, Chun Ting ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

Bacterial genome; COG; Essential gene; Essentiality; Expressiveness; Functionality; Strand bias

Indexed keywords

AMINO ACID; CARBOHYDRATE; NUCLEOTIDE;

AMINO ACID METABOLISM; AMINO ACID TRANSPORT; ARTICLE; BACTERIAL CELL WALL; BACTERIAL GENE; BACTERIAL GENOME; BIOGENESIS; CARBOHYDRATE METABOLISM; CARBOHYDRATE TRANSPORT; CELL CYCLE REGULATION; CONTROLLED STUDY; ENERGY CONVERSION; ENERGY YIELD; ESSENTIAL GENE; GENE FUNCTION; GENE LOCATION; NUCLEOTIDE METABOLISM; NUCLEOTIDE TRANSPORT; PRIORITY JOURNAL; PROTEIN PROCESSING; SEQUENCE HOMOLOGY;

BACTERIA; DATABASES, GENETIC; GENES, ESSENTIAL; GENOME, BACTERIAL;

BACTERIA (MICROORGANISMS);

EID: 77952744822     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2010.04.119     Document Type: Article

References (15)

1. Kobayashi K., Ehrlich S.D., Albertini A., et al. Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100 (2003) 4678-4683
2. Zhang R., Ou H.Y., and Zhang C.T. DEG: a database of essential genes. Nucleic Acids Res. 32 (2004) D271-D272
3. Zhang R., and Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 37 (2009) D455-D458
4. Zeigler D.R., and Dean D.H. Orientation of genes in the Bacillus subtilis chromosome. Genetics 125 (1990) 703-708
5. McLean M.J., Wolfe K.H., and Devine K.M. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47 (1998) 691-696
6. Rocha E.P., and Danchin A. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat. Genet. 34 (2003) 377-378
7. Rocha E.P., and Danchin A. Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res. 31 (2003) 6570-6577
8. Tatusov R.L., Koonin E.V., and Lipman D.J. A genomic perspective on protein families. Science 278 (1997) 631-637
9. Tatusov R.L., Fedorova N.D., Jackson J.D., et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4 (2003) 41
10. Gao F., and Zhang C.T. DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 23 (2007) 1866-1867
11. Rocha E.P. The organization of the bacterial genome. Annu. Rev. Genet. 42 (2008) 211-233
12. Ochman H., and Davalos L.M. The nature and dynamics of bacterial genomes. Science 311 (2006) 1730-1733
13. Kanehisa M., and Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28 (2000) 27-30
14. Kanehisa M., Goto S., Hattori M., et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34 (2006) D354-D357
15. Kanehisa M., Goto S., Furumichi M., et al. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38 (2010) D355-D360