Detecting alien genes in bacterial genomes

Annals of the New York Academy of Sciences

Volumn 870, Issue , 1999, Pages 314-329

  Mrázek, Jan ^a   Karlin, Samuel ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN; ELONGATION FACTOR; HEAT SHOCK PROTEIN; RIBOSOME PROTEIN; TRANSPOSASE;

BACTERIAL GENE; BACTERIAL GENETICS; CODON; CONFERENCE PAPER; CYANOBACTERIUM; GENE EXPRESSION; GENOME; METHANOBACTERIALES; METHANOGENESIS; NONHUMAN; OPEN READING FRAME; PHOTOSYSTEM II;

BACTERIA (MICROORGANISMS); METHANOBACTERIALES; METHANOCALDOCOCCUS JANNASCHII; METHANOCOCCUS; SYNECHOCYSTIS;

EID: 0032804381     PISSN: 00778923     EISSN: None     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.1999.tb08893.x     Document Type: Conference Paper

References (22)

1. LORENZ, M.G. & W. WACKERNAGEL. 1994. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58: 563-602.
2. SOLOMON, J.M. & A.D. GROSSMAN. 1996. Who's competent and when: Regulation of natural genetic competence in bacteria. Trends Genet. 12: 150-155.
3. BROWN, J.R., Y. MASUCHI, F.T. ROBB, & W.F. DOOLITTLE. 1994. Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J. Mol. Evol. 38: 566-576.
4. BENACHENHOU-LAHFA, N., P. FORTEREE & B. LABEDAN. 1994. Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. J. Mol. Evol. 36: 335-346.
5. BALDAUF, S.L., J.D. PALMER & W.F. DOOLITTLE. 1996. The root of the universal tree and the origin of eukaryotes based on clongation factor phylogeny. Proc. Natl. Acad. Sci. USA 93: 7749-7754.
6. ROSENTHAL, B., Z.M. MAI, D. CAPLIVSKI, S. GHOSH, H. DELAVEGA, T. GRAF & J. SAMUELSON. 1997. Evidence for the bacterial origin of genes encoding fermentation enzymes of the amitochondriate protozoan parasite Entamoeba histolytica. J. Bacteriol. 179: 3736-3745.
7. SHARP, P.M. & W.-H. LI. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15: 1281-1295.
8. SHARP, P.M. & G. MATASSI. 1994. Codon usage and genome evolution. Curr. Opin. Genet. Dev. 4: 851-860.
9. VANBOGELEN, R.A., K.Z. ABSHIRE, A. PERTSEMLIDIS, R.L. CLARK & F.C. NEIDHART. 1996. Gene-protein database of Escherichia coli K-12, edition 6. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd Ed.: 2067-2117. F.C. Neidhardt, R. Curtiss, III, J.L. Ingraham, E.C.C. Lin, K.B. Low, B. Magasanik, W.S. Reznikoff, M. Riley, M. Schaechter & H.E. Umbarger, Eds. ASM Press. Washington, DC.
10. MÉDIGUE, C., T. ROUXEL, P. VIGIER, A. HENAUT & A. DANCHIN. 1991. Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222: 851-856.
11. LAWRENCE, J.G. & H. OCHMAN. 1997. Amclioration of bacterial genomes: Rates of change and exchange. J. Mol. Evol. 44: 383-397.
12. KARLIN, S., A.M. CAMPBELL & J. MRAZEK. 1998. Codon usages in different gene classes of the E. coli genome. Mol. Microbiol. 29: 1341-1355.
13. KARLIN, S., A.M. CAMPBELL & J. MRÁZEK. 1998. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32: 185-225.
14. FLEISCHMANN, R.D., M.D. ADAMS, O. WHITE, R.A. CLAYTON, E.F. KIRKNESS, A.R. KERLAVAGE, C.J. BULT, J.F. TOMB, B.A. DOUGHERTY, J.M. MERRICK et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
15. SMITH, H.O., J.-F. TOMB, B.A. DOUGHERTY, R.D. FLEISCHMANN & J.C. VENTER. 1995. Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. Science 269: 538-540.
16. KARLIN, S., J. MRÁZEK & A.M. CAMPBELL. 1996. Frequent oligonucleotides and peptides of the Haemophilus influenzae genome. Nucleic Acids Res. 24: 4263-4272.
17. HENDRICKS, R.W., M.C.M. SMITH, R.N. BURNS, M.E. FORD & G.F. HATFULL. 1999. Evolutionary relationships among diverse bacteriophage and prophage: All the world's a phage. Proc. Natl. Acad. Sci. USA. In press.
18. KARLIN, S. 1998. Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol. 1: 598-610.
19. LAWRENCE, J.G. & J.R. ROTH. 1996. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143: 1843-1860.
20. LOBRY, J.R. 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13: 660-665.
21. FRANCINO, M.P. & H. OCHMAN. 1997. Strand asymmetries in DNA evolution. Trends Genet. 13: 240-245.
22. MRÁZEK, J. & S. KARLIN. 1998. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95: 3720-3725.