Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes.
BACKGROUND
Most bacterial chromosomes exhibit asymmetry of base composition with respect to leading vs. lagging strands (GC and AT skews). These skews reflect mainly those in protein coding sequences, which are driven by asymmetric mutation pressures during replication and transcription (notably asymmetric cytosine deamination) plus subsequent selection for preferred structures, signals, amino acid or codons. The transcription-associated effects but not the replication-associated effects contribute to the overall skews through the uneven distribution of the coding sequences on the leading and lagging strands.


RESULTS
Analysis of 185 representative bacterial chromosomes showed diverse and characteristic patterns of skews among different clades. The base composition skews in the coding sequences were used to derive quantitatively the effect of replication-driven mutation plus subsequent selection ('replication-associated pressure', RAP), and the effect of transcription-driven mutation plus subsequent selection at translation level ('transcription-associate pressure', TAP). While different clades exhibit distinct patterns of RAP and TAP, RAP is absent or nearly absent in some bacteria, but TAP is present in all. The selection pressure at the translation level is evident in all bacteria based on the analysis of the skews at the three codon positions. Contribution of asymmetric cytosine deamination was found to be weak to TAP in most phyla, and strong to RAP in all the Proteobacteria but weak in most of the Firmicutes. This possibly reflects the differences in their chromosomal replication machineries. A strong negative correlation between TAP and G+C content and between TAP and chromosomal size were also revealed.


CONCLUSIONS
The study reveals the diverse mutation and selection forces associated with replication and transcription in various groups of bacteria that shape the distinct patterns of base composition skews in the chromosomes during evolution. Some closely relative species with distinct base composition parameters are uncovered in this study, which also provides opportunities for comparative bioinformatic and genetic investigations to uncover the underlying principles for mutation and selection.
Chen
Chi
C
Institute of Biomedical Informatics, National Yang-Ming University, Shih-Pai, Taipei 111, Taiwan. g39008006@ym.edu.tw
Chen
Carton W
CW
D001482:Base Composition; D002876:Chromosomes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D009154:Mutation; D012641:Selection, Genetic
J Mol Evol. 1998 Dec;47(6):691-6
9847411
Trends Microbiol. 2002 Sep;10(9):393-5
12217498
Mol Biol Evol. 2001 Sep;18(9):1789-99
11504858
J Biotechnol. 2000 Mar 31;78(3):209-19
10751682
J Bacteriol. 1999 Oct;181(20):6425-40
10515934
J Mol Evol. 2000 Mar;50(3):249-57
10754068
Mutat Res. 1995 Mar;336(2):101-13
7885381
Nucleic Acids Res. 1984 Feb 10;12(3):1749-63
6583663
Curr Opin Microbiol. 1999 Oct;2(5):524-8
10508724
Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13919-24
8943036
Nucleic Acids Res. 2004;32(13):3781-91
15258248
Comput Appl Biosci. 1996 Dec;12(6):519-24
9021271
J Appl Genet. 2001;42(4):553-77
14564030
J Mol Evol. 1999 Jul;49(1):49-62
10368434
Gene. 1999 Sep 30;238(1):65-77
10570985
Annu Rev Genet. 1998;32:185-225
9928479
Mol Microbiol. 1999 Apr;32(1):11-6
10216855
Genome Biol. 2002 Sep 26;3(10):RESEARCH0058
12372146
J Bacteriol. 1997 Jun;179(12):3899-913
9190805
Gene. 1998 Sep 14;217(1-2):57-67
9795135
Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3720-5
9520433
Gene. 1984 Oct;30(1-3):157-66
6096212
J Mol Evol. 2001 May;52(5):426-33
11443346
Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10698-703
9724767
BMC Genomics. 2003 May 5;4(1):17
12732098
Genome Res. 2006 Dec;16(12):1537-47
17068325
Genome Res. 2001 Apr;11(4):540-6
11282969
Nucleic Acids Res. 1999 Apr 1;27(7):1642-9
10075995
Trends Genet. 1997 Jun;13(6):240-5
9196330
Genome Res. 1999 May;9(5):409-16
10330120
Microbiology. 2004 Jun;150(Pt 6):1609-27
15184548
Mol Biol Evol. 2001 Jun;18(6):1147-50
11371605
Curr Opin Microbiol. 2003 Apr;6(2):101-8
12732297
Biol Chem. 1998 Apr-May;379(4-5):549-51
9628351
Science. 2001 Nov 23;294(5547):1716-9
11721055
Mol Biol Evol. 1996 May;13(5):660-5
8676740
Proc Natl Acad Sci U S A. 1987 Jan;84(1):166-9
3467347
Annu Rev Genet. 2004;38:771-92
15568993
Cell. 1996 May 31;85(5):625-7
8646771
Environ Microbiol. 2006 Feb;8(2):353-61
16423021
Science. 1996 Apr 5;272(5258):107-9
8600517
J Bacteriol. 2002 Jul;184(14):3801-7
12081949