Codon Usage Patterns in Corynebacterium glutamicum: Mutational Bias, Natural Selection and Amino Acid Conservation.
The alternative synonymous codons in Corynebacterium glutamicum, a well-known bacterium used in industry for the production of amino acid, have been investigated by multivariate analysis. As C. glutamicum is a GC-rich organism, G and C are expected to predominate at the third position of codons. Indeed, overall codon usage analyses have indicated that C and/or G ending codons are predominant in this organism. Through multivariate statistical analysis, apart from mutational selection, we identified three other trends of codon usage variation among the genes. Firstly, the majority of highly expressed genes are scattered towards the positive end of the first axis, whereas the majority of lowly expressed genes are clustered towards the other end of the first axis. Furthermore, the distinct difference in the two sets of genes was that the C ending codons are predominate in putatively highly expressed genes, suggesting that the C ending codons are translationally optimal in this organism. Secondly, the majority of the putatively highly expressed genes have a tendency to locate on the leading strand, which indicates that replicational and transciptional selection might be invoked. Thirdly, highly expressed genes are more conserved than lowly expressed genes by synonymous and nonsynonymous substitutions among orthologous genes fromthe genomes of C. glutamicum and C. diphtheriae. We also analyzed other factors such as the length of genes and hydrophobicity that might influence codon usage and found their contributions to be weak.
Liu
Guiming
G
James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, Zhejiang 310008, China.
Wu
Jinyu
J
Yang
Huanming
H
Bao
Qiyu
Q
Genetics. 1994 Mar;136(3):927-35
8005445
Acta Biochim Biophys Sin (Shanghai). 2005 Sep;37(9):625-33
16143818
Nucleic Acids Res. 1999 Apr 1;27(7):1642-9
10075995
Nucleic Acids Res. 1981 Jan 10;9(1):r43-74
7208352
Microbiology (Reading). 1996 Apr;142 ( Pt 4):915-925
8936318
Gene. 2000 Jan 25;242(1-2):307-11
10721724
J Mol Evol. 1997 Nov;45(5):514-23
9342399
Biochem Biophys Res Commun. 2007 Mar 16;354(3):693-9
17258174
Bioessays. 2006 Jul;28(7):726-38
16850406
J Mol Biol. 1998 Aug 7;281(1):31-48
9680473
J Mol Biol. 1991 Dec 20;222(4):851-6
1762151
Gene. 2000 Mar 21;245(2):291-8
10717480
Genetics. 2006 Mar;172(3):1567-76
16361241
J Mol Evol. 1996 May;42(5):525-36
8662004
Biochem Biophys Res Commun. 2000 Mar 24;269(3):692-6
10720478
Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10698-703
9724767
Gene. 1993 Nov 30;134(1):15-24
8244028
Nat Rev Genet. 2009 Oct;10(10):715-24
19763154
Nat Rev Genet. 2006 Feb;7(2):98-108
16418745
Proteins. 2005 Jul 1;60(1):27-35
15849754
Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4482-7
10200288
J Biotechnol. 2003 Sep 4;104(1-3):5-25
12948626
DNA Res. 2009 Apr;16(2):91-104
19221094
J Mol Evol. 2000 Jan;50(1):45-55
10654259
Int J Parasitol. 2000 May;30(6):715-22
10856505
J Mol Evol. 2001 Mar;52(3):275-80
11428464
Biosystems. 2006 Aug;85(2):107-13
16442213
Trends Genet. 2000 Jul;16(7):287-9
10858656
FEBS Lett. 1998 Aug 28;434(1-2):93-6
9738458
Biochem Biophys Res Commun. 2004 May 7;317(3):957-64
15081433
J Mol Biol. 1981 Sep 25;151(3):389-409
6175758
APMIS. 2003 Sep;111(9):843-7
14510641
Nucleic Acids Res. 2000 May 15;28(10):2084-90
10773076
Mol Biol Evol. 2010 Apr;27(4):800-10
20018979
J Mol Evol. 1989 Apr;28(4):286-98
2499685
Mol Biol Evol. 2007 Feb;24(2):374-81
17101719
Nucleic Acids Res. 1990 Mar 25;18(6):1565-9
2326195
Microbiology (Reading). 2003 Apr;149(Pt 4):855-863
12686628
Biochem Biophys Res Commun. 2009 Dec 11;390(2):177-81
19769943
Nat Genet. 2003 Aug;34(4):377-8
12847524
Biosystems. 2004 Feb;73(2):89-97
15013221
Gene. 2006 Mar 1;368:117-25
16380221
DNA Res. 2005;12(2):91-102
16303741
BMC Evol Biol. 2007 Jan 29;7:9
17257443
Genome Res. 2002 Jun;12(6):962-8
12045149
Nucleic Acids Res. 1998 Jul 1;26(13):3188-93
9628917