Basak Surajit, Ghosh Tapash Chandra
Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
FEBS Lett. 2006 Jul 10;580(16):3895-9. doi: 10.1016/j.febslet.2006.06.014. Epub 2006 Jun 16.
Synonymous codon usage of homologous sequences between Methanococcus jannaschii and Methanococcus maripaludis have been analyzed in three broad functional categories of genes namely: (i) information storage and processing; (ii) metabolism; and (iii) cellular processes and signaling. Average values of synonymous nucleotide substitutions per synonymous site are significantly lower for information processing genes compared to either metabolic or cellular processing genes. These results suggests that synonymous codon usage has been subject to greater constraint in the information storage and processing group of genes compared to other functional categories of genes. For metabolic and cellular processing genes, correspondence analysis based on relative synonymous codon usage (RSCU) values separates the genes along the first major axes according to the genome type; while in the information processing group, genes are separated along the second major axes according to the genome type. Further study on synonymous substitution rate for information processing genes shows a stronger selective constraint on synonymous codon usage of six amino acids, G,A,R,P,Y,F. Randomization of the original transcript of M. jannaschii for information processing genes suggests that variation in selective constraint between synonymous codon usage is related to the potential formation of mRNA secondary structures which contribute to the folding stability.
已对詹氏甲烷球菌和沼泽甲烷球菌之间同源序列的同义密码子使用情况在三类广泛的基因功能类别中进行了分析，即：（i）信息存储与处理；（ii）代谢；以及（iii）细胞过程与信号传导。与代谢或细胞处理基因相比，信息处理基因每个同义位点的同义核苷酸替换平均值显著更低。这些结果表明，与其他功能类别的基因相比，同义密码子使用在信息存储与处理基因组中受到了更大的限制。对于代谢和细胞处理基因，基于相对同义密码子使用（RSCU）值的对应分析根据基因组类型在第一主轴上分离基因；而在信息处理组中，基因根据基因组类型在第二主轴上分离。对信息处理基因同义替换率的进一步研究表明，对六个氨基酸G、A、R、P、Y、F的同义密码子使用存在更强的选择限制。对詹氏甲烷球菌信息处理基因原始转录本的随机化表明，同义密码子使用之间选择限制的差异与有助于折叠稳定性的mRNA二级结构的潜在形成有关。
