Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411-8540, Japan.
DNA Res. 2011 Jun;18(3):177-87. doi: 10.1093/dnares/dsr010. Epub 2011 May 17.
The primary role of a protein coding gene is to encode amino acids. Therefore, synonymous sites of codons, which do not change the encoded amino acid, are regarded as evolving neutrally. However, if a certain region of a protein coding gene contains a functional nucleotide element (e.g. splicing signals), synonymous sites in the region may have selective pressure. The existence of such elements would be detected by searching regions of low nucleotide substitution. We explored invariant nucleotide sequences in 10,790 orthologous genes of six mammalian species (Homo sapiens, Macaca mulatta, Mus musculus, Rattus norvegicus, Bos taurus, and Canis familiaris), and extracted 4150 sequences whose conservation is significantly stronger than other regions of the gene and named them significantly conserved coding sequences (SCCSs). SCCSs are observed in 2273 genes. The genes are mainly involved with development, transcriptional regulation, and the neurons, and are expressed in the nervous system and the head and neck organs. No strong influence of conventional factors that affect synonymous substitution was observed in SCCSs. These results imply that SCCSs may have double function as nucleotide element and protein coding sequence and retained in the course of mammalian evolution.
蛋白质编码基因的主要作用是编码氨基酸。因此，密码子的同义位点不会改变编码的氨基酸，被认为是中性进化的。然而，如果蛋白质编码基因的某个区域包含功能性核苷酸元件（例如剪接信号），则该区域的同义位点可能受到选择压力。通过搜索核苷酸替换率低的区域，可以检测到这些元件的存在。我们探索了六种哺乳动物（智人、猕猴、小家鼠、褐家鼠、牛和犬）的 10790 个直系同源基因中的不变核苷酸序列，并提取了 4150 个序列，它们的保守性明显强于基因的其他区域，并将其命名为显著保守编码序列（SCCSs）。SCCS 在 2273 个基因中观察到。这些基因主要参与发育、转录调控以及神经元的活动，并在神经系统和头颈部器官中表达。在 SCCSs 中没有观察到对影响同义替换的常规因素的强烈影响。这些结果表明，SCCS 可能具有核苷酸元件和蛋白质编码序列的双重功能，并在哺乳动物进化过程中保留下来。
