McWeeney S K, Valdes A M
Department of Integrative Biology, 3060 Valley Life Sciences Building, University of California at Berkeley, Berkeley, CA 94720-3140, USA.
Immunogenetics. 1999 Apr;49(4):272-9. doi: 10.1007/s002510050493.
Codon bias and base composition in major histocompatibility complex (MHC) sequences have been studied for both class I and II loci in Homo sapiens and Pan troglodytes. There is low to moderate codon bias for the MHC of humans and chimpanzees. In the class I loci, the same level of moderate codon bias is seen for HLA-B, HLA-C, Patr-A, Patr-B, and Patr-C, while at HLA-A the level of codon bias is lower. There is a correlation between codon usage bias and G+C content in the A and B loci in humans and chimps, but not at the C locus. To examine the effect of diversifying selection on codon bias, we subdivided class I alleles into antigen recognition site (ARS) and non-ARS codons. ARS codons had lower bias than non-ARS codons. This may indicate that the constraint of codon bias on nucleotide substitution may be selected against in ARS codons. At the class II loci, there are distinct differences between alpha and beta chain genes with respect to codon usage, with the beta chain genes being much more biased. Species-specific differences in base composition were seen in exon 2 at the DRB1 locus, with lower GC content in chimpanzees. Considering the complex evolutionary history of MHC genes, the study of codon usage patterns provides us with a better understanding of both the evolutionary history of these genes and the evolution of synonymous codon usage in genes under natural selection.
人们已经对智人和黑猩猩主要组织相容性复合体（MHC）序列中的密码子偏好和碱基组成进行了研究，涉及I类和II类基因座。人类和黑猩猩的MHC存在低到中度的密码子偏好。在I类基因座中，HLA - B、HLA - C、Patr - A、Patr - B和Patr - C的密码子偏好程度相同，而HLA - A的密码子偏好程度较低。人类和黑猩猩的A和B基因座中，密码子使用偏好与G + C含量之间存在相关性，但在C基因座中不存在这种相关性。为了研究多样化选择对密码子偏好的影响，我们将I类等位基因细分为抗原识别位点（ARS）密码子和非ARS密码子。ARS密码子的偏好性低于非ARS密码子。这可能表明，在ARS密码子中，密码子偏好对核苷酸替换的限制可能会受到选择淘汰。在II类基因座中，α链和β链基因在密码子使用方面存在明显差异，β链基因的偏好性更强。在DRB1基因座的第2外显子中观察到了碱基组成的物种特异性差异，黑猩猩的GC含量较低。考虑到MHC基因复杂的进化历史，对密码子使用模式的研究有助于我们更好地理解这些基因的进化历史以及自然选择下基因中同义密码子使用的进化情况。
