Characterization of the gorilla carboxyl ester lipase locus, and the appearance of the carboxyl ester lipase pseudogene during primate evolution.

In this study we report on the isolation and characterization of the gorilla carboxyl ester lipase gene, CEL, and the corresponding CEL pseudogene. We also report on the age of the CEL pseudogene.The gorilla CEL gene is 10.5kb long and comprises 11exons intervened by introns similar to the situation in man, mouse and rat. The encoded protein is 998amino acids long and includes a 23amino acid-long leader peptide. Comparison of the coding sequence, excluding exon 11, of CEL from gorilla and man reveals a 97% similarity. Exon 11, which encodes the characteristic proline rich repeats, contains 39 repeated units in gorilla compared to 16 in man. A truncated CEL pseudogene, with the same organization as that found in man, is also shown to be present in the gorilla genome. The gorilla CEL pseudogene is 4.9kb in length and consists of 5exons interrupted by introns. Southern analysis of the gorilla CEL locus shows that the locus is arranged in a similar way as in man with the functional CEL gene being the most 5' one.To bring further insight to the events involved in the rearrangement of the CEL locus, genomic Southern analyses were performed across several primates; Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo pygmaeus and Macaca arctoides. Results presented show that the CEL gene duplication occurred prior to the separation of Hominidae (man, chimpanzee, gorilla and orangutan) from Old World monkeys (macaque). The deletion of the original CEL gene giving rise to the truncated version of the CEL gene seems, however, to be restricted to man and the great apes only.     

人猿超科和旧大陆猴7种高等灵长类FKN全基因序列的测定及进化分析

测定人猿超科(人、黑猩猩、大猩猩、红毛猩猩和长臂猿)和旧大陆猴(猕猴和叶猴)7种高等灵长类FKN全基因序列, 探讨其系统进化分析。用简并引物PCR(Degenerated PCR)法分别扩增FKN的3个外显子, 其产物经琼脂糖凝胶回收、纯化后测序, 然后用BioEdit软件剪切拼接FKN基因全序列, 用DNAStar比对后比较基因和氨基酸序列同源性, Mega软件重构FKN基因进化树, 应用Datamonkey分析FKN的负选择位点。序列分析发现人猿超科较旧大陆猴FKN基因除了有散在的点突变外, 还有一明显的30 bp的核苷酸缺失突变; 人FKN基因序列与黑猩猩、大猩猩、红毛猩猩、长臂猿、猕猴和叶猴的同源性分别是99.2%、98.4%、98.1%、96.5%、95.9%和93.8%, 由此推导的氨基酸序列同源性分别是98.5%、98.0%、97.7%、94.7%、93.7%和90.5%; FKN基因进化树表明人与黑猩猩关系更近, FKN基因进化和通常认为的物种进化一致; Datamonkey分析结果显示FKN存在3个负选择位点53Q、84D、239N。成功获得人、黑猩猩、大猩猩、红毛猩猩、长臂猿、猕猴和叶猴7种高等灵长类物种FKN全基因序列, 为后续探讨FKN在高等灵长类物种进化过程中免疫学功能演变及其结构与功能的关系奠定基础。     

Genomic organization and tissue-specific expression of splice variants of mouse organic anion transporting polypeptide 2

cDNAs that code for mouse organic anion transporting polypeptide 2 (oatp2) have been cloned. At least three forms of mouse oatp2 cDNAs containing the same coding sequence were isolated. The common coding sequence is for a protein of 670 amino acids with 12 putative transmembrane domains. The deduced amino acid sequence of the mouse oatp2 shares 89% identity with the reported rat oatp2. Cloning and analysis of mouse oatp2 gene indicates that these isoforms are alternatively spliced products from the same gene. Heterogeneity was observed in the 5'-untranslated region of the cDNAs. Two of the three isoforms lacked the noncoding exon 3 sequence. Northern-blot hybridization analysis using the exon 3-specific probes demonstrated that mouse oatp2 mRNA containing exon 3 sequence is expressed in heart and lung, whereas exon 1-, 2-, and 17-specific probes detected mRNA only in brain and liver. The mouse oatp2 gene consists of 17 exons, including three noncoding exons, and 16 introns. All of the introns are flanked by GT-AG splice sequences except for intron 10 that is flanked by GC-AG splice sequence.     

Comparative analysis of amino acid usage and protein length distribution between alternatively and non-alternatively spliced genes across six eukaryotic genomes

Alternative splicing has been discovered in nearly all metazoan organisms as a mechanism to increase the diversity of gene products. However, the origin and evolution of alternatively spliced genes are still poorly understood. To understand the mechanisms for the evolution of alternatively spliced genes, it may be important to study the differences between alternatively and non-alternatively spliced genes. The aim of this research was to compare amino acid usage and protein length distribution between alternatively and non-alternatively spliced genes across six nearly complete eukaryotic genomes, including those of human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), fruit fly (Drosophila melanogaster), Caenorhabditis elegans, and bovine (Bos taurus). Our results have suggested the following: (1) across the six species, alternatively and non-alternatively spliced genes have very similar tendency for amino acids usage for not only the overall scale but also those highly expressed genes, with all of the highly expressed genes having preferred amino acids including A, E, G, K, L, P, S, V, R, T, and D. (2) For not only the overall genes but also those highly expressed ones, the average length of the protein products of alternatively spliced genes is significantly greater than that of non-alternatively spliced ones. In contrast, distributions of protein lengths for the two groups of genes are very similar among all six species. Based on these results, we propose that alternatively spliced genes may have originated from non-alternatively spliced ones through events such as DNA mutations or gene fusion.     

Evidence of functional selection pressure for alternative splicingevents that accelerate evolution of protein subsequences

Recently, it was proposed that alternative splicing may act as a mechanism for opening accelerated paths of evolution, by reducing negative selection pressure, but there has been little evidence so far whether this could produce adaptive benefit. Here we employ metrics of very different types of selection pressures (e.g. against amino acid mutations (Ka/Ks); against mutations at synonymous sites (Ks); and for protein reading-frame preservation) to address this question via genome-wide analyses of human, chimpanzee, mouse, and rat. These data show that alternative splicing relaxes Ka/Ks selection pressure up to seven-fold, but intriguingly that this effect is accompanied by a strong increase in selection pressure against synonymous mutations, which propagates into the adjacent intron, and correlates strongly with the alternative splicing level observed for each exon. These effects are highly local to the alternatively spliced exon. Comparisons of these four genomes consistently show an increase in the density of amino acid mutations (Ka) in alternatively spliced exons, and a decrease in the density of synonymous mutations (Ks). This selection pressure against synonymous mutations in alternatively spliced exons was accompanied in all four genomes by a striking increase in selection pressure for protein reading-frame preservation, and both increased markedly with increasing evolutionary age. Restricting our analysis to a subset of exons with strong evidence for biologically functional alternative splicing produced identical results. Thus alternative splicing apparently can create evolutionary “hotspots” within a protein sequence, and these events have evidently been selected for during mammalian evolution.