Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila
Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila
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DOI：
10.1101/gr.089391.108
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发表时间：
2009-05-01
期刊：
影响因子：
7
通讯作者：
Swanson, Willie J.
中科院分区：
文献类型：
--
作者：
Findlay, Geoffrey D.;MacCoss, Michael J.;Swanson, Willie J.
随着基因组序列越来越容易获得，鸟枪蛋白质组学将在基因组注释中发挥越来越重要的作用。通过蛋白质组学，研究人员可以确认和修改现有的基因组注释，并发现全新的基因。基于蛋白质组学的从头基因发现应该特别适用于具有使其难以用基因发现算法预测的特征的基因集。在这里，我们报告的蛋白质组学发现的19个以前未注释的基因编码精液蛋白（SFPs），从男性转移到女性在果蝇交配。使用生物信息学，我们检测到这些基因的推定直系同源物，以及在以前的研究中通过相同的方法检测到的其他19个基因，跨越几个相关物种。基因表达分析显示，几乎所有预测的直系同源物都被转录，并且大多数以男性特异性或男性偏好的方式表达。我们提出了这些基因逃脱计算预测的几个原因。像注释的Sfps一样，许多这些新蛋白质显示出适应性进化的模式，与它们在影响男性精子竞争能力方面的潜在作用一致。然而，与注释的Sfps相反，这些新基因更短，具有更高的非同义替换率，并且在编码区中具有明显更低的GC含量。我们的数据表明，应用蛋白质组学基因发现方法，以一个特定的生物过程的效用，并提供了一个更完整的图片的分子，是至关重要的果蝇生殖成功。
As genomic sequences become easier to acquire, shotgun proteomics will play an increasingly important role in genome annotation. With proteomics, researchers can confirm and revise existing genome annotations and discover completely new genes. Proteomic-based de novo gene discovery should be especially useful for sets of genes with characteristics that make them difficult to predict with gene-finding algorithms. Here, we report the proteomic discovery of 19 previously unannotated genes encoding seminal fluid proteins (Sfps) that are transferred from males to females during mating in Drosophila. Using bioinformatics, we detected putative orthologs of these genes, as well as 19 others detected by the same method in a previous study, across several related species. Gene expression analysis revealed that nearly all predicted orthologs are transcribed and that most are expressed in a male-specific or male-biased manner. We suggest several reasons why these genes escaped computational prediction. Like annotated Sfps, many of these new proteins show a pattern of adaptive evolution, consistent with their potential role in influencing male sperm competitive ability. However, in contrast to annotated Sfps, these new genes are shorter, have a higher rate of nonsynonymous substitution, and have a markedly lower GC content in coding regions. Our data demonstrate the utility of applying proteomic gene discovery methods to a specific biological process and provide a more complete picture of the molecules that are critical to reproductive success in Drosophila.