Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.
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DOI：
10.1093/molbev/mss100
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发表时间：
2012-09
影响因子：
10.7
通讯作者：
Tress ML
中科院分区：
文献类型：
--
作者：
Ezkurdia I;del Pozo A;Frankish A;Rodriguez JM;Harrow J;Ashman K;Valencia A;Tress ML
高通量质谱技术的进步使蛋白质组学成为基因组注释项目中越来越重要的工具。在质谱实验中检测到的肽可用于验证基因模型和验证推定编码序列（CDS）的翻译。在这里，我们已经确定了肽，涵盖了35%的基因注释的GENCODE财团的人类基因组作为一个全面的分析实验光谱的一部分，从两个大型的公开可用的质谱数据库。我们检测到翻译为蛋白质的“新的”和“推定的”蛋白质编码转录本，以及转录注释为假基因和无义介导的衰变目标。我们提供了一个详细的概述人口的选择性剪接蛋白质亚型，可检测的肽鉴定方法。我们发现150个基因表达多种可选择的蛋白质异构体。这构成了迄今为止发现的最大的一组可靠确认的可变剪接蛋白质。三组基因被高度过度表达。我们检测到的25个可能的异质核核糖核蛋白，蛋白质的剪接过程中的关键作用的10个替代亚型。从可互换的同源外显子和短插入缺失产生的替代异构体也显着丰富，无论是在人类实验和小鼠和果蝇蛋白质组学实验的平行分析。我们的研究结果表明，一个令人惊讶的高比例（近25%）的检测到的替代亚型只是微妙的不同，从他们的组成对应。产生这些选择性同种型的许多选择性剪接事件在小鼠中是保守的。令人惊讶的是，这些保守的剪接事件很少破坏Pfam功能结构域或破坏球状蛋白结构。CDS和可能保守的细胞功能和结构的细微差异的强烈偏见的证据是显着的，并强烈表明，替代转录本的翻译可能受到选择性的限制。
Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of “novel” and “putative” protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and strongly suggests that the translation of alternative transcripts may be subject to selective constraints.
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影响因子：
9.8
作者：
Church DM;Goodstadt L;Hillier LW;Zody MC;Goldstein S;She X;Bult CJ;Agarwala R;Cherry JL;DiCuccio M;Hlavina W;Kapustin Y;Meric P;Maglott D;Birtle Z;Marques AC;Graves T;Zhou S;Teague B;Potamousis K;Churas C;Place M;Herschleb J;Runnheim R;Forrest D;Amos-Landgraf J;Schwartz DC;Cheng Z;Lindblad-Toh K;Eichler EE;Ponting CP;Mouse Genome Sequencing Consortium
通讯作者：
Mouse Genome Sequencing Consortium
影响因子：
3.3
作者：
Gillingham, AK;Pfeifer, AC;Munro, S
通讯作者：
Munro, S
影响因子：
4.4
作者：
Craig, R;Cortens, JP;Beavis, RC
通讯作者：
Beavis, RC
影响因子：
5.8
作者：
Craig, R;Beavis, RC
通讯作者：
Beavis, RC
影响因子：
4.5
作者：
Han, Siew Ping;Kassahn, Karin S.;Smith, Ross
通讯作者：
Smith, Ross