The zebrafish secretome
The zebrafish secretome
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DOI：
10.1089/zeb.2008.0529
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发表时间：
2008-06-01
期刊：
影响因子：
2
通讯作者：
Klee, Eric W.
中科院分区：
文献类型：
--
作者：
Klee, Eric W.
分泌组是一个功能丰富的蛋白质组亚群，包括通过分泌途径加工的细胞膜和细胞外蛋白。在这项研究中，用SignalP、TargetP、Phobius和pTarget算法分析了斑马鱼和智人RefSeq蛋白。大约16.5%的斑马鱼蛋白质组和17.0%的人类蛋白质组具有预测的N端信号序列。这些蛋白质中有近一半随后被归类为可溶性的，因为它们缺乏预测的跨膜结构域。可溶性蛋白质进一步细分，预测1345（3.8%）斑马鱼和1207（3.2%）人类蛋白质为胞外。斑马鱼和人类可溶性分泌蛋白的比较确定了372个直系同源物，基于相互BLAST最佳命中。斑马鱼蛋白质的计算表征发现了比SwissProt数据库中注释的更多的分泌组成员。2078个斑马鱼SwissProt蛋白条目中只有180个和19，294个人类SwissProt蛋白条目中只有995个用分泌蛋白位置注释。对成纤维细胞生长因子和基质金属蛋白酶（MMP）蛋白家族的具体研究证实了预测数据，并生成了另外三种推定MMP斑马鱼蛋白的注释。这项研究提出了自斑马鱼基因组测序计划完成以来第一个已知的斑马鱼分泌组的描述。
The secretome is a functionally rich proteome subset, including cellular membrane and extracellular proteins processed through the secretory pathway. In this study, Danio rerio and Homo sapiens RefSeq proteins were analyzed with SignalP, TargetP, Phobius, and pTarget algorithms. About 16.5% of the zebrafish proteome and 17.0% of the human proteome possessed predicted N-terminal signal sequences. Nearly half of these proteins were subsequently classified as soluble, as they lacked predicted transmembrane domains. The soluble proteins were further subclassified, predicting 1345 (3.8%) zebrafish and 1207 (3.2%) human proteins as extracellular. Comparison of the zebrafish and human soluble secretome proteins identified 372 as orthologs, on the basis of reciprocal BLAST best hits. The computational characterization of the zebrafish proteins found many more members of the secretome than annotated in the SwissProt database. Only 180 of the 2078 zebrafish SwissProt protein entries, and 995 of the 19,294 human SwissProt protein entries were annotated with secreted protein locales. A specific investigation of the fibroblast growth factor and matrix metalloproteinase (MMP) protein families confirmed the prediction data and generated annotation of three additional putative MMP zebrafish proteins. This study presents the first known published description of the zebrafish secretome since the completion of the zebrafish genome sequencing project.