Identification of putative crustacean neuropeptides using in silico analyses of publicly accessible expressed sequence tags
Identification of putative crustacean neuropeptides using in silico analyses of publicly accessible expressed sequence tags
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DOI：
10.1016/j.ygcen.2008.01.018
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发表时间：
2008-04-01
影响因子：
2.7
通讯作者：
Dickinson, Patsy S.
中科院分区：
文献类型：
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作者：
Christie, Andrew E.;Cashman, Christopher R.;Dickinson, Patsy S.
甲壳类cDNA文库表达序列标签（est）的开发及其在公共数据库中的存储为这一具有重要商业和生态意义的节肢动物亚门的肽发现提供了丰富的资源。在这里，我们使用BLAST程序tblastn对这些数据库进行了计算机搜索，寻找编码假定的神经肽前体的未注释的est，并预测了它们编码的肽的成熟形式。使用的主要策略是查询数据库中已知的十足动物激素前原序列，或者在某些情况下，昆虫前体蛋白序列。对于不知道前激素的神经肽，肽本身被用作查询。对于那些预计来自共同前体的肽，将单个序列组合起来，每个肽的两侧都有一个双碱加工位点，如果经过修饰，则有一个甘氨酸残基。使用这些方法，发现了13个未注释的est编码假定的神经肽前体。例如，使用第一种策略，确定了日本有袋绦虫（Marsupenaeus japonicus）编码b型allatostins、神经肽F （NPF）和orcokinins的前激素。同样，也发现了几个美洲Homarus americanus的est编码假定的orcokinin前体。除了十足动物的前体激素外，从支足动物大水蚤（Daphnia magna）中鉴定出推定编码NPF异构体和红色色素浓缩激素样肽的EST，以及从等足动物Eurydice pulchra中推定编码多个速激肽相关肽的EST。使用第二种策略，我们确定了致癌maenas EST编码HIGSLYRamide，这是一种最近通过质谱分析从癌症产品中发现的肽。利用质谱方法，我们证实了这种肽也存在于癌中。从鉴定的ESTs中预测了50多个新的甲壳类肽，为进一步研究这些肽及其相关分子在该节肢动物分类单元中的进化、调控和功能提供了坚实的基础。(C) 2008爱思唯尔公司版权所有。
The development of expressed sequence tags (ESTs) for crustacean cDNA libraries and their deposition in publicly accessible databases has generated a rich resource for peptide discovery in this commercially and ecologically important arthropod subphylum. Here, we have conducted in silico searches of these databases for unannotated ESTs encoding putative neuropeptide precursors using the BLAST program tblastn, and have predicted the mature forms of the peptides encoded by them. The primary strategy used was to query the database with known decapod prepro-hormone sequences or, in some instances, insect precursor protein sequences. For neuropeptides for which no prepro-hormones are known, the peptides themselves were used as queries. For those peptides expected to originate from a common precursor, the individual sequences were combined, with each peptide flanked by a dibasic processing site and, if amidated, a glycine residue. Using these approaches, 13 unannotated ESTs encoding putative neuropeptide precursors were found. For example, using the first strategy, putative Marsupenaeus japonicus prepro-hormones encoding B-type allatostatins, neuropeptide F (NPF), and orcokinins were identified. Similarly, several Homarus americanus ESTs encoding putative orcokinin precursors were found. In addition to the decapod prepro-hormones, ESTs putatively encoding a NPF isoform and a red pigment concentrating hormone-like peptide were identified from the cladoceran Daphnia magna, as was one EST putatively encoding multiple tachykinin-related peptides from the isopod Eurydice pulchra. Using the second strategy, we identified a Carcinus maenas EST encoding HIGSLYRamide, a peptide recently discovered via mass spectrometry from Cancer productus. Using mass spectral methods we confirmed that this peptide is also present in Carcinus maenas. Collectively over 50 novel crustacean peptides were predicted from the identified ESTs, providing a strong foundation for future investigations of the evolution, regulation and function of these and related molecules in this arthropod taxon. (C) 2008 Elsevier Inc. All rights reserved.