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首页> 外文期刊>Animal Genetics >Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences
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Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences

机译：马支气管肺泡灌洗液蛋白质组的功能建模提供了马基因组序列的实验确认和功能注释

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摘要

The equine genome sequence enables the use of high-throughput genomic technologies in equine research, but accurate identification of expressed gene products and interpreting their biological relevance require additional structural and functional genome annotation. Here, we employ the equine genome sequence to identify predicted and known proteins using proteomics and model these proteins into biological pathways, identifying 582 proteins in normal cell-free equine bronchoalveolar lavage fluid (BALF). We improved structural and functional annotation by directly confirming the in vivo expression of 558 (96%) proteins, which were computationally predicted previously, and adding Gene Ontology (GO) annotations for 174 proteins, 108 of which lacked functional annotation. Bronchoalveolar lavage is commonly used to investigate equine respiratory disease, leading us to model the associated proteome and its biological functions. Modelling of protein functions using Ingenuity Pathway Analysis identified carbohydrate metabolism, cell-to-cell signalling, cellular function, inflammatory response, organ morphology, lipid metabolism and cellular movement as key biological processes in normal equine BALF. Comparative modelling of protein functions in normal cell-free bronchoalveolar lavage proteomes from horse, human, and mouse, performed by grouping GO terms sharing common ancestor terms, confirms conservation of functions across species. Ninety-one of 92 human GO categories and 105 of 109 mouse GO categories were conserved in the horse. Our approach confirms the utility of the equine genome sequence to characterize protein networks without antibodies or mRNA quantification, highlights the need for continued structural and functional annotation of the equine genome and provides a framework for equine researchers to aid in the annotation effort.
机译：马基因组序列可在马研究中使用高通量基因组技术，但要准确鉴定表达的基因产物并解释其生物学相关性，则需要额外的结构和功能基因组注释。在这里，我们利用马蛋白质组学序列使用蛋白质组学来鉴定预测和已知的蛋白质，并将这些蛋白质建模为生物学途径，从而在正常的无细胞马支气管肺泡灌洗液（BALF）中鉴定出582种蛋白质。我们通过直接确认先前通过计算预测的558种蛋白质（96％）的体内表达并添加174种蛋白质的基因本体论（GO）注释来改善结构和功能注释，其中174种蛋白质缺乏功能注释。支气管肺泡灌洗通常用于研究马呼吸道疾病，这使我们对相关的蛋白质组及其生物学功能进行建模。使用Ingenuity Pathway Analysis对蛋白质功能进行建模，将碳水化合物代谢，细胞间信号传导，细胞功能，炎症反应，器官形态，脂质代谢和细胞运动确定为正常马BALF的关键生物学过程。通过对共享共同祖先术语的GO术语进行分组，对来自马，人和小鼠的正常无细胞支气管肺泡灌洗蛋白质组中蛋白质功能进行了比较建模，证实了物种间功能的保守性。马中保存了92个人类GO类别中的91个和109个鼠标GO类别中的105个。我们的方法证实了马基因组序列在无需抗体或mRNA定量的情况下表征蛋白质网络的实用性，强调了对马基因组进行连续结构和功能注释的必要性，并为马研究人员提供了有助于注释工作的框架。

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  • 来源
    《Animal Genetics》 |2011年第4期|395-405|共11页
  • 作者

    L. A. Bright; N. Mujahid; B. Nanduri; F. M. McCarthy; L. R. R. Costa; S. C. Burgess; C. E. Swiderski;

  • 作者单位

    Department of Clinical Sciences College of Veterinary Medicine Mississippi State University PO Box 6100 Mississippi State MS 39762 USA.;

    Institute for Digital Biology Mississippi State University Mississippi State MS 39762 USA.;

    Department of Basic Sciences College of Veterinary Medicine Mississippi State University PO Box 6100 Mississippi State MS 39762 USA.;

    Department of Clinical Sciences Cummings School of Veterinary Medicine Tufts University North Grafton MA 01536 USA.;

    Mississippi Agricultural and Forestry Experiment Station Mississippi State University Mississippi State MS 39762 USA;

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  • 正文语种 eng
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  • 关键词

    bronchoalveolar lavage; equine; genome annotation; proteomics;

    机译：支气管肺泡灌洗;马;基因组注释;蛋白质组学;

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