Modeling a whole organ using proteomics: The avian bursa of Fabricius
Modeling a whole organ using proteomics: The avian bursa of Fabricius
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DOI：
10.1002/pmic.200500648
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发表时间：
2006-05-01
期刊：
影响因子：
3.4
通讯作者：
Burgess, Shane C.
中科院分区：
文献类型：
--
作者：
McCarthy, Fiona M.;Cooksey, Amanda M.;Burgess, Shane C.
虽然蛋白质组学的进展改善了蛋白质组的覆盖范围并增强了生物建模，但对多细胞生物体的功能建模需要了解细胞如何相互作用。在这里，我们使用Fabricius的鸡法氏囊，一个常见的B细胞功能实验系统，从蛋白质组学数据中模拟器官功能。法氏囊有两种主要的功能细胞类型：B细胞和支持基质细胞。我们使用差示洗涤剂分离-多维蛋白质鉴定技术(DDF-MudPIT)从所有细胞隔室中鉴定了5198种蛋白质。其中，1753个是B细胞特异性的，1972个是基质特异性的，1473个是两者共同的。通过模拟细胞程序性死亡(PCD)、细胞分化和增殖以及转录激活，我们改进了鸡蛋白的功能注释，并利用系统发育学将鸡特异性死亡受体加入到PCD过程中。我们已经确定了114个转录因子(TF)；其中42个法氏囊B细胞转录因子以前从未在任何B细胞中报道过。我们还改进了一个新测序的基因组的结构注释，证实了4006“预测！”和6623从头算，ORF的体内表达。最后，我们开发了一种新的结构注释方法--“表达的肽序列标签”(EPSTs)，并通过从鸡的“未分配染色体”中识别521个潜在的新蛋白来证明其有效性。
While advances in proteomics have improved proteome coverage and enhanced biological modeling, modeling function in multicellular organisms requires understanding how cells interact. Here we used the chicken bursa of Fabricius, a common experimental system for B cell function, to model organ function from proteomics data. The bursa has two major functional cell types: B cells and the supporting stromal cells. We used differential detergent fractionation-multidimensional protein identification technology (DDF-MudPIT) to identify 5198 proteins from all cellular compartments. Of these, 1753 were B cell specific, 1972 were stroma specific and 1473 were shared between the two. By modeling programmed cell death (PCD), cell differentiation and proliferation, and transcriptional activation, we have improved functional annotation of chicken proteins and placed chicken-specific death receptors into the PCD process using phylogenetics. We have identified 114 transcription factors (TFs); 42 of the bursal B cell TFs have not been reported before in any B cells. We have also improved the structural annotation of a newly sequenced genome by confirming the in vivo expression of 4006 "predicted!', and 6623 ab initio, ORFs. Finally, we have developed a novel method for facilitating structural annotation, "expressed peptide sequence tags" (ePSTs) and demonstrate its utility by identifying 521 potential novel proteins from the chicken "unassigned chromosome".