Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs
Novel DNA coding regions and protein arginylation reveal unexplored T. cruzi proteome and PTMs
复制标题
DOI：
10.1016/j.ijms.2016.11.020
复制
发表时间：
2017-07-01
影响因子：
1.8
通讯作者：
Palmisano, Giuseppe
中科院分区：
文献类型：
--
作者：
de Oliveira, Gilberto Santos;Kawahara, Rebeca;Palmisano, Giuseppe
查加斯病，也被称为美洲锥虫病，是一种被忽视的热带疾病，由克氏锥虫寄生虫引起。为了开发诊断和治疗解决方案，已经使用组学技术（例如基因组学、转录组学、脂质组学和蛋白质组学）对寄生虫生物学进行了密集的研究。特别是，大规模的基于质谱的蛋白质组学研究已经允许在不同的生物条件下鉴定和定量蛋白质和选择的PTM。在这项研究中，我们调查了未分配的MS/MS光谱通常观察到的大规模自下而上的蛋白质组学实验，在T。cruzi（Sylvio X10/1）蛋白质组。使用蛋白质基因组学和非限制性PTM搜索方法进行的深入蛋白质组学数据分析使我们能够注释30%以上的MS/MS光谱，并确定锥虫中新的DNA编码区和未表征的PTM，例如蛋白质的酰基化。总的来说，这项研究表明：（1）在大规模基于质谱的蛋白质组学数据中分配蛋白质修饰、分析伪像和PTM以深入剖析锥虫蛋白质组的重要性。(2)需要更好地表征样品制备步骤对蛋白质和蛋白质修饰鉴定的影响。（3）在T.克鲁兹(4)在锥虫中发现蛋白质去乙酰化。(C)2016爱思唯尔B. V.保留所有权利。
Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the Trypanosoma cruzi parasite. In order to develop diagnostic and therapeutic solutions, there has been an intense investigation on the parasite biology using omics technologies such as genomics, transcriptomics lipidomics and proteomics. In particular, large scale mass spectrometry-based proteomics studies have allowed the identification and quantification of proteins and selected PTMs in different biological conditions. In this study, we investigated the unassigned MS/MS spectra commonly observed in large scale bottom up proteomics experiments looking at the T. cruzi (Sylvio X10/1) proteome. A deep proteomics data analysis using proteogenomic and unrestrictive PTMs search approaches allowed us to annotate 30% more MS/MS spectra and identify novel DNA coding regions and uncharacterized PTMs in Trypanosomatids, such as protein arginylation. Overall, this study shows: (1) the importance of assigning protein modifications, analytical artefacts and PTMs, in large-scale mass spectrometry-based proteomics data to deeply profile the trypanosomatids proteome. (2) The need of a better characterization of the influence of sample preparation steps on the identification of proteins and protein modifications. (3)The identification of novel DNA coding regions in T. cruzi. (4) The discovery of protein arginylation in trypanosomatids. (C) 2016 Elsevier B.V. All rights reserved.