Integrated top-down and bottom-up proteomics mass spectrometry for the characterization of endogenous ribosomal protein heterogeneity.
Integrated top-down and bottom-up proteomics mass spectrometry for the characterization of endogenous ribosomal protein heterogeneity.
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集成自上而下和自下而上的蛋白质组学质谱用于表征内源核糖体蛋白质异质性
DOI：
10.1016/j.jpha.2022.11.003
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发表时间：
2023-01
影响因子：
8.8
通讯作者：
Li, Huilin
中科院分区：
文献类型：
--
作者：
Zhang, Ying;Cai, Qinghua;Luo, Yuxiang;Zhang, Yu;Li, Huilin
核糖体是丰富的大型RNA -蛋白质复合物，是细胞中所有蛋白质合成的场所。核糖体蛋白（RPs）的缺陷，包括由基因变异、RNA转录本的可变剪接、翻译后修饰以及蛋白质表达水平的改变所产生的蛋白质亚型，已与多种疾病相关，包括癌症和衰老。核糖体蛋白质亚型的全面表征具有挑战性，但对于发现潜在的疾病生物标志物或蛋白质靶点非常重要。在本研究中，以大肠杆菌70S核糖体蛋白为例，我们首先在沃特世Synapt G2 Si质谱（MS）系统上开发了一种自上而下的蛋白质组学方法，然后将其应用于海拉细胞80S核糖体。自下而上的方法对结果进行了补充。通过自上而下的方法，总共鉴定出55种核糖体蛋白中的50种。其中，发现30多种核糖体蛋白的N端甲硫氨酸被去除。还观察到了甲基化、乙酰化和羟基化等其他修饰，并且通过自下而上的质谱确定了修饰位点。在海拉细胞80S核糖体样本中，我们鉴定出98种核糖体蛋白质亚型，其中观察到多种截短的80S核糖体蛋白质亚型，这种信息在自下而上的实验中经常被忽视。尽管它们与疾病的相关性尚不清楚，但自上而下和自下而上的蛋白质组学方法的整合为发现蛋白质亚型特异性疾病生物标志物或靶点铺平了道路。
一种用于表征核糖体蛋白质异质性的自上而下和自下而上相结合的蛋白质组学方法。
在大肠杆菌和海拉核糖体中都观察到了由基因变异、可变剪接和翻译后修饰产生的核糖体蛋白质亚型。
在海拉核糖体中经常观察到截短的核糖体蛋白质亚型。
Ribosomes are abundant, large RNA-protein complexes that are the sites of all protein synthesis in cells. Defects in ribosomal proteins (RPs), including proteoforms arising from genetic variations, alternative splicing of RNA transcripts, post-translational modifications and alterations of protein expression level, have been linked to a diverse range of diseases, including cancer and aging. Comprehensive characterization of ribosomal proteoforms is challenging but important for the discovery of potential disease biomarkers or protein targets. In the present work, using E.coli 70S RPs as an example, we first developed a top-down proteomics approach on a Waters Synapt G2 Si mass spectrometry (MS) system, and then applied it to the HeLa 80S ribosome. The results were complemented by a bottom-up approach. In total, 50 out of 55 RPs were identified using the top-down approach. Among these, more than 30 RPs were found to have their N-terminal methionine removed. Additional modifications such as methylation, acetylation, and hydroxylation were also observed, and the modification sites were identified by bottom-up MS. In a HeLa 80S ribosomal sample, we identified 98 ribosomal proteoforms, among which multiple truncated 80S ribosomal proteoforms were observed, the type of information which is often overlooked by bottom-up experiments. Although their relevance to diseases is not yet known, the integration of top-down and bottom-up proteomics approaches paves the way for the discovery of proteoform-specific disease biomarkers or targets. An integrated top-down and bottom-up proteomics approach for characterizing ribosomal protein heterogeneity. Ribosomal proteoforms arisen from genetic variations, alternative splicing, and PTMs were observed for both E.coli and Hela ribosome. Truncated ribosomal proteoforms were frequently observed in Hela ribosome.
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影响因子：
2.9
作者：
Brown, Kyle A.;Anderson, Corey;Reilly, Louise;Sondhi, Kunal;Ge, Ying;Eckhardt, Lee L.
通讯作者：
Eckhardt, Lee L.
影响因子：
64.5
作者：
Challa S;Khulpateea BR;Nandu T;Camacho CV;Ryu KW;Chen H;Peng Y;Lea JS;Kraus WL
通讯作者：
Kraus WL
DOI：
10.1016/j.bbrc.2014.02.041
发表时间：
2014-03-21
影响因子：
3.1
作者：
Catherman, Adam D.;Skinner, Owen S.;Kelleher, Neil L.
通讯作者：
Kelleher, Neil L.
替代剪接和蛋白质功能。
影响因子：
3
作者：
Neverov AD;Artamonova II;Nurtdinov RN;Frishman D;Gelfand MS;Mironov AA
通讯作者：
Mironov AA
影响因子：
4.3
作者：
Burton B;Zimmermann MT;Jernigan RL;Wang Y
通讯作者：
Wang Y