A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis.
A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis.
复制标题
以半胰蛋白酶肽为中心的宏蛋白质组学挖掘方法及其在捕获肠道微生物蛋白水解特征中的潜在用途
DOI：
10.1186/s40168-020-00967-x
复制
发表时间：
2021-01-12
期刊：
影响因子：
15.5
通讯作者：
Shan H
中科院分区：
文献类型：
--
作者：
Yan Z;He F;Xiao F;He H;Li D;Cong L;Lin L;Zhu H;Wu Y;Yan R;Li X;Shan H
研究背景蛋白水解调节使肠道微生物通过快速降解错误折叠的蛋白质和激活调节蛋白对动态肠道环境做出快速反应。然而，尚未研究复杂疾病状态如炎性肠病（IBD，包括克罗恩病（CD）和溃疡性结肠炎（UC））下肠道微生物蛋白水解特征的改变。Metaproteoms具有潜在的调查肠道微生物蛋白水解，因为半胰蛋白酶肽主要来自内源性proteolysis.ResultsWe已经开发出一种半胰蛋白酶肽为中心的metaproteoms挖掘方法，以获得人类肠道微生物蛋白水解签名的快照。这种方法采用了一个全面的元数据库，两步多引擎数据库搜索，并与高分辨率的碎片光谱数据集，以增加半胰蛋白酶肽鉴定的信心。该方法通过发现大肠杆菌热休克反应的蛋白质水解特征的改变进行了验证。利用两个已发表的大规模元蛋白质组学数据集，其中包含来自IBD患者和健康个体的447个粪便和176个粘膜管腔界面（MLI）样本的623个元蛋白质组，我们在分类学，功能和切割位点基序水平上获得了肠道微生物蛋白水解改变的潜在特征。功能改变主要涉及微生物碳水化合物的运输和代谢、氧化应激、细胞运动、蛋白质合成和成熟。CD和UC的微生物蛋白水解特征的改变主要分别发生在回肠末端和降结肠。微生物蛋白水解模式与β多样性呈低相关性，与微生物蛋白酶和伴侣蛋白水平呈中等相关性。人类蛋白酶抑制剂和免疫球蛋白主要与微生物蛋白水解模式呈负相关，可能是因为这些宿主因素对肠道微生物蛋白水解事件的抑制作用。ConclusionsThis semi-tryptic peptide centric mining strategy provides a label-free approach to discover signals of in vivo gut microbial proteolysis events if experimental conditions are well controlled.它还可以捕获体外蛋白水解特征，以促进实验条件的评估和优化。我们的研究结果突出了肠道微生物组复杂多样的蛋白水解事件，提供了一个超越分类和蛋白质组丰度的独特信息层。视频摘要
BackgroundProteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut microbial proteolytic signatures under complex disease status such as inflammatory bowel disease (IBD, including Crohn’s disease (CD) and ulcerative colitis (UC)), have not been investigated. Metaproteomics holds the potential to investigate gut microbial proteolysis because semi-tryptic peptides mainly derive from endogenous proteolysis.ResultsWe have developed a semi-tryptic peptide centric metaproteomic mining approach to obtain a snapshot of human gut microbial proteolysis signatures. This approach employed a comprehensive meta-database, two-step multiengine database search, and datasets with high-resolution fragmentation spectra to increase the confidence of semi-tryptic peptide identification. The approach was validated by discovering altered proteolysis signatures ofEscherichia coliheat shock response. Utilizing two published large-scale metaproteomics datasets containing 623 metaproteomes from 447 fecal and 176 mucosal luminal interface (MLI) samples from IBD patients and healthy individuals, we obtain potential signatures of altered gut microbial proteolysis at taxonomic, functional, and cleavage site motif levels. The functional alterations mainly involved microbial carbohydrate transport and metabolism, oxidative stress, cell motility, protein synthesis, and maturation. Altered microbial proteolysis signatures of CD and UC mainly occurred in terminal ileum and descending colon, respectively. Microbial proteolysis patterns exhibited low correlations with β-diversity and moderate correlations with microbial protease and chaperones levels, respectively. Human protease inhibitors and immunoglobulins were mainly negatively associated with microbial proteolysis patterns, probably because of the inhibitory effects of these host factors on gut microbial proteolysis events.ConclusionsThis semi-tryptic peptide centric mining strategy offers a label-free approach to discover signatures of in vivo gut microbial proteolysis events if experimental conditions are well controlled. It can also capture in vitro proteolysis signatures to facilitate the evaluation and optimization of experimental conditions. Our findings highlight the complex and diverse proteolytic events of gut microbiome, providing a unique layer of information beyond taxonomic and proteomic abundance.Video abstract
登录
查看更多内容
影响因子：
9.3
作者：
Beyter D;Lin MS;Yu Y;Pieper R;Bafna V
通讯作者：
Bafna V
影响因子：
4.4
作者：
Cox, Juergen;Neuhauser, Nadin;Mann, Matthias
通讯作者：
Mann, Matthias
影响因子：
4.4
作者：
Gurdeep Singh, Robbert;Tanca, Alessandro;Mesuere, Bart
通讯作者：
Mesuere, Bart
组氨酸激酶 VgrS 的蛋白水解抑制其自磷酸化并促进野油菜黄单胞菌的渗透压抵抗
影响因子：
16.6
作者：
Deng CY;Zhang H;Wu Y;Ding LL;Pan Y;Sun ST;Li YJ;Wang L;Qian W
通讯作者：
Qian W
影响因子：
4.7
作者：
Deter, Heather S.;Abualrahi, Alawiah H.;Butzin, Nicholas C.
通讯作者：
Butzin, Nicholas C.