通过核糖体谱分析和蛋白质基因组学解析植物共生体的小蛋白质组

Unraveling the small proteome of the plant symbiont by ribosome profiling and proteogenomics.

作者信息

Hadjeras Lydia, Heiniger Benjamin, Maaß Sandra, Scheuer Robina, Gelhausen Rick, Azarderakhsh Saina, Barth-Weber Susanne, Backofen Rolf, Becher Dörte, Ahrens Christian H, Sharma Cynthia M, Evguenieva-Hackenberg Elena

机构信息

Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany.

Molecular Ecology, Agroscope and SIB Swiss Institute of Bioinformatics, 8046 Zurich, Switzerland.

出版信息

Microlife. 2023 Mar 10;4:uqad012. doi: 10.1093/femsml/uqad012. eCollection 2023.

Abstract

The soil-dwelling plant symbiont is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from to Bacteria, suggesting important physiological functions.

摘要

土壤栖息植物共生体是α-变形菌纲的主要模式生物。尽管有大量详细的组学研究,但关于小开放阅读框(sORF)编码蛋白(SEP)的信息在很大程度上仍缺失,因为sORF注释不佳且SEP难以通过实验检测。然而,鉴于SEP可发挥重要功能,鉴定已翻译的sORF对于分析它们在细菌生理学中的作用至关重要。核糖体谱分析(Ribo-seq)能够高灵敏度地检测已翻译的sORF,但尚未常规应用于细菌,因为必须针对每个物种进行调整。在此,我们基于核糖核酸酶I消化建立了2011年的Ribo-seq程序,并在基本培养基中生长期间检测到60%注释编码序列的翻译。使用基于Ribo-seq数据、后续筛选和人工整理的ORF预测工具,自信地预测了37个氨基酸数≤70的未注释sORF的翻译。Ribo-seq数据通过来自三种样品制备方法和两种整合蛋白质基因组搜索数据库(iPtgxDB)类型的质谱(MS)分析得到补充。针对标准和比Ribo-seq数据小20倍的定制iPtgxDB进行搜索,证实了47个注释的SEP,并鉴定出另外11个新的SEP。表位标签和蛋白质印迹分析证实了从翻译组图谱中选择的20个SEP中有15个的翻译。总体而言,通过结合MS和Ribo-seq方法,2011年的小蛋白质组因48个新的SEP而大幅扩展。其中一些是预测操纵子的一部分和/或从2011年到细菌是保守的,表明具有重要的生理功能。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/660d/10117765/eb5e5a9bb8d9/uqad012fig1.jpg

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