Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

BMC Genomics

Research Article

Harald Marx¹  Bernhard Kuster²  Andrea Schafferhans³  Tatyana Goldberg³  Burkhard Rost³  Olga N. Ozoline⁴  Daniel A. Keim⁵  Svenja Simon⁵  Siegfried Scherer⁶  Lea Fellner⁶  Klaus Neuhaus⁶  Richard Landstorfer⁶ 

[1] Chair of Proteomics and Bioanalytics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany;Chair of Proteomics and Bioanalytics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354, Freising, Germany;Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany;Department of Informatics - Bioinformatics & TUM-IAS, Technische Universität München, Boltzmannstraße 3, 85748, Garching, Germany;Institute of Cell Biophysics, Russian Academy of Sciences, Moscow Region, 142290, Pushchino, Russia;Lehrstuhl für Datenanalyse und Visualisierung, Fachbereich Informatik und Informationswissenschaft, Universität Konstanz, Box 78, 78457, Konstanz, Germany;Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs- und Lebensmittelforschung, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany;

关键词: Translatome;    Riboseq;    Proteome;    Novel genes;    Orphans;    EHEC;   

DOI  :  10.1186/s12864-016-2456-1

 received in 2015-05-27, accepted in 2016-02-09,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundGenomes of E. coli, including that of the human pathogen Escherichia coli O157:H7 (EHEC) EDL933, still harbor undetected protein-coding genes which, apparently, have escaped annotation due to their small size and non-essential function. To find such genes, global gene expression of EHEC EDL933 was examined, using strand-specific RNAseq (transcriptome), ribosomal footprinting (translatome) and mass spectrometry (proteome).ResultsUsing the above methods, 72 short, non-annotated protein-coding genes were detected. All of these showed signals in the ribosomal footprinting assay indicating mRNA translation. Seven were verified by mass spectrometry. Fifty-seven genes are annotated in other enterobacteriaceae, mainly as hypothetical genes; the remaining 15 genes constitute novel discoveries. In addition, protein structure and function were predicted computationally and compared between EHEC-encoded proteins and 100-times randomly shuffled proteins. Based on this comparison, 61 of the 72 novel proteins exhibit predicted structural and functional features similar to those of annotated proteins. Many of the novel genes show differential transcription when grown under eleven diverse growth conditions suggesting environmental regulation. Three genes were found to confer a phenotype in previous studies, e.g., decreased cattle colonization.ConclusionsThese findings demonstrate that ribosomal footprinting can be used to detect novel protein coding genes, contributing to the growing body of evidence that hypothetical genes are not annotation artifacts and opening an additional way to study their functionality. All 72 genes are taxonomically restricted and, therefore, appear to have evolved relatively recently de novo.

【 授权许可】

CC BY   
© Neuhaus et al. 2016