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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-02-24

AUTHORS

Klaus Neuhaus, Richard Landstorfer, Lea Fellner, Svenja Simon, Andrea Schafferhans, Tatyana Goldberg, Harald Marx, Olga N. Ozoline, Burkhard Rost, Bernhard Kuster, Daniel A. Keim, Siegfried Scherer

ABSTRACT

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. More... »

PAGES

133

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s12864-016-2456-1

    DOI

    http://dx.doi.org/10.1186/s12864-016-2456-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1039788317

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26911138


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