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

BMC Genomics
Klaus NeuhausSiegfried Scherer

Abstract

Genomes 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). Using 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 g...Continue Reading

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Citations

Apr 13, 2018·Proteomics·Caitlin E VanOrsdelMatthew R Hemm
Jul 22, 2020·BMC Genomics·Mariana Buongermino PereiraErik Kristiansson
Sep 15, 2020·Frontiers in Molecular Biosciences·Zachary ArdernSiegfried Scherer
May 10, 2020·The Journal of Biological Chemistry·Alina GlaubZachary Ardern
Feb 3, 2021·Toxins·Richard DietrichPer Einar Granum
Mar 11, 2021·International Journal of Medical Microbiology : IJMM·Thomas C A HitchThomas Clavel
May 10, 2020·EcoSal Plus·Matthew R HemmGisela Storz
Jan 16, 2018·Journal of Proteome Research·Armando JardimChristoph H Borchers

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Methods Mentioned

BETA
electrophoresis
footprinting

Software Mentioned

Matrix Science
PredictProtein
mfold
Scaffold
REPFIND
PROFbval
METADISORDER
Mascot
NGS
COILS

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