ArticleBMC genomics2016
Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes.Nucleic acids research · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines.International journal of molecular sciences · 2024Article
- Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers.BMC microbiology · 2023Article
- The Lost and Found: Unraveling the Functions of Orphan Genes.Journal of developmental biology · 2023Review
- Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933.Microbiology spectrum · 2023Article
- Article
- The Food Poisoning Toxins ofToxins · 2021Review
- A comprehensive survey of integron-associated genes present in metagenomes.BMC genomics · 2020Article
- Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.The Journal of biological chemistry · 2020Article
- Review
- Are Antisense Proteins in Prokaryotes Functional?Frontiers in molecular biosciences · 2020Article
- A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding GeneFrontiers in microbiology · 2020Article
- Differences Between the Raw Material and the Products ofGenetics · 2019Article
- The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase.Scientific reports · 2018Article
- Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor.Nucleic acids research · 2018Article
- Identifying New Small Proteins in Escherichia coli.Proteomics · 2018Article
- A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting.BMC evolutionary biology · 2018Article
- The Novel Anaerobiosis-Responsive Overlapping GeneFrontiers in microbiology · 2018Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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