Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933
ABSTRACT The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escheri...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-02-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.02351-22 |
| _version_ | 1811164386465677312 |
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| author | Franziska Graf Barbara Zehentner Lea Fellner Siegfried Scherer Klaus Neuhaus |
| author_facet | Franziska Graf Barbara Zehentner Lea Fellner Siegfried Scherer Klaus Neuhaus |
| author_sort | Franziska Graf |
| collection | DOAJ |
| description | ABSTRACT The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes. IMPORTANCE The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated, since such genes are not allowed in genome annotations. However, ribosome profiling catches mRNA in the moment of being template for protein production. Using this technique and subsequent experiments, we verified 3 novel overlapping genes encoded in antisense of known genes. This adds more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes. |
| first_indexed | 2024-04-10T15:20:42Z |
| format | Article |
| id | doaj.art-a433a119bb7b48bc91202fe9ec9dc259 |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-10T15:20:42Z |
| publishDate | 2023-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-a433a119bb7b48bc91202fe9ec9dc2592023-02-14T14:15:50ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972023-02-0111110.1128/spectrum.02351-22Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933Franziska Graf0Barbara Zehentner1Lea Fellner2Siegfried Scherer3Klaus Neuhaus4Core Facility Microbiome, ZIEL – Institute for Food & Health, Technische Universität München, Freising, GermanyChair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Freising, GermanyChair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Freising, GermanyCore Facility Microbiome, ZIEL – Institute for Food & Health, Technische Universität München, Freising, GermanyCore Facility Microbiome, ZIEL – Institute for Food & Health, Technische Universität München, Freising, GermanyABSTRACT The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes. IMPORTANCE The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated, since such genes are not allowed in genome annotations. However, ribosome profiling catches mRNA in the moment of being template for protein production. Using this technique and subsequent experiments, we verified 3 novel overlapping genes encoded in antisense of known genes. This adds more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes.https://journals.asm.org/doi/10.1128/spectrum.02351-22overlapping genesEHEC O157:H7proteinprokaryotic genomescompetitive growth assaysphenotype |
| spellingShingle | Franziska Graf Barbara Zehentner Lea Fellner Siegfried Scherer Klaus Neuhaus Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933 Microbiology Spectrum overlapping genes EHEC O157:H7 protein prokaryotic genomes competitive growth assays phenotype |
| title | Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933 |
| title_full | Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933 |
| title_fullStr | Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933 |
| title_full_unstemmed | Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933 |
| title_short | Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933 |
| title_sort | three novel antisense overlapping genes in e coli o157 h7 edl933 |
| topic | overlapping genes EHEC O157:H7 protein prokaryotic genomes competitive growth assays phenotype |
| url | https://journals.asm.org/doi/10.1128/spectrum.02351-22 |
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