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Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1

The annotated genome sequences of prokaryotes seldom include overlapping genes encoded opposite each other by the same stretch of DNA. However, antisense transcription is becoming recognized as a widespread phenomenon in eukaryotes, and examples have been linked to important biological processes. Ps...

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Autores principales: Silby, Mark W., Levy, Stuart B.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396522/
https://www.ncbi.nlm.nih.gov/pubmed/18551168
http://dx.doi.org/10.1371/journal.pgen.1000094
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author Silby, Mark W.
Levy, Stuart B.
author_facet Silby, Mark W.
Levy, Stuart B.
author_sort Silby, Mark W.
collection PubMed
description The annotated genome sequences of prokaryotes seldom include overlapping genes encoded opposite each other by the same stretch of DNA. However, antisense transcription is becoming recognized as a widespread phenomenon in eukaryotes, and examples have been linked to important biological processes. Pseudomonas fluorescens inhabits aquatic and terrestrial environments, and can be regarded as an environmental generalist. The genetic basis for this ecological success is not well understood. In a previous search for soil-induced genes in P. fluorescens Pf0-1, ten antisense genes were discovered. These were termed ‘cryptic’ genes, as they had escaped detection by gene-hunting algorithms, and lacked easily recognizable promoters. In this communication, we designate such genes as ‘non-predicted’ or ‘hidden’. Using reverse transcription PCR, we show that at each of six non-predicted gene loci chosen for study, transcription occurs from both ‘sense’ and ‘antisense’ DNA strands. Further, at least one of these hidden antisense genes, iiv14, encodes a protein, as does the sense transcript, both identified by poly-histidine tags on the C-terminus of the proteins. Mutational and complementation studies showed that this novel antisense gene was important for efficient colonization of soil, and multiple copies in the wildtype host improved the speed of soil colonization. Introduction of a stop codon early in the gene eliminated complementation, further implicating the protein in colonization of soil. We therefore designate iiv14 “cosA”. These data suggest that, as is the case with eukaryotes, some bacterial genomes are more densely coded than currently recognized.
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spelling pubmed-23965222008-06-13 Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1 Silby, Mark W. Levy, Stuart B. PLoS Genet Research Article The annotated genome sequences of prokaryotes seldom include overlapping genes encoded opposite each other by the same stretch of DNA. However, antisense transcription is becoming recognized as a widespread phenomenon in eukaryotes, and examples have been linked to important biological processes. Pseudomonas fluorescens inhabits aquatic and terrestrial environments, and can be regarded as an environmental generalist. The genetic basis for this ecological success is not well understood. In a previous search for soil-induced genes in P. fluorescens Pf0-1, ten antisense genes were discovered. These were termed ‘cryptic’ genes, as they had escaped detection by gene-hunting algorithms, and lacked easily recognizable promoters. In this communication, we designate such genes as ‘non-predicted’ or ‘hidden’. Using reverse transcription PCR, we show that at each of six non-predicted gene loci chosen for study, transcription occurs from both ‘sense’ and ‘antisense’ DNA strands. Further, at least one of these hidden antisense genes, iiv14, encodes a protein, as does the sense transcript, both identified by poly-histidine tags on the C-terminus of the proteins. Mutational and complementation studies showed that this novel antisense gene was important for efficient colonization of soil, and multiple copies in the wildtype host improved the speed of soil colonization. Introduction of a stop codon early in the gene eliminated complementation, further implicating the protein in colonization of soil. We therefore designate iiv14 “cosA”. These data suggest that, as is the case with eukaryotes, some bacterial genomes are more densely coded than currently recognized. Public Library of Science 2008-06-13 /pmc/articles/PMC2396522/ /pubmed/18551168 http://dx.doi.org/10.1371/journal.pgen.1000094 Text en Silby, Levy. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Silby, Mark W.
Levy, Stuart B.
Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1
title Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1
title_full Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1
title_fullStr Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1
title_full_unstemmed Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1
title_short Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1
title_sort overlapping protein-encoding genes in pseudomonas fluorescens pf0-1
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396522/
https://www.ncbi.nlm.nih.gov/pubmed/18551168
http://dx.doi.org/10.1371/journal.pgen.1000094
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