Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts

ABSTRACT Prokaryotic genomes encode a plethora of small noncoding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly...

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Autores principales:	Daniel Dar, Rotem Sorek
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	transcriptome mRNA degradation ncRNA sRNA Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ab9dd11446ad46ffb3dffd7b4b73eede
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spelling	oai:doaj.org-article:ab9dd11446ad46ffb3dffd7b4b73eede2021-11-15T15:58:21ZBacterial Noncoding RNAs Excised from within Protein-Coding Transcripts10.1128/mBio.01730-182150-7511https://doaj.org/article/ab9dd11446ad46ffb3dffd7b4b73eede2018-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01730-18https://doaj.org/toc/2150-7511ABSTRACT Prokaryotic genomes encode a plethora of small noncoding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly to protein-coding genes. In addition, recent studies have shown that functional ncRNAs can also be derived from gene 3′ untranslated regions (3′UTRs) via an alternative biogenesis pathway, in which the ncRNA segment is separated from the mRNA via RNase cleavage. Here, we report the detection of a large set of decay-generated noncoding RNAs (decRNAs), many of which are completely embedded within protein-coding mRNA regions rather than in the UTRs. We show that these decRNAs are “carved out” of the mRNA through the action of RNase E and that they are predicted to fold into highly stable RNA structures, similar to those of known ncRNAs. A subset of these decRNAs is predicted to interact with Hfq or ProQ or both, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. These results suggest that mRNA protein-coding regions may harbor a large set of potentially functional small RNAs. IMPORTANCE Bacteria and archaea utilize regulatory small noncoding RNAs (ncRNAs) to control the expression of specific genetic programs. These ncRNAs are almost exclusively encoded within intergenic regions and are independently transcribed. Here, we report on a large set ncRNAs that are “carved out” from within the protein-coding regions of Escherichia coli mRNAs by cellular RNases. These protected mRNA fragments fold into energetically stable RNA structures, reminiscent of those of intergenic regulatory ncRNAs. In addition, a subset of these ncRNAs coprecipitate with the major ncRNA chaperones Hfq and ProQ and display evolutionarily conserved sequences and conserved expression patterns between different bacterial species. Our data suggest that protein-coding genes can potentially act as a reservoir of regulatory ncRNAs.Daniel DarRotem SorekAmerican Society for MicrobiologyarticletranscriptomemRNA degradationncRNAsRNAMicrobiologyQR1-502ENmBio, Vol 9, Iss 5 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	transcriptome mRNA degradation ncRNA sRNA Microbiology QR1-502
spellingShingle	transcriptome mRNA degradation ncRNA sRNA Microbiology QR1-502 Daniel Dar Rotem Sorek Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts
description	ABSTRACT Prokaryotic genomes encode a plethora of small noncoding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly to protein-coding genes. In addition, recent studies have shown that functional ncRNAs can also be derived from gene 3′ untranslated regions (3′UTRs) via an alternative biogenesis pathway, in which the ncRNA segment is separated from the mRNA via RNase cleavage. Here, we report the detection of a large set of decay-generated noncoding RNAs (decRNAs), many of which are completely embedded within protein-coding mRNA regions rather than in the UTRs. We show that these decRNAs are “carved out” of the mRNA through the action of RNase E and that they are predicted to fold into highly stable RNA structures, similar to those of known ncRNAs. A subset of these decRNAs is predicted to interact with Hfq or ProQ or both, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. These results suggest that mRNA protein-coding regions may harbor a large set of potentially functional small RNAs. IMPORTANCE Bacteria and archaea utilize regulatory small noncoding RNAs (ncRNAs) to control the expression of specific genetic programs. These ncRNAs are almost exclusively encoded within intergenic regions and are independently transcribed. Here, we report on a large set ncRNAs that are “carved out” from within the protein-coding regions of Escherichia coli mRNAs by cellular RNases. These protected mRNA fragments fold into energetically stable RNA structures, reminiscent of those of intergenic regulatory ncRNAs. In addition, a subset of these ncRNAs coprecipitate with the major ncRNA chaperones Hfq and ProQ and display evolutionarily conserved sequences and conserved expression patterns between different bacterial species. Our data suggest that protein-coding genes can potentially act as a reservoir of regulatory ncRNAs.
format	article
author	Daniel Dar Rotem Sorek
author_facet	Daniel Dar Rotem Sorek
author_sort	Daniel Dar
title	Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts
title_short	Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts
title_full	Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts
title_fullStr	Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts
title_full_unstemmed	Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts
title_sort	bacterial noncoding rnas excised from within protein-coding transcripts
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/ab9dd11446ad46ffb3dffd7b4b73eede
work_keys_str_mv	AT danieldar bacterialnoncodingrnasexcisedfromwithinproteincodingtranscripts AT rotemsorek bacterialnoncodingrnasexcisedfromwithinproteincodingtranscripts
_version_	1718427045697945600

Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts

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