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Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping

Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and ope...

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Autores principales: Adams, Philip P, Baniulyte, Gabriele, Esnault, Caroline, Chegireddy, Kavya, Singh, Navjot, Monge, Molly, Dale, Ryan K, Storz, Gisela, Wade, Joseph T
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815308/
https://www.ncbi.nlm.nih.gov/pubmed/33460557
http://dx.doi.org/10.7554/eLife.62438
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author Adams, Philip P
Baniulyte, Gabriele
Esnault, Caroline
Chegireddy, Kavya
Singh, Navjot
Monge, Molly
Dale, Ryan K
Storz, Gisela
Wade, Joseph T
author_facet Adams, Philip P
Baniulyte, Gabriele
Esnault, Caroline
Chegireddy, Kavya
Singh, Navjot
Monge, Molly
Dale, Ryan K
Storz, Gisela
Wade, Joseph T
author_sort Adams, Philip P
collection PubMed
description Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs.
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spelling pubmed-78153082021-01-21 Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping Adams, Philip P Baniulyte, Gabriele Esnault, Caroline Chegireddy, Kavya Singh, Navjot Monge, Molly Dale, Ryan K Storz, Gisela Wade, Joseph T eLife Microbiology and Infectious Disease Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs. eLife Sciences Publications, Ltd 2021-01-18 /pmc/articles/PMC7815308/ /pubmed/33460557 http://dx.doi.org/10.7554/eLife.62438 Text en https://creativecommons.org/publicdomain/zero/1.0/This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication (https://creativecommons.org/publicdomain/zero/1.0/) .
spellingShingle Microbiology and Infectious Disease
Adams, Philip P
Baniulyte, Gabriele
Esnault, Caroline
Chegireddy, Kavya
Singh, Navjot
Monge, Molly
Dale, Ryan K
Storz, Gisela
Wade, Joseph T
Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
title Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
title_full Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
title_fullStr Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
title_full_unstemmed Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
title_short Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping
title_sort regulatory roles of escherichia coli 5' utr and orf-internal rnas detected by 3' end mapping
topic Microbiology and Infectious Disease
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815308/
https://www.ncbi.nlm.nih.gov/pubmed/33460557
http://dx.doi.org/10.7554/eLife.62438
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