Cargando…
Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function
Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and t...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619774/ https://www.ncbi.nlm.nih.gov/pubmed/26495981 http://dx.doi.org/10.1371/journal.pgen.1005613 |
_version_ | 1782397180021047296 |
---|---|
author | Del Campo, Cristian Bartholomäus, Alexander Fedyunin, Ivan Ignatova, Zoya |
author_facet | Del Campo, Cristian Bartholomäus, Alexander Fedyunin, Ivan Ignatova, Zoya |
author_sort | Del Campo, Cristian |
collection | PubMed |
description | Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. |
format | Online Article Text |
id | pubmed-4619774 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-46197742015-10-29 Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function Del Campo, Cristian Bartholomäus, Alexander Fedyunin, Ivan Ignatova, Zoya PLoS Genet Research Article Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. Public Library of Science 2015-10-23 /pmc/articles/PMC4619774/ /pubmed/26495981 http://dx.doi.org/10.1371/journal.pgen.1005613 Text en © 2015 Del Campo et al 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 Del Campo, Cristian Bartholomäus, Alexander Fedyunin, Ivan Ignatova, Zoya Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function |
title | Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function |
title_full | Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function |
title_fullStr | Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function |
title_full_unstemmed | Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function |
title_short | Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function |
title_sort | secondary structure across the bacterial transcriptome reveals versatile roles in mrna regulation and function |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619774/ https://www.ncbi.nlm.nih.gov/pubmed/26495981 http://dx.doi.org/10.1371/journal.pgen.1005613 |
work_keys_str_mv | AT delcampocristian secondarystructureacrossthebacterialtranscriptomerevealsversatilerolesinmrnaregulationandfunction AT bartholomausalexander secondarystructureacrossthebacterialtranscriptomerevealsversatilerolesinmrnaregulationandfunction AT fedyuninivan secondarystructureacrossthebacterialtranscriptomerevealsversatilerolesinmrnaregulationandfunction AT ignatovazoya secondarystructureacrossthebacterialtranscriptomerevealsversatilerolesinmrnaregulationandfunction |