Cargando…

Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli

Bacterial small RNAs (sRNAs) regulate protein production by binding to mRNAs and altering their translation and degradation. sRNAs are smaller than most mRNAs but larger than many proteins. Therefore it is uncertain whether sRNAs can enter the nucleoid to target nascent mRNAs. Here, we investigate t...

Descripción completa

Detalles Bibliográficos
Autores principales: Sheng, Huanjie, Stauffer, Weston T., Hussein, Razika, Lin, Chris, Lim, Han N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389542/
https://www.ncbi.nlm.nih.gov/pubmed/28119418
http://dx.doi.org/10.1093/nar/gkx023
_version_ 1782521288229650432
author Sheng, Huanjie
Stauffer, Weston T.
Hussein, Razika
Lin, Chris
Lim, Han N.
author_facet Sheng, Huanjie
Stauffer, Weston T.
Hussein, Razika
Lin, Chris
Lim, Han N.
author_sort Sheng, Huanjie
collection PubMed
description Bacterial small RNAs (sRNAs) regulate protein production by binding to mRNAs and altering their translation and degradation. sRNAs are smaller than most mRNAs but larger than many proteins. Therefore it is uncertain whether sRNAs can enter the nucleoid to target nascent mRNAs. Here, we investigate the intracellular localization of sRNAs transcribed from plasmids in Escherichia coli using RNA fluorescent in-situ hybridization. We found that sRNAs (GlmZ, OxyS, RyhB and SgrS) have equal preference for the nucleoid and cytoplasm, and no preferential localization at the cell membrane. We show using the gfp mRNA (encoding green fluorescent protein) that non-sRNAs can be engineered to have different proportions of nucleoid and cytoplasmic localization by altering their length and/or translation. The same localization as sRNAs was achieved by decreasing gfp mRNA length and translation, which suggests that sRNAs and other RNAs may enter the densely packed DNA of the nucleoid if they are sufficiently small. We also found that the Hfq protein, which binds sRNAs, minimally affects sRNA localization. Important implications of our findings for engineering synthetic circuits are: (i) sRNAs can potentially bind nascent mRNAs in the nucleoid, and (ii) localization patterns and distribution volumes of sRNAs can differ from some larger RNAs.
format Online
Article
Text
id pubmed-5389542
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-53895422017-04-24 Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli Sheng, Huanjie Stauffer, Weston T. Hussein, Razika Lin, Chris Lim, Han N. Nucleic Acids Res Synthetic Biology and Bioengineering Bacterial small RNAs (sRNAs) regulate protein production by binding to mRNAs and altering their translation and degradation. sRNAs are smaller than most mRNAs but larger than many proteins. Therefore it is uncertain whether sRNAs can enter the nucleoid to target nascent mRNAs. Here, we investigate the intracellular localization of sRNAs transcribed from plasmids in Escherichia coli using RNA fluorescent in-situ hybridization. We found that sRNAs (GlmZ, OxyS, RyhB and SgrS) have equal preference for the nucleoid and cytoplasm, and no preferential localization at the cell membrane. We show using the gfp mRNA (encoding green fluorescent protein) that non-sRNAs can be engineered to have different proportions of nucleoid and cytoplasmic localization by altering their length and/or translation. The same localization as sRNAs was achieved by decreasing gfp mRNA length and translation, which suggests that sRNAs and other RNAs may enter the densely packed DNA of the nucleoid if they are sufficiently small. We also found that the Hfq protein, which binds sRNAs, minimally affects sRNA localization. Important implications of our findings for engineering synthetic circuits are: (i) sRNAs can potentially bind nascent mRNAs in the nucleoid, and (ii) localization patterns and distribution volumes of sRNAs can differ from some larger RNAs. Oxford University Press 2017-03-17 2017-01-24 /pmc/articles/PMC5389542/ /pubmed/28119418 http://dx.doi.org/10.1093/nar/gkx023 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Synthetic Biology and Bioengineering
Sheng, Huanjie
Stauffer, Weston T.
Hussein, Razika
Lin, Chris
Lim, Han N.
Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli
title Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli
title_full Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli
title_fullStr Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli
title_full_unstemmed Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli
title_short Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli
title_sort nucleoid and cytoplasmic localization of small rnas in escherichia coli
topic Synthetic Biology and Bioengineering
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389542/
https://www.ncbi.nlm.nih.gov/pubmed/28119418
http://dx.doi.org/10.1093/nar/gkx023
work_keys_str_mv AT shenghuanjie nucleoidandcytoplasmiclocalizationofsmallrnasinescherichiacoli
AT staufferwestont nucleoidandcytoplasmiclocalizationofsmallrnasinescherichiacoli
AT husseinrazika nucleoidandcytoplasmiclocalizationofsmallrnasinescherichiacoli
AT linchris nucleoidandcytoplasmiclocalizationofsmallrnasinescherichiacoli
AT limhann nucleoidandcytoplasmiclocalizationofsmallrnasinescherichiacoli