Cargando…

Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis

Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs (sRNAs), some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhao, Tingting, Zhang, Ren, Wang, Mingbo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Editorial Department of Journal of Biomedical Research 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596533/
https://www.ncbi.nlm.nih.gov/pubmed/23554609
http://dx.doi.org/10.1016/S1674-8301(10)60006-1
_version_ 1782262515798900736
author Zhao, Tingting
Zhang, Ren
Wang, Mingbo
author_facet Zhao, Tingting
Zhang, Ren
Wang, Mingbo
author_sort Zhao, Tingting
collection PubMed
description Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs (sRNAs), some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base pairs. Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.
format Online
Article
Text
id pubmed-3596533
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher Editorial Department of Journal of Biomedical Research
record_format MEDLINE/PubMed
spelling pubmed-35965332013-04-02 Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis Zhao, Tingting Zhang, Ren Wang, Mingbo J Biomed Res Research Paper Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs (sRNAs), some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base pairs. Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes. Editorial Department of Journal of Biomedical Research 2010-01 /pmc/articles/PMC3596533/ /pubmed/23554609 http://dx.doi.org/10.1016/S1674-8301(10)60006-1 Text en © 2010 by the Journal of Biomedical Research. All rights reserved. This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/
spellingShingle Research Paper
Zhao, Tingting
Zhang, Ren
Wang, Mingbo
Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis
title Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis
title_full Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis
title_fullStr Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis
title_full_unstemmed Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis
title_short Prediction of candidate small non-coding RNAs in Agrobacterium by computational analysis
title_sort prediction of candidate small non-coding rnas in agrobacterium by computational analysis
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596533/
https://www.ncbi.nlm.nih.gov/pubmed/23554609
http://dx.doi.org/10.1016/S1674-8301(10)60006-1
work_keys_str_mv AT zhaotingting predictionofcandidatesmallnoncodingrnasinagrobacteriumbycomputationalanalysis
AT zhangren predictionofcandidatesmallnoncodingrnasinagrobacteriumbycomputationalanalysis
AT wangmingbo predictionofcandidatesmallnoncodingrnasinagrobacteriumbycomputationalanalysis