skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

Abstract

Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenicmore » candidates and other Desulfovibrio genomes indicated that eight candidates were likely portions of ORFs not previously annotated in the D. vulgaris genome. Comparison of the intergenic and antisense data sets to the bioinformatical predicted candidates, resulted in ~;;54 common candidates. Current approaches using Northern analysis and qRT-PCR are being used toverify expression of the candidates and to further develop the role these sRNAs play in D. vulgaris regulation.« less

Authors:
; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Physical Biosciences Division
OSTI Identifier:
985922
Report Number(s):
LBNL-3742E-Poster
TRN: US1006345
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Technical Report
Resource Relation:
Conference: 110th General Meeting of the American Society for Microbiology, San Diego, CA, May 23-27, 2010
Country of Publication:
United States
Language:
English
Subject:
59; 54; ALIGNMENT; DESULFOVIBRIO; GENE REGULATION; NITRATES; NUCLEOTIDES; REMOVAL; RNA; URANIUM; Desulfovibrio vulgaris regulation, uranium reduction

Citation Formats

Burns, Andrew, Joachimiak, Marcin, Deutschbauer, Adam, Arkin, Adam, and Bender, Kelly. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough. United States: N. p., 2010. Web. doi:10.2172/985922.
Burns, Andrew, Joachimiak, Marcin, Deutschbauer, Adam, Arkin, Adam, & Bender, Kelly. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough. United States. doi:10.2172/985922.
Burns, Andrew, Joachimiak, Marcin, Deutschbauer, Adam, Arkin, Adam, and Bender, Kelly. Mon . "Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough". United States. doi:10.2172/985922. https://www.osti.gov/servlets/purl/985922.
@article{osti_985922,
title = {Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough},
author = {Burns, Andrew and Joachimiak, Marcin and Deutschbauer, Adam and Arkin, Adam and Bender, Kelly},
abstractNote = {Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenic candidates and other Desulfovibrio genomes indicated that eight candidates were likely portions of ORFs not previously annotated in the D. vulgaris genome. Comparison of the intergenic and antisense data sets to the bioinformatical predicted candidates, resulted in ~;;54 common candidates. Current approaches using Northern analysis and qRT-PCR are being used toverify expression of the candidates and to further develop the role these sRNAs play in D. vulgaris regulation.},
doi = {10.2172/985922},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2010},
month = {5}
}