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Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria
BACKGROUND: Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches i...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2005
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1262725/ https://www.ncbi.nlm.nih.gov/pubmed/16202131 http://dx.doi.org/10.1186/1471-2180-5-54 |
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author | Seliverstov, Alexander V Putzer, Harald Gelfand, Mikhail S Lyubetsky, Vassily A |
author_facet | Seliverstov, Alexander V Putzer, Harald Gelfand, Mikhail S Lyubetsky, Vassily A |
author_sort | Seliverstov, Alexander V |
collection | PubMed |
description | BACKGROUND: Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches in proteobacteria and Firmicutes, but not in other groups of bacteria. RESULTS: Comparative analysis of amino acid biosynthesis operons in Actinobacteria resulted in identification of conserved regions upstream of several operons. Classical attenuators were predicted upstream of trp operons in Corynebacterium spp. and Streptomyces spp., and trpS and leuS genes in some Streptomyces spp. Candidate leader peptides with terminators were observed upstream of ilvB genes in Corynebacterium spp., Mycobacterium spp. and Streptomyces spp. Candidate leader peptides without obvious terminators were found upstream of cys operons in Mycobacterium spp. and several other species. A conserved pseudoknot (named LEU element) was identified upstream of leuA operons in most Actinobacteria. Finally, T-boxes likely involved in the regulation of translation initiation were observed upstream of ileS genes from several Actinobacteria. CONCLUSION: The metabolism of tryptophan, cysteine and leucine in Actinobacteria seems to be regulated on the RNA level. In some cases the mechanism is classical attenuation, but in many cases some components of attenuators are missing. The most interesting case seems to be the leuA operon preceded by the LEU element that may fold into a conserved pseudoknot or an alternative structure. A LEU element has been observed in a transposase gene from Bifidobacterium longum, but it is not conserved in genes encoding closely related transposases despite a very high level of protein similarity. One possibility is that the regulatory region of the leuA has been co-opted from some element involved in transposition. Analysis of phylogenetic patterns allowed for identification of ML1624 of M. leprae and its orthologs as the candidate regulatory proteins that may bind to the LEU element. T-boxes upstream of the ileS genes are unusual, as their regulatory mechanism seems to be inhibition of translation initiation via a hairpin sequestering the Shine-Dalgarno box. |
format | Text |
id | pubmed-1262725 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-12627252005-10-22 Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria Seliverstov, Alexander V Putzer, Harald Gelfand, Mikhail S Lyubetsky, Vassily A BMC Microbiol Research Article BACKGROUND: Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches in proteobacteria and Firmicutes, but not in other groups of bacteria. RESULTS: Comparative analysis of amino acid biosynthesis operons in Actinobacteria resulted in identification of conserved regions upstream of several operons. Classical attenuators were predicted upstream of trp operons in Corynebacterium spp. and Streptomyces spp., and trpS and leuS genes in some Streptomyces spp. Candidate leader peptides with terminators were observed upstream of ilvB genes in Corynebacterium spp., Mycobacterium spp. and Streptomyces spp. Candidate leader peptides without obvious terminators were found upstream of cys operons in Mycobacterium spp. and several other species. A conserved pseudoknot (named LEU element) was identified upstream of leuA operons in most Actinobacteria. Finally, T-boxes likely involved in the regulation of translation initiation were observed upstream of ileS genes from several Actinobacteria. CONCLUSION: The metabolism of tryptophan, cysteine and leucine in Actinobacteria seems to be regulated on the RNA level. In some cases the mechanism is classical attenuation, but in many cases some components of attenuators are missing. The most interesting case seems to be the leuA operon preceded by the LEU element that may fold into a conserved pseudoknot or an alternative structure. A LEU element has been observed in a transposase gene from Bifidobacterium longum, but it is not conserved in genes encoding closely related transposases despite a very high level of protein similarity. One possibility is that the regulatory region of the leuA has been co-opted from some element involved in transposition. Analysis of phylogenetic patterns allowed for identification of ML1624 of M. leprae and its orthologs as the candidate regulatory proteins that may bind to the LEU element. T-boxes upstream of the ileS genes are unusual, as their regulatory mechanism seems to be inhibition of translation initiation via a hairpin sequestering the Shine-Dalgarno box. BioMed Central 2005-10-03 /pmc/articles/PMC1262725/ /pubmed/16202131 http://dx.doi.org/10.1186/1471-2180-5-54 Text en Copyright © 2005 Seliverstov et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Seliverstov, Alexander V Putzer, Harald Gelfand, Mikhail S Lyubetsky, Vassily A Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria |
title | Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria |
title_full | Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria |
title_fullStr | Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria |
title_full_unstemmed | Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria |
title_short | Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria |
title_sort | comparative analysis of rna regulatory elements of amino acid metabolism genes in actinobacteria |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1262725/ https://www.ncbi.nlm.nih.gov/pubmed/16202131 http://dx.doi.org/10.1186/1471-2180-5-54 |
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