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GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization

BACKGROUND: Mycobacterium smegmatis is fast growing non-pathogenic mycobacteria. This organism has been widely used as a model organism to study the biology of other virulent and extremely slow growing species like Mycobacterium tuberculosis. Based on the homology of the N-terminal DNA binding domai...

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Autores principales: Vindal, Vaibhav, Suma, Katta, Ranjan, Akash
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2018728/
https://www.ncbi.nlm.nih.gov/pubmed/17714599
http://dx.doi.org/10.1186/1471-2164-8-289
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author Vindal, Vaibhav
Suma, Katta
Ranjan, Akash
author_facet Vindal, Vaibhav
Suma, Katta
Ranjan, Akash
author_sort Vindal, Vaibhav
collection PubMed
description BACKGROUND: Mycobacterium smegmatis is fast growing non-pathogenic mycobacteria. This organism has been widely used as a model organism to study the biology of other virulent and extremely slow growing species like Mycobacterium tuberculosis. Based on the homology of the N-terminal DNA binding domain, the recently sequenced genome of M. smegmatis has been shown to possess several putative GntR regulators. A striking characteristic feature of this family of regulators is that they possess a conserved N-terminal DNA binding domain and a diverse C-terminal domain involved in the effector binding and/or oligomerization. Since the physiological role of these regulators is critically dependent upon effector binding and operator sites, we have analysed and classified these regulators into their specific subfamilies and identified their potential binding sites. RESULTS: The sequence analysis of M. smegmatis putative GntRs has revealed that FadR, HutC, MocR and the YtrA-like regulators are encoded by 45, 8, 8 and 1 genes respectively. Further out of 45 FadR-like regulators, 19 were classified into the FadR group and 26 into the VanR group. All these proteins showed similar secondary structural elements specific to their respective subfamilies except MSMEG_3959, which showed additional secondary structural elements. Using the reciprocal BLAST searches, we further identified the orthologs of these regulators in Bacillus subtilis and other mycobacteria. Since the expression of many regulators is auto-regulatory, we have identified potential operator sites for a number of these GntR regulators by analyzing the upstream sequences. CONCLUSION: This study helps in extending the annotation of M. smegmatis GntR proteins. It identifies the GntR regulators of M. smegmatis that could serve as a model for studying orthologous regulators from virulent as well as other saprophytic mycobacteria. This study also sheds some light on the nucleotide preferences in the target-motifs of GntRs thus providing important leads for initiating the experimental characterization of these proteins, construction of the gene regulatory network for these regulators and an understanding of the influence of these proteins on the physiology of the mycobacteria.
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spelling pubmed-20187282007-10-12 GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization Vindal, Vaibhav Suma, Katta Ranjan, Akash BMC Genomics Research Article BACKGROUND: Mycobacterium smegmatis is fast growing non-pathogenic mycobacteria. This organism has been widely used as a model organism to study the biology of other virulent and extremely slow growing species like Mycobacterium tuberculosis. Based on the homology of the N-terminal DNA binding domain, the recently sequenced genome of M. smegmatis has been shown to possess several putative GntR regulators. A striking characteristic feature of this family of regulators is that they possess a conserved N-terminal DNA binding domain and a diverse C-terminal domain involved in the effector binding and/or oligomerization. Since the physiological role of these regulators is critically dependent upon effector binding and operator sites, we have analysed and classified these regulators into their specific subfamilies and identified their potential binding sites. RESULTS: The sequence analysis of M. smegmatis putative GntRs has revealed that FadR, HutC, MocR and the YtrA-like regulators are encoded by 45, 8, 8 and 1 genes respectively. Further out of 45 FadR-like regulators, 19 were classified into the FadR group and 26 into the VanR group. All these proteins showed similar secondary structural elements specific to their respective subfamilies except MSMEG_3959, which showed additional secondary structural elements. Using the reciprocal BLAST searches, we further identified the orthologs of these regulators in Bacillus subtilis and other mycobacteria. Since the expression of many regulators is auto-regulatory, we have identified potential operator sites for a number of these GntR regulators by analyzing the upstream sequences. CONCLUSION: This study helps in extending the annotation of M. smegmatis GntR proteins. It identifies the GntR regulators of M. smegmatis that could serve as a model for studying orthologous regulators from virulent as well as other saprophytic mycobacteria. This study also sheds some light on the nucleotide preferences in the target-motifs of GntRs thus providing important leads for initiating the experimental characterization of these proteins, construction of the gene regulatory network for these regulators and an understanding of the influence of these proteins on the physiology of the mycobacteria. BioMed Central 2007-08-23 /pmc/articles/PMC2018728/ /pubmed/17714599 http://dx.doi.org/10.1186/1471-2164-8-289 Text en Copyright © 2007 Vindal 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
Vindal, Vaibhav
Suma, Katta
Ranjan, Akash
GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
title GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
title_full GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
title_fullStr GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
title_full_unstemmed GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
title_short GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization
title_sort gntr family of regulators in mycobacterium smegmatis: a sequence and structure based characterization
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2018728/
https://www.ncbi.nlm.nih.gov/pubmed/17714599
http://dx.doi.org/10.1186/1471-2164-8-289
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