| Conservation of the LexA repressor binding site in Deinococcus radiodurans. | |
| | |
MedLine Citation:
|
PMID: 20134056 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
The LexA protein is a transcriptional repressor of the bacterial SOS DNA repair system, which comprises a set of DNA repair and cellular survival genes that are induced in response to DNA damage. Its varied DNA binding motifs have been characterized and reported in the Escherichia coli, Bacillus subtilis, rhizobia family members, marine magnetotactic bacterium, Salmonella typhimurium and recently in Mycobacterium tuberculosis and this motifs information has been used in our theoretical analysis to detect its novel regulated genes in radio-resistant Deinococcus radiodurans genome. This bacterium showed presence of SOS-box like consensus sequence in the upstream sequences of 3166 genes with >60% motif score similarity percentage (MSSP) on both strands. Attempts to identify LexA-binding sites and the composition of the putative SOS regulon in D. radiodurans have been unsuccessful so far. To resolve the problem we performed theoretical analysis with modifications on reported data set of genes related to DNA repair (61 genes), stress response (145 genes) and some unusual predicted operons (21 clusters). Expression of some of the predicted SOS-box regulated operon members then was examined through the previously reported microarray data which confirm the expression of only single predicted operon i.e. DRB0143 (AAA superfamily NTPase related to 5-methylcytosine specific restriction enzyme subunit McrB) and DRB0144 (homolog of the McrC subunit of the McrBC restriction modification system). The methodology involved weight matrix construction through CONSENSUS algorithm using information of conserved upstream sequences of eight known genes including dinB, tagC, lexA, recA, uvrB, yneA of B. subtilis while lexA and recA of D. radiodurans through phylogenetic footprinting method and later detection of similar conserved SOS-box like LexA binding motifs through both RSAT & PoSSuMsearch programs. The resultant DNA consensus sequence had highly conserved 14 bp SOS-box like binding site. |
| | |
Authors:
|
Feroz Khan; S P Singh; B N Mishra |
Related Documents
:
|
2687236 - Nucleotide sequence and expression in escherichia coli of the 3-hydroxy-3-methylglutary... 3308846 - Promoter region of the nar operon of escherichia coli: nucleotide sequence and transcri... 12835266 - A bayesian network approach to operon prediction. 6258016 - The structure of unstable constitutive revertants of mutant galop-308::is2-i. 20058486 - Poisson approach to clustering analysis of regulatory sequences. 1820216 - Repositioning of an alternative exon sequence of mouse igm pre-mrna activates splicing ... |
Publication Detail:
|
Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2008-01-24 |
Journal Detail:
|
Title: Journal of integrative bioinformatics Volume: 5 ISSN: 1613-4516 ISO Abbreviation: J Integr Bioinform Publication Date: 2008 |
Date Detail:
|
Created Date: 2010-02-05 Completed Date: 2010-04-16 Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 101503361 Medline TA: J Integr Bioinform Country: Germany |
Other Details:
|
Languages: eng Pagination: - Citation Subset: IM |
Affiliation:
|
Department of Biotechnology, Institute of Engineering & Technology, U. P. Technical University, Lucknow, India. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Algorithms Animals Bacterial Proteins / genetics, metabolism* Base Sequence Binding Sites / genetics Consensus Sequence / genetics DNA Repair DNA, Bacterial / metabolism Deinococcus / metabolism* Genome, Bacterial Molecular Sequence Data Operon Protein Binding Repressor Proteins / genetics, metabolism* SOS Response (Genetics) Serine Endopeptidases / genetics, metabolism* |
| Chemical | |
Reg. No./Substance:
|
0/Bacterial Proteins; 0/DNA, Bacterial; 0/LexA protein, Bacteria; 0/Repressor Proteins; EC 3.4.21.-/Serine Endopeptidases |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: WebStruct and VisualStruct: web interfaces and visualization for Structure software implemented in a...
Next Document: 2.5D Visualisation of Overlapping Biological Networks.