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The GlxR regulon of the amino acid producer Corynebacterium glutamicum: In silico and in vitro detection of DNA binding sites of a global transcription regulator

Paper ID Volume ID Publish Year Pages File Format Full-Text
24913 43545 2008 11 PDF Available
Title
The GlxR regulon of the amino acid producer Corynebacterium glutamicum: In silico and in vitro detection of DNA binding sites of a global transcription regulator
Abstract

The glxR (cg0350) gene of Corynebacterium glutamicum ATCC 13032 encodes a DNA-binding trancription regulator of the CRP/FNR protein family. Five genomic DNA regions known to be bound by GlxR provided the seed information for DNA binding site discovery by expectation maximization and Gibbs sampling approaches. The detection of additional motifs in the genome sequence of C. glutamicum was performed with a position weight matrix and a profile hidden Markov model, both deduced from the initial motif discovery. A combined iterative search for GlxR binding sites revealed 201 potential operator sequences. The interaction of purified GlxR protein with 51 selected binding sites was demonstrated in vitro by performing electrophoretic mobility shift assays with double-stranded 40-mer oligonucleotides. Considering potential operon structures and the genomic organization of C. glutamicum, the expression of 53 transcription units comprising 96 genes may be controlled directly by GlxR. The DNA binding site of GlxR is apparently specified by the consensus sequence TGTGANNTANNTCACA. Integration of the data into the transcriptional regulatory network model of C. glutamicum revealed a high connectivity of the deduced regulatory interactions and suggested that GlxR controls at least (i) sugar uptake, glycolysis, and gluconeogenesis, (ii) acetate, lactate, gluconate, and ethanol metabolism, (iii) aromatic compound degradation, (iv) aerobic and anaerobic respiration, (v) glutamate uptake and nitrogen assimilation, (vi) fatty acid biosynthesis, (vii) deoxyribonucleotide biosynthesis, (viii) the cellular stress response, and (ix) resuscitation.

Keywords
Corynebacterium glutamicum; Transcriptional regulatory network; Motif discovery; Transcription factor binding site; Global regulator; GlxR
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The GlxR regulon of the amino acid producer Corynebacterium glutamicum: In silico and in vitro detection of DNA binding sites of a global transcription regulator
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 135, Issue 4, 31 July 2008, Pages 340–350
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us