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. Export

@article{citeulike:2931328, 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 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.}, address = {Institut f\"{u}r Genomforschung und Systembiologie, Centrum f\"{u}r Biotechnologie, Universit\"{a}t Bielefeld, Universit\"{a}tsstra{\ss}e 25, D-33615 Bielefeld, Germany; International NRW Graduate School in Bioinformatics and Genome Research, Centrum f\"{u}r Biotechnologie, Universit\"{a}t Bielefeld, Universit\"{a}tsstra{\ss}e 25, D-33615 Bielefeld, Germany.}, author = {Kohl, Thomas A A. and Baumbach, Jan and Jungwirth, Britta and P\"{u}hler, Alfred and Tauch, Andreas}, citeulike-article-id = {2931328}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jbiotec.2008.05.011}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18573287}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18573287}, day = {3}, doi = {10.1016/j.jbiotec.2008.05.011}, issn = {0168-1656}, journal = {Journal of biotechnology}, keywords = {application}, month = {June}, posted-at = {2008-06-26 16:32:01}, priority = {2}, 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.}, url = {http://dx.doi.org/10.1016/j.jbiotec.2008.05.011}, year = {2008} }

TY - JOUR ID - citeulike:2931328 L3 - citeulike-article-id:2931328 N2 - 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 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. JF - Journal of biotechnology SN - 0168-1656 AD - Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany; International NRW Graduate School in Bioinformatics and Genome Research, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany. TI - 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. KW - application AU - Kohl, Thomas A AU - Baumbach, Jan AU - Jungwirth, Britta AU - Pühler, Alfred AU - Tauch, Andreas PY - 2008/06/03/ UR - http://dx.doi.org/10.1016/j.jbiotec.2008.05.011 ER -