The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model
Kohl T, Tauch A (2009)
JOURNAL OF BIOTECHNOLOGY 143(4): 239-246.
Zeitschriftenaufsatz
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Einrichtung
Abstract / Bemerkung
Corynebacterium glutamicum is an industrially important producer of amino acids and an emerging model system for the Corynebacterineae. The glxR gene of C. glutamicum ATCC 13032 encodes a DNA binding transcription factor of the Crp-Fnr protein family. Available data indicated a prominent role of GlxR in the transcriptional regulatory network of C. glutamicum. We have used recently published whole-genome annotations of several corynebacteria to derive further evidence for GlxR-mediated transcriptional regulation from a comparative genomics approach. A bioinformatic strategy detected 22 genes belonging to a proposed GlxR core regulon in corynebacteria. Binding of purified GlxR protein to 40-mer oligonucleotides representing predicted GlxR binding sites in the upstream region of core genes from C. glutamicum ATCC 13032 was verified in vitro by electrophoretic mobility shift assays. Based on current data, a reliable genome-scale prediction of GlxR binding sites was performed, indicating that about 14% of the annotated C. glutamicum genes might be under direct transcriptional control by GlxR. Integration of GlxR-mediated regulatory interactions with the data stored in CoryneRegNet enabled the reconstruction of a refined transcriptional regulatory network model for C. glutamicum. This network model exhibited a hierarchical and modular structure and is characterized by the presence of master regulators in each functional module, with GlxR serving as the dominating regulatory hub. (C) 2009 Elsevier B.V. All rights reserved.
Stichworte
Corynebacterium glutamicum;
Transcriptional;
regulatory network;
Transcription factor binding site;
Global;
Comparative genomics;
GlxR;
regulator
Erscheinungsjahr
2009
Zeitschriftentitel
JOURNAL OF BIOTECHNOLOGY
Band
143
Ausgabe
4
Seite(n)
239-246
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/1589932
Zitieren
Kohl T, Tauch A. The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model. JOURNAL OF BIOTECHNOLOGY. 2009;143(4):239-246.
Kohl, T., & Tauch, A. (2009). The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model. JOURNAL OF BIOTECHNOLOGY, 143(4), 239-246. https://doi.org/10.1016/j.jbiotec.2009.08.005
Kohl, Thomas, and Tauch, Andreas. 2009. “The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model”. JOURNAL OF BIOTECHNOLOGY 143 (4): 239-246.
Kohl, T., and Tauch, A. (2009). The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model. JOURNAL OF BIOTECHNOLOGY 143, 239-246.
Kohl, T., & Tauch, A., 2009. The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model. JOURNAL OF BIOTECHNOLOGY, 143(4), p 239-246.
T. Kohl and A. Tauch, “The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model”, JOURNAL OF BIOTECHNOLOGY, vol. 143, 2009, pp. 239-246.
Kohl, T., Tauch, A.: The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model. JOURNAL OF BIOTECHNOLOGY. 143, 239-246 (2009).
Kohl, Thomas, and Tauch, Andreas. “The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model”. JOURNAL OF BIOTECHNOLOGY 143.4 (2009): 239-246.
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PMID: 18599074
Martinez-Antonio A, Janga SC, Thieffry D., J. Mol. Biol. 381(1), 2008
PMID: 18599074
The phosphotransferase system of Corynebacterium glutamicum: features of sugar transport and carbon regulation.
Moon MW, Park SY, Choi SK, Lee JK., J. Mol. Microbiol. Biotechnol. 12(1-2), 2007
PMID: 17183210
Moon MW, Park SY, Choi SK, Lee JK., J. Mol. Microbiol. Biotechnol. 12(1-2), 2007
PMID: 17183210
Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens.
Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K, Gojobori T., Genome Res. 13(7), 2003
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Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K, Gojobori T., Genome Res. 13(7), 2003
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In vitro reconstitution of catabolite repression in Escherichia coli.
Park YH, Lee BR, Seok YJ, Peterkofsky A., J. Biol. Chem. 281(10), 2006
PMID: 16407219
Park YH, Lee BR, Seok YJ, Peterkofsky A., J. Biol. Chem. 281(10), 2006
PMID: 16407219
Bacterial nucleotide-based second messengers.
Pesavento C, Hengge R., Curr. Opin. Microbiol. 12(2), 2009
PMID: 19318291
Pesavento C, Hengge R., Curr. Opin. Microbiol. 12(2), 2009
PMID: 19318291
From dormant to germinating spores of Streptomyces coelicolor A3(2): new perspectives from the crp null mutant.
Piette A, Derouaux A, Gerkens P, Noens EE, Mazzucchelli G, Vion S, Koerten HK, Titgemeyer F, De Pauw E, Leprince P, van Wezel GP, Galleni M, Rigali S., J. Proteome Res. 4(5), 2005
PMID: 16212423
Piette A, Derouaux A, Gerkens P, Noens EE, Mazzucchelli G, Vion S, Koerten HK, Titgemeyer F, De Pauw E, Leprince P, van Wezel GP, Galleni M, Rigali S., J. Proteome Res. 4(5), 2005
PMID: 16212423
Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis.
Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF., FEMS Microbiol. Lett. 273(1), 2007
PMID: 17559405
Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF., FEMS Microbiol. Lett. 273(1), 2007
PMID: 17559405
A novel method for accurate operon predictions in all sequenced prokaryotes.
Price MN, Huang KH, Alm EJ, Arkin AP., Nucleic Acids Res. 33(3), 2005
PMID: 15701760
Price MN, Huang KH, Alm EJ, Arkin AP., Nucleic Acids Res. 33(3), 2005
PMID: 15701760
Modular analysis of the transcriptional regulatory network of E. coli.
Resendis-Antonio O, Freyre-Gonzalez JA, Menchaca-Mendez R, Gutierrez-Rios RM, Martinez-Antonio A, Avila-Sanchez C, Collado-Vides J., Trends Genet. 21(1), 2005
PMID: 15680508
Resendis-Antonio O, Freyre-Gonzalez JA, Menchaca-Mendez R, Gutierrez-Rios RM, Martinez-Antonio A, Avila-Sanchez C, Collado-Vides J., Trends Genet. 21(1), 2005
PMID: 15680508
A member of the cAMP receptor protein family of transcription regulators in Mycobacterium tuberculosis is required for virulence in mice and controls transcription of the rpfA gene coding for a resuscitation promoting factor.
Rickman L, Scott C, Hunt DM, Hutchinson T, Menendez MC, Whalan R, Hinds J, Colston MJ, Green J, Buxton RS., Mol. Microbiol. 56(5), 2005
PMID: 15882420
Rickman L, Scott C, Hunt DM, Hutchinson T, Menendez MC, Whalan R, Hinds J, Colston MJ, Green J, Buxton RS., Mol. Microbiol. 56(5), 2005
PMID: 15882420
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Puhler A., J. Bacteriol. 187(13), 2005
PMID: 15968079
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Puhler A., J. Bacteriol. 187(13), 2005
PMID: 15968079
Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids.
Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH, Arnold W, Blom J, Brinkrolf K, Brune I, Gotker S, Weisshaar B, Goesmann A, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18430482
Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH, Arnold W, Blom J, Brinkrolf K, Brune I, Gotker S, Weisshaar B, Goesmann A, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18430482
The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.
Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Gotker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18367281
Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Gotker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Droge M, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18367281
Architectural requirements for optimal activation by tandem CRP molecules at a class I CRP-dependent promoter.
Tebbutt J, Rhodius VA, Webster CL, Busby SJ., FEMS Microbiol. Lett. 210(1), 2002
PMID: 12023077
Tebbutt J, Rhodius VA, Webster CL, Busby SJ., FEMS Microbiol. Lett. 210(1), 2002
PMID: 12023077
Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R.
Yukawa H, Omumasaba CA, Nonaka H, Kos P, Okai N, Suzuki N, Suda M, Tsuge Y, Watanabe J, Ikeda Y, Vertes AA, Inui M., Microbiology (Reading, Engl.) 153(Pt 4), 2007
PMID: 17379713
Yukawa H, Omumasaba CA, Nonaka H, Kos P, Okai N, Suzuki N, Suda M, Tsuge Y, Watanabe J, Ikeda Y, Vertes AA, Inui M., Microbiology (Reading, Engl.) 153(Pt 4), 2007
PMID: 17379713
Mechanism of activation of catabolite-sensitive genes: a positive control system.
Zubay G, Schwartz D, Beckwith J., Proc. Natl. Acad. Sci. U.S.A. 66(1), 1970
PMID: 4320461
Zubay G, Schwartz D, Beckwith J., Proc. Natl. Acad. Sci. U.S.A. 66(1), 1970
PMID: 4320461
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