The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum

Journal of Biotechnology - Tập 129 - Trang 191-211 - 2007
Karina Brinkrolf1,2, Iris Brune1, Andreas Tauch1
1Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
2International NRW Graduate School in Bioinformatics and Genome Research, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany

Tài liệu tham khảo

Aderem, 2005, Systems biology: its practice and challenges, Cell, 121, 511, 10.1016/j.cell.2005.04.020 Aínsa, 2000, WhiA, a protein of unknown function conserved among gram-positive bacteria, is essential for sporulation in Streptomyces coelicolor A3(2), J. Bacteriol., 182, 5470, 10.1128/JB.182.19.5470-5478.2000 Aravind, 2005, The many faces of the helix-turn-helix domain: transcription regulation and beyond, FEMS Microbiol. Rev., 29, 231, 10.1016/j.fmrre.2004.12.008 Barreiro, 2004, Transcriptional analysis of the groES-groEL1, groEL2, and dnaK genes in Corynebacterium glutamicum: characterization of heat shock-induced promoters, J. Bacteriol., 186, 4813, 10.1128/JB.186.14.4813-4817.2004 Barriuso-Iglesias, 2006, Transcriptional analysis of the F0F1 ATPase operon of Corynebacterium glutamicum ATCC 13032 reveals strong induction by alkaline pH, Microbiology, 152, 11, 10.1099/mic.0.28383-0 Baumbach, 2006, CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks, BMC Genomics, 7, 24, 10.1186/1471-2164-7-24 Baumbach, 2006, CoryneRegNet 2: an integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes, J. Integr. Bioinf., 3, 24, 10.1515/jib-2006-24 Beckers, 2004, Molecular identification of the urea uptake system and transcriptional analysis of urea transporter- and urease-encoding genes in Corynebacterium glutamicum, J. Bacteriol., 186, 7645, 10.1128/JB.186.22.7645-7652.2004 Bellmann, 2001, Expression control and specificity of the basic amino acid exporter LysE of Corynebacterium glutamicum, Microbiology, 147, 1765, 10.1099/00221287-147-7-1765 Bijlsma, 2003, Making informed decisions: regulatory interactions between two-component systems, Trends Microbiol., 11, 359, 10.1016/S0966-842X(03)00176-8 Borovok, 2004, Alternative oxygen-dependent and oxygen-independent ribonucleotide reductases in Streptomyces: cross-regulation and physiological role in response to oxygen limitation, Mol. Microbiol., 54, 1022, 10.1111/j.1365-2958.2004.04325.x Brinkrolf, 2006, Transcriptional regulation of catabolic pathways for aromatic compounds in Corynebacterium glutamicum, Genet. Mol. Res., 5, 773 Brune, 2005, The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences, BMC Genomics, 7, 86, 10.1186/1471-2164-6-86 Brune, 2006, The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum, BMC Genomics, 7, 21, 10.1186/1471-2164-7-21 Burkovski, 2003, Ammonium assimilation and nitrogen control in Corynebacterium glutamicum and its relatives: an example for new regulatory mechanisms in actinomycetes, FEMS Microbiol. Rev., 27, 617, 10.1016/S0168-6445(03)00067-6 Busenlehner, 2003, The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance, FEMS Microbiol. Rev., 27, 131, 10.1016/S0168-6445(03)00054-8 Canneva, 2005, Rv2358 and FurB: two transcriptional regulators from Mycobacterium tuberculosis which respond to zinc, J. Bacteriol., 187, 5837, 10.1128/JB.187.16.5837-5840.2005 Cases, 2003, Transcription regulation and environmental adaptation in bacteria, Trends Microbiol., 11, 248, 10.1016/S0966-842X(03)00103-3 Cerdeño-Tárraga, 2003, The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129, Nucl. Acids Res., 31, 6516, 10.1093/nar/gkg874 Chen, 2003, Quantitative Petri net model of gene regulated metabolic networks in the cell, In Silico Biol., 3, 347 Chung, 2006, Molecular analysis of pyrH gene encoding UMP kinase in Corynebacterium glutamicum, 138 Cramer, 2006, Identification of RamA, a novel LuxR-type transcriptional regulator of genes involved in acetate metabolism of Corynebacterium glutamicum, J. Bacteriol., 188, 2554, 10.1128/JB.188.7.2554-2567.2006 Croft, 2003, Is prokaryotic complexity limited by accelerated growth in regulatory overhead?, Genome Biol., 5, P2, 10.1186/gb-2003-5-1-p2 Dobrin, 2004, Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network, BMC Bioinf., 5, 10, 10.1186/1471-2105-5-10 Engels, 2004, clpC and clpP1P2 gene expression in Corynebacterium glutamicum is controlled by a regulatory network involving the transcriptional regulators ClgR and HspR as well as the ECF sigma factor σH, Mol. Microbiol., 52, 285, 10.1111/j.1365-2958.2003.03979.x Engels, 2005, The transcriptional activator ClgR controls transcription of genes involved in proteolysis and DNA repair in Corynebacterium glutamicum, Mol. Microbiol., 57, 576, 10.1111/j.1365-2958.2005.04710.x Gao, 2006, Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups, Antonie van Leeuwenhoek, 90, 69, 10.1007/s10482-006-9061-2 Geiman, 2006, Differential gene expression in response to exposure to antimycobacterial agents and other stress conditions among seven Mycobacterium tuberculosis whiB-like genes, Antimicrob. Agents Chemother., 50, 2836, 10.1128/AAC.00295-06 Gerstmeir, 2004, RamB, a novel transcriptional regulator of genes involved in acetate metabolism of Corynebacterium glutamicum, J. Bacteriol., 186, 2798, 10.1128/JB.186.9.2798-2809.2004 Goldberg, 2006, A sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes, Proc. Natl. Acad. Sci. USA, 103, 11240, 10.1073/pnas.0604351103 Gomez, 2000, whmD is an essential mycobacterial gene required for proper septation and cell division, Proc. Natl. Acad. Sci. USA, 97, 8554, 10.1073/pnas.140225297 Gough, 2001, Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure, J. Mol. Biol., 313, 903, 10.1006/jmbi.2001.5080 Grandvalet, 1999, The ClpB ATPase of Streptomyces albus G belongs to the HspR heat shock regulon, Mol. Microbiol., 31, 521, 10.1046/j.1365-2958.1999.01193.x Gualerzi, 2003, Transcriptional and post-transcriptional control of cold-shock genes, J. Mol. Biol., 331, 527, 10.1016/S0022-2836(03)00732-0 Halgasova, 2001, Cloning and transcriptional characterization of two sigma factor genes, sigA and sigB, from Brevibacterium flavum, Curr. Microbiol., 43, 249, 10.1007/s002840010296 Halgasova, 2002, The Brevibacterium flavum sigma factor SigB has a role in the environmental stress response, FEMS Microbiol. Lett., 216, 77, 10.1111/j.1574-6968.2002.tb11418.x Hansmeier, 2006, The surface (S)-layer gene cspB of Corynebacterium glutamicum is transcriptionally activated by a LuxR-type regulator and located on a 6kb genomic island absent from the type strain ATCC 13032, Microbiology, 152, 923, 10.1099/mic.0.28673-0 Hermann, 2003, Industrial production of amino acids by coryneform bacteria, J. Biotechnol., 104, 155, 10.1016/S0168-1656(03)00149-4 Herrgård, 2004, Reconstruction of microbial transcriptional regulatory networks, Curr. Opin. Biotechnol., 15, 70, 10.1016/j.copbio.2003.11.002 Huang, 2006, Genetic characterization of the resorcinol catabolic pathway in Corynebacterium glutamicum, Appl. Environ. Microbiol., 72, 7238, 10.1128/AEM.01494-06 Ishige, 2003, The phosphate starvation stimulon of Corynebacterium glutamicum determined by DNA microarray analyses, J. Bacteriol., 185, 4519, 10.1128/JB.185.15.4519-4529.2003 Ishihama, 2000, Functional modulation of Escherichia coli RNA polymerase, Annu. Rev. Microbiol., 54, 499, 10.1146/annurev.micro.54.1.499 Itou, 2005, The CGL2612 protein from Corynebacterium glutamicum is a drug resistance-related transcriptional repressor: structural and functional analysis of a newly identified transcription factor from genomic DNA analysis, J. Biol. Chem., 280, 38711, 10.1074/jbc.M505999200 Jakimowicz, 2006, Developmental control of a parAB promoter leads to formation of sporulation-associated ParB complexes in Streptomyces coelicolor, J. Bacteriol., 188, 1710, 10.1128/JB.188.5.1710-1720.2006 Jáuregui, 2003, Conservation of DNA curvature signals in regulatory regions of prokaryotic genes, Nucl. Acids Res., 31, 6770, 10.1093/nar/gkg882 Kalinowski, 2003, The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of l-aspartate-derived amino acids and vitamins, J. Biotechnol., 104, 5, 10.1016/S0168-1656(03)00154-8 Kato, 2005, Regulatory network of the initiation of chromosomal replication in Escherichia coli, Crit. Rev. Biochem. Mol. Biol., 40, 331, 10.1080/10409230500366090 Kennerknecht, 2002, Export of l-isoleucine from Corynebacterium glutamicum: a two-gene-encoded member of a new translocator family, J. Bacteriol., 184, 3947, 10.1128/JB.184.14.3947-3956.2002 Kim, 2004, Identification and characterization of glxR, a gene involved in regulation of glyoxylate bypass in Corynebacterium glutamicum, J. Bacteriol., 186, 3453, 10.1128/JB.186.11.3453-3460.2004 Kim, 2005, Functional analysis of sigH expression in Corynebacterium glutamicum, Biochem. Biophys. Res. Commun., 331, 1542, 10.1016/j.bbrc.2005.04.073 Kim, 2005, The whcE gene of Corynebacterium glutamicum is important for survival following heat and oxidative stress, Biochem. Biophys. Res. Commun., 337, 757, 10.1016/j.bbrc.2005.09.115 Kim, 2006, Organization and regulation of arginine biosynthesis genes in Corynebacterium glutamicum, 187 Kimura, 2002, Triggering mechanism of l-glutamate overproduction by DtsR1 in coryneform bacteria, J. Biosci. Bioeng., 94, 545, 10.1016/S1389-1723(02)80193-1 Kočan, 2006, Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response, J. Bacteriol., 188, 724, 10.1128/JB.188.2.724-732.2006 Koch, 2005, The transcriptional regulator SsuR activates expression of the Corynebacterium glutamicum sulphonate utilization genes in the absence of sulphate, Mol. Microbiol., 58, 480, 10.1111/j.1365-2958.2005.04836.x Konstantinidis, 2004, Trends between gene content and genome size in prokaryotic species with larger genomes, Proc. Natl. Acad. Sci. USA, 101, 3160, 10.1073/pnas.0308653100 Krug, 2005, Identification of AcnR, a TetR-type repressor of the aconitase gene acn in Corynebacterium glutamicum, J. Biol. Chem., 280, 585, 10.1074/jbc.M408271200 Letek, 2006, Characterization and use of catabolite-repressed promoters from gluconate genes in Corynebacterium glutamicum, J. Bacteriol., 188, 409, 10.1128/JB.188.2.409-423.2006 Leuchtenberger, 2005, Biotechnological production of amino acids and derivatives: current status and prospects, Appl. Microbiol. Biotechnol., 69, 1, 10.1007/s00253-005-0155-y Lozada-Chávez, 2006, Bacterial regulatory networks are extremely flexible in evolution, Nucl. Acids Res., 34, 3434, 10.1093/nar/gkl423 Lucchini, 2001, Microarrays for microbiologists, Microbiology, 147, 1403, 10.1099/00221287-147-6-1403 Ma, 2004, Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach, BMC Bioinf., 5, 199, 10.1186/1471-2105-5-199 Ma, 2004, An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs, Nucl. Acids Res., 32, 6643, 10.1093/nar/gkh1009 Madan Babu, 2003, Evolution of transcription factors and the gene regulatory network in Escherichia coli, Nucl. Acids Res., 31, 1234, 10.1093/nar/gkg210 Mangan, 2003, Structure and function of the feed-forward loop network motif, Proc. Natl. Acad. Sci. USA, 100, 11980, 10.1073/pnas.2133841100 Marchler-Bauer, 2005, CDD: a conserved domain database for protein classification, Nucl. Acids Res., 33, D192, 10.1093/nar/gki069 Margulies, 2005, Genome sequencing in microfabricated high-density picolitre reactors, Nature, 437, 376, 10.1038/nature03959 Martínez-Antonio, 2003, Identifying global regulators in transcriptional regulatory networks in bacteria, Curr. Opin. Microbiol., 6, 482, 10.1016/j.mib.2003.09.002 Martínez-Antonio, 2006, Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli, Trends Microbiol., 14, 22, 10.1016/j.tim.2005.11.002 McHardy, 2003, Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum, J. Biotechnol., 104, 229, 10.1016/S0168-1656(03)00161-5 Merkens, 2005, Vanillate metabolism in Corynebacterium glutamicum, Curr. Microbiol., 51, 59, 10.1007/s00284-005-4531-8 Milano, 2004, The Mycobacterium tuberculosis Rv2358-furB operon is induced by zinc, Res. Microbiol., 155, 192, 10.1016/j.resmic.2003.11.009 Möker, 2004, Deletion of the genes encoding the MtrA–MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection, Mol. Microbiol., 54, 420, 10.1111/j.1365-2958.2004.04249.x Moon, 2005, Analyses of enzyme II gene mutants for sugar transport and heterologous expression of fructokinase gene in Corynebacterium glutamicum ATCC 13032, FEMS Microbiol. Lett., 244, 259, 10.1016/j.femsle.2005.01.053 Moreno-Campuzano, 2006, Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes—a genomic approach, BMC Genomics, 7, 147, 10.1186/1471-2164-7-147 Nikolskaya, 2002, A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family, Nucl. Acids Res., 30, 2453, 10.1093/nar/30.11.2453 Nishio, 2003, Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens, Genome Res., 13, 1572, 10.1101/gr.1285603 Oguiza, 1996, Multiple sigma factor genes in Brevibacterium lactofermentum: characterization of sigA and sigB, J. Bacteriol., 178, 550, 10.1128/jb.178.2.550-553.1996 Oguiza, 1997, Transcriptional analysis of the sigA and sigB genes of Brevibacterium lactofermentum, FEMS Microbiol. Lett., 153, 111, 10.1111/j.1574-6968.1997.tb10471.x Ordóñez, 2005, Analysis of genes involved in arsenic resistance in Corynebacterium glutamicum ATCC 13032, Appl. Environ. Microbiol., 71, 6206, 10.1128/AEM.71.10.6206-6215.2005 Pabo, 1992, Transcription factors: structural families and principles of DNA recognition, Annu. Rev. Biochem., 61, 1053, 10.1146/annurev.bi.61.070192.005201 Pátek, 2003, Promoters of Corynebacterium glutamicum, J. Biotechnol., 104, 311, 10.1016/S0168-1656(03)00155-X Pérez-Martín, 1994, Promoters responsive to DNA bending: a common theme in prokaryotic gene expression, Microbiol. Rev., 58, 268, 10.1128/MMBR.58.2.268-290.1994 Pérez-Rueda, 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12, Nucleic Acids Res., 28, 1838, 10.1093/nar/28.8.1838 Pérez-Rueda, 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea, Comput. Biol. Chem., 28, 341, 10.1016/j.compbiolchem.2004.09.004 Phadtare, 1999, Cold-shock response and cold-shock proteins, Curr. Opin. Microbiol., 2, 175, 10.1016/S1369-5274(99)80031-9 Ranea, 2004, Evolution of protein superfamilies and bacterial genome size, J. Mol. Biol., 336, 871, 10.1016/j.jmb.2003.12.044 Reed, 2003, Thirteen years of building constraint-based in silico models of Escherichia coli, J. Bacteriol., 185, 2692, 10.1128/JB.185.9.2692-2699.2003 Resendis-Antonio, 2005, Modular analysis of the transcriptional regulatory network of E. coli, Trends Genet., 21, 16, 10.1016/j.tig.2004.11.010 Rey, 2003, The putative transcriptional repressor McbR, member of the TetR-family, is involved in the regulation of the metabolic network directing the synthesis of sulfur containing amino acids in Corynebacterium glutamicum, J. Biotechnol., 103, 51, 10.1016/S0168-1656(03)00073-7 Rey, 2005, The McbR repressor modulated by the effector substance S-adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism of Corynebacterium glutamicum ATCC 13032, Mol. Microbiol., 56, 871, 10.1111/j.1365-2958.2005.04586.x Rice, 2005, Reconstructing biological networks using conditional correlation analysis, Bioinformatics, 21, 765, 10.1093/bioinformatics/bti064 Rodionov, 2005, Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling, Trends Genet., 21, 385, 10.1016/j.tig.2005.05.011 Rückert, C., Koch, D., Rey, A., Pühler, A., Kalinowski, J., 2006. The transcriptional activator CysR of Corynebacterium glutamicum and its regulon. In: 2nd European Conference on Prokaryotic Genomes. Dechema e.V., Frankfurt am Main, p. 80. Shen, 2005, Genomic analysis and identification of catabolic pathways for aromatic compounds in Corynebacterium glutamicum, Microbes Environ., 20, 160, 10.1264/jsme2.20.160 Shen, 2005, Functional identification of novel genes involved in the glutathione-independent gentisate pathway in Corynebacterium glutamicum, Appl. Environ. Microbiol., 71, 3442, 10.1128/AEM.71.7.3442-3452.2005 Shen-Orr, 2002, Network motifs in the transcriptional regulation network of Escherichia coli, Nat. Genet., 31, 64, 10.1038/ng881 Silberbach, 2006, Application of global analysis techniques to Corynebacterium glutamicum: new insights into nitrogen regulation, J. Biotechnol., 126, 101, 10.1016/j.jbiotec.2006.03.039 Soliveri, 2000, Multiple paralogous genes related to the Streptomyces coelicolor developmental regulatory gene whiB are present in Streptomyces and other actinomycetes, Microbiology, 146, 333, 10.1099/00221287-146-2-333 Song, 2003, RshA, an anti-sigma factor that regulates the activity of the mycobacterial stress response sigma factor SigH, Mol. Microbiol., 50, 949, 10.1046/j.1365-2958.2003.03739.x Stock, 2000, Two-component signal transduction, Annu. Rev. Biochem., 69, 183, 10.1146/annurev.biochem.69.1.183 Stormo, 2002, Mining genome databases to identify and understand new gene regulatory systems, Curr. Opin. Microbiol., 5, 149, 10.1016/S1369-5274(02)00309-0 Switzer, 1999, Regulation of the Bacillus subtilis pyrimidine biosynthetic operon by transcriptional attenuation: control of gene expression by an mRNA-binding protein, Prog. Nucl. Acid Res. Mol. Biol., 62, 329, 10.1016/S0079-6603(08)60512-7 Tauch, 2005, Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora, J. Bacteriol., 187, 4671, 10.1128/JB.187.13.4671-4682.2005 Tauch, 2006, Ultrafast de novo sequencing of Corynebacterium urealyticum using the Genome Sequencer 20 System, Biochemica, 4, 4 Teichmann, 2004, Gene regulatory network growth by duplication, Nat. Genet., 36, 492, 10.1038/ng1340 Tompa, 2005, Assessing computational tools for the discovery of transcription factor binding sites, Nat. Biotechnol., 23, 137, 10.1038/nbt1053 van Nimwegen, 2003, Scaling laws in the functional content of genomes, Trends Genet., 19, 479, 10.1016/S0168-9525(03)00203-8 Vrljic, 1996, A new type of transporter with a new type of cellular function: l-lysine export from Corynebacterium glutamicum, Mol. Microbiol., 22, 815, 10.1046/j.1365-2958.1996.01527.x Wang, 2004, The sufR gene (sll0088 in Synechocystis sp. strain PCC 6803) functions as a repressor of the sufBCDS operon in iron-sulfur cluster biogenesis in cyanobacteria, J. Bacteriol., 186, 956, 10.1128/JB.186.4.956-967.2004 Wendisch, 2003, Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays, J. Biotechnol., 104, 273, 10.1016/S0168-1656(03)00147-0 Wennerhold, 2006, The DtxR regulon of Corynebacterium glutamicum, J. Bacteriol., 188, 2907, 10.1128/JB.188.8.2907-2918.2006 Wennerhold, 2005, The AraC-type regulator RipA represses aconitase and other iron proteins from Corynebacterium under iron limitation and is itself repressed by DtxR, J. Biol. Chem., 280, 40500, 10.1074/jbc.M508693200 Wösten, 1998, Eubacterial sigma-factors, FEMS Microbiol. Rev., 22, 127, 10.1016/S0168-6445(98)00011-4 Yu, 2003, Genomic analysis of gene expression relationships in transcriptional regulatory networks, Trends Genet., 19, 422, 10.1016/S0168-9525(03)00175-6