More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Göhler, Anna Katharina ^a   Kökpinar, Öznur ^b,c   Schmidt Heck, Wolfgang ^d   Geffers, Robert ^b   Guthke, Reinhard ^d   Rinas, Ursula ^b,c   Schuster, Stefan ^e   Jahreis, Knut ^a   Kaleta, Christoph ^e  

^a UNIVERSITY OF OSNABRÜCK   (Germany)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^c LEIBNIZ UNIVERSITY HANNOVER   (Germany)

^d HANS KNÖLL INSTITUTE   (Germany)

^e FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

ESCHERICHIA COLI PROTEIN; PDHR PROTEIN, E COLI; REPRESSOR PROTEIN;

ARTICLE; BACTERIAL GENE; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; METHODOLOGY; PHYSIOLOGY; REGULON; SYSTEMS BIOLOGY;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; GENES, BACTERIAL; METABOLIC NETWORKS AND PATHWAYS; REGULON; REPRESSOR PROTEINS; SYSTEMS BIOLOGY;

EID: 84856228299     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-197     Document Type: Article

References (37)

1. Quail MA, Guest JR. Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli. Mol Microbiol 1995, 15(3):519-529.
2. Quail MA, Haydon DJ, Guest JR. The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex. Mol Microbiol 1994, 12(1):95-104.
3. Haydon DJ, Guest JR. A new family of bacterial regulatory proteins. FEMS Microbiol Lett 1991, 63(2-3):291-295.
4. Ogasawara H, Ishida Y, Yamada K, Yamamoto K, Ishihama A. PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli. J Bacteriol 2007, 189(15):5534-5541.
5. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007, 5(1):e8.
6. Blankenhorn D, Phillips J, Slonczewski JL. Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis. J Bacteriol 1999, 181(7):2209-2216.
7. Kaleta C, Göhler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S. Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis. BMC Syst Biol 2010, 4:116.
8. Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res 2008, (36 Database):D866-870.
9. Freyre-Gonzalez JA, Alonso-Pavon JA, Trevino-Quintanilla LG, Collado-Vides J. Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach. Genome Biol 2008, 9(10):R154.
10. Vicente M, Gomez MJ, Ayala JA. Regulation of transcription of cell division genes in the Escherichia coli dcw cluster. Cell Mol Life Sci 1998, 54(4):317-324.
11. Pao SS, Paulsen IT, Saier MH. Major facilitator superfamily. Microbiol Mol Biol Rev 1998, 62(1):1-34.
12. Janga SC, Salgado H, Martinez-Antonio A. Transcriptional regulation shapes the organization of genes on bacterial chromosomes. Nucleic Acids Res 2009, 37(11):3680-3688.
13. Pellicer MT, Fernandez C, Badia J, Aguilar J, Lin EC, Baldom L. Cross-induction of glc and ace operons of Escherichia coli attributable to pathway intersection. Characterization of the glc promoter. J Biol Chem 1999, 274(3):1745-1752.
14. Kornberg HL, Krebs HA. Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle. Nature 1957, 179(4568):988-991.
15. Kornberg HL, Lascelles J. The formation of isocitratase by the Athiorhodaceae. J Gen Microbiol 1960, 23:511-517.
16. Kornberg HL, Phizackerley PJ, Sadler JR. The metabolism of C2 compounds in micro-organisms. 5. Biosynthesis of cell materials from acetate in Escherichia coli. Biochem J 1960, 77:438-445.
17. Chao YP, Patnaik R, Roof WD, Young RF, Liao JC. Control of gluconeogenic growth by pps and pck in Escherichia coli. J Bacteriol 1993, 175(21):6939-6944.
18. d'Ari R. The SOS system. Biochimie 1985, 67(3-4):343-347.
19. Giese KC, Michalowski CB, Little JW. RecA-dependent cleavage of LexA dimers. J Mol Biol 2008, 377(1):148-161.
20. Bi EF, Lutkenhaus J. FtsZ ring structure associated with division in Escherichia coli. Nature 1991, 354(6349):161-164.
21. Vicente M, Kushner SR, Garrido T, Aldea M. The role of the 'gearbox' in the transcription of essential genes. Mol Microbiol 1991, 5(9):2085-2091.
22. Kotte O, Zaugg JB, Heinemann M. Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 2010, 6:355.
23. Zeppenfeld T, Larisch C, Lengeler JW, Jahreis K. Glucose transporter mutants of Escherichia coli K-12 with changes in substrate recognition of IICB(Glc) and induction behavior of the ptsG gene. J Bacteriol 2000, 182(16):4443-4452.
24. Tanaka S, Lerner SA, Lin EC. Replacement of a phosphoenolpyruvate-dependent phosphotransferase by a nicotinamide adenine dinucleotide-linked dehydrogenase for the utilization of mannitol. J Bacteriol 1967, 93(2):642-648.
25. Morrison TB, Parkinson JS. Liberation of an interaction domain from the phosphotransfer region of CheA, a signaling kinase of Escherichia coli. Proc Natl Acad Sci USA 1994, 91(12):5485-5489.
26. Yanisch-Perron C, Vieira J, Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 1985, 33(1):103-119.
27. Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 2000, 97(12):6640-6645.
28. Arber W. Transduction of chromosomal genes and episomes in Escherichia coli. Virology 1960, 11:273-288.
29. Lengeler J. Studies on the glucose effect in the synthesis of the galactose enzyme of Escherichia coli. Z Vererbungsl 1966, 98(3):203-229.
30. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80.
31. Sammon JW. A nonlinear mapping for data structure analysis. IEEE Transactions on Computers 1969, 18:401-409.
32. Venables WN, Ripley BD. Modern Applied Statistics with S. 2002, New York: Springer, 4.
33. Fraley C, Raftery AE. MCLUST Version 3 for R: Normal Mixture Modeling and Model-based Clustering. Technical Report 504 2006, Department of Statistics, University of Washington.
34. Bembom O, Keles S, van der Laan MJ. Supervised detection of conserved motifs in DNA sequences with cosmo. Stat Appl Genet Mol Biol 2007, 6:Article8.
35. McCue L, Thompson W, Carmack C, Ryan MP, Liu JS, Derbyshire V, Lawrence CE. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res 2001, 29(3):774-782.
36. McCue LA, Thompson W, Carmack CS, Lawrence CE. Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res 2002, 12(10):1523-1532.
37. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, et al. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 2011, (39 Database):D583-590.