Reprogramming of escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Trotter, Eleanor W ^a   Rolfe, Matthew D ^a   Hounslow, Andrea M ^a   Craven, C Jeremy ^a   Williamson, Michael P ^a   Sanguinetti, Guido ^b   Poole, Robert K ^a   Green, Jeffrey ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PYRUVATE DEHYDROGENASE COMPLEX; ESCHERICHIA COLI PROTEIN; FNR PROTEIN, E COLI; IRON SULFUR PROTEIN; MESSENGER RNA; OXYGEN; PDHR PROTEIN, E COLI; PYRUVIC ACID; REPRESSOR PROTEIN; TRANSCRIPTOME;

ANAEROBIC METABOLISM; ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIUM CULTURE; BIOMASS PRODUCTION; CONTROLLED STUDY; ESCHERICHIA COLI K 12; GENE EXPRESSION; METABOLOMICS; OXYGEN CONSUMPTION; STEADY STATE; ADAPTATION; AEROBIC METABOLISM; ANAEROBIC GROWTH; BIOREACTOR; CULTURE TECHNIQUE; DRUG EFFECT; ENVIRONMENT; FERMENTATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METABOLOME; TIME;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI K12;

ADAPTATION, PHYSIOLOGICAL; AEROBIOSIS; ANAEROBIOSIS; BIOREACTORS; CULTURE TECHNIQUES; ENVIRONMENT; ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; FERMENTATION; IRON-SULFUR PROTEINS; METABOLOME; OXYGEN; PYRUVIC ACID; REPRESSOR PROTEINS; RNA, MESSENGER; TIME FACTORS; TRANSCRIPTOME;

EID: 80053187971     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025501     Document Type: Article

References (25)

1. Guest JR, Green J, Irvine AS, Spiro S, (1996) The FNR modulon and FNR-regulated gene expression. In: Lin ECC, Lynch AS, editors. Regulation of Gene Expression in Escherichia coli Austin, Texas RG Landes & Co pp. 317-342.
2. Sawers G, (1999) The aerobic/anaerobic interface. Curr Opin Microbiol 2: 181-187.
3. Unden G, Bongaerts J, (1997) Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation. Biochim Biophys Acta 1320: 217-234.
4. Gennis RB, Stewart V, (1996) Respiration. In: Neidhardt FC, editors. Escherichia coli and Salmonella Cellular and Molecular Biology. Volume 1. 2nd edition Washington DC ASM Press pp. 217-261.
5. Bock A, Sawers G, (1996) Fermentation. In: Neidhardt FC, editors. Escherichia coli and Salmonella Cellular and Molecular Biology. Volume 1. 2nd edition Washington DC ASM Press pp. 262-282.
6. Quail MA, Guest JR, (1995) Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli. Mol Microbiol 15: 519-529.
7. Wyborn NR, Messenger SL, Henderson RA, Sawers G, Roberts RE, et al. (2002) Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products. Microbiology 148: 1015-1026.
8. Ogasawara H, Ishida Y, Yamada K, Yamamoto K, Ishihama A, (2007) PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory transport system of Escherichia coli. J Bacteriol 189: 5534-5541.
9. Green J, Paget MS, (2004) Bacterial redox sensors. Nat Rev Microbiol 2: 954-966.
10. Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR, (2005) Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187: 135-1160.
11. Marshall FA, Messenger SL, Wyborn NR, Guest JR, Wing H, et al. (2001) A novel promoter architecture for microaerobic activitation by the anaerobic transcription factor FNR. Mol Microbiol 39: 747-753.
12. Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, et al. (2003) Global gene expression profiling in Escherichia coli K12: the effects of oxygen availability and FNR. J Biol Chem 278: 29837-29855.
13. Alexeeva S, Hellingwerf KJ, Teixeira de Mattos MJ, (2002) Quantitative assessment of oxygen availability: perceived aerobiosis and its effect on flux distribution in the respiratory chain of Escherichia coli. J Bacteriol 184: 1402-1406.
14. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO, (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
15. Partridge JD, Scott C, Tang Y, Poole RK, Green J, (2006) Escherichia coli transcriptome dynamics during the transition from anaerobic to aerobic conditions. J Biol Chem 281: 27806-27815.
16. Wagner AF, Schultz S, Bomke J, Pils T, Knappe J, (2001) YfiD of Escherichia coli YO61 of bacteriophage T4 as autonomous glycyl radical cofactors reconstituting the catalytic center of oxygen-fragmented pyruvate formate-lyase. Biochim Biophys Res Commun 285: 456-462.
17. Keseler IM, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, et al. (2009) EcoCyc: a comprehensive view of Escherichia coli biology. Nucl Acids Res 37: D464-470.
18. Taymaz-Nikerel H, Borujeni AE, Veheijan PJT, Heijen JJ, van Gulik WM, (2010) Genome-derived minimal metabolic models for Escherichia coli MG1655 with essential in vivo respiratory ATP stoichiometry. Biotechnol Bioeng 107: 369-381.
19. Rolfe MD, Ter Beek A, Graham AI, Trotter EW, Asif HA, et al. (2011) Transcript profiling and inference of Escherichia coli K-12 ArcA activity across the range of physiologically relevant oxygen concentrations. J Biol Chem 286: 10147-10154.
20. Asif HMS, Rolfe MD, Green J, Lawrence ND, Rattray M, et al. (2010) TFinfer: A tool for probabilistic inference of transcription factor activities. Bioinformatics 26: 2635-2636.
21. Partridge JD, Sanguinetti G, Dibden DP, Roberts RE, Poole RK, et al. (2007) Transition of Escherichia coli from aerobic to micro-aerobic conditions involves fast and slow reacting regulatory components. J Biol Chem 282: 11230-11237.
22. Evans CGT, Herbert D, Tempest DW, (1970) The continuous cultivation of micro-organisms. Methods Microbiol 2: 278-327.
23. Kessler D, Herth W, Knappe J, (1992) Ultrastructure and pyruvate formate-lyase quenching property of the multi-meric AdhE protein of Escherichia coli. J Biol Chem 267: 18073-18079.
24. Reyes-Ramirez F, Sawers RG, (2006) Aerobic activation of transcription of the anaerobically inducible Escherichia coli focA-pfl operon by fumarate nitrate regulator. FEMS Microbiol Lett 255: 262-267.
25. Laemmli UK, (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.