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Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions

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Bioreactor Engineering Research and Industrial Applications I

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 155))

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Abbreviations

CIT:

Citrate

E4P:

Erythrose-4-phosphate

FBP:

Fructose-1,6-bisphosphate

F1P:

Fructose 1-phosphate

F6P:

Fructose-6-phosphate

G6P:

Glucose-6-phosphate

GAP:

Glyceraldehyde-3-phosphate

GOX:

Glyoxylate

ICI:

Isocitrate

KDPG:

2-keto-3-deoxy-6-phosphogluconate

αKG:

α-ketoglutarate

MAL:

Malate

OAA:

Oxaloacetate

PEP:

Phosphoenolpyruvate

6PG:

6-phosphogluconate

PYR:

Pyruvate

Ack:

Acetate kinase

Acs:

Acetyl-coenzyme A synthetase

Adk:

Adenylate kinase

CS:

Citrate synthase

Cya:

Adenylate cyclase

EI:

Enzyme I

EII:

Enzyme II

Fdp:

Fructose bisphosphatase

FDH:

Formate dehydrogenase

Fhl:

Formate hydrogen lyase

GAD:

Glutamate decarboxylase

G6PDH:

Glucose-6-phosphate dehydrogenase

GAPDH:

Glyceraldehyde-3-phosphate dehydrogenase

GOGAT:

Glutamate synthase

GS:

Glutamine synthetase

HPr:

Histidine-phosphorylatable protein

Hyc:

Hydrogenase

ICDH:

Isocitrate dehydrogenase

Icl:

Isocitrate lyase

KGDH:

α-ketoglutaric acid dehydrogenase

LDH:

Lactate dehydrogenase

Mez:

Malic enzyme

MS:

Malate synthase

NOX:

NADH oxidase

Pck:

Phosphoenolpyruvate carboxykinase

PDH:

Pyruvate dehydrogenase

Pfk:

Phosphofructokinase

PGDH:

6-phosphogluconate dehydrogenase

Pgi:

Phosphoglucose isomerase

Pox:

Pyruvate oxidase

Ppc:

Phosphoenolpyruvate carboxylase

Pps:

Phosphoenolpyruvate synthase

Pta:

Phosphotransacetylase

Pyk:

Pyruvate kinase

SOD:

Superoxide dismutase

ED pathway:

Entner–Doudoroff pathway

EMP pathway:

Embden–Meyerhof–Parnas pathway

PMF:

Proton motive force

PP pathway:

Pentose phosphate pathway

PTS:

Phosphotransferase system

ROS:

Reactive oxygen species

TCA cycle:

Tricarboxylic acid cycle

References

Introduction

  1. Jone RG, Thompson CB (2009) Tumor suppressors and cell metabolism: a recipe for cancer growth. Genes Dev 23:537–548

    Article  CAS  Google Scholar 

  2. Hsu PP, Sabatini DM (2008) Cancer cell metabolism: Warburg and beyond. Cell 134:703–707

    Article  CAS  Google Scholar 

  3. Kroemer G, Pouyssegur J (2008) Tumor cell metabolism: cancer’s Achilles’ heel. Cancer Cell 13:472–482

    Article  CAS  Google Scholar 

  4. Folger O et al (2011) Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol 7:501

    Article  Google Scholar 

  5. McInerney MJ, Sieber JR, Gunsalus RP (2009) Syntrophy in anaerobic global carbon cycles. Curr Opin Biotechnol 20:623–632

    Article  CAS  Google Scholar 

  6. Dolfing J, Jiang B, Henstra AM, Stams AJ, Plugge CM (2008) Syntrophic growth on formate: a new microbial niche in anoxic environments. Appl Environ Microbiol 74:6126–6131

    Article  CAS  Google Scholar 

  7. Lin LH et al (2006) Long-term sustainability of a high-energy, low-diversity crustal biome. Science 314:479–482

    Article  CAS  Google Scholar 

  8. Peralta-Yahya PP, Zhang F, del Cardayre SB, Keasling JD (2012) Microbial engineering for the production of advanced biofuels. Nature 488:320–328

    Article  CAS  Google Scholar 

  9. Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–90

    Article  CAS  Google Scholar 

  10. Yim H et al (2011) Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7:445–452

    Article  CAS  Google Scholar 

  11. Dellomonaco C, Clomburg JM, Miller EN, Gonzalez R (2011) Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature 476:355–359

    Article  CAS  Google Scholar 

  12. Bond-Watts BB, Bellerose RJ, Chang MC (2011) Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat Chem Biol 7:222–227

    Article  CAS  Google Scholar 

  13. Shen CR et al (2011) Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl Environ Microbiol 77:2905–2915

    Article  CAS  Google Scholar 

  14. Keasling JD (2010) Manufacturing molecules through metabolic engineering. Science 330:1355–1358

    Article  CAS  Google Scholar 

  15. Shimizu K (2014) Biofuels and biochemicals production by microbes. NOVA Publishing Co., USA

    Google Scholar 

  16. Bar-Even A, Flamholz A, Noor E, Mil R (2012) Rethinking of glycolysis: on the biochemical logic of metabolic pathways. Nat Chem Biol 8:509–517

    Article  CAS  Google Scholar 

  17. Flamholz A, Noor E, Bar-Even A, Liebermeister W, Milo R (2013) Glycolytic strategy as a tradeoff between energy yield and protein cost. PNAS USA 110(24):10039–10044

    Article  Google Scholar 

  18. Shimizu K (2013) Metabolic regulation of a bacterial cell system with emphasis on Escherichia coli metabolism. ISRN Biochemistry, doi:10.1155/2013/645983 (Article ID 645983)

  19. Shimizu K (2014) Metabolic regulation of Escherichia coli in response to nutrient limitation and environmental stress conditions. Metabolites 4:1–35

    Article  CAS  Google Scholar 

  20. Chubukov V, Gerosa L, Kochanowski K, Sauer U (2014) Coordination of microbial metabolism. Nat Rev 12:327–340

    CAS  Google Scholar 

Transport of Nutrient and Waste

  1. de la Cruz MA, Fernandez-Mora M, Guadarrama C et al (2007) LeuO antagonizes H-NS and StpA-dependent repression in Salmonella enterica ompS1. Mol Microbiol 66(3):727–743

    Article  CAS  Google Scholar 

  2. Nikaido H (2003) Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 67(4):593–656

    Article  CAS  Google Scholar 

  3. Nikaido H, Vaara M (1985) Molecular basis of bacterial outer membrane permeability. Microbiol Rev 49(1):1–32

    CAS  Google Scholar 

  4. Death A, Ferenci T (1994) Between feast and famine: endogenous inducer synthesis in the adaptation of Escherichia coli to growth with limiting carbohydrates. J Bacteriol 176(16):5101–5107

    CAS  Google Scholar 

  5. Gunnewijk MGW, van den Bogaard PTC, Veenhoff LM et al (2001) Hierarchical control versus autoregulation of carbohydrate utilization in bacteria. J Mol Microbiol Biotechnol 3(3):401–413

    CAS  Google Scholar 

  6. Poolman B, Konings WN (1993) Secondary solute transport in bacteria. Biochim Biophy Acta 1183(1):5–39

    Article  CAS  Google Scholar 

  7. Deutscher J, Francke C, Postoma PW (2006) How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 70(4):939–1031

    Article  CAS  Google Scholar 

  8. Palm K, Luthman K, Ros J, Grasjo J, Artursson P (1999) Effect of molecular charge on intestinal epithelial drug transport: pH-dependent transport of cationic drugs. J Pharmacol Exp Ther 291:435–443

    CAS  Google Scholar 

  9. Chakrabarti AC, Deamer DW (1992) Permeability of lipid bilayers to amino acids and phosphate. Biochim Biophys Acta 1111:171–177

    Article  CAS  Google Scholar 

  10. Chakrabarti AC, Deamer DW (1994) Permeation of membranes by the neutral form of amino acids and peptides: relevance to the origin of peptide translocation. J Mol Evol 39:1–5

    Google Scholar 

  11. Finkelstein A (1976) Water and nonelectrolyte permeability of lipid bilayer membranes. J Gen Physiol 68:127–135

    Article  CAS  Google Scholar 

  12. Winiwarter S et al (1998) Correlation of human jejunal permeability (in vivo) of drugs with experimentally and theoretically derived parameters. A multivariate data analysis approach. J Med Chem 41:4939–4949

    Article  CAS  Google Scholar 

  13. Davis BD (1958) On the importance of being ionized. Arch Biochem Biophys 78:497–509

    Article  CAS  Google Scholar 

  14. Westheimer FH (1987) Why nature chose phosphates. Science 235:1173–1178

    Article  CAS  Google Scholar 

PTS and Carbon Catabolite Regulation

  1. Gorke B, Stulke J (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6:613–624

    Article  CAS  Google Scholar 

  2. Inada T, Kimata K, Aiba H (1996) Genes Cells 1:293–301

    Article  CAS  Google Scholar 

  3. Gosset G (2005) Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate: sugar phosphotransferase system. Microb Cell Fact 4:14

    Article  CAS  Google Scholar 

  4. Hogema BM, Arents JC, Bader R, Eijkemans K et al (1998) Inducer exclusion in Escherichia coli by non-PTS substrates: the role of the PEP to pyruvate ratio in deter-mining the phosphorylation state of enzyme IIAGlc. Mol Microbiol 30:487–498

    Article  CAS  Google Scholar 

  5. Bettenbrock K, Sauter T, Jahreis K, Klemling A, Lengeler JW, Gilles ED (2007) Correlation be-tween growth rates, EIIACrr phosphorylation, and intra-cellular cyclic AMP levels in Escherichia coli K-12. J Bacteriol 189:6891–6900

    Article  CAS  Google Scholar 

  6. Schaub J, Reuss M (2008) In vivo dynamics of glycolysis in E. coli shows need for gowth-rate dependent metabolome analysis. Biotechnol Prog 24:1402–1407

    Article  CAS  Google Scholar 

  7. Kochanowski K, Volkmer B, Gerosa L, van Rijsewijk HBR, Schmidt A, Heinemann M (2013) Functioning of a metabolic flux sensor in Escherichia coli. PNAS USA 110:1130–1135

    Article  Google Scholar 

  8. Kotte O, Zaugg JB, Heinemann M (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 6:355

    Article  CAS  Google Scholar 

  9. Huberts DH, Niebel B, Heinemann M (2012) A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 12(2):118–128

    Article  CAS  Google Scholar 

  10. Kremling A, Bettenbrock K, Gilles ED (2008) A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake. Bioinformatics 24:704–710

    Article  CAS  Google Scholar 

  11. Matsuoka Y, Shimizu K (2013) Catabolite regulation analysis of Escherichia coli for acetate overflow mechanism and co-consumption of multiple sugars based on systems biology approach using computer simulation. J Biotechnol 168:155–173

    Article  CAS  Google Scholar 

  12. Shimada T, Yamamoto K, Ishihama A (2011) Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. J Bacteriol 193(3):649–659

    Article  CAS  Google Scholar 

  13. Saier MH Jr, Ramseier TM (1996) The catabolite repressor/activator (Cra) protein of enteric bacteria. J Bacteriol 178:3411–3417

    CAS  Google Scholar 

  14. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316:593–597

    Article  CAS  Google Scholar 

  15. Valgepea K, Adamberg K, Nahku R, Lahtvee PJ, Arike L, Vilu R (2010) Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase. BMC Syst Biol 4:166

    Article  CAS  Google Scholar 

  16. Yao R, Hirose Y, Sarkar D, Nakahigashi K, Ye Q, Shimizu K (2011) Catabolic regulation analysis of Escherichia coli and its crp, mlc, mgsA, pgi and ptsG mutants. Microb Cell Fact 10:67

    Article  CAS  Google Scholar 

  17. Wolf RE, Prather DM, Shea FM (1979) Growth-rate dependent alteration of 6-phosphogluconate dehydrogenase and glucose 6-phosphate dehydrogenase levels in Escherichia coli K-12. J Bacteriol 139:1093–1096

    CAS  Google Scholar 

Acetate Overflow Metabolism and Reduction of Acetate Formation in E. coli

  1. Wong MS, Wu S, Causey TB, Bennet GN, San KY (2008) Reduction of acetate accumulation in Escherichia coli cultures for increased recombinant protein production. Metab Eng 10:97–108

    Article  CAS  Google Scholar 

  2. Russel JB et al (2007) The energy spilling reactions of bacteria and other organisms. J Mol Microbiol Biotechnol 13:1–11

    Article  CAS  Google Scholar 

  3. Valgepea K, Adamberg K, Vilu R (2011) Decrease of energy spilling in Escherichia coli continuous cultures with rising specific growth rate and carbon wasting. BMC Syst Biol 5:106

    Article  CAS  Google Scholar 

  4. Kayser A, Weber J, Hecht V, Rinas U (2005) Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate dependent metabolic efficiency at steady state. Microbiology 151:693–706

    Article  CAS  Google Scholar 

  5. Wolfe AJ (2005) The acetate switch. Microbiol Mol Biol Rev 69:12–50

    Article  CAS  Google Scholar 

  6. Majewski RA, Domach MM (1990) Simple constrained-optimization view of acetate overflow in Escherichia coli. Biotech Bioeng 35:732–738

    Article  CAS  Google Scholar 

  7. Yang C, Hua Q, Baba T, Mori H et al (2003) Analysis of E. coli anaplerotic metabolism and its regulation mechanism from the metabolic responses to alter dilution rates and pck knockout. Biotechnol Bioeng 84:129–144

    Article  CAS  Google Scholar 

  8. Lee SY (1996) High cell-density cultivation of Escherichia coli. Trends Biotechnol 14:98–105

    Article  CAS  Google Scholar 

  9. Hardiman T, Lemuth K, Keller MA, Reuss M, Siemann-Herzberg M (2007) Topology of the global regulatory network of carbon limitation in Escherichia coli. J Biotechnol 132:359–374

    Article  CAS  Google Scholar 

  10. Konstantinov K, Kishimoto M, Seki T, Yoshida T (1990) A balanced DO-stat and its application to the control of acetic acid excretion by recombinant Eshcherichia coli. Biotechnol Bioeng 36(7):750–758

    Article  CAS  Google Scholar 

  11. Ferreira AR, Ataide F, von Stosch M, Jias JML et al (2012) Application of adaptive DO-stat feeding control to Pichia pastoris X33 cultures expressing a single chain antibody fragment (scFv). Bioprocess Biosyst Eng 35(9):1603–1614

    Article  CAS  Google Scholar 

  12. Li K-T, Liu D-H, Chu J, Wang Y-H et al (2008) An efficient and simplified pH-stat control strategy for the industrial fermentation of vitamin B12 by Pseudomonas denitrificans. Bioprocess Byosyst Eng 31:605–610

    Article  CAS  Google Scholar 

  13. Pirt SJ (1982) Maintenance energy: a general model for energy-limited and energy-sufficient growth. Arch Microbiol 133:300–302

    Article  CAS  Google Scholar 

  14. Hewitt, CJ, Caron NV, Nienow AW, McFarlane CM (1999) Use of multi-staining flow cytometry to characterise the physiological state of Escherichia coli W3110 in high cell density fed-batch cultures. Biotechnol Bioeng 63:705–711

    Google Scholar 

  15. Hewitt CJ, Caron NV, Axelsson B, McFarlane CM, Nienow AW (2000) Studies related to the scale-up of high-cell-density E. coli fed-batch fermentations using multiparameter flow cytometry: effect of a changing microenvironment with respect to glucose and dissolved oxygen concentration. Biotechnol Bioeng 70(4):381–390

    Google Scholar 

  16. Hewitt CJ, Nebe-Von-Caron G (2001) An industrial application of multiparameter flow cytometry: Assessment of cell physiological state and its application to the study of microbial fermentations. Cytometry 44:179–187

    Article  CAS  Google Scholar 

  17. Peebo K, Valgepea K, Nahku R, Riis G, Õun M, Adamberg K, Vilu R (2014) Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli. Appl Microbiol Biotechnol, doi: 10.1007/s00253-014-5613-y

Catabolite Regulation for the Uptake of Various Carbon Sources

  1. Vasudevan P, Briggs M (2008) Biodiesel production–current state of the art and challenges. J Ind Microbiol Biotechnol 35:421–430

    Article  CAS  Google Scholar 

  2. Dharmadi Y, Murarka A, Gonzalez R (2006) Anaerobic fermentation of glycerol by Escherichia coli: a new platform for metabolic engineering. Biotechnol Bioeng 94:821–829

    Article  CAS  Google Scholar 

  3. Clomburg JM, Gonzalez Ramon (2013) Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicals. Trends Biotechnol 31(1):20–28

    Article  CAS  Google Scholar 

  4. Almeida JRM, Fávaro LCL, Betania F, Quirino BF (2012) Biodiesel biorefinery: opportunities and challenges for microbial production of fuels and chemicals from glycerol waste. Biotechnol Biofuels 5:48

    Article  CAS  Google Scholar 

  5. Martínez-Gómez K, Flores N, Castañeda HM, Martínez-Batallar G, Hernández-Chávez G, Ramírez OT, Gosset G, Encarnación S, Bolivar F (2012) New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol. Micob Cell Fact 11:46

    Article  CAS  Google Scholar 

  6. Peng L, Shimizu K (2003) Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement. Appl Microbiol Biotechnol 61:163–178

    Article  CAS  Google Scholar 

  7. Oh MK, Liao JC (2000) Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol Prog 16:278–286

    Article  CAS  Google Scholar 

  8. Applebee MK, Joyce AR, Conrad TM, Pettigrew DW, Palsson BO (2011) Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli. J Biol Chem 286(26):23150–23159

    Article  CAS  Google Scholar 

  9. Cheng K-K, Lee B-S, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson BO, Robert M (2014) Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun 5:3233

    Google Scholar 

  10. Kornberg HL (2001) Routes for fructose utilization by Escherichia coli. J Mol Microbiol Biotechnol 3:355–359

    CAS  Google Scholar 

  11. Yao R, Kurata H, Shimizu K (2013) Effect of cra gene mutation on the metabolism of Escherichia coli for a mixture of multiple carbon sources. Adv Biosci Biotechnol 4:477−486

    Google Scholar 

  12. Sarkar D, Shimizu K (2008) Effect of cra gene knockout together with other genes knockouts on the improvement of substrate consumption rate in Escherichia coli under microaerobic conditions. Biochem Eng J 42:224–228

    Article  CAS  Google Scholar 

  13. Sarkar D, Siddiquee KAZ, Arauzo-Bravo MJ, Oba T, Shimizu K (2008) Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli. Arch Microbiol 190:559–571

    Article  CAS  Google Scholar 

  14. Crasnier-Mednansky M, Park MC, Studley WK, Saier MH Jr (1997) Cra-mediated regulations of Escherichia coli adenylate cyclase. Microbiology 143:785–792

    Article  CAS  Google Scholar 

  15. Griffith JK, Baker ME, Rouch DA, Page MG, Skurray RA, Paulsen IT, Chater KF, Baldwin SA, Henderson PJ (1992) Membrane transport proteins: implications of sequence comparisons. Curr Opin Cell Biol 4:684–695

    Article  CAS  Google Scholar 

  16. Sumiya M, Davis EO, Packman LC, McDonald TP, Henderson PJ (1995) Molecular genetics of a receptor protein for D-xylose, encoded by the gene xylF, in Escherichia coli. Receptors Channels 3:117–128

    CAS  Google Scholar 

  17. Song S, Park C (1997) Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator. J Bacteriol 179:7025–7032

    CAS  Google Scholar 

  18. Hasona A, Kim Y, Healy FG, Ingram LO, Shanmugam KT (2004) Pyruvate formate lyase and acetate kinase are essential for anaerobic growth of Escherichia coli on xylose. J Bacteriol 186:7593–7600

    Article  CAS  Google Scholar 

  19. Novotny CP, Englesberg E (1966) The L-arabinose permease system in Escherichia coli B/r. Biochim Biophys Acta 117:217–230

    Article  CAS  Google Scholar 

  20. Schleif R (1969) An L-arabinose binding protein and arabinose permeation in Escherichia coli. J Mol Biol 46:185–196

    Article  CAS  Google Scholar 

  21. Doyle ME, Brown C, Hogg RW, Helling RB (1972) Induction of the ara operon of Escherichia coli B-r. J Bacteriol 110:56–65

    CAS  Google Scholar 

  22. Davidson CJ, Narang A, Surette MG (2010) Integration of transcriptional inputs at promoters of the arabinose catabolic pathway. BMC Syst Biol 4:75

    Article  CAS  Google Scholar 

  23. Madar D, Dekel E, Bren A, Alon U (2011) Negative auto-regulation increases the input dynamical-range of the arabinose system of Escherichia coli. BMC Syst Biol 5:111

    Article  Google Scholar 

  24. Desai TA, Rao CV (2010) Regulation of arabinose and xylose metabolism in Escherichia coli. Appl Environ Microbiol 76:1524–1532

    Article  CAS  Google Scholar 

  25. Groff D, Benke PI, Batth TS, Bokinsky G, Petzold CJ, Adams PD, Keasling JD (2012) Supplementation of intracellular XylR leads to co-utilization of hemicellulose sugars. Appl Environ Microbiol 78:2221–2229

    Article  CAS  Google Scholar 

Transition of the Metabolism during Batch Culture

  1. Toya Y, Ishii N, Nakahigashi K, Tomita M, Shimizu K (2010) 13C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol Prog 26:975–992

    CAS  Google Scholar 

  2. Schuetz R, Zamboni N, Zampieri M, Heinemann M et al (2012) Multidimensional optimality of microbial metabolism. Science 336:601–604

    Google Scholar 

  3. Enjalbert B, Letisse F, Portais J-C (2013) Physiological and molecular timing of the glucose to acetate transition in Escherichia coli. Metabolites 3:820–837

    Article  CAS  Google Scholar 

  4. Xu Y-F, Amador-Noguez D, Reaves ML, Feng XJ et al (2012) Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase. Nat Chem Biol 8:562–568

    Article  CAS  Google Scholar 

  5. Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181:6361–6370

    CAS  Google Scholar 

  6. Bradley MD, Beach MB, Jason de Koning AP, Pratt TS, Osuna R (2007) Effects of Fis on Escherichia coli gene expression during different growth stages. Microbiology 153:2922–2940

    Article  CAS  Google Scholar 

  7. Mallik P, Pratt TS, Beach MB, Bradley MD, Undamatla J, Osuna R (2004) Growth phase-dependent regulation and stringent control of fis are conserved processes in enteric bacteria and involve a single promoter (fis P) in Escherichia coli. J Bacteriol 186:122–135

    Article  CAS  Google Scholar 

  8. Mallik P, Paul BJ, Rutherford ST, Gourse RL, Osuna R (2006) DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J Bacteriol 188:5775–5782

    Article  CAS  Google Scholar 

  9. Paul BJ, Berkmen MB, Gourse RL (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. PNAS USA 102:7823–7828

    Article  CAS  Google Scholar 

  10. Ferenci T (2001) Hungry bacteria—definition and properties of a nutritional state. Environ Microbiol 3:605–611

    Article  CAS  Google Scholar 

  11. Braeken K, Moris M, Daniels R, Vanderleyden J, Michiels J (2006) New horizons for (p)ppGpp in bacterial and plant physiology. Trends Microbiol 14(1):45–54

    Article  CAS  Google Scholar 

  12. Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S (2004) Structural basis for transcription regulation by alarmone ppGpp. Cell 117:299–310

    Article  CAS  Google Scholar 

  13. Kanjee U, Ogata K, Houry WA (2012) Direct binding targets of the stringent response alarmone (p)ppGpp. Mol Micobiol 85(6):1029–1043

    Article  CAS  Google Scholar 

  14. Hengge-Aronis R (2002) Signal transduction and regulatory mechanisms involved in control of the σS (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 66:373–395

    Article  CAS  Google Scholar 

  15. Patten CL, Kirchhof MG, Schertzberg MR, Morton RA, Schellhorn HE (2004) Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12. Mol Genet Genom 272(5):580–591

    Article  CAS  Google Scholar 

  16. Jishage M, Kvint K, Shingler V, Nystrom T (2002) Regulation of σ factor competition by the alarmone ppGpp. Genes Dev 16:1260–1270

    Article  CAS  Google Scholar 

  17. Lacour S, Landini P (2004) σ S-dependent gene expression at the onset of stationary phase in Escherichia coli: function of σ s-dependent genes and identification of their promoter sequences. J of Bacteriol 186(21):7186–7195

    Article  CAS  Google Scholar 

  18. Vijayakumar SRV, Kirchhof MG, Patten CL, Schellhorn HE (2004) RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis. J of Bacteriol 186(24):8499–8507

    Article  CAS  Google Scholar 

  19. Rahman M, Shimizu K (2008) Altered acetate metabolism and biomass production in several Escherichia coli mutants lacking rpoS-dependent metabolic pathway genes. Mol BioSyst 4(2):160–169

    Article  CAS  Google Scholar 

  20. Rahman M, Hasan MM, Shimizu K (2008) Growth phase-dependent changes in the expression of global regulatory genes and associated metabolic pathways in Escherichia coli. Biotechnol Lett 30:853–860

    Article  CAS  Google Scholar 

  21. Llorens NJM, Tormo A, Martínez-García E (2010) Stationary phase in gram-negative bacteria. FEMS Microbiol Rev 34:476–495

    Article  CAS  Google Scholar 

  22. Desnues B, Cuny C, Gregori G, Dukan S, Aguilaniu H, Nyström T (2003) Differential oxidative damage and expression of stress defence regulons in culturable and non-culturable Escherichia coli cells. EMBO Rep 4:400–404

    Article  CAS  Google Scholar 

  23. Nagamitsu H, Murata M, Kosaka T, Kawaguchi J, Mori H, Yamada M (2013) Crucial roles of MicA and RybB as vital factors for σE-Dependent cell lysis in Escherichia coli long-term stationary phase. J Mol Microbiol Biotechnol 23:227–232

    Article  CAS  Google Scholar 

  24. Murata M, Noor R, Nagamitsu H, Tanaka S, Yamada M (2012) Novel pathway directed by sigma E to cause cell lysis in Escherichia coli. Genes Cells 17:234–247

    Article  CAS  Google Scholar 

  25. Noor R, Murata M, Yamada M (2009) Oxidative stress as a trigger for growth phase-specific sigma E-dependent cell lysis in Escherichia coli. J Mol Microbiol Biotechnol 17:177–187

    Article  CAS  Google Scholar 

Carbon Storage Regulation

  1. Yamamotoya T, Dose H, Tian Z, Faure A, Toya Y, Honma M, Igarashi K, Nakahigashi K, Soga T, Mori H, Matsuno H (2012) Glycogen is the primary source of glucose during the lag phase of E. coli proliferation. Biochim Biophys Acta 1824:1442–1448

    Article  CAS  Google Scholar 

  2. Timmermans J, van Melderen L (2010) Post-transcriptional global regulation by CsrA in bacteria. Cell Mol Life Sci 67(17):2897–2908

    Article  CAS  Google Scholar 

  3. Jonas K, Edwards AN, Ahmad I, Romeo T, Romling U, Melefors O (2010) Complex regulatory network encompassing the Csr, c-di-GMP and motility systems of Salmonella typhimurium. Environ Microbiol 12(2):524–540

    Article  CAS  Google Scholar 

  4. Yakhnin H, Pandit P, Petty TJ, Baker CS, Romeo T, Babitzke P (2007) CsrA of Bacillus subtilis regulates translation initiation of the gene encoding the flagellin protein (hag) by blocking ribosome binding. Mol Microbiol 64(6):1605–1620

    Article  CAS  Google Scholar 

  5. Romeo T, Vakulskas CA, Babitzke P (2013) Post-transcriptional regulation on a global scale: from and function of Csr/Rsm systems. Environ Microbiol 15(2):313–324

    Google Scholar 

  6. Dubey AK, Baker CS, Romeo T, Babitzke P (2005) RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction. RNA 11(10):1579–1587

    Article  CAS  Google Scholar 

  7. Suzuki K, Wang X, Weilbacher T et al (2002) Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli. J of Bacteriol 184(18):5130–5140

    Article  CAS  Google Scholar 

  8. Weilbacher T, Suzuki K, Dubey AK et al (2003) A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol Microbiol 48(3):657–670

    Article  CAS  Google Scholar 

  9. Baker CS, Morozov I, Suzuki K, Romeo T, Babitzke P (2002) CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli. Mol Microbiol 44(6):1599–1610

    Article  CAS  Google Scholar 

  10. Dong T, Schellhorn HE (2009) Control of RpoS in global gene expression of Escherichia coli in minimal media. Mol Genet Genomics 281:19–33

    Article  CAS  Google Scholar 

  11. Edwards AN, Patterson-Fortin LM, Vakulskas CA, Mercante JW, Potrykus K, Vinella D, Camacho MI, Fields JA, Thompson SA, Georgellis D et al (2011) Circuitry linking the Csr and stringent response global regulatory systems. Mol Microbiol 80:1561–1580

    Article  CAS  Google Scholar 

  12. McKee AE, Rutherford BJ, Chivian DC, Baidoo EK, Juminaga D, Kuo D, Benke PI, Dietrich JA, Ma SM, Arkin AP, Petzold CJ, Adams PD, Keasling JD, Chhabra SR (2012) Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. Microb Cell Fact 11:79

    Article  CAS  Google Scholar 

  13. Revelles O, Millard P, Nougayrede J-P, Dpbrindt U, Osward E, Letisse F, Portais, J-C (2013) The carbon storage regulator (Csr) system exerts a nutrient-specific control over central metabolism in Escherichia coli strain Nissle 1917. Plos One 8(6):e66386 (1–12)

    Google Scholar 

  14. Tatarko M, Romeo T (2001) Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli. Current Microbiol 43(1):26–32

    Article  CAS  Google Scholar 

Nitrogen Regulation

  1. Van Heeswijk WC, Westerhoff HV, Boogerd FC (2013) Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 77(4):628–695

    Article  CAS  Google Scholar 

  2. Kim M, Zhang Z, Okano H, Yan D, Groisman A, Hwa T (2012) Need-based activation of ammonium uptake in Escherichia coli. Mol Syst Biol 8:616

    Google Scholar 

  3. Gruswitz F, O’Connell J, Stroud RM (2007) Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A. PNAS USA 104:42–47

    Article  CAS  Google Scholar 

  4. Radchenko MV, Thornton J, Merrick M (2010) Control of AmtB-GlnK complex formation by intracellular levels of ATP, ADP, and 2-oxoglutarate. J Biol Chem 285:31037–31045

    Article  CAS  Google Scholar 

  5. Truan D, Huergo LF, Chubatsu LS, Merrick M, Li XD, Winkler FK (2010) A new P(II) protein structure identifies the 2-oxoglutarate binding site. J Mol Biol 400:531–539

    Article  CAS  Google Scholar 

  6. Yuan J, Doucette CD, Fowler WU, Feng X-J, Piazza M, Rabitz HA, Wingreen NS, Rabinowitz JD (2009) Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol Syst Biol 5:302

    Article  CAS  Google Scholar 

  7. Ninfa AJ, Jiang P, Atkinson MR, Peliska JA (2000) Integration of antagonistic signals in the regulation of nitrogen assimilation in Escherichia coli. Curr Topics Cell Regul 36:31–75

    Article  CAS  Google Scholar 

  8. Gerosa L, Kochanowski K, Heinemann M, Sauer U (2013) Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol Syst Biol 9:658

    Article  Google Scholar 

  9. Kiupakis AK, Reitzer L (2002) ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli. J Bacteriol 184(11):2940–2950

    Article  CAS  Google Scholar 

  10. Commichau FM, Forchhammer K, Stulke J (2006) Regulatory links between carbon and nitrogen metabolism. Curr Opin Microbiol 9(2):167–172

    Article  CAS  Google Scholar 

  11. Mao XJ, Huo YX, Buck M, Kolb A, Wang YP (2007) Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli. Nucleic Acids Res 35(5):1432–1440

    Article  CAS  Google Scholar 

  12. Kumar R, Shimizu K (2010) Metabolic regulation of Escherichia coli and its gdhA, glnL, gltB, D mutants under different carbon and nitrogen limitations in the continuous culture. Microb Cell Fact 9:8

    Google Scholar 

  13. Jiang P, Ninfa AJ (2007) Escherichia coli PII signal transduction protein controlling nitrogen assimilation acts as a sensor of adenylate energy charge in vitro. Biochemistry 46(45):12979–12996

    Article  CAS  Google Scholar 

  14. Ninfa J, Jiang P (2005) PII signal transduction proteins: sensors of -ketoglutarate that regulate nitrogen metabolism. Curr Opin Microbiol 8(2):168–173

    Article  CAS  Google Scholar 

  15. Brauer MJ, Yuan J, Bennet BD, Lu W, Kimball E, Botstein D, Rabinowitz JD (2006) Conservation of the metabolomic response to starvation across two divergent microbes. PNAS USA 103:19302–19307

    Article  CAS  Google Scholar 

  16. Hart Y, Madar D, Yuan J, Bren A, Mayo AE, Rabinowitz JD, Alon U (2011) Robust control of nitrogen assimilation by a bifunctional enzyme in E. coli. Moleculae Cell 41:117–127

    Article  CAS  Google Scholar 

  17. Doucette CD, Schwab DJ, Wingreen NS, Rabinowitz JD (2011) Alpha-ketoglutarate coordinates carbon and nitrogen utilization via enzyme i inhibition. Nat Chem Biol 7:894–901

    Article  CAS  Google Scholar 

  18. You C, Okano H, Hui S, Zhang Z, Kim M, Gunderson CW, Wang Y-P, Lenz P, Yan D, Hwa T (2013) Coordination of bacterial proteome with metabolism by cyclic AMP signaling. Nature 500:301–306

    Article  CAS  Google Scholar 

  19. Powell BS, Court DL, Inada T, Nakamura Y, Michotey V, Cui X et al (1995) Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. Enzyme IIANtr affects growth on organic nitrogen and the conditional lethality of an erats mutant. J Biol Chem 270:4822–4839

    Article  CAS  Google Scholar 

  20. Peterkofski A, Wang G, Seok Y-J (2006) Parallel PTS systems. Arch Biochem Biophys 453(1):101–107

    Article  CAS  Google Scholar 

  21. Pflüger-Grau K, Görke B (2010) Regulatory roles of the bacterial nitrogen-related phosphotransferase system. Trend Microbiol 18(5):205–214

    Article  CAS  Google Scholar 

  22. Lee CR, Cho SH, Yoon MJ, Peterkofsky A, Seok YJ (2007) Escherichia coli enzyme IIANtr regulates the K+ transporter TrkA. PNAS USA 104:4124–4129

    Article  CAS  Google Scholar 

  23. Lüttmann D, Heermann R, Zimmer B, Hillmann A, Rampp IS, Jung K, Görke B (2009) Stimulation of the potassium sensor KdpD kinase activity by interaction with the phosphotransferase protein IIANtr in Escherichia coli. Mol Micobiol 72(4):978–994

    Article  CAS  Google Scholar 

  24. Lee C-R, Cho S-H, Kim H-J, Kim M, Peterkofsky A, Seok Y-J (2010) Potassium mediates Escherichia coli enzyme IIANtr-dependent regulation of sigma factor selectivity. Mol Microbiol 78(6):1468–1483

    Article  CAS  Google Scholar 

  25. Lüttmann D, Göpel Y, Görke B (2012) The phosphotransferase protein EIIANtr modulates the phosphate starvation response through interaction with histidine kinase PhoR in Escherichia coli. Mol Microbiol 86(1):96–110

    Article  CAS  Google Scholar 

  26. Kim H-J, Lee C-R, Kim M, Peterkofsky A, Seok Y-J (2011) Dephosphorylated NPr of the nitrogen PTS regulates lipid a biosynthesis by direct interaction with LpxD. Biochem Biophys Res Commun 409(3):556–561

    Article  CAS  Google Scholar 

  27. Lee C-R, Park Y-H, Kim M, Kim Y-R, Park S, Peterkofsky A, Seok Y-J (2013) Reciprocal regulation of the autophosphorylation of enzyme INtr by glutamine and α-ketoglutarate in Escherichia coli. Mol Microbiol 88(3):473–485

    Article  CAS  Google Scholar 

Sulfur Regulation

  1. Bykowski T, van der Ploeg JR, Iwanicka-Nowicka R, Hryniewicz MM (2002) The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5′-phosphosulphate (APS) as a signalling molecule for sulphate excess. Mol Microbiol 43:1347–1358

    Article  CAS  Google Scholar 

  2. Kredich NM (1996) Biosynthesis of cysteine. In: Neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HH (eds) Escherichia coli and Salmonella: cellular and molecular biology, vol 1, 2nd edn. ASM Press, Washington DC, pp 514–527

    Google Scholar 

  3. Iwanicka-Nowicka R, Hryniewicz MM (1995) A new gene, cbl, encoding a member of the LysR family of transcriptional regulators belongs to Escherichia coli cys regulon. Gene 166:11–17

    Article  CAS  Google Scholar 

  4. Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky BJ, Peter R, Bender A, Kustu S (2000) Nitrogen regulatory protein controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. PNAS USA 97:14674–14679

    Article  CAS  Google Scholar 

  5. Gyaneshwar P, Paliy O, McAuliffe J, Popham DL, Jordan MI, Kustu S (2005) Sulfur and Nitrogen Limitation in Escherichia coli K-12: specific homeostatic responses. J Bacteriol 187(3):1074–1090

    Article  CAS  Google Scholar 

Phosphate Regulation

  1. Wanner BL (1996) Phosphorus assimilation and control of the phosphate regulon. In: Neidhardt FC, Curtiss IIIR, Ingraham JL et al (eds) Escherichia coli and salmonella: cellular and molecular biology, pp 1357–1381. ASM Press, Washington DC

    Google Scholar 

  2. Wanner BL (1993) Gene regulation by phosphate in enteric bacteria. J Cellr Biochem 51(1):47–54

    Article  CAS  Google Scholar 

  3. Baek JH, Lee SY (2007) Transcriptome analysis of phosphate starvation response in Escherichia coli. J Microbiol Biotechnol 17(2):244–252

    CAS  Google Scholar 

  4. Van Dien SJ, Keasling JD (1998) A dynamic model of the Escherichia coli phosphate-starvation response. J Theoret Biol 190(1):37–49

    Article  Google Scholar 

  5. Marzan LW, Shimizu K (2011) Metabolic regulation of Escherichia coli and its phoB and phoR gene knockout mutants under phosphate and nitrogen limitations as well as acidic condition. Microb Cell Fact 10:39

    Article  CAS  Google Scholar 

  6. Spira B, Silberstein N, Yagil E (1995) Guanosine 3′,5′-bispyrophosphate (ppGpp) synthesis in cells of Escherichia coli starved for Pi. J Bacteriol 177(14):4053–4058

    CAS  Google Scholar 

Metal Ion Regulation and Oxidative Stress Regulation

  1. Frey PA, Reed GH (2012) The ubiquity of iron. ACS Chem Biol 7:1477–1481

    Article  CAS  Google Scholar 

  2. Dixon SJ, Stockwell BR (2014) The role of iron and reactive oxygen species in cell death. Nat Chem Biol 10:9–17

    Article  CAS  Google Scholar 

  3. Dann CEIII, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winker WC (2007) Structure and mechanism of a metal-sensing regulatory RNA. Cell 130:878–892

    Article  CAS  Google Scholar 

  4. Helmann JD (2007) Measuring metals with RNA. Mol Cell 27:859–860

    Article  CAS  Google Scholar 

  5. Zheng M, Doan B, Schneider TD, Storz G (1999) OxyR and SoxRS regulation of fur. J Biotechnol 181:4639–4643

    CAS  Google Scholar 

  6. McHugh JP, Rodríguez-Quiñones F, Abdul-Tehrani H, Svistunenko DA, Poole RK, Cooper CE, Andrews SC (2003) Global iron-dependent gene regulation in Escherichia coli. J Biol Chem 278:29478–29486

    Article  CAS  Google Scholar 

  7. Storz G, Imlay JA (1999) Oxidative stress. Curr Opin Microbiol 2:188–194

    Article  CAS  Google Scholar 

  8. Jovanovic G, Lloyde LJ, Stumpf MP, Mayhew AJ, Buck M (2006) Induction and function of the phase shock protein extracytoplasmic stress response in Escherichia coli. J Biol Chem 281:21147–21161

    Google Scholar 

  9. Blanchard JR, Wholey WY, Conlon EM, Pomposiello PJ (2007) Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS dependent and independent transcriptional network. PLoS One 2:e1186

    Article  CAS  Google Scholar 

  10. Brynildsen MP, Liao JC (2009) An integrated network approach indentifies the isobutanol response network of Escherichia coli. Mol Syst Biol 5:34

    Article  CAS  Google Scholar 

  11. Braun V, Hantke K, Koster W (1998) Bacterial ion transport: mechanisms, genetics, and regulation. In: Sigel A, Sigel H (eds) Metal ions in biological systems. Marcel Dekker, New York, pp 67–145

    Google Scholar 

  12. Azpiroz MF, Lavińa M (2004) Involvement of enterobactin synthesis pathway in production of Microcin H47. Antimicrob Agents Chemother 48:1235–1241

    Article  CAS  Google Scholar 

  13. Semsey S, Andersson AM, Krishna S, Jensen MH, Masse E, Sneppen K (2006) Genetic regulation of fluxes: iron homeostasis of Escherichia coli. Nucleic Acids Res 34:4960–4967

    Article  CAS  Google Scholar 

  14. Hantash FM, Ammerlaan M, Earhart CF (1997) Enterobactin synthase polypeptides of Escherichia coli are present in an osmotic-shock-sensitive cytoplasmic locality. Microbiol 143:147–156

    Article  CAS  Google Scholar 

  15. Kumar R, Shimizu K (2011) Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures. Microb Cell Fact 10:3

    Article  CAS  Google Scholar 

  16. Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, Saier MH Jr (2005) Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli. J Bacteriol 187:980–990

    Article  CAS  Google Scholar 

  17. Perera IC, Grove A (2010) Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators. J Mol Cell Biol 2:243–254

    Article  CAS  Google Scholar 

  18. Hao Z, Lou H, Zhu R, Zhu J, Zhang D, Zhao BS, Zeng S, Chen X, Chan J, He C, Chen PR (2014) The multiple antibiotic resistance regulator MarR is a copper sensor in Escherichia coli. Nat Chem Biol 10:21–28

    Article  CAS  Google Scholar 

  19. Pomposiello PJ, Demple B (2001) Redox-operated genetic switches: the SoxR and OxyR transcription factors. Trends Biotechnol 19(3):109–114

    Article  CAS  Google Scholar 

  20. Gaudu P, Weiss B (1996) SoxR, a [2Fe–2S] transcription factor, is active only in its oxidized form. PNAS USA 93(19):10094–10098

    Article  CAS  Google Scholar 

  21. Mailloux RJ, Bériault R, Lemire J, Singh R, Chénier RR, Hamel RD, Appanna VD (2007) The tricarboxylic acid cycle, an ancient metabolic network with a novel twist. Plos One 2(8):e690

    Article  CAS  Google Scholar 

  22. DeNicola GM et al (2011) Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis. Nature 475:106–109

    Article  CAS  Google Scholar 

  23. Son J et al (2013) Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature 496:101–105

    Article  CAS  Google Scholar 

  24. Maddocks OD et al (2013) Serine starvation induces stress and p53-dependent metabolic remodeling in cancer cells. Nature 493:542–546

    Article  CAS  Google Scholar 

  25. Trachootham D, Alexandre J, Huang P (2009) Targeting cancer cells by ROS-mediated mechanisms: a radical therapeutic approach ? Nat Rev Drug Discov 8:579–591

    Article  CAS  Google Scholar 

Redox State Regulation

  1. Gunsalus RP (1992) Control of electron flow in Escherichia coli: coordinated transcription of respiratory pathway genes. J Bacteriol 174(22):7069–7074

    CAS  Google Scholar 

  2. Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003) Global gene expression profiling in Escherichia coli K12: the effects of oxygen availability and FNR. J Biol Chem 278(32):29837–29855

    Article  CAS  Google Scholar 

  3. Alexeeva S, Hellingwerf KJ, de Mattos MJT (2003) Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions. J Bacteriol 185(1):204–209

    Article  CAS  Google Scholar 

  4. Zhu J, Shalel-Levanon S, Bennett G, San KY (2006) Effect of the global redox sensing/ regulation networks on Escherichia coli and metabolic flux distribution based on C-13 labeling experiments. Metab Eng 8(6):619–627

    Article  CAS  Google Scholar 

  5. Georgellis D, Kwon O, Lin ECC (2001) Quinones as the redox signal for the arc two-component system of bacteria. Science 292(5525):2314–2316

    Article  CAS  Google Scholar 

  6. Malpica R, Franco B, Rodriguez C, Kwon O, Georgellis D (2004) Identification of a quinone-sensitive redox switch in the ArcB sensor kinase. PNAS USA 101(36):13318–13323

    Article  CAS  Google Scholar 

  7. Constantinidou C, Hobman JL, Grifiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006) A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J Biol Chem 281(8):4802–4815

    Article  CAS  Google Scholar 

  8. Kessler D, Knappe J (1996) Anaerobic dissimilation of pyruvate. In: Neidhardt FC, Curtiss R, Ingraham JI et al (eds) E. Coli and salmonella: cellular and molecular biology, 2nd edn, vol 1, pp 199–205. ASM Press, Washington, DC

    Google Scholar 

  9. Toya Y, Nakahigashi K, Tomita M, Shimizu K (2012) Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data. Mol Biosyst 8:2593–2604

    Article  CAS  Google Scholar 

  10. Maeda T, Sanchez-Torres V, Wood TK (2007) Enhanced hydrogen production from glucose by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 77:879–890

    Article  CAS  Google Scholar 

  11. Zhu J, Shimizu K (200) The effect of pfl genes knockout on the metabolism for optically pure d-lactate production by Escherichia coli. Applied Microbiol Biotechnol 64:367–75

    Google Scholar 

  12. Zhu J, Shimizu K (2005) Effect of a single-gene knockout on the metabolic regulation in E. coli for d-lactate production under microaerobic conditions. Metabolic Eng 7:104–115

    Article  CAS  Google Scholar 

  13. Vemuri GN, Altman E, Sangurdekar DP, Khodursky AB, Eiteman MA (2006) Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio. Appl Environ Microbiol 72(5):3653–3661

    Article  CAS  Google Scholar 

  14. Valgepea K, Adamberg K, Seiman A, Vilu R (2014) Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins. Mol BioSyst 9:2344–2358

    Article  CAS  Google Scholar 

  15. Nizam SA, Zhu J, Ho PY, Shimizu K (2009) Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under aerobic condition. Biochem Eng J 44(2–3):240–250

    Article  CAS  Google Scholar 

  16. Vemuri GN, Eiteman MA, Altman E (2006) Increased recombinant protein production in Escherichia coli strains with overexpressed water-forming NADH oxidase and a deleted ArcA regulatory protein. Biotechnol Bioeng 94(3):538–542

    Article  CAS  Google Scholar 

  17. Nizam SA, Shimizu K (2008) Effects of arc A and arc B genes knockout on the metabolism in Escherichia coli under anaerobic and microaerobic conditions. Biocheml Eng J 42:229–236

    Article  CAS  Google Scholar 

Acid Shock

  1. Foster JW (2004) Escherichia coli acid resistance: tales of an amateur acidophile. Nat Rev Microbiol 2(11):898–907

    Article  CAS  Google Scholar 

  2. Stincone A, Daudi N, Rahman AS et al (2011) A systems biology approach sheds new light on Escherichia coli acid resistance. Nucleic Acids Res 39(17):7512–7528

    Google Scholar 

  3. Richard HT, Foster JW (2003) Acid resistance in Escherichia coli. Adv Appl Microbiol 52:167–186

    Article  CAS  Google Scholar 

  4. Richard HT, Foster JW (2004) Escherichia coli glutamate-and arginine-dependent acid resistance systems increase internal pH and reverse transmembrane potential. J Bacteriol 86(18):6032–6041

    Article  CAS  Google Scholar 

  5. Gong S, Richard H, Foster JW (2003) YjdE (AdiC) is the arginine: agmatine antiporter essential for arginine-dependent acid resistance in Escherichia coli. J Bacteriol 185(15):4402–4409

    Article  CAS  Google Scholar 

  6. Iyer R, Williams C, Miller C (2003) Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli. J Bacteriol 185:6556–6561

    Article  CAS  Google Scholar 

  7. Martin-Galiano AJ, Ferrandiz MJ, de La Campa AG (2001) The promoter of the operon encoding the F0F1 ATPase of Streptococcus pneumonia is inducible by pH. Molr Microbiol 41:327–338

    Google Scholar 

  8. Castanie-Cornet MP, Foster JW (2001) Escherichia coli acid resistance: cAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes. Microbiol 147:709–715

    Article  CAS  Google Scholar 

  9. Marzan LW, Shimizu K (2011) Metabolic regulation of Escherichia coli and its phoB and phoR genes knockout mutants under phosphate and nitrogen limitations as well as at acidic condition. Microb Cell Fact 10:39

    Article  CAS  Google Scholar 

  10. Greenberg JT, Monach P, Chou JH, Josephy PD, Demple B (1990) Positive control of a global antioxidant defense regulon activated by superoxide-generating agents in Escherichia coli. PNAS USA 87(16):6181–6185

    Article  CAS  Google Scholar 

  11. Suziedeliene E, Suziedelis K, Garbenciute V, Normark S (1999) The acid-inducible asr gene in Escherichia coli: transcriptional control by the phoBR operon. J Bacteriol 181(7):2084–2093

    CAS  Google Scholar 

  12. Wu X, Altman R, Eiteman MA, Altman E (2013) Effect of overexpressing nhaA and nhaR on sodium tolerance and lactate production in Escherichia coli. J Biol Eng 7:3

    Article  CAS  Google Scholar 

Heat Shock

  1. Kitagawa M, Miyakawa M, Matsumura Y, Tsuchido T (2002) Escherichia coli small heat shock proteins, IbpA and IbpB, protect enzymes from inactivation by heat and oxidants. Eur J Biochem 269(12):2907–2917

    Article  CAS  Google Scholar 

  2. Sørensen HP, Mortensen KK (2005) Soluble expression of recombinant proteins in the cytoplasm of Escherichia coli. Microb Cell Fact 4:1

    Article  CAS  Google Scholar 

  3. Hoffmann F, Weber J, Rinas U (2002 Metabolic adaptation of Escherichia coli during temperature-induced recombinant protein production: 1. Readjustment of metabolic enzyme synthesis. Biotechnol Bioeng 80(3):313–319

    Google Scholar 

  4. Tilly K, Erickson J, Sharma S, Georgopoulos C (1986) Heat shock regulatory gene rpoH mRNA level increases after heat shock in Escherichia coli. J Bacteriol 168(3):1155–1158

    CAS  Google Scholar 

  5. Tilly K, Spence J, Georgopoulos C (1989) Modulation of stability of the Escherichia coli heat shock regulatory factor 32. J Bacteriol 171(3):1585–1589

    CAS  Google Scholar 

  6. Shin D, Lim S, Seok YJ, Ryu S (2001) Heat shock RNA polymerase (E 32) is involved in the transcription of mlc and Crucial for Induction of the Mlc regulon by glucose in Escherichia coli. J Biol Chem 276(28):25871–25875

    Article  CAS  Google Scholar 

  7. Hasan CM, Shimizu K (2008) Effect of temperature up-shift on fermentation and metabolic characteristics in view of gene expressions in Escherichia coli. Microb Cell Fact 7:35

    Google Scholar 

  8. Kumari S, Beatty CM, Browning DF et al (2000) Regulation of acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 182(15):4173–4179

    Article  CAS  Google Scholar 

  9. Browning DF, Beatty CM, Wolfe AJ, Cole JA, Busby SJW (2002) Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region. Mol Microbiol 43(3):687–701

    Article  CAS  Google Scholar 

  10. Beatty CM, Browning DF, Busby SJW, Wolfe AJ (2003) Cyclic AMP receptor protein-dependent activation of the Escherichia coliacs P2 promoter by a synergistic class III mechanism. J Bacteriol 185(17):5148–5157

    Article  CAS  Google Scholar 

  11. Browning DF, Beatty CM, Sanstad EA, Gunn KE, Busby SJW, Wolfe AJ (2004) Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF. Mol Microbiol 51(1):241–254

    Article  CAS  Google Scholar 

  12. Privalle CT, Fridovich I (1987) Induction of superoxide dismutase in Escherichia coli by heat shock. PNAS USA 84(9):2723–2726

    Article  CAS  Google Scholar 

Cold Shock

  1. Etchegaray J-P, Inoue M (1999) CspA, CspB, and CspG, major cold shock proteins of Escherichia coli, are induced at low temperature under conditions that completely block protein synthesis. J Bacteriol 181(6):1827–1830

    Google Scholar 

  2. White-Ziegler CA, Um S, Perez NM, Berns AL, Malhowski AJ, Young S (2008) Low temperature (23 °C) increases expression of biofilm-, cold shock-, and RpoS-dependent genes in Escherichia coli K-12. Microbiol 154:148–166

    Article  CAS  Google Scholar 

  3. Kim Y-H, Han KY, Lee K, Lee J (2005) Proteome response of Escherichia coli fed-batch culture to temperature downshift. Appl Microbiol Biotechnol 68:786–793

    Article  CAS  Google Scholar 

Solvent Stress Regulation

  1. Dunlop MJ (2011) Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels 4:32

    Article  CAS  Google Scholar 

  2. Isken S, de Bont JAM (1998) Bacteria tolerant to organic solvents. Extremophiles 2:229–238

    Article  CAS  Google Scholar 

  3. Ramos JL, Duque E, Gallegos M-T, Godoy P, Ramos-Gonzalez MI, Rojas A, Teran W, Segura A (2002) Mechanisms of solvent tolerance in Gram-negative bacteria. Annu Rev Microbiol 56:743–768

    Article  CAS  Google Scholar 

  4. Nicolaou SA, Gaida SM, Papoutsakis ET (2010) A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation. Metab Eng 12:307–331

    Article  CAS  Google Scholar 

  5. Takatsuka Y, Chen C, Nikaido H (2010) Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of Escherichia coli. PNAS USA 107:6559–6565

    Article  Google Scholar 

  6. Ankarloo J, Wikman S, Nicholls IA (2010) Escherichia coli mar and acrAB mutants display no tolerance to simple alcohols. Int J Mol Sci 11:1403–1412

    Article  CAS  Google Scholar 

  7. Piper P (1995) The heat-shock and ethanol stress responses of yeast exhibit extensive similarity and functional overlap. FEMS Microbiol Lett 134:121–127

    Article  CAS  Google Scholar 

  8. Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD (2010) Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl Environ Microbiol 76:1935–1945

    Article  CAS  Google Scholar 

  9. Tomas C, Beamish J, Papoutsakis E (2004) Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum. J Bacteriol 186:2006–2018

    Article  CAS  Google Scholar 

  10. Fiocco D, Capozzi V, Goffin P, Hols P, Spano G (2007) Improved adaptation to heat, cold, and solvent tolerance in Lactobacillus plantarum. Appl Microbiol Biotechnol 77:909–915

    Article  CAS  Google Scholar 

  11. Reyes LH, Almario MP, Kao KC (2011) Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli. PLoS One 6:e17678

    Article  CAS  Google Scholar 

  12. Sikkema J, de Bont JAM, Poolman B (1995) Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59:201–222

    CAS  Google Scholar 

  13. Holtwick R, Meinhardt F, Keweloh H (1997) cis-trans isomerization of unsaturated fatty acids: cloning and sequencing of the cti gene from Pseudomonas putida P8. Appl Environ Microb 63:4292–4297

    CAS  Google Scholar 

  14. Kiran M, Prakash J, Annapoorni S, Dube S, Kusano T, Okuyama H, Murata N, Shivaji S (2004) Psychrophilic Pseudomonas syringae requires transmonounsaturated fatty acid for growth at higher temperature. Extremophiles 8:401–410

    Article  CAS  Google Scholar 

Osmoregulation

  1. Kramer R (2010) Bacterial stimulus perception and signal transduction: response to osmotic stress. Chem Res 10:217–229

    Google Scholar 

  2. Wood JM (2011) Bacterial osmoregulation: a paradigm for the study of cellular homeostasis. Ann Rev Microbiol 65:215–238

    Article  CAS  Google Scholar 

  3. Walderhaug MO, Polarek JW, Voelkner P, Daniel JM, Hesse JE, Altendorf K, Epstein W (1992) KdpD and KdpE, proteins that control expression of the kdpABC operon, are members of the two-component sensor-effector class of regulators. J Bacteriol 174:2152–2159

    CAS  Google Scholar 

  4. Sugiura A, Hirokawa K, Nakashima K, Mizuno T (1994) Signal-sensing mechanisms of the putative osmosensor KdpD in Escherichia coli. Mol Microbiol 14:929–938

    Article  CAS  Google Scholar 

  5. Hamann K, Zimmann P, Altendorf K (2008) Reduction of turgor is not the stimulus for the sensor kinase KdpD of Escherichia coli. J Bacteriol 190:2360–2367

    Article  CAS  Google Scholar 

  6. Heermann R, Jung K (2010) The complexity of the ‘simple’ two-component system KdpD/KdpE in Escherichia coli. Microbiol Lett 304:97–106

    Article  CAS  Google Scholar 

  7. Sevin DC, Sauer U (2014) Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli. Nat Chem Biol 10:266–272

    Article  CAS  Google Scholar 

  8. Piuri M, Sanchez-Rivas C, Ruzal SM (2005) Cell wall modifications during osmotic stress in Lactobacullus casei. J Appl Microbiol 98:84–95

    Article  CAS  Google Scholar 

  9. Clarke CF, Rowat AC, Gober JW (2014) Is CoQ a membrane stabilizer? Nat Chem Biol 10:242–243

    Article  CAS  Google Scholar 

  10. Calamita G, Bishai WR, Preston GM, Guggino WB, Agre P (1995) Molecular cloning and characterization of AqpZ, a water channel from Escherichia coli. J Biol Chem 270:29063–29066

    Article  CAS  Google Scholar 

  11. Lamins LA, Rhoads DB, Epstein W (1981) Osmotic control of kdp operon expression in Escherichia coli. PNAS USA 78:464–468

    Article  Google Scholar 

  12. Record MT Jr, Courtenary ES, Cayley DS, Guttman HJ (1998) Responses of E. coli to osmotic stress: large changes in amounts of cytoplasmic solutes and water. Trends Biochem Sci 23:143–148

    Article  CAS  Google Scholar 

  13. Grothe S, Krogsrud RL, McClellan DJ, Milner JL, Wood JM (1986) Proline transport and osmotic response in Escherichia coli K-12. J Bacteriol 166:253–259

    CAS  Google Scholar 

  14. Von Weyman N, Nyyssola A, Reinikainen T, Leisola M, Ojamo H (2001) Improved osmotolerance of recombinant Escherichia coli by de novo glycine betaine biosynthesis. Appl Microbiol Biotechnol 55:214–218

    Article  Google Scholar 

  15. Giaever HM, Styrvoid OB, Kaasen I, Strom AR (1998) Biochemical and genetic characterization of osmoregulatory trehalose synthesis in Escherichia coli. J Bacteriol 170:2841–2849

    Google Scholar 

  16. Elbein AD, Pan YT, Pastuszak I, Carroll D (2003) New insights on trehalose: a multifunctional molecule. Glycobiology 13:17R–27R

    Article  CAS  Google Scholar 

  17. Klein W, Ehmann U, Boos W (2991) The repression of trehalose transport and metabolism in Escherichia coli by high osmolarity is mediated by trehalose-6-phosphate phosphatase. Res Microbiol 142:359–371

    Google Scholar 

  18. Turunen M, Olsson J, Dallner G (2004) Metabolism and function of coenzyme Q. Biochim Biophys ACTA Biomembr 1660:171–199

    Article  CAS  Google Scholar 

Biofilm, Motility and Quarum Sensing

  1. Wang X, Dubey AK, Suzuki K, Baker CS, Babitzke P, Romeo T (2005) CsrA post-transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli. Mol Microbiol 56:1648–1663

    Article  CAS  Google Scholar 

  2. Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7:263–273

    Article  CAS  Google Scholar 

  3. Barnhart MM, Chapman MR (2006) Curli biogenesis and function. Annu Rev Microbiol 60:131–147

    Article  CAS  Google Scholar 

  4. Thomason MK, Fontaine F, De Lay N, Storz1 G (2012) A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli. Mol Microbiol 84(1):17–35

    Google Scholar 

  5. Jackson DW, Simecka JW, Romeo T (2002) Catabolite repression of Escherichia coli biofilm formation. J Bacteriol 184:3406–3410

    Article  CAS  Google Scholar 

  6. Waters CM, Bassler BL (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21:319–346

    Article  CAS  Google Scholar 

  7. De Lay N, Gottesman S (2009) The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J Bacteriol 191:461–476

    Article  CAS  Google Scholar 

Systems Biology Approach

  1. Yu Matsuoka, Shimizu K (2015) Current status and future perspectives of kinetic modeling for the cell metabolism with incorporation of the metabolic regulation mechanism. Bioreses Bioprocess 2:4

    Google Scholar 

  2. Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M (2014) Kinetic models in industrial biotechnology-improving cell factory performance. Metab Eng 24:38–60

    Article  CAS  Google Scholar 

  3. Chassagnole C, Noisommitt-Rizzi N, Schmid JW, Mauch K, Reuss M (2002) Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79:53–73

    Article  CAS  Google Scholar 

  4. Kadir TA, Mannan AA, Kierzek AM, McFadden J, Shimizu K (2010) Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification. Microb Cell Fact 9:88

    Article  CAS  Google Scholar 

  5. Nishio Y, Usuda Y, Matsui K, Kurata H (2008) Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol Syst Biol 4:160

    Article  CAS  Google Scholar 

  6. Usuda Y, Nishio Y, Iwatani S, Van Dien SJ, Imaizumi A, Shimbo K, Kageyama N, Iwahata D, Miyano H, Matsui K (2010) Dynamic modeling of Escherichia coli metabolic and regulatory systems for amino-acid production. J Biotechnol 147:17–30

    Article  CAS  Google Scholar 

  7. Matsuoka Y, Shimizu K (2013) Catabolite regulation analysis of Escherichia coli for acetate overflow mechanism and co-consumption of multiple sugars based on systems biology approach using computer simulation. J Biotechnol 168:155−173

    Article  CAS  Google Scholar 

Concluding Remarks

  1. Gutierrez-Rios RM, Rosenblueth DA, Loza JA, Huerta AM, Glasner JD, Blattner FR, Collado-Vides J (2003) Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. Genome Res 13:2435–2443

    Article  CAS  Google Scholar 

  2. Maheswaran M, Forchhammer K (2003) Carbon-source-dependent nitrogen regulation in Escherichia coli is mediated through glutamine-dependent GlnB signaling. Microbiology 149:2163–2172

    Article  CAS  Google Scholar 

  3. Quan JA, Schneider BL, Paulsen IT, Yamada M, Kredich NM, Saier MH Jr (2002) Regulation of carbon utilization by sulfur availability in Escherichia coli and Salmonella typhimurium. Microbiology 148:123–131

    Article  CAS  Google Scholar 

  4. De Lorenzo V, Herrero M, Giovannini F, Neilands JB (1998) Fur (ferric uptake regulation) protein and CAP (catabolite-activator protein) modulate transcription of fur gene in Escherichia coli. Eur J Biochem 173:537–546

    Article  Google Scholar 

  5. Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, Saier MH Jr (2005) Functional interactions between the carbon and iron utilization regulators, Crp and Fur, Escherichia coli. J Bacteriol 187(3):980–990

    Article  CAS  Google Scholar 

  6. Gyaneshwar P, Paliy O, McAuliffe J, Popham DL, Jordan MI, Kustu S (2005) Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses. J Bacteriol 187(3):1074–1090

    Article  CAS  Google Scholar 

  7. Dragosits M, Mozhayskiy V, Quinones-Soto S, Park J, Tagkopoulos I (2013) Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli. Mol Syst Biol 9:643

    Article  Google Scholar 

  8. Weber H, Polen T, Heuveling J, Wendisch V, Hengge R (2005) Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J Bacteriol 187:1591–1603

    Article  CAS  Google Scholar 

  9. Jenkins D, Schultz J, Matin A (1988) Starvation-induced cross protection against heat or H2O2 challenge in Escherichia coli. J Bacteriol 170:3910–3914

    CAS  Google Scholar 

  10. Jenkins D, Auger E, Matin A (1991) Role of RpoH, a heat shock regulator protein, in Escherichia coli carbon starvation protein synthesis and survival. J Bacteriol 173:1992–1996

    CAS  Google Scholar 

  11. Gunasekera T, Csonka L, Paliy O (2008) Genome-wide transcriptional responses of Escherichia coli K-12 to continuous osmotic and heat stresses. J Bacteriol 190:3712–3720

    Article  CAS  Google Scholar 

  12. White-Ziegler C, Um S, Pérez N, Berns A, Malhowski A, Young S (2008) Low temperature (23 degrees C) increases expression of biofilm-, cold-shock- and RpoS-dependent genes in Escherichia coli K-12. Microbiology 154:148–166

    Article  CAS  Google Scholar 

  13. Rutherford B, Dahl R, Price R, Szmidt H, Benke P, Mukhopadhyay A, Keasling J (2012) Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl Environ Microbiol 76:1935–1945

    Article  CAS  Google Scholar 

  14. Rabinowitz J, Silhavy TJ (2012) Metabolite turns master regulator. Nature 500:283–284

    Article  CAS  Google Scholar 

  15. Klumpp S, Zhang Z, Hwa T (2009) Growth rate-dependent global effects on gene expression in bacteria. Cell 139:1366–1375

    Article  Google Scholar 

  16. Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T (2010) Interdependence of cell growth and gene expression: origins and consequences. Science 330:1099–1102

    Article  CAS  Google Scholar 

  17. Koebman BJ, Westerhoff HV, Snoep JL, Nilsson D, Jensen PR (2002) The glycolytic flux in Escherichia coli is controlled by the demand for ATP. J Bacteriol 184:3909

    Article  CAS  Google Scholar 

  18. Luo Y, Zhang T, Wu H (2014) The transport and mediation mechanisms of the common sugars in Escherichia coli. Biotechnol Adv 32:905–919

    Article  CAS  Google Scholar 

  19. Yao R, Shimizu K (2012) Recent progress in metabolic engineering for the production of biofuels and biochemical from renewable sources with particular emphasis on catabolite regulation and its modulation. Process Biochem 48(9):1409–1417

    Article  CAS  Google Scholar 

  20. Aidelberg G, Towbin BD, Rothschild D, Dekel E, Bren A, Alon U (2014) Hierarchy of non-glucose sugars in Escherichia coli. BMC Syst Biol 8:133

    Article  Google Scholar 

  21. Balsalobre C, Johansson J, Uhlin BE (2006) Cyclic AMP-dependent osmoregulation of crp gene expression in Escherichia coli. J Bacteriol 188(16):5935–5944

    Article  CAS  Google Scholar 

  22. Zhang H, Chong H, Ching CB, Jiang R (2012) Random mutagenesis of global transcription factor cAMP receptor protein for improved osmotolerance. Biotechnol Bioeng 109(5):1165–1172

    Article  CAS  Google Scholar 

  23. Basak S, Jiang R (2012) Enhancing E. coli tolerance towards oxidative stress via engineering its global regulator cAMP receptor protein (CRP). PLOS One 7(12):e51179

    Article  CAS  Google Scholar 

  24. Basak S, Geng H, Jiang R (2013) Rewiring global regulator cAMP receptor protein (CRP) to improve E. coli tolerance towards low pH. J Biotechnol 173:68–75

    Google Scholar 

  25. Chong H, Yeow J, Wang I, Song H, Jiang R (2013) Improving acetate tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PLOS One 8(10):e77422

    Article  CAS  Google Scholar 

  26. Chong H, Huang L, Yeow J, Wang I, Zhang H, Song H, Jiang R (2013) Improving ethanol tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PLOS One 8(2):e57628

    Article  CAS  Google Scholar 

  27. Zhang H, Chong H, Ching CB, Song H, Jiang R (2012) Engineering global transcription factor cyclic AMP receptor protein of Escherichia coli for improved 1-butanol tolerance. Appl Microbiol Biotechnol 94:1107–1117

    Article  CAS  Google Scholar 

  28. Khankal R, Chin JW, Ghosh D, Cirino PC (2009) Transcriptional effects of CRP* expression in Escherichia coli. J Biol Eng 3:13

    Article  CAS  Google Scholar 

  29. Gosset G, Zhang Z, Nayyar S, Cuevas WA, Saier MH Jr (2004) Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli. J Bacteriol 186(11):3516–3524

    Article  CAS  Google Scholar 

  30. Valgepea K, Adamberg K, Seiman A, Vilu R (2014) Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins. Mol BioSyst 9:2344–2358

    Article  CAS  Google Scholar 

  31. Baste DJV, Nol K, Niedenfuhr Mendum TA, Hawkins ND, Ward JL, Beale MH, Wiechert W, McFadden J (2013) 13C-Flux spectral analysis of host-pathogen metabolism reveals a mixed diet for intracellular Mycobacterium tuberculosis. Chem Biol 20:1–10

    Article  CAS  Google Scholar 

  32. Shimizu K (2004) Metabolic flux analysis based on 13C-labeling experiments and integration of the information with gene and protein expression patterns. Adv Biochem Eng Biotechnol 91:1–49

    CAS  Google Scholar 

  33. Shimizu K (2013) Bacterial cellular metabolic systems. Woodhead Publ. Co., Oxford

    Book  Google Scholar 

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Authors and Affiliations

  1. Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan

    Kazuyuki Shimizu

  2. Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan

    Kazuyuki Shimizu

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  1. Kazuyuki Shimizu
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Editors and Affiliations

  1. East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, School of Biotechnology, Shanghai, China

    Qin Ye

  2. East China University of Science and Technology, State Key Laboratory of Bioreactor Engineering, School of Biotechnology, Shanghai, China

    Jie Bao

  3. Shanghai Jiao Tong University, School of Life Sciences and Biotechnology, Shanghai, China

    Jian-Jiang Zhong

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Shimizu, K. (2015). Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions. In: Ye, Q., Bao, J., Zhong, JJ. (eds) Bioreactor Engineering Research and Industrial Applications I. Advances in Biochemical Engineering/Biotechnology, vol 155. Springer, Berlin, Heidelberg. https://doi.org/10.1007/10_2015_320

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