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Buchtitelbild

2016 | OriginalPaper | Buchkapitel

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

verfasst von : Kazuyuki Shimizu

Erschienen in: Bioreactor Engineering Research and Industrial Applications I

Verlag: Springer Berlin Heidelberg

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Abstract

Living organisms have sophisticated but well-organized regulation system. It is important to understand the metabolic regulation mechanisms in relation to growth environment for the efficient design of cell factories for biofuels and biochemicals production. Here, an overview is given for carbon catabolite regulation, nitrogen regulation, ion, sulfur, and phosphate regulations, stringent response under nutrient starvation as well as oxidative stress regulation, redox state regulation, acid-shock, heat- and cold-shock regulations, solvent stress regulation, osmoregulation, and biofilm formation, and quorum sensing focusing on Escherichia coli metabolism and others. The coordinated regulation mechanisms are of particular interest in getting insight into the principle which governs the cell metabolism. The metabolism is controlled by both enzyme-level regulation and transcriptional regulation via transcription factors such as cAMP–Crp, Cra, Csr, Fis, PII(GlnB), NtrBC, CysB, PhoR/B, SoxR/S, Fur, MarR, ArcA/B, Fnr, NarX/L, RpoS, and (p)ppGpp for stringent response, where the timescales for enzyme-level and gene-level regulations are different. Moreover, multiple regulations are coordinated by the intracellular metabolites, where fructose 1,6-bisphosphate (FBP), phosphoenolpyruvate (PEP), and acetyl-CoA (AcCoA) play important roles for enzyme-level regulation as well as transcriptional control, while α-ketoacids such as α-ketoglutaric acid (αKG), pyruvate (PYR), and oxaloacetate (OAA) play important roles for the coordinated regulation between carbon source uptake rate and other nutrient uptake rate such as nitrogen or sulfur uptake rate by modulation of cAMP via Cya.

Graphical Abstract

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Nächstes Kapitel Efficient Biocatalytic Synthesis of Chiral Chemicals
Literatur
1.
Jone RG, Thompson CB (2009) Tumor suppressors and cell metabolism: a recipe for cancer growth. Genes Dev 23:537–548CrossRef
2.
Hsu PP, Sabatini DM (2008) Cancer cell metabolism: Warburg and beyond. Cell 134:703–707CrossRef
3.
Kroemer G, Pouyssegur J (2008) Tumor cell metabolism: cancer’s Achilles’ heel. Cancer Cell 13:472–482CrossRef
4.
Folger O et al (2011) Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol 7:501CrossRef
5.
McInerney MJ, Sieber JR, Gunsalus RP (2009) Syntrophy in anaerobic global carbon cycles. Curr Opin Biotechnol 20:623–632CrossRef
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 74:6126–6131CrossRef
7.
Lin LH et al (2006) Long-term sustainability of a high-energy, low-diversity crustal biome. Science 314:479–482CrossRef
8.
Peralta-Yahya PP, Zhang F, del Cardayre SB, Keasling JD (2012) Microbial engineering for the production of advanced biofuels. Nature 488:320–328CrossRef
9.
Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–90CrossRef
10.
Yim H et al (2011) Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7:445–452CrossRef
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 476:355–359CrossRef
12.
Bond-Watts BB, Bellerose RJ, Chang MC (2011) Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat Chem Biol 7:222–227CrossRef
13.
Shen CR et al (2011) Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl Environ Microbiol 77:2905–2915CrossRef
14.
Keasling JD (2010) Manufacturing molecules through metabolic engineering. Science 330:1355–1358CrossRef
15.
Shimizu K (2014) Biofuels and biochemicals production by microbes. NOVA Publishing Co., USA
16.
Bar-Even A, Flamholz A, Noor E, Mil R (2012) Rethinking of glycolysis: on the biochemical logic of metabolic pathways. Nat Chem Biol 8:509–517CrossRef
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):10039–10044CrossRef
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 4:1–35CrossRef
20.
Chubukov V, Gerosa L, Kochanowski K, Sauer U (2014) Coordination of microbial metabolism. Nat Rev 12:327–340
21.
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):727–743CrossRef
22.
Nikaido H (2003) Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 67(4):593–656CrossRef
23.
Nikaido H, Vaara M (1985) Molecular basis of bacterial outer membrane permeability. Microbiol Rev 49(1):1–32
24.
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
25.
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
26.
Poolman B, Konings WN (1993) Secondary solute transport in bacteria. Biochim Biophy Acta 1183(1):5–39CrossRef
27.
Deutscher J, Francke C, Postoma PW (2006) How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 70(4):939–1031CrossRef
28.
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
29.
Chakrabarti AC, Deamer DW (1992) Permeability of lipid bilayers to amino acids and phosphate. Biochim Biophys Acta 1111:171–177CrossRef
30.
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
31.
Finkelstein A (1976) Water and nonelectrolyte permeability of lipid bilayer membranes. J Gen Physiol 68:127–135CrossRef
32.
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 41:4939–4949CrossRef
33.
Davis BD (1958) On the importance of being ionized. Arch Biochem Biophys 78:497–509CrossRef
34.
Westheimer FH (1987) Why nature chose phosphates. Science 235:1173–1178CrossRef
35.
Gorke B, Stulke J (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6:613–624CrossRef
36.
37.
Gosset G (2005) Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate: sugar phosphotransferase system. Microb Cell Fact 4:14CrossRef
38.
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 30:487–498CrossRef
39.
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 189:6891–6900CrossRef
40.
Schaub J, Reuss M (2008) In vivo dynamics of glycolysis in E. coli shows need for gowth-rate dependent metabolome analysis. Biotechnol Prog 24:1402–1407CrossRef
41.
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 110:1130–1135CrossRef
42.
Kotte O, Zaugg JB, Heinemann M (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 6:355CrossRef
43.
Huberts DH, Niebel B, Heinemann M (2012) A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 12(2):118–128CrossRef
44.
Kremling A, Bettenbrock K, Gilles ED (2008) A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake. Bioinformatics 24:704–710CrossRef
45.
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 168:155–173CrossRef
46.
Shimada T, Yamamoto K, Ishihama A (2011) Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. J Bacteriol 193(3):649–659CrossRef
47.
Saier MH Jr, Ramseier TM (1996) The catabolite repressor/activator (Cra) protein of enteric bacteria. J Bacteriol 178:3411–3417
48.
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 316:593–597CrossRef
49.
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 4:166CrossRef
50.
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 10:67CrossRef
51.
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
52.
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 10:97–108CrossRef
53.
Russel JB et al (2007) The energy spilling reactions of bacteria and other organisms. J Mol Microbiol Biotechnol 13:1–11CrossRef
54.
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 5:106CrossRef
55.
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 151:693–706CrossRef
56.
Wolfe AJ (2005) The acetate switch. Microbiol Mol Biol Rev 69:12–50CrossRef
57.
Majewski RA, Domach MM (1990) Simple constrained-optimization view of acetate overflow in Escherichia coli. Biotech Bioeng 35:732–738CrossRef
58.
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 84:129–144CrossRef
59.
Lee SY (1996) High cell-density cultivation of Escherichia coli. Trends Biotechnol 14:98–105CrossRef
60.
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 132:359–374CrossRef
61.
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):750–758CrossRef
62.
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):1603–1614CrossRef
63.
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 31:605–610CrossRef
64.
Pirt SJ (1982) Maintenance energy: a general model for energy-limited and energy-sufficient growth. Arch Microbiol 133:300–302CrossRef
65.
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
66.
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
67.
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 44:179–187CrossRef
68.
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
69.
Vasudevan P, Briggs M (2008) Biodiesel production–current state of the art and challenges. J Ind Microbiol Biotechnol 35:421–430CrossRef
70.
Dharmadi Y, Murarka A, Gonzalez R (2006) Anaerobic fermentation of glycerol by Escherichia coli: a new platform for metabolic engineering. Biotechnol Bioeng 94:821–829CrossRef
71.
Clomburg JM, Gonzalez Ramon (2013) Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicals. Trends Biotechnol 31(1):20–28CrossRef
72.
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 5:48CrossRef
73.
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 11:46CrossRef
74.
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 61:163–178CrossRef
75.
Oh MK, Liao JC (2000) Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol Prog 16:278–286CrossRef
76.
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):23150–23159CrossRef
77.
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
78.
Kornberg HL (2001) Routes for fructose utilization by Escherichia coli. J Mol Microbiol Biotechnol 3:355–359
79.
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
80.
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 42:224–228CrossRef
81.
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 190:559–571CrossRef
82.
Crasnier-Mednansky M, Park MC, Studley WK, Saier MH Jr (1997) Cra-mediated regulations of Escherichia coli adenylate cyclase. Microbiology 143:785–792CrossRef
83.
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 4:684–695CrossRef
84.
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
85.
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
86.
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 186:7593–7600CrossRef
87.
Novotny CP, Englesberg E (1966) The L-arabinose permease system in Escherichia coli B/r. Biochim Biophys Acta 117:217–230CrossRef
88.
Schleif R (1969) An L-arabinose binding protein and arabinose permeation in Escherichia coli. J Mol Biol 46:185–196CrossRef
89.
Doyle ME, Brown C, Hogg RW, Helling RB (1972) Induction of the ara operon of Escherichia coli B-r. J Bacteriol 110:56–65
90.
Davidson CJ, Narang A, Surette MG (2010) Integration of transcriptional inputs at promoters of the arabinose catabolic pathway. BMC Syst Biol 4:75CrossRef
91.
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 5:111CrossRef
92.
Desai TA, Rao CV (2010) Regulation of arabinose and xylose metabolism in Escherichia coli. Appl Environ Microbiol 76:1524–1532CrossRef
93.
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 78:2221–2229CrossRef
94.
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
95.
Schuetz R, Zamboni N, Zampieri M, Heinemann M et al (2012) Multidimensional optimality of microbial metabolism. Science 336:601–604
96.
Enjalbert B, Letisse F, Portais J-C (2013) Physiological and molecular timing of the glucose to acetate transition in Escherichia coli. Metabolites 3:820–837CrossRef
97.
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 8:562–568CrossRef
98.
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
99.
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 153:2922–2940CrossRef
100.
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 186:122–135CrossRef
101.
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 188:5775–5782CrossRef
102.
Paul BJ, Berkmen MB, Gourse RL (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. PNAS USA 102:7823–7828CrossRef
103.
Ferenci T (2001) Hungry bacteria—definition and properties of a nutritional state. Environ Microbiol 3:605–611CrossRef
104.
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):45–54CrossRef
105.
Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S (2004) Structural basis for transcription regulation by alarmone ppGpp. Cell 117:299–310CrossRef
106.
Kanjee U, Ogata K, Houry WA (2012) Direct binding targets of the stringent response alarmone (p)ppGpp. Mol Micobiol 85(6):1029–1043CrossRef
107.
Hengge-Aronis R (2002) Signal transduction and regulatory mechanisms involved in control of the σS (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 66:373–395CrossRef
108.
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):580–591CrossRef
109.
Jishage M, Kvint K, Shingler V, Nystrom T (2002) Regulation of σ factor competition by the alarmone ppGpp. Genes Dev 16:1260–1270CrossRef
110.
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):7186–7195CrossRef
111.
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):8499–8507CrossRef
112.
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):160–169CrossRef
113.
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 30:853–860CrossRef
114.
Llorens NJM, Tormo A, Martínez-García E (2010) Stationary phase in gram-negative bacteria. FEMS Microbiol Rev 34:476–495CrossRef
115.
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 4:400–404CrossRef
116.
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 23:227–232CrossRef
117.
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 17:234–247CrossRef
118.
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 17:177–187CrossRef
119.
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 1824:1442–1448CrossRef
120.
Timmermans J, van Melderen L (2010) Post-transcriptional global regulation by CsrA in bacteria. Cell Mol Life Sci 67(17):2897–2908CrossRef
121.
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):524–540CrossRef
122.
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):1605–1620CrossRef
123.
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
124.
Dubey AK, Baker CS, Romeo T, Babitzke P (2005) RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction. RNA 11(10):1579–1587CrossRef
125.
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):5130–5140CrossRef
126.
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):657–670CrossRef
127.
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):1599–1610CrossRef
128.
Dong T, Schellhorn HE (2009) Control of RpoS in global gene expression of Escherichia coli in minimal media. Mol Genet Genomics 281:19–33CrossRef
129.
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 80:1561–1580CrossRef
130.
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 11:79CrossRef
131.
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)
132.
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):26–32CrossRef
133.
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):628–695CrossRef
134.
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
135.
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 104:42–47CrossRef
136.
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 285:31037–31045CrossRef
137.
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 400:531–539CrossRef
138.
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 5:302CrossRef
139.
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 36:31–75CrossRef
140.
Gerosa L, Kochanowski K, Heinemann M, Sauer U (2013) Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol Syst Biol 9:658CrossRef
141.
Kiupakis AK, Reitzer L (2002) ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli. J Bacteriol 184(11):2940–2950CrossRef
142.
Commichau FM, Forchhammer K, Stulke J (2006) Regulatory links between carbon and nitrogen metabolism. Curr Opin Microbiol 9(2):167–172CrossRef
143.
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):1432–1440CrossRef
144.
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
145.
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):12979–12996CrossRef
146.
Ninfa J, Jiang P (2005) PII signal transduction proteins: sensors of -ketoglutarate that regulate nitrogen metabolism. Curr Opin Microbiol 8(2):168–173CrossRef
147.
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 103:19302–19307CrossRef
148.
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 41:117–127CrossRef
149.
Doucette CD, Schwab DJ, Wingreen NS, Rabinowitz JD (2011) Alpha-ketoglutarate coordinates carbon and nitrogen utilization via enzyme i inhibition. Nat Chem Biol 7:894–901CrossRef
150.
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 500:301–306CrossRef
151.
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 270:4822–4839CrossRef
152.
Peterkofski A, Wang G, Seok Y-J (2006) Parallel PTS systems. Arch Biochem Biophys 453(1):101–107CrossRef
153.
Pflüger-Grau K, Görke B (2010) Regulatory roles of the bacterial nitrogen-related phosphotransferase system. Trend Microbiol 18(5):205–214CrossRef
154.
Lee CR, Cho SH, Yoon MJ, Peterkofsky A, Seok YJ (2007) Escherichia coli enzyme IIANtr regulates the K+ transporter TrkA. PNAS USA 104:4124–4129CrossRef
155.
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):978–994CrossRef
156.
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):1468–1483CrossRef
157.
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):96–110CrossRef
158.
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):556–561CrossRef
159.
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):473–485CrossRef
160.
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 43:1347–1358CrossRef
161.
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
162.
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 166:11–17CrossRef
163.
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 97:14674–14679CrossRef
164.
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):1074–1090CrossRef
165.
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
166.
Wanner BL (1993) Gene regulation by phosphate in enteric bacteria. J Cellr Biochem 51(1):47–54CrossRef
167.
Baek JH, Lee SY (2007) Transcriptome analysis of phosphate starvation response in Escherichia coli. J Microbiol Biotechnol 17(2):244–252
168.
Van Dien SJ, Keasling JD (1998) A dynamic model of the Escherichia coli phosphate-starvation response. J Theoret Biol 190(1):37–49CrossRef
169.
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 10:39CrossRef
170.
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
171.
Frey PA, Reed GH (2012) The ubiquity of iron. ACS Chem Biol 7:1477–1481CrossRef
172.
Dixon SJ, Stockwell BR (2014) The role of iron and reactive oxygen species in cell death. Nat Chem Biol 10:9–17CrossRef
173.
Dann CEIII, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winker WC (2007) Structure and mechanism of a metal-sensing regulatory RNA. Cell 130:878–892CrossRef
174.
175.
Zheng M, Doan B, Schneider TD, Storz G (1999) OxyR and SoxRS regulation of fur. J Biotechnol 181:4639–4643
176.
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 278:29478–29486CrossRef
177.
Storz G, Imlay JA (1999) Oxidative stress. Curr Opin Microbiol 2:188–194CrossRef
178.
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
179.
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:e1186CrossRef
180.
Brynildsen MP, Liao JC (2009) An integrated network approach indentifies the isobutanol response network of Escherichia coli. Mol Syst Biol 5:34CrossRef
181.
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
182.
Azpiroz MF, Lavińa M (2004) Involvement of enterobactin synthesis pathway in production of Microcin H47. Antimicrob Agents Chemother 48:1235–1241CrossRef
183.
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 34:4960–4967CrossRef
184.
Hantash FM, Ammerlaan M, Earhart CF (1997) Enterobactin synthase polypeptides of Escherichia coli are present in an osmotic-shock-sensitive cytoplasmic locality. Microbiol 143:147–156CrossRef
185.
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 10:3CrossRef
186.
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 187:980–990CrossRef
187.
Perera IC, Grove A (2010) Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators. J Mol Cell Biol 2:243–254CrossRef
188.
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 10:21–28CrossRef
189.
Pomposiello PJ, Demple B (2001) Redox-operated genetic switches: the SoxR and OxyR transcription factors. Trends Biotechnol 19(3):109–114CrossRef
190.
Gaudu P, Weiss B (1996) SoxR, a [2Fe–2S] transcription factor, is active only in its oxidized form. PNAS USA 93(19):10094–10098CrossRef
191.
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):e690CrossRef
192.
DeNicola GM et al (2011) Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis. Nature 475:106–109CrossRef
193.
Son J et al (2013) Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature 496:101–105CrossRef
194.
Maddocks OD et al (2013) Serine starvation induces stress and p53-dependent metabolic remodeling in cancer cells. Nature 493:542–546CrossRef
195.
Trachootham D, Alexandre J, Huang P (2009) Targeting cancer cells by ROS-mediated mechanisms: a radical therapeutic approach ? Nat Rev Drug Discov 8:579–591CrossRef
196.
Gunsalus RP (1992) Control of electron flow in Escherichia coli: coordinated transcription of respiratory pathway genes. J Bacteriol 174(22):7069–7074
197.
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):29837–29855CrossRef
198.
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):204–209CrossRef
199.
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):619–627CrossRef
200.
Georgellis D, Kwon O, Lin ECC (2001) Quinones as the redox signal for the arc two-component system of bacteria. Science 292(5525):2314–2316CrossRef
201.
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):13318–13323CrossRef
202.
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):4802–4815CrossRef
203.
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
204.
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 8:2593–2604CrossRef
205.
Maeda T, Sanchez-Torres V, Wood TK (2007) Enhanced hydrogen production from glucose by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 77:879–890CrossRef
206.
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
207.
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 7:104–115CrossRef
208.
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):3653–3661CrossRef
209.
Valgepea K, Adamberg K, Seiman A, Vilu R (2014) Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins. Mol BioSyst 9:2344–2358CrossRef
210.
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):240–250CrossRef
211.
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):538–542CrossRef
212.
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 42:229–236CrossRef
213.
Foster JW (2004) Escherichia coli acid resistance: tales of an amateur acidophile. Nat Rev Microbiol 2(11):898–907CrossRef
214.
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
215.
Richard HT, Foster JW (2003) Acid resistance in Escherichia coli. Adv Appl Microbiol 52:167–186CrossRef
216.
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):6032–6041CrossRef
217.
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):4402–4409CrossRef
218.
Iyer R, Williams C, Miller C (2003) Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli. J Bacteriol 185:6556–6561CrossRef
219.
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
220.
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 147:709–715CrossRef
221.
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 10:39CrossRef
222.
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):6181–6185CrossRef
223.
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
224.
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 7:3CrossRef
225.
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):2907–2917CrossRef
226.
Sørensen HP, Mortensen KK (2005) Soluble expression of recombinant proteins in the cytoplasm of Escherichia coli. Microb Cell Fact 4:1CrossRef
227.
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
228.
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
229.
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
230.
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):25871–25875CrossRef
231.
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
232.
Kumari S, Beatty CM, Browning DF et al (2000) Regulation of acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 182(15):4173–4179CrossRef
233.
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):687–701CrossRef
234.
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):5148–5157CrossRef
235.
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):241–254CrossRef
236.
Privalle CT, Fridovich I (1987) Induction of superoxide dismutase in Escherichia coli by heat shock. PNAS USA 84(9):2723–2726CrossRef
237.
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
238.
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 154:148–166CrossRef
239.
Kim Y-H, Han KY, Lee K, Lee J (2005) Proteome response of Escherichia coli fed-batch culture to temperature downshift. Appl Microbiol Biotechnol 68:786–793CrossRef
240.
Dunlop MJ (2011) Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels 4:32CrossRef
241.
Isken S, de Bont JAM (1998) Bacteria tolerant to organic solvents. Extremophiles 2:229–238CrossRef
242.
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 56:743–768CrossRef
243.
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 12:307–331CrossRef
244.
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 107:6559–6565CrossRef
245.
Ankarloo J, Wikman S, Nicholls IA (2010) Escherichia coli mar and acrAB mutants display no tolerance to simple alcohols. Int J Mol Sci 11:1403–1412CrossRef
246.
Piper P (1995) The heat-shock and ethanol stress responses of yeast exhibit extensive similarity and functional overlap. FEMS Microbiol Lett 134:121–127CrossRef
247.
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 76:1935–1945CrossRef
248.
Tomas C, Beamish J, Papoutsakis E (2004) Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum. J Bacteriol 186:2006–2018CrossRef
249.
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 77:909–915CrossRef
250.
Reyes LH, Almario MP, Kao KC (2011) Genomic library screens for genes involved in n-butanol tolerance in Escherichia coli. PLoS One 6:e17678CrossRef
251.
Sikkema J, de Bont JAM, Poolman B (1995) Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59:201–222
252.
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
253.
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 8:401–410CrossRef
254.
Kramer R (2010) Bacterial stimulus perception and signal transduction: response to osmotic stress. Chem Res 10:217–229
255.
Wood JM (2011) Bacterial osmoregulation: a paradigm for the study of cellular homeostasis. Ann Rev Microbiol 65:215–238CrossRef
256.
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
257.
Sugiura A, Hirokawa K, Nakashima K, Mizuno T (1994) Signal-sensing mechanisms of the putative osmosensor KdpD in Escherichia coli. Mol Microbiol 14:929–938CrossRef
258.
Hamann K, Zimmann P, Altendorf K (2008) Reduction of turgor is not the stimulus for the sensor kinase KdpD of Escherichia coli. J Bacteriol 190:2360–2367CrossRef
259.
Heermann R, Jung K (2010) The complexity of the ‘simple’ two-component system KdpD/KdpE in Escherichia coli. Microbiol Lett 304:97–106CrossRef
260.
Sevin DC, Sauer U (2014) Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli. Nat Chem Biol 10:266–272CrossRef
261.
Piuri M, Sanchez-Rivas C, Ruzal SM (2005) Cell wall modifications during osmotic stress in Lactobacullus casei. J Appl Microbiol 98:84–95CrossRef
262.
Clarke CF, Rowat AC, Gober JW (2014) Is CoQ a membrane stabilizer? Nat Chem Biol 10:242–243CrossRef
263.
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 270:29063–29066CrossRef
264.
Lamins LA, Rhoads DB, Epstein W (1981) Osmotic control of kdp operon expression in Escherichia coli. PNAS USA 78:464–468CrossRef
265.
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 23:143–148CrossRef
266.
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
267.
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 55:214–218CrossRef
268.
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
269.
Elbein AD, Pan YT, Pastuszak I, Carroll D (2003) New insights on trehalose: a multifunctional molecule. Glycobiology 13:17R–27RCrossRef
270.
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
271.
Turunen M, Olsson J, Dallner G (2004) Metabolism and function of coenzyme Q. Biochim Biophys ACTA Biomembr 1660:171–199CrossRef
272.
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 56:1648–1663CrossRef
273.
Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7:263–273CrossRef
274.
Barnhart MM, Chapman MR (2006) Curli biogenesis and function. Annu Rev Microbiol 60:131–147CrossRef
275.
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
276.
Jackson DW, Simecka JW, Romeo T (2002) Catabolite repression of Escherichia coli biofilm formation. J Bacteriol 184:3406–3410CrossRef
277.
Waters CM, Bassler BL (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21:319–346CrossRef
278.
De Lay N, Gottesman S (2009) The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J Bacteriol 191:461–476CrossRef
279.
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
280.
Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M (2014) Kinetic models in industrial biotechnology-improving cell factory performance. Metab Eng 24:38–60CrossRef
281.
Chassagnole C, Noisommitt-Rizzi N, Schmid JW, Mauch K, Reuss M (2002) Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79:53–73CrossRef
282.
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 9:88CrossRef
283.
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 4:160CrossRef
284.
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 147:17–30CrossRef
285.
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 168:155−173CrossRef
286.
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 13:2435–2443CrossRef
287.
Maheswaran M, Forchhammer K (2003) Carbon-source-dependent nitrogen regulation in Escherichia coli is mediated through glutamine-dependent GlnB signaling. Microbiology 149:2163–2172CrossRef
288.
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 148:123–131CrossRef
289.
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 173:537–546CrossRef
290.
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):980–990CrossRef
291.
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):1074–1090CrossRef
292.
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 9:643CrossRef
293.
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 187:1591–1603CrossRef
294.
Jenkins D, Schultz J, Matin A (1988) Starvation-induced cross protection against heat or H2O2 challenge in Escherichia coli. J Bacteriol 170:3910–3914
295.
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
296.
Gunasekera T, Csonka L, Paliy O (2008) Genome-wide transcriptional responses of Escherichia coli K-12 to continuous osmotic and heat stresses. J Bacteriol 190:3712–3720CrossRef
297.
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 154:148–166CrossRef
298.
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 76:1935–1945CrossRef
299.
Rabinowitz J, Silhavy TJ (2012) Metabolite turns master regulator. Nature 500:283–284CrossRef
300.
Klumpp S, Zhang Z, Hwa T (2009) Growth rate-dependent global effects on gene expression in bacteria. Cell 139:1366–1375CrossRef
301.
Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T (2010) Interdependence of cell growth and gene expression: origins and consequences. Science 330:1099–1102CrossRef
302.
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 184:3909CrossRef
303.
Luo Y, Zhang T, Wu H (2014) The transport and mediation mechanisms of the common sugars in Escherichia coli. Biotechnol Adv 32:905–919CrossRef
304.
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):1409–1417CrossRef
305.
Aidelberg G, Towbin BD, Rothschild D, Dekel E, Bren A, Alon U (2014) Hierarchy of non-glucose sugars in Escherichia coli. BMC Syst Biol 8:133CrossRef
306.
Balsalobre C, Johansson J, Uhlin BE (2006) Cyclic AMP-dependent osmoregulation of crp gene expression in Escherichia coli. J Bacteriol 188(16):5935–5944CrossRef
307.
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):1165–1172CrossRef
308.
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):e51179CrossRef
309.
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
310.
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):e77422CrossRef
311.
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):e57628CrossRef
312.
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 94:1107–1117CrossRef
313.
Khankal R, Chin JW, Ghosh D, Cirino PC (2009) Transcriptional effects of CRP* expression in Escherichia coli. J Biol Eng 3:13CrossRef
314.
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):3516–3524CrossRef
315.
Valgepea K, Adamberg K, Seiman A, Vilu R (2014) Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins. Mol BioSyst 9:2344–2358CrossRef
316.
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 20:1–10CrossRef
317.
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
318.
Shimizu K (2013) Bacterial cellular metabolic systems. Woodhead Publ. Co., OxfordCrossRef
Metadaten
Titel
Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions
verfasst von
Kazuyuki Shimizu
Copyright-Jahr
2016
Verlag
Springer Berlin Heidelberg
Buch
Bioreactor Engineering Research and Industrial Applications I

Print ISBN: 978-3-662-49159-1

Electronic ISBN: 978-3-662-49161-4

Copyright-Jahr: 2016

DOI
https://doi.org/10.1007/10_2015_320