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.
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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
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Nitrogen Regulation
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Sulfur Regulation
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Phosphate Regulation
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Metal Ion Regulation and Oxidative Stress Regulation
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Redox State Regulation
Gunsalus RP (1992) Control of electron flow in Escherichia coli: coordinated transcription of respiratory pathway genes. J Bacteriol 174(22):7069–7074
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Acid Shock
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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
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
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Heat Shock
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
Sørensen HP, Mortensen KK (2005) Soluble expression of recombinant proteins in the cytoplasm of Escherichia coli. Microb Cell Fact 4:1
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
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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
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Cold Shock
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
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Solvent Stress Regulation
Dunlop MJ (2011) Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels 4:32
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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
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Osmoregulation
Kramer R (2010) Bacterial stimulus perception and signal transduction: response to osmotic stress. Chem Res 10:217–229
Wood JM (2011) Bacterial osmoregulation: a paradigm for the study of cellular homeostasis. Ann Rev Microbiol 65:215–238
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Biofilm, Motility and Quarum Sensing
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
Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7:263–273
Barnhart MM, Chapman MR (2006) Curli biogenesis and function. Annu Rev Microbiol 60:131–147
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
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Waters CM, Bassler BL (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21:319–346
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
Systems Biology Approach
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
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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
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
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
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
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Concluding Remarks
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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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