-
1
-
-
34547887655
-
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
-
DOI 10.1073/pnas.0609845104
-
Beg QK, Vazquez A, Ernst J, de Menezes M, Bar-Joseph Z, Barabási A, Oltvai ZN (2007) Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc Natl Acad Sci USA 104: 12663-12668 (Pubitemid 47255211)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.31
, pp. 12663-12668
-
-
Beg, Q.K.1
Vazquez, A.2
Ernst, J.3
De Menezes, M.A.4
Bar-Joseph, Z.5
Barabasi, A.-L.6
Oltvai, Z.N.7
-
2
-
-
0021886039
-
Cell shape and division in Escherichia coli: Experiments with shape and division mutants
-
Begg KJ, Donachie WD (1985) Cell shape and division in Escherichia coli: experiments with shape and division mutants. J Bacteriol 163: 615-622 (Pubitemid 15012635)
-
(1985)
Journal of Bacteriology
, vol.163
, Issue.2
, pp. 615-622
-
-
Begg, K.J.1
Donachie, W.D.2
-
3
-
-
68949158532
-
Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase
-
Bekker M, de Vries S, Ter Beek A, Hellingwerf KJ, de Mattos MJ (2009) Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase. J Bacteriol 191: 5510-5517
-
(2009)
J Bacteriol
, vol.191
, pp. 5510-5517
-
-
Bekker, M.1
De Vries, S.2
Ter Beek, A.3
Hellingwerf, K.J.4
De Mattos, M.J.5
-
4
-
-
68049100110
-
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
-
Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien S, Rabinowitz JD (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 5: 593-599
-
(2009)
Nat Chem Biol
, vol.5
, pp. 593-599
-
-
Bennett, B.D.1
Kimball, E.H.2
Gao, M.3
Osterhout, R.4
Van Dien, S.5
Rabinowitz, J.D.6
-
5
-
-
0029401476
-
Physiological constraints in the aerobic performance of hummingbirds
-
Bicudo JE, Zerbinatti CV (1995) Physiological constraints in the aerobic performance of hummingbirds. Braz J Med Biol Res 28: 1139-1145
-
(1995)
Braz J Med Biol Res
, vol.28
, pp. 1139-1145
-
-
Bicudo, J.E.1
Zerbinatti, C.V.2
-
6
-
-
0025841651
-
+-dependent isocitrate dehydrogenase: Cloning, nucleotide sequence, and disruption of the IDH2 gene from saccharomyces cerevisiae
-
Cupp JR, McAlister-Henn L (1991) NAD(+)-dependent isocitrate dehydrogenase. Cloning, nucleotide sequence, and disruption of the IDH2 gene from Saccharomyces cerevisiae. J Biol Chem 266: 22199-22205 (Pubitemid 21908635)
-
(1991)
Journal of Biological Chemistry
, vol.266
, Issue.33
, pp. 22199-22205
-
-
Cupp, J.R.1
McAlister-Henn, L.2
-
8
-
-
17844363250
-
Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture
-
DOI 10.1111/j.1462-2920.2005.00731.x
-
Esteve-Nunez A, Rothermich M, Sharma M, Lovley D (2005) Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ Microbiol 7: 641-648 (Pubitemid 40580584)
-
(2005)
Environmental Microbiology
, vol.7
, Issue.5
, pp. 641-648
-
-
Esteve-Nunez, A.1
Rothermich, M.2
Sharma, M.3
Lovley, D.4
-
9
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3: 121
-
(2007)
Mol Syst Biol
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
Broadbelt, L.J.7
Hatzimanikatis, V.8
Palsson, B.O.9
-
10
-
-
0034537304
-
Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon
-
DOI 10.1046/j.1365-2958.2000.02215.x
-
Govantes F, Orjalo AV, Gunsalus RP (2000) Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon. Mol Microbiol 38: 1061-1073 (Pubitemid 32009680)
-
(2000)
Molecular Microbiology
, vol.38
, Issue.5
, pp. 1061-1073
-
-
Govantes, F.1
Orjalo, A.V.2
Gunsalus, R.P.3
-
11
-
-
11944264976
-
Studies on hydrogenase activity and chlorobenzene respiration in Dehalococcoides sp. strain CBDB1
-
DOI 10.1007/s00203-004-0734-9
-
Jayachandran G, Gorisch H, Adrian L (2004) Studies on hydrogenase activity and chlorobenzene respiration in Dehalococcoides sp. strain CBDB1. Arch Microbiol 182: 498-504 (Pubitemid 40100811)
-
(2004)
Archives of Microbiology
, vol.182
, Issue.6
, pp. 498-504
-
-
Jayachandran, G.1
Gorisch, H.2
Adrian, L.3
-
12
-
-
0025769570
-
Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S
-
Lange R, Hengge-Aronis R (1991) Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S. J Bacteriol 173: 4474-4481
-
(1991)
J Bacteriol
, vol.173
, pp. 4474-4481
-
-
Lange, R.1
Hengge-Aronis, R.2
-
13
-
-
47149099785
-
The tragedy of the commons in microbial populations: Insights from theoretical, comparative and experimental studies
-
DOI 10.1038/sj.hdy.6801073, PII 6801073
-
MacLean RC (2008) The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies. Heredity 100: 471-477 (Pubitemid 351972598)
-
(2008)
Heredity
, vol.100
, Issue.5
, pp. 471-477
-
-
MacLean, R.C.1
-
14
-
-
0025405421
-
Simple constrained-optimization view of acetate overflow in E. coli
-
DOI 10.1002/bit.260350711
-
Majewski RA, Domach MM (1990) Simple constrained-optimization view of acetate overflow in E. coli. Biotechnol Bioeng 35: 732-738 (Pubitemid 20150014)
-
(1990)
Biotechnology and Bioengineering
, vol.35
, Issue.7
, pp. 732-738
-
-
Majewski, R.A.1
Domach, M.M.2
-
15
-
-
0015829997
-
Oxidative phosphorylation in bacteria which contain different cytochrome oxidases
-
Meyer DJ, Jones CW (1973) Oxidative phosphorylation in bacteria which contain different cytochrome oxidases. Eur J Biochem 36: 144-151
-
(1973)
Eur J Biochem
, vol.36
, pp. 144-151
-
-
Meyer, D.J.1
Jones, C.W.2
-
17
-
-
68949163858
-
Metabolic flux analysis of Escherichia coli creB and arcA mutants reveals shared control of carbon catabolism under microaerobic growth conditions
-
Nikel P, Zhu J, San K, Mendez BS, Bennet GN (2009) Metabolic flux analysis of Escherichia coli creB and arcA mutants reveals shared control of carbon catabolism under microaerobic growth conditions. J Bacteriol 191: 5538-5548
-
(2009)
J Bacteriol
, vol.191
, pp. 5538-5548
-
-
Nikel, P.1
Zhu, J.2
San, K.3
Mendez, B.S.4
Bennet, G.N.5
-
18
-
-
33747363488
-
Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli
-
Novak M, Pfeiffer T, Lenski RE, Sauer U, Bonhoeffer S (2006) Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli. Am Nat 168: 242-251
-
(2006)
Am Nat
, vol.168
, pp. 242-251
-
-
Novak, M.1
Pfeiffer, T.2
Lenski, R.E.3
Sauer, U.4
Bonhoeffer, S.5
-
19
-
-
0033764285
-
The challenges of in silico biology
-
Palsson B (2000) The challenges of in silico biology. Nat Biotechnol 18: 1147-1150
-
(2000)
Nat Biotechnol
, vol.18
, pp. 1147-1150
-
-
Palsson, B.1
-
20
-
-
13444278821
-
Reconstruction of cellular signalling networks and analysis of their properties
-
DOI 10.1038/nrm1570
-
Papin JA, Hunter T, Palsson BO, Subramaniam S (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6: 99-111 (Pubitemid 40215806)
-
(2005)
Nature Reviews Molecular Cell Biology
, vol.6
, Issue.2
, pp. 99-111
-
-
Papin, J.A.1
Hunter, T.2
Palsson, B.O.3
Subramaniam, S.4
-
21
-
-
0036333748
-
Evolutionary consequences of tradeoffs between yield and rate of ATP production
-
Pfeiffer T, Bonhoeffer S (2002) Evolutionary consequences of tradeoffs between yield and rate of ATP production. Z Phys Chem 216: 51-63
-
(2002)
Z Phys Chem
, vol.216
, pp. 51-63
-
-
Pfeiffer, T.1
Bonhoeffer, S.2
-
22
-
-
34548079773
-
Evolution of cross-feeding in microbial populations
-
Pfeiffer T, Bonhoeffer S (2004) Evolution of cross-feeding in microbial populations. Am Nat 163: E126-E136
-
(2004)
Am Nat
, vol.163
-
-
Pfeiffer, T.1
Bonhoeffer, S.2
-
23
-
-
0035917865
-
Cooperation and competition in the evolution of ATP-producing pathways
-
Pfeiffer T, Schuster S, Bonhoeffer S (2001) Cooperation and competition in the evolution of ATP-producing pathways. Science 292: 504-507 (Pubitemid 32335953)
-
(2001)
Science
, vol.292
, Issue.5516
, pp. 504-507
-
-
Pfeiffer, T.1
Schuster, S.2
Bonhoeffer, S.3
-
24
-
-
76049087452
-
A feeling for the numbers in biology
-
Phillips R, Milo R (2009) A feeling for the numbers in biology. PNAS 106: 21465-21471
-
(2009)
PNAS
, vol.106
, pp. 21465-21471
-
-
Phillips, R.1
Milo, R.2
-
25
-
-
57449102586
-
Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain
-
Portnoy VA, Herrgård M, Palsson B (2008) Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain. Appl Environ Microbiol 74: 7561-7569
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 7561-7569
-
-
Portnoy, V.A.1
Herrgård, M.2
Palsson, B.3
-
26
-
-
0025796578
-
Properties of the two terminal oxidases of Escherichia coli
-
Puustinen A, Finel M, Haltia T, Gennis RB, Wikstrom M (1991) Properties of the two terminal oxidases of Escherichia coli. Biochemistry 30: 3936-3942
-
(1991)
Biochemistry
, vol.30
, pp. 3936-3942
-
-
Puustinen, A.1
Finel, M.2
Haltia, T.3
Gennis, R.B.4
Wikstrom, M.5
-
27
-
-
0025912489
-
In vivo assembly of yeast mitochondrial α-ketoglutarate dehydrogenase complex
-
Repetto B, Tzagoloff A (1991) In vivo assembly of yeast mitochondrial alpha-ketoglutarate dehydrogenase complex. Mol Cell Biol 11: 3931-3939 (Pubitemid 21895782)
-
(1991)
Molecular and Cellular Biology
, vol.11
, Issue.8
, pp. 3931-3939
-
-
Repetto, B.1
Tzagoloff, A.2
-
28
-
-
70350460030
-
Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens
-
Risso C, Sun J, Zhuang K, Mahadevan R, DeBoy R, Ismail W, Shrivastava S, Huot H, Kothari S, Daugherty S, Bui O, Schilling CH, Lovley DR, Methe BA (2009) Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens. BMC Genomics 10: 447
-
(2009)
BMC Genomics
, vol.10
, pp. 447
-
-
Risso, C.1
Sun, J.2
Zhuang, K.3
Mahadevan, R.4
Deboy, R.5
Ismail, W.6
Shrivastava, S.7
Huot, H.8
Kothari, S.9
Daugherty, S.10
Bui, O.11
Schilling, C.H.12
Lovley, D.R.13
Methe, B.A.14
-
29
-
-
43449132092
-
Is maximization of molar yield in metabolic networks favoured by evolution?
-
Schuster S, Pfeiffer T, Fell DA (2008) Is maximization of molar yield in metabolic networks favoured by evolution? J Theor Biol 252: 497-504
-
(2008)
J Theor Biol
, vol.252
, pp. 497-504
-
-
Schuster, S.1
Pfeiffer, T.2
Fell, D.A.3
-
30
-
-
36248971737
-
Control of key metabolic intersections in Bacillus subtilis
-
DOI 10.1038/nrmicro1772, PII NRMICRO1772
-
Sonenshein AL (2007) Control of key metabolic intersections in Bacillus subtilis. Nat Rev Microbiol 5: 917-927 (Pubitemid 350131180)
-
(2007)
Nature Reviews Microbiology
, vol.5
, Issue.12
, pp. 917-927
-
-
Sonenshein, A.L.1
-
31
-
-
0022736565
-
Growth of Saccharomyces cerevisiae is controlled by its limited respiratory capacity: Formulation and verification of a hypothesis
-
Sonnleitner B, Kappeli O (1986) Growth of Saccharomyces cerevisiae is controlled by its limited respiratory capacity: formulation and verification of a hypothesis. Biotechnol Bioeng 28: 927-937 (Pubitemid 16568397)
-
(1986)
Biotechnology and Bioengineering
, vol.28
, Issue.6
, pp. 927-937
-
-
Sonnleitner, B.1
Kaeppeli, O.2
-
32
-
-
0030067649
-
Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli
-
Tseng CP, Albrecht J, Gunsalus RP (1996) Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli. J Bacteriol 178: 1094-1098 (Pubitemid 26048026)
-
(1996)
Journal of Bacteriology
, vol.178
, Issue.4
, pp. 1094-1098
-
-
Tseng, C.-P.1
Albrecht, J.2
Gunsalus, R.P.3
-
33
-
-
66249108601
-
Understanding theWarburg effect: The metabolic requirements of cell proliferation
-
Vander Heiden MG, Cantley LC, Thompson CB (2009) Understanding theWarburg effect: the metabolic requirements of cell proliferation. Science 324: 1029-1033
-
(2009)
Science
, vol.324
, pp. 1029-1033
-
-
Vander Heiden, M.G.1
Cantley, L.C.2
Thompson, C.B.3
-
34
-
-
0028146781
-
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
-
Varma A, Palsson BO (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 60: 3724-3731 (Pubitemid 24298868)
-
(1994)
Applied and Environmental Microbiology
, vol.60
, Issue.10
, pp. 3724-3731
-
-
Varma, A.1
Palsson, B.O.2
-
35
-
-
41149087177
-
Impact of the solvent capacity constraint on E. coli metabolism
-
Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, Barabasi AL, Boros LG, Oltvai ZN (2008) Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst Biol 2: 7
-
(2008)
BMC Syst Biol
, vol.2
, pp. 7
-
-
Vazquez, A.1
Beg, Q.K.2
Demenezes, M.A.3
Ernst, J.4
Bar-Joseph, Z.5
Barabasi, A.L.6
Boros, L.G.7
Oltvai, Z.N.8
-
36
-
-
33846827387
-
Global gene expression analysis of glucose overflow metabolism in Escherichia coli and reduction of aerobic acetate formation
-
DOI 10.1007/s00253-006-0680-3
-
Veit A, Polen T, Wendisch VF (2007) Global gene expression analysis of glucose overflow metabolism in Escherichia coli and reduction of aerobic acetate formation. Appl Microbiol Biotechnol 74: 406-421 (Pubitemid 46204517)
-
(2007)
Applied Microbiology and Biotechnology
, vol.74
, Issue.2
, pp. 406-421
-
-
Veit, A.1
Polen, T.2
Wendisch, V.F.3
-
37
-
-
33646578756
-
Overflow metabolism in Escherichia coli during steady-state growth: Transcriptional regulation and effect of the redox ratio
-
DOI 10.1128/AEM.72.5.3653-3661.2006
-
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: 3653-3661 (Pubitemid 43728022)
-
(2006)
Applied and Environmental Microbiology
, vol.72
, Issue.5
, pp. 3653-3661
-
-
Vemuri, G.N.1
Altman, E.2
Sangurdekar, D.P.3
Khodursky, A.B.4
Eiteman, M.A.5
-
38
-
-
33847785682
-
Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae
-
DOI 10.1073/pnas.0607469104
-
Vemuri GN, Eiteman MA, McEwen JE, Olsson L, Nielsen J (2007) Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 104: 2402-2407 (Pubitemid 46391409)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.7
, pp. 2402-2407
-
-
Vemuri, G.N.1
Eiteman, M.A.2
McEwen, J.E.3
Olsson, L.4
Nielsen, J.5
-
39
-
-
0031441724
-
Optimization of glycolysis: A new look at the efficiency of energy coupling
-
Waddell TG, Repovic P, Meléndez-Hevia E, Heinrich R, Montero F (1997) Optimization of glycolysis: a new look at the efficiency of energy coupling. Biochem Educ 25: 204-205
-
(1997)
Biochem Educ
, vol.25
, pp. 204-205
-
-
Waddell, T.G.1
Repovic, P.2
Meléndez-Hevia, E.3
Heinrich, R.4
Montero, F.5
-
40
-
-
34848823739
-
Consequences of membrane protein overexpression in Escherichia coli
-
DOI 10.1074/mcp.M600431-MCP200
-
Wagner S, Baars L, Ytterberg AJ, Klussmeier A, Wagner CS, Nord O, Nygren PA, van Wijk K, de Gier J (2007) Consequences of membrane protein overexpression in Escherichia coli. Mol Cell Proteomics 6: 1527-1550 (Pubitemid 47506165)
-
(2007)
Molecular and Cellular Proteomics
, vol.6
, Issue.9
, pp. 1527-1550
-
-
Wagner, S.1
Baarst, L.2
Ytterberg, A.J.3
Klussmerer, A.4
Wagner, C.S.5
Nord, O.6
Nygren, P.-A.7
Van Wijks, K.J.8
De Gier, J.-W.9
-
41
-
-
0028943972
-
Effects of growth conditions on mitochondrial morphology in Saccharomyces cerevisiae
-
Visser W, Spronsen E, Nanninga N, Pronk J, Kuenen JG, Dijken JP (1995) Effects of growth conditions on mitochondrial morphology in Saccharomyces cerevisiae. Antonie van Leeuwenhoek 67: 243-253
-
(1995)
Antonie Van Leeuwenhoek
, vol.67
, pp. 243-253
-
-
Visser, W.1
Spronsen, E.2
Nanninga, N.3
Pronk, J.4
Kuenen, J.G.5
Dijken, J.P.6
-
42
-
-
78751584992
-
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
-
Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, Mahadevan R, Lovley DR (2011) Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J 5: 305-316
-
(2011)
ISME J
, vol.5
, pp. 305-316
-
-
Zhuang, K.1
Izallalen, M.2
Mouser, P.3
Richter, H.4
Risso, C.5
Mahadevan, R.6
Lovley, D.R.7
|