The metabolic potential of Escherichia coli BL21 in defined and rich medium

Microbial Cell Factories

Volumn 13, Issue 1, 2014, Pages

  Li, Zhaopeng ^a,b   Nimtz, Manfred ^a   Rinas, Ursula ^a,b  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b LEIBNIZ UNIVERSITY HANNOVER   (Germany)

Author keywords

Escherichia coli; Growth rate control; Metabolic balance; Overflow metabolism; Proteome; Stationary phase response; Transcriptional control; Two dimensional gel electrophoresis

Indexed keywords

PROTEOME; PYRUVATE DEHYDROGENASE; PYRUVATE DEHYDROGENASE COMPLEX;

AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL PHENOMENA AND FUNCTIONS; BIOMASS; CARBON METABOLISM; CELL PROTECTION; CITRIC ACID CYCLE; CULTURE MEDIUM; ESCHERICHIA COLI; ESCHERICHIA COLI BL21; GLYCOLYSIS; METABOLIC BALANCE; METABOLISM; NONHUMAN; NUTRIENT AVAILABILITY; PENTOSE PHOSPHATE CYCLE; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN SYNTHESIS; RESPIRATORY CHAIN; TRANSCRIPTION REGULATION; TWO DIMENSIONAL GEL ELECTROPHORESIS;

AMINO ACIDS; CARBON; CITRIC ACID CYCLE; CULTURE MEDIA; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ENERGY METABOLISM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GLYCOLYSIS; KETONE OXIDOREDUCTASES; PENTOSE PHOSPHATE PATHWAY; PROTEOME;

EID: 84899525935     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-13-45     Document Type: Article

References (96)

1. Shiloach J, Rinas U. Glucose and acetate metabolism in E. coli - System level analysis and biotechnological applications in protein production processes. Systems biology and biotechnology of Escherichia coli 2009, 377-400. Berlin, Heidelberg, New York: Springer-Verlag, Lee SY.
2. Yoon SH, Han MJ, Jeong H, Lee CH, Xia XX, Lee DH, Shim JH, Lee SY, Oh TK, Kim JF. Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. Genome Biol 2012, 13:R37. 10.1186/gb-2012-13-5-r37, 3446290, 22632713.
3. Korz DJ, Rinas U, Hellmuth K, Sanders EA, Deckwer WD. Simple fed-batch technique for high cell density cultivation of Escherichia coli. J Biotechnol 1995, 39:59-65. 10.1016/0168-1656(94)00143-Z, 7766011.
4. Martin VJ, Pitera DJ, Withers ST, Newman JD, Keasling JD. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 2003, 21:796-802. 10.1038/nbt833, 12778056.
5. Tsuruta H, Paddon CJ, Eng D, Lenihan JR, Horning T, Anthony LC, Regentin R, Keasling JD, Renninger NS, Newman JD. High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS ONE 2009, 4:e4489. 10.1371/journal.pone.0004489, 2637983, 19221601.
6. Chavez-Bejar MI, Balderas-Hernandez VE, Gutierrez-Alejandre A, Martinez A, Bolivar F, Gosset G. Metabolic engineering of Escherichia coli to optimize melanin synthesis from glucose. Microb Cell Fact 2013, 12:108. 10.1186/1475-2859-12-108, 3842659, 24225202.
7. Park JH, Lee SY. Fermentative production of branched chain amino acids: a focus on metabolic engineering. Appl Microbiol Biotechnol 2010, 85:491-506. 10.1007/s00253-009-2307-y, 19844702.
8. Julsing MK, Kuhn D, Schmid A, Buhler B. Resting cells of recombinant E. coli show high epoxidation yields on energy source and high sensitivity to product inhibition. Biotechnol Bioeng 2012, 109:1109-1119. 10.1002/bit.24404, 22170310.
9. Leonardo MR, Cunningham PR, Clark DP. Anaerobic regulation of the adhE gene, encoding the fermentative alcohol dehydrogenase of Escherichia coli. J Bacteriol 1993, 175:870-878. 196234, 8423158.
10. Leonardo MR, Dailly Y, Clark DP. Role of NAD in regulating the adhE gene of Escherichia coli. J Bacteriol 1996, 178:6013-6018. 178460, 8830700.
11. Holland-Staley CA, Lee K, Clark DP, Cunningham PR. Aerobic activity of Escherichia coli alcohol dehydrogenase is determined by a single amino acid. J Bacteriol 2000, 182:6049-6054. 10.1128/JB.182.21.6049-6054.2000, 94738, 11029424.
12. Anderson KB, von Meyenburg K. Are growth rates of Escherichia coli in batch cultures limited by respiration?. J Bacteriol 1980, 144:114-123. 294601, 6998942.
13. Mizuno T, Shinkai A, Matsui K, Mizushima S. Osmoregulatory expression of porin genes in Escherichia coli: a comparative study on strains B and K-12. FEMS Microbiol Lett 1990, 68:289-293.
14. Schneider D, Duperchy E, Depeyrot J, Coursange E, Lenski R, Blot M. Genomic comparisons among Escherichia coli strains B, K-12, and O157:H7 using IS elements as molecular markers. BMC Microbiol 2002, 2:18. 10.1186/1471-2180-2-18, 117601, 12106505.
15. Studier FW, Daegelen P, Lenski RE, Maslov S, Kim JF. Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. J Mol Biol 2009, 394:653-680. 10.1016/j.jmb.2009.09.021, 19765592.
16. Matuszewska M, Kuczynska-Wisnik D, Laskowska E, Liberek K. The small heat shock protein IbpA of Escherichia coli cooperates with IbpB in stabilization of thermally aggregated proteins in a disaggregation competent state. J Biol Chem 2005, 280:12292-12298. 10.1074/jbc.M412706200, 15665332.
17. Ratajczak E, Zietkiewicz S, Liberek K. Distinct activities of Escherichia coli small heat shock proteins IbpA and IbpB promote efficient protein disaggregation. J Mol Biol 2009, 386:178-189. 10.1016/j.jmb.2008.12.009, 19101567.
18. Goloubinoff P, Mogk A, Ben Zvi AP, Tomoyasu T, Bukau B. Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network. Proc Natl Acad Sci U S A 1999, 96:13732-13737. 10.1073/pnas.96.24.13732, 24133, 10570141.
19. Rosenzweig R, Moradi S, Zarrine-Afsar A, Glover JR, Kay LE. Unraveling the mechanism of protein disaggregation through a ClpB-DnaK interaction. Science 2013, 339:1080-1083. 10.1126/science.1233066, 23393091.
20. Brown TDK, Jones-Mortimer MC, Kornberg HL. The enzymic interconversion of acetate and acetyl-coenzyme in Escherichia coli. J Gen Microbiol 1977, 102:327-336. 10.1099/00221287-102-2-327, 21941.
21. Phue JN, Shiloach J. Transcription levels of key metabolic genes are the cause for different glucose utilization pathways in E. coli B (BL21) and E. coli K (JM109). J Biotechnol 2004, 109:21-30. 10.1016/j.jbiotec.2003.10.038, 15063611.
22. Shimada T, Yamamoto K, Ishihama A. Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. J Bacteriol 2011, 193:649-659. 10.1128/JB.01214-10, 3021228, 21115656.
23. Fic E, Bonarek P, Gorecki A, Kedracka-Krok S, Mikolajczak J, Polit A, Tworzydlo M, Dziedzicka-Wasylewska M, Wasylewski Z. cAMP receptor protein from Escherichia coli as a model of signal transduction in proteins - a review. J Mol Microbiol Biotechnol 2009, 17:1-11. 10.1159/000178014, 19033675.
24. Georgellis D, Kwon O, Lin EC. Quinones as the redox signal for the arc two-component system of bacteria. Science 2001, 292:2314-2316. 10.1126/science.1059361, 11423658.
25. Malpica R, Sandoval GR, Rodriguez C, Franco B, Georgellis D. Signaling by the arc two-component system provides a link between the redox state of the quinone pool and gene expression. Antioxid Redox Signal 2006, 8:781-795. 10.1089/ars.2006.8.781, 16771670.
26. Shimada T, Fujita N, Maeda M, Ishihama A. Systematic search for the Cra-binding promoters using genomic SELEX system. Genes Cells 2005, 10:907-918. 10.1111/j.1365-2443.2005.00888.x, 16115199.
27. Ramseier TM, Negre D, Cortay JC, Scarabel M, Cozzone AJ, Saier MH. In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium. J Mol Biol 1993, 234:28-44. 10.1006/jmbi.1993.1561, 8230205.
28. Nègre D, Bonod-Bidaud C, Geourjon C, Deleage G, Cozzone AJ, Cortay JC. Definition of a consensus DNA-binding site for the Escherichia coli pleiotropic regulatory protein, FruR. Mol Microbiol 1996, 21:257-266. 10.1046/j.1365-2958.1996.6341350.x, 8858581.
29. Ishizuka H, Hanamura A, Inada T, Aiba H. Mechanism of the down-regulation of cAMP receptor by glucose in Escherichia coli: role of autoregulation of the crp gene. EMBO J 1994, 13:3077-3082. 395198, 7518773.
30. Charpentier B, Branlant C. The Escherichia coli gapA gene is transcribed by the vegetative RNA polymerase holoenzyme Eσ70 and by the heat shock RNA polymerase Eσ32. J Bacteriol 1994, 176:830-839. 205121, 8300536.
31. Quail MA, Guest JR. Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli. Mol Microbiol 1995, 15:519-529. 10.1111/j.1365-2958.1995.tb02265.x, 7783622.
32. Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, Saier MH. Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli. J Bacteriol 2005, 187:980-990. 10.1128/JB.187.3.980-990.2005, 545712, 15659676.
33. Wilde RJ, Guest JR. Transcript analysis of the citrate synthase and succinate dehydrogenase genes of Escherichia coli K12. J Gen Microbiol 1986, 132:3239-3251.
34. Cunningham L, Gruer MJ, Guest JR. Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli. Microbiology 1997, 143:3795-3805. 10.1099/00221287-143-12-3795, 9421904.
35. Cunningham L, Guest JR. Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli. Microbiology 1998, 144:2113-2123. 10.1099/00221287-144-8-2113, 9720032.
36. Chen YP, Lin HH, Yang CD, Huang SH, Tseng CP. Regulatory role of cAMP receptor protein over Escherichia coli fumarase genes. J Microbiol 2012, 50:426-433. 10.1007/s12275-012-1542-6, 22752906.
37. Göhler A-G, Kökpinar T, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C. More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli. BMC Syst Biol 2011, 5:197. 10.1186/1752-0509-5-197, 3265435, 22168595.
38. Shalel-Levanon S, San KY, Bennett GN. Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions. Biotechnol Bioeng 2005, 92:147-159. 10.1002/bit.20583, 15988767.
39. Pinske C, Bonn M, Kruger S, Lindenstrauss U, Sawers RG. Metabolic deficiences revealed in the biotechnologically important model bacterium Escherichia coli BL21(DE3). PLoS ONE 2011, 6:e22830. 10.1371/journal.pone.0022830, 3149613, 21826210.
40. Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP. Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem 2005, 280:15084-15096. 10.1074/jbc.M414030200, 15699038.
41. Phue JN, Noronha SB, Hattacharyya R, Wolfe AJ, Shiloach J. Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microoarrys and northern blot analyses. Biotechnol Bioeng 2005, 90:805-820. 10.1002/bit.20478, 15806547.
42. Dittrich CR, Bennett GN, San KY. Characterization of the acetate-producing pathways in Escherichia coli. Biotechnol Prog 2005, 21:1062-1067.
43. Mather MW, Gennis RB. Kinetic studies of the lipid-activated pyruvate oxidase flavoprotein of Escherichia coli. J Biol Chem 1985, 260:16148-16155.
44. Marchal D, Pantigny J, Laval JM, Moiroux J, Bourdillon C. Rate constants in two dimensions of electron transfer between pyruvate oxidase, a membrane enzyme, and ubiquinone (coenzyme Q8), its water-insoluble electron carrier. Biochemistry 2001, 40:1248-1256. 10.1021/bi002325y, 11170450.
45. Kumari S, Beatty CM, Browning DF, Busby SJ, Simel EJ, Hovel-Miner G, Wolfe AJ. Regulation of acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 2000, 182:4173-4179. 10.1128/JB.182.15.4173-4179.2000, 101899, 10894724.
46. Wolfe AJ. The acetate switch. Microbiol Mol Biol Rev 2005, 69:12-50. 10.1128/MMBR.69.1.12-50.2005, 1082793, 15755952.
47. Browning DF, Beatty CM, Wolfe AJ, Cole JA, Busby SJ. Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region. Mol Microbiol 2002, 43:687-701. 10.1046/j.1365-2958.2002.02776.x, 11929525.
48. Browning DF, Beatty CM, Sanstad EA, Gunn KE, Busby SJ, Wolfe AJ. 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 2004, 51:241-254.
49. Ball CA, Osuna R, Ferguson KC, Johnson RC. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol 1992, 174:8043-8056. 207543, 1459953.
50. Nafissi M, Chau J, Xu J, Johnson RC. Robust translation of the nucleoid protein Fis requires a remote upstream AU element and is enhanced by RNA secondary structure. J Bacteriol 2012, 194:2458-2469. 10.1128/JB.00053-12, 3347164, 22389479.
51. Valgepea K, Adamberg K, Nahku R, Lahtvee PJ, Arike L, Vilu R. 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 2010, 4:166. 10.1186/1752-0509-4-166, 3014970, 21122111.
52. Shin S, Song SG, Lee DS, Pan JG, Park C. Involvement of iclR and rpoS in the induction of acs, the gene for acetyl coenzyme A synthetase of Escherichia coli K-12. FEMS Microbiol Lett 1997, 146:103-108. 10.1111/j.1574-6968.1997.tb10178.x, 8997713.
53. Nahku R, Valgepea K, Lahtvee PJ, Erm S, Abner K, Adamberg K, Vilu R. Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures. J Biotechnol 2010, 145:60-65. 10.1016/j.jbiotec.2009.10.007, 19861135.
54. Nyström T. Stationary-phase physiology. Annu Rev Microbiol 2004, 58:161-181. 10.1146/annurev.micro.58.030603.123818, 15487934.
55. Magnusson LU, Farewell A, Nyström T. ppGpp: a global regulator in Escherichia coli. Trends Microbiol 2005, 13:236-242. 10.1016/j.tim.2005.03.008, 15866041.
56. Traxler MF, Zacharia VM, Marquardt S, Summers SM, Nguyen HT, Stark SE, Conway T. Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli. Mol Microbiol 2011, 79:830-845. 10.1111/j.1365-2958.2010.07498.x, 3073637, 21299642.
57. Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL. Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA. Proc Natl Acad Sci U S A 2011, 108:5712-5717. 10.1073/pnas.1019383108, 3078377, 21402902.
58. Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muniz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, Garcia-Sotelo JS, Lopez-Fuentes A, Porron-Sotelo L, Alquicira-Hernandez S, Medina-Rivera A, Martinez-Flores I, Alquicira-Hernandez K, Martinez-Adame R, Bonavides-Martinez C, Miranda-Rios J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J. RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res 2011, 39:D98-105. 10.1093/nar/gkq1110, 3013702, 21051347.
59. Rinas U, Hellmuth K, Kang R, Seeger A, Schlieker H. Entry of Escherichia coli into stationary phase is indicated by endogenous and exogenous accumulation of nucleobases. Appl Environ Microbiol 1995, 61:4147-4151. 167726, 8534082.
60. Zundel MA, Basturea GN, Deutscher MP. Initiation of ribosome degradation during starvation in Escherichia coli. RNA 2009, 15:977-983. 10.1261/rna.1381309, 2673067, 19324965.
61. Piir K, Paier A, Liiv A, Tenson T, Maivali U. Ribosome degradation in growing bacteria. EMBO Rep 2011, 12:458-462. 10.1038/embor.2011.47, 3090016, 21460796.
62. Paul BJ, Berkmen MB, Gourse RL. DksA potentiates direct activation of amino acid promoters by ppGpp. Proc Natl Acad Sci U S A 2005, 102:7823-7828. 10.1073/pnas.0501170102, 1142371, 15899978.
63. Srivatsan A, Wang JD. Control of bacterial transcription, translation and replication by (p)ppGpp. Curr Opin Microbiol 2008, 11:100-105. 10.1016/j.mib.2008.02.001, 18359660.
64. Lee JH, Lennon CW, Ross W, Gourse RL. Role of the coiled-coil tip of Escherichia coli DksA in promoter control. J Mol Biol 2012, 416:503-517. 10.1016/j.jmb.2011.12.028, 3288215, 22200485.
65. Weissbach H, Brot N. Regulation of methionine synthesis in Escherichia coli. Mol Microbiol 1991, 5:1593-1597. 10.1111/j.1365-2958.1991.tb01905.x, 1943695.
66. Gollop N, Chipman DM, Barak Z. Inhibition of acetohydroxy acid synthase by leucine. Biochim Biophys Acta 1983, 748:34-39. 10.1016/0167-4838(83)90024-9, 6351926.
67. Rhee KY, Senear DF, Hatfield GW. Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex. J Biol Chem 1998, 273:11257-11266. 10.1074/jbc.273.18.11257, 9556617.
68. Opel ML, Hatfield GW. DNA supercoiling-dependent transcriptional coupling between the divergently transcribed promoters of the ilvYC operon of Escherichia coli is proportional to promoter strengths and transcript lengths. Mol Microbiol 2001, 39:191-198. 10.1046/j.1365-2958.2001.02249.x, 11123701.
69. Monroe RS, Ostrowski J, Hryniewicz MM, Kredich NM. In vitro interactions of CysB protein with the cysK and cysJIH promoter regions of Salmonella typhimurium. J Bacteriol 1990, 172:6919-6929. 210811, 2254265.
70. Hindson VJ. Serine acetyltransferase of Escherichia coli: substrate specificity and feedback control by cysteine. Biochem J 2003, 375:745-752. 10.1042/BJ20030429, 1223735, 12940772.
71. Yamamoto K, Oshima T, Nonaka G, Ito H, Ishihama A. Induction of the Escherichia coli cysK gene by genetic and environmental factors. FEMS Microbiol Lett 2011, 323:88-95. 10.1111/j.1574-6968.2011.02364.x, 22092684.
72. Brown L, Gentry D, Elliott T, Cashel M. DksA affects ppGpp induction of RpoS at a translational level. J Bacteriol 2002, 184:4455-4465. 10.1128/JB.184.16.4455-4465.2002, 135238, 12142416.
73. Rajkumari K, Kusano S, Ishihama A, Mizuno T, Gowrishankar J. Effects of H-NS and potassium glutamate on σS- and σ70-directed transcription in vitro from osmotically regulated P1 and P2 promoters of proU in Escherichia coli. J Bacteriol 1996, 178:4176-4181. 178175, 8763946.
74. Lacour S, Landini P. σS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sS-dependent genes and identification of their promoter sequences. J Bacteriol 2004, 186:7186-7195. 10.1128/JB.186.21.7186-7195.2004, 523212, 15489429.
75. Hengge-Aronis R, Klein W, Lange R, Rimmele M, Boss W. Trehalose synthesis genes are controlled by the putative sigma factor encoded by rpoS and are involved in stationary-phase thermotolerance in Escherichia coli. J Bacteriol 1991, 173:7918-7924. 212585, 1744047.
76. Kiupakis AK, Reitzer L. ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli. J Bacteriol 2002, 184:2940-2950. 10.1128/JB.184.11.2940-2950.2002, 135064, 12003934.
77. Waterman SR, Small PL. Transcriptional expression of Escherichia coli glutamate-dependent acid resistance genes gadA and gadBC in an hns rpoS mutant. J Bacteriol 2003, 185:4644-4647. 10.1128/JB.185.15.4644-4647.2003, 165754, 12867478.
78. Metzner M, Germer J, Hengge R. Multiple stress signal integration in the regulation of the complex σS-dependent csiD-ygaF-gabDTP operon in Escherichia coli. Mol Microbiol 2004, 51:799-811.
79. Dong T, Schellhorn HE. Control of RpoS in global gene expression of Escherichia coli in minimal media. Mol Genet Genomics 2009, 281:19-33. 10.1007/s00438-008-0389-3, 18843507.
80. Hengge-Aronis R. Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in Escherichia coli. Cell 1993, 72:165-168. 10.1016/0092-8674(93)90655-A, 8425216.
81. Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolivar F. Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation. PLoS ONE 2009, 4:e7466. 10.1371/journal.pone.0007466, 2759082, 19838295.
82. Rahman M, Hasan MR, Shimizu K. Growth phase-dependent changes in the expression of global regulatory genes and associated metabolic pathways in Escherichia coli. Biotechnol Lett 2008, 30:853-860. 10.1007/s10529-007-9621-1, 18175070.
83. Chang YY, Wang AY, Cronan J. Expression of Escherichia coli pyruvate oxidase (PoxB) depends on the sigma factor encoded by the rpoS(katF) gene. Mol Microbiol 1994, 11:1019-1028. 10.1111/j.1365-2958.1994.tb00380.x, 8022274.
84. Mallik P, Paul BJ, Rutherford ST, Gourse RL, Osuna R. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J Bacteriol 2006, 188:5775-5782. 10.1128/JB.00276-06, 1540068, 16885445.
85. Farewell A, Diez AA, DiRusso CC, Nyström T. Role of the Escherichia coli FadR regulator in stasis survival and growth phase-dependent expression of the uspA, fad, and fab genes. J Bacteriol 1996, 178:6443-6450. 178529, 8932299.
86. Kim SJ, Han YH, Kim IH, Kim HK. Involvement of ArcA and Fnr in expression of Escherichia coli thiol peroxidase gene. IUBMB Life 1999, 48:215-218. 10.1080/713803496, 10794600.
87. Ogasawara H, Teramoto J, Yamamoto S, Hirao K, Yamamoto K, Ishihama A, Utsumi R. Negative regulation of DNA repair gene (uvrA) expression by ArcA/ArcB two-component system in Escherichia coli. FEMS Microbiol Lett 2005, 251:243-249. 10.1016/j.femsle.2005.08.006, 16140472.
88. Price MN, Deutschbauer AM, Skerker JM, Wetmore KM, Ruths T, Mar JS, Kuehl JV, Shao W, Arkin AP. Indirect and suboptimal control of gene expression is widespread in bacteria. Mol Syst Biol 2013, 9:660. 3658271, 23591776.
89. Li Z, Kessler W, van den Heuvel J, Rinas U. Simple defined autoinduction medium for high-level recombinant protein production for T7-based Escherichia coli expression systems. Appl Microbiol Biotechnol 2011, 91:1203-1213. 10.1007/s00253-011-3407-z, 21698378.
90. Li Z, Nimtz M, Rinas U. Optimized procedure to generate heavy isotope and selenomethionine-labeled proteins for structure determination using Escherichia coli-based expression systems. Appl Microbiol Biotechnol 2011, 92:823-833. 10.1007/s00253-011-3603-x, 21983707.
91. Wessel D, Flügge UI. A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem 1984, 138:141-143. 10.1016/0003-2697(84)90782-6, 6731838.
92. Lu X, Sun J, Nimtz M, Wissing J, Zeng AP, Rinas U. The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate. Microb Cell Fact 2010, 9:23. 10.1186/1475-2859-9-23, 2874515, 20406453.
93. Candiano G, Bruschi M, Musante L, Santucci L, Ghiggeri GM, Carnemolla B, Orecchia P, Zardi L, Righetti PG. Blue silver: a very sensitive colloidal Coomassie G-250 staining for proteome analysis. Electrophoresis 2004, 25:1327-1333. 10.1002/elps.200305844, 15174055.
94. Wang W, Sun J, Nimtz M, Deckwer W-D, Zeng A-P. Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences. Proteome Sci 2003, 1:6. 10.1186/1477-5956-1-6, 317362, 14653859.
95. Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martinez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muniz-Rascado L, Ong Q, Paley S, Schroder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 2013, 41:D605-D612. 10.1093/nar/gks1027, 3531154, 23143106.
96. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.