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Escherichia coli K-12 substr. MG1655 Enzyme: phosphoglucose isomerase



Gene: pgi Accession Numbers: EG10702 (EcoCyc), b4025, ECK4017

Regulation Summary Diagram: ?

Regulation summary diagram for pgi

Subunit composition of phosphoglucose isomerase = [Pgi]2

Summary:
Phosphoglucose isomerase catalyzes the interconversion of glucose-6-phosphate and fructose-6-phosphate, an essential step of the glycolysis and gluconeogenesis pathways.

The enzyme is dimeric in solution, but an additional higher molecular weight form that is less active and more negatively charged was found as well [Schreyer80]. The crystal structure of dimeric Pgi from E. coli K-12 has been solved at 2.05 Å resolution [Totir12].

A pgi mutant grows slowly on glucose and utilizes glucose primarily via the pentose phosphate pathway as the source of NADPH [Fraenkel67, Csonka77, Canonaco01, Hua03]; the Entner-Doudoroff pathway I is also used to a lesser degree [Loomis66]. The glyoxylate shunt is also active in a pgi mutant strain [Hua03]. The increased flux through the pentose phosphate pathway leads to overproduction of NADPH and thus disturbs the redox balance [Kabir03a, Kabir03], which may be restored by overexpressing SthA [Canonaco01] or a heterologous NADPH-utilizing pathway [Kabir03a, Kabir03]. Deletion of pgi is a common strategy for metabolic engineering of E. coli, e.g. [Simkhada09, Kurumbang10, Chemler10, Kim10b, Kim11a, Ahn11, Siedler11, Chin11, Yao11, Callura12, Malla13, Pandey13, Lin14, Shiue15, Ghimire15].

pgi mutant strains that were allowed to evolve for 600-800 generations have been characterized [Fong06, Charusanti10]. When grown on maltose, pgi mutants accumulate maltodextrin and thus stain blue with iodine (the "maltose Blu phenotype") [Roehl79]. pgi expression is induced by oxidative stress, and a pgi deletion mutant is hypersensitive to oxidative stress induced by paraquat [Rungrassamee08]. pgi insertion mutants were identified in a genetic screen for genes that are important for survival of exposure to ionizing radiation (IR). A pgi deletion mutant has a moderate decrease in IR survival [Byrne14].

Deletion of pgi can suppress the effects of a dnaB8(ts) mutation [Maciag11]. In an E. coli MG1655 strain pgi was identified as a knockout target for increasing plasmid DNA production [Goncalves13, Goncalves14]. The effect of perturbation (rather than knockout) of pgi gene expression on central carbon metabolism has been studied using 13C metabolic flux analysis [Usui12]. A series of vectors inducibly expressing paired-terminus antisense RNAs was constructed to silence central carbon metabolism in host E. coli K-12 MG1655. A vector that silenced pgi at 90% efficacy resulted in a defect in carbon catabolite repression [Nakashima14].

Phosphoglucose isomerase activity is positively regulated by CsrA [Sabnis95].

pgi is one of a network of genes believed to play a role in promoting the stress-induced mutagenesis (SIM) response of E. coli K-12 [Al12].

Pgi: "phosphoglucose isomerase" [Fraenkel67]

Citations: [Fraenkel67a]

Locations: periplasmic space, cytosol

Map Position: [4,231,781 -> 4,233,430] (91.21 centisomes, 328°)
Length: 1650 bp / 549 aa

Molecular Weight of Polypeptide: 61.53 kD (from nucleotide sequence), 59.0 kD (experimental) [Schreyer80 ]

Molecular Weight of Multimer: 125.0 kD (experimental) [Schreyer80]

Unification Links: ASAP:ABE-0013163 , CGSC:409 , DIP:DIP-35887N , EchoBASE:EB0696 , EcoGene:EG10702 , EcoliWiki:b4025 , ModBase:P0A6T1 , OU-Microarray:b4025 , PortEco:pgi , PR:PRO_000025181 , Pride:P0A6T1 , Protein Model Portal:P0A6T1 , RefSeq:NP_418449 , RegulonDB:EG10702 , SMR:P0A6T1 , String:511145.b4025 , Swiss-Model:P0A6T1 , UniProt:P0A6T1

Relationship Links: InterPro:IN-FAMILY:IPR001672 , InterPro:IN-FAMILY:IPR018189 , InterPro:IN-FAMILY:IPR023096 , Panther:IN-FAMILY:PTHR11469 , PDB:Structure:3NBU , Pfam:IN-FAMILY:PF00342 , Prints:IN-FAMILY:PR00662 , Prosite:IN-FAMILY:PS00174 , Prosite:IN-FAMILY:PS00765 , Prosite:IN-FAMILY:PS51463

In Paralogous Gene Group: 486 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for pgi

GO Terms:

Biological Process: GO:0006096 - glycolytic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01, Fraenkel67]
GO:0034599 - cellular response to oxidative stress Inferred from experiment [Rungrassamee08]
GO:0006094 - gluconeogenesis Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
Molecular Function: GO:0004347 - glucose-6-phosphate isomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Schreyer80, Loomis66, Ishii07]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Lasserre06]
GO:0042803 - protein homodimerization activity Inferred from experiment [Schreyer80]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]
GO:0030288 - outer membrane-bounded periplasmic space [Friedberg72]

MultiFun Terms: metabolism central intermediary metabolism
metabolism energy metabolism, carbon glycolysis

Essentiality data for pgi knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Created 14-Jun-2010 by Keseler I , SRI International
Curated 15-Jun-2010 by Keseler I , SRI International
Last-Curated ? 04-May-2015 by Fulcher C , SRI International


Enzymatic reaction of: phosphoglucose isomerase

Synonyms: glucose-6-phosphate isomerase, D-glucose-6-phosphate-ketol-isomerase

EC Number: 5.3.1.9

β-D-glucose 6-phosphate <=> β-D-fructofuranose 6-phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible. [Ishii07]

In Pathways: colanic acid building blocks biosynthesis , O-antigen building blocks biosynthesis (E. coli) , superpathway of glycolysis and Entner-Doudoroff , superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass , GDP-mannose biosynthesis , gluconeogenesis I , UDP-N-acetyl-D-glucosamine biosynthesis I , glycolysis I (from glucose 6-phosphate)

Summary:
The equilibrium constant for the reaction is 0.30 [Ishii07].

The data from [Schreyer80] are for E. coli K 10.

Early work suggested that low cellular pH inhibits the phosphoglucose isomerase reaction [Klungsoyr64].

Inhibitors (Competitive): phosphoenolpyruvate [Ogawa07]

Inhibitors (Unknown Mechanism): D-gluconate 6-phosphate [Schreyer80]

Kinetic Parameters:

Substrate
Km (μM)
Citations
β-D-fructofuranose 6-phosphate
200.0
[Schreyer80, BRENDA14]
β-D-fructofuranose 6-phosphate
78.0
[Ogawa07]
β-D-glucose 6-phosphate
1018.0
[Ogawa07]

pH(opt): 8 [Schreyer80]


Sequence Features

Protein sequence of Pgi with features indicated

Feature Class Location Citations Comment
N6-acetyllysine-Modification 80
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
N6-acetyllysine-Modification 228
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
N6-acetyllysine-Modification 234
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Sequence-Conflict 317
[Smith92b, Froman89, UniProt10a]
UniProt: (in Ref. 1 and 2);
Active-Site 355
[UniProt10]
UniProt: Proton donor; Non-Experimental Qualifier: by similarity;
Active-Site 386
[UniProt10]
UniProt: Non-Experimental Qualifier: by similarity;
Acetylation-Modification 449
[Yu08]
 
Active-Site 514
[UniProt10]
UniProt: Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b4025 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10702; confirmed by SwissProt match.


References

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Al12: Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM (2012). "Identity and function of a large gene network underlying mutagenic repair of DNA breaks." Science 338(6112);1344-8. PMID: 23224554

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Byrne14: Byrne RT, Chen SH, Wood EA, Cabot EL, Cox MM (2014). "Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation." J Bacteriol 196(20);3534-45. PMID: 25049088

Callura12: Callura JM, Cantor CR, Collins JJ (2012). "Genetic switchboard for synthetic biology applications." Proc Natl Acad Sci U S A 109(15);5850-5. PMID: 22454498

Canonaco01: Canonaco F, Hess TA, Heri S, Wang T, Szyperski T, Sauer U (2001). "Metabolic flux response to phosphoglucose isomerase knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA." FEMS Microbiol Lett 204(2);247-52. PMID: 11731130

Charusanti10: Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, Gao Y, Palsson BO (2010). "Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene." PLoS Genet 6(11);e1001186. PMID: 21079674

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Feist07: 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. PMID: 17593909

Fong06: Fong SS, Nanchen A, Palsson BO, Sauer U (2006). "Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes." J Biol Chem 281(12);8024-33. PMID: 16319065

Fraenkel67: Fraenkel DG, Levisohn SR (1967). "Glucose and gluconate metabolism in an Escherichia coli mutant lacking phosphoglucose isomerase." J Bacteriol 93(5);1571-8. PMID: 5337843

Fraenkel67a: Fraenkel DG (1967). "Genetic mapping of mutations affecting phosphoglucose isomerase and fructose diphosphatase in Escherichia coli." J Bacteriol 93(5);1582-7. PMID: 4290578

Friedberg72: Friedberg I (1972). "Localization of phosphoglucose isomerase in Escherichia coli and its relation to the induction of the hexose phosphate transport system." J Bacteriol 1972;112(3);1201-5. PMID: 4344919

Froman89: Froman BE, Tait RC, Gottlieb LD (1989). "Isolation and characterization of the phosphoglucose isomerase gene from Escherichia coli." Mol Gen Genet 1989;217(1);126-31. PMID: 2549364

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Ghimire15: Ghimire GP, Koirala N, Pandey RP, Jung HJ, Sohng JK (2015). "Modification of emodin and aloe-emodin by glycosylation in engineered Escherihia coli." World J Microbiol Biotechnol 31(4);611-9. PMID: 25663173

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Goncalves13: Goncalves GA, Prazeres DM, Monteiro GA, Prather KL (2013). "De novo creation of MG1655-derived E. coli strains specifically designed for plasmid DNA production." Appl Microbiol Biotechnol 97(2);611-20. PMID: 22885693

Goncalves14: Goncalves GA, Prather KL, Monteiro GA, Carnes AE, Prazeres DM (2014). "Plasmid DNA production with Escherichia coli GALG20, a pgi-gene knockout strain: fermentation strategies and impact on downstream processing." J Biotechnol 186;119-27. PMID: 24995846

Hua03: Hua Q, Yang C, Baba T, Mori H, Shimizu K (2003). "Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts." J Bacteriol 185(24);7053-67. PMID: 14645264

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Ishii07: Ishii N, Suga Y, Hagiya A, Watanabe H, Mori H, Yoshino M, Tomita M (2007). "Dynamic simulation of an in vitro multi-enzyme system." FEBS Lett 581(3);413-20. PMID: 17239859

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kabir03: Kabir MM, Shimizu K (2003). "Gene expression patterns for metabolic pathway in pgi knockout Escherichia coli with and without phb genes based on RT-PCR." J Biotechnol 105(1-2);11-31. PMID: 14511906

Kabir03a: Kabir MM, Shimizu K (2003). "Fermentation characteristics and protein expression patterns in a recombinant Escherichia coli mutant lacking phosphoglucose isomerase for poly(3-hydroxybutyrate) production." Appl Microbiol Biotechnol 62(2-3);244-55. PMID: 12883871

Kim10b: Kim J, Reed JL (2010). "OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains." BMC Syst Biol 4(1);53. PMID: 20426856

Kim11a: Kim S, Lee CH, Nam SW, Kim P (2011). "Alteration of reducing powers in an isogenic phosphoglucose isomerase (pgi)-disrupted Escherichia coli expressing NAD(P)-dependent malic enzymes and NADP-dependent glyceraldehyde 3-phosphate dehydrogenase." Lett Appl Microbiol 52(5);433-40. PMID: 21272045

Klungsoyr64: Klungsoyr L, Endresen A "Intracellular pH effect upon phosphoglucose isomerase in Escherichia coli." Biochim Biophys Acta 1964;92:378-387. PMID: 14249126

Kurumbang10: Kurumbang NP, Liou K, Sohng JK (2010). "Biosynthesis of paromamine derivatives in engineered Escherichia coli by heterologous expression." J Appl Microbiol 108(5);1780-8. PMID: 19895652

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

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Maciag11: Maciag M, Nowicki D, Janniere L, Szalewska-Palasz A, Wegrzyn G (2011). "Genetic response to metabolic fluctuations: correlation between central carbon metabolism and DNA replication in Escherichia coli." Microb Cell Fact 10;19. PMID: 21453533

Malla13: Malla S, Pandey RP, Kim BG, Sohng JK (2013). "Regiospecific modifications of naringenin for astragalin production in Escherichia coli." Biotechnol Bioeng 110(9);2525-35. PMID: 23568509

Nakashima14: Nakashima N, Ohno S, Yoshikawa K, Shimizu H, Tamura T (2014). "A vector library for silencing central carbon metabolism genes with antisense RNAs in Escherichia coli." Appl Environ Microbiol 80(2);564-73. PMID: 24212579

Ogawa07: Ogawa T, Mori H, Tomita M, Yoshino M (2007). "Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli." Res Microbiol 158(2);159-63. PMID: 17307338

Pandey13: Pandey RP, Malla S, Simkhada D, Kim BG, Sohng JK (2013). "Production of 3-O-xylosyl quercetin in Escherichia coli." Appl Microbiol Biotechnol 97(5);1889-901. PMID: 23053089

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

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Rungrassamee08: Rungrassamee W, Liu X, Pomposiello PJ (2008). "Activation of glucose transport under oxidative stress in Escherichia coli." Arch Microbiol 190(1):41-9. PMID: 18368388

Sabnis95: Sabnis NA, Yang H, Romeo T (1995). "Pleiotropic regulation of central carbohydrate metabolism in Escherichia coli via the gene csrA." J Biol Chem 1995;270(49);29096-104. PMID: 7493933

Schreyer80: Schreyer R, Bock A (1980). "Phosphoglucose isomerase from Escherischia coli K 10: purification, properties and formation under aerobic and anaerobic condition." Arch Microbiol 127(3);289-98. PMID: 7004378

Shiue15: Shiue E, Brockman IM, Prather KL (2015). "Improving product yields on D-glucose in Escherichia coli via knockout of pgi and zwf and feeding of supplemental carbon sources." Biotechnol Bioeng 112(3);579-87. PMID: 25258165

Siedler11: Siedler S, Bringer S, Bott M (2011). "Increased NADPH availability in Escherichia coli: improvement of the product per glucose ratio in reductive whole-cell biotransformation." Appl Microbiol Biotechnol 92(5);929-37. PMID: 21670981

Simkhada09: Simkhada D, Kim E, Lee HC, Sohng JK (2009). "Metabolic engineering of Escherichia coli for the biological synthesis of 7-O-xylosyl naringenin." Mol Cells 28(4);397-401. PMID: 19812897

Smith92b: Smith MW, Doolittle RF (1992). "Anomalous phylogeny involving the enzyme glucose-6-phosphate isomerase." J Mol Evol 34(6);544-5. PMID: 1593646

Thomson79: Thomson J, Gerstenberger PD, Goldberg DE, Gociar E, Orozco de Silva A, Fraenkel DG (1979). "ColE1 hybrid plasmids for Escherichia coli genes of glycolysis and the hexose monophosphate shunt." J Bacteriol 1979;137(1);502-6. PMID: 368027

Totir12: Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T (2012). "Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization." PLoS One 7(2);e32498. PMID: 22393408

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Usui12: Usui Y, Hirasawa T, Furusawa C, Shirai T, Yamamoto N, Mori H, Shimizu H (2012). "Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using (13)C metabolic flux analysis." Microb Cell Fact 11;87. PMID: 22721472

Vinopal75b: Vinopal RT, Hillman JD, Schulman H, Reznikoff WS, Fraenkel DG (1975). "New phosphoglucose isomerase mutants of Escherichia coli." J Bacteriol 122(3);1172-4. PMID: 1097391

Yao11: Yao R, Hirose Y, Sarkar D, Nakahigashi K, Ye Q, Shimizu K (2011). "Catabolic regulation analysis of Escherichia coli and its crp, mlc, mgsA, pgi and ptsG mutants." Microb Cell Fact 10;67. PMID: 21831320

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Zhang09: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Martin02: Martin RG, Rosner JL (2002). "Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data." Mol Microbiol 44(6);1611-24. PMID: 12067348

Olvera09: Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolivar F (2009). "Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation." PLoS One 4(10);e7466. PMID: 19838295


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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