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Escherichia coli K-12 substr. MG1655 Enzyme: isoleucyl-tRNA synthetase



Gene: ileS Accession Numbers: EG10492 (EcoCyc), b0026, ECK0027

Synonyms: ilvS

Regulation Summary Diagram: ?

Summary:
Isoleucyl-tRNA synthetase (IleRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. IleRS belongs to the Class I aminoacyl tRNA synthetases [Eriani90, Landes95].

IleRS contains two zinc atoms per active site [Xu94]. One zinc atom bound near the N-terminal catalytic core is important for amino acid binding and utilization [Landro94]. The second zinc binding site has been mapped near the C terminus of IleRS [Landro94a] and is required for the tRNA binding step in aminoacylation [Zhou95a]. The C-terminal peptide containing this site can complement the specific tRNA binding and catalytic activity of the N-terminal domain in trans [Glasfeld96, Glasfeld97]. If separately expressed, the three domains of IleRS can form an active complex and complement each other in trans [Shiba92]. IleRS binds one molecule of tRNA per molecule of enzyme [Hustedt77]. A dispensable sequence interrupts the nucleotide binding domain within IleRS [Starzyk87].

Specificity determinants within tRNAIle that are important for recognition by IleRS have been identified [Schoemaker76, Schoemaker77, Schoemaker77a, Nureki91, Pallanck91, Niimi93, Nureki94]. Residues within IleRS that interact with tRNAIle have been identified [Schmidt95, Auld96].

The reaction mechanism of IleRS has been studied [Freist82]. Aminoacylation proceeds via the aminoacyl adenylate pathway [Fersht76, Kim77].

Binding specificity of IleRS for various aliphatic amino acids and aminoalkyl adenylates has been determined; none of the tested isoleucine analogs bind as tightly as isoleucine and isoleucinol-AMP itself [Flossdorf76, Hinz76, Flossdorf77, Kohda87]. Both amino acid discrimination and proofreading contribute to the specificity of Ile charging onto tRNAIle [Freist87, Freist88], and experimental data is consistent with the existence of both a pre- and a post-transfer editing capability of the enzyme, depending on the amino acid [Fersht77, Yamane77, Freist87a, Cramer91].

Although valine is discriminated against at the amino acid recognition stage, IleRS misactivates valine at a significant rate. A single point mutation, G56A, eliminates the ability to discriminate against valine, and valine is then discriminated against by hydrolytic editing [Schmidt94].

The presence of misacylated tRNA is required for pre- and post-transfer editing [Nordin03]. The editing site maps to the CP1 domain, an insertion that interrupts the Rossman fold nucleotide-binding domain [Schmidt95]. The editing response appears to be triggered by specific bases in the effector and does not require a tRNA-like structure, active acceptor hydroxyl groups [Hale96] or joining of the amino acid to the nucleic acid [Farrow01]. The editing site is distinct from the active site for aminoacylation [Hendrickson00]. Translocation of misactivated valine from the active site to the editing site is is required for editing [Bishop02, Bishop03] and is dependent on tRNAIle [Nomanbhoy99]. Distinct residues within the editing site are required for editing the misactivated adenylate form and the aninoacyl ester [Hendrickson02]. Misactivated homocysteine undergoes pretransfer editing [Jakubowski81].

Site-directed mutagenesis identified the isoleucine binding site [Clarke88]. Labeling studies with pyridoxal-5'-phosphate identified residues that may be important for binding of the phosphates of ATP [Kalogerakos94]. An editing-deficient IleRS mutant strain has a growth yield advantage under specialized conditions, generating "statistical proteins" containing norvaline [Pezo04], but under most conditions, it has a lower growth rate [Bacher05].

Reviews: [Ibba00, Burbaum90, Hughes05]

Gene Citations: [Tokunaga85, Regue84, Innis84, Miller87, Kamio85, Miller87a, Brissette91]

Locations: cytosol

Map Position: [22,391 -> 25,207] (0.48 centisomes)
Length: 2817 bp / 938 aa

Molecular Weight of Polypeptide: 104.3 kD (from nucleotide sequence), 102 kD (experimental) [Durekovic73 ]

Unification Links: ASAP:ABE-0000094 , CGSC:613 , DIP:DIP-10017N , EchoBASE:EB0487 , EcoGene:EG10492 , EcoliWiki:b0026 , Mint:MINT-1232480 , ModBase:P00956 , OU-Microarray:b0026 , PortEco:ileS , PR:PRO_000023000 , Pride:P00956 , Protein Model Portal:P00956 , RefSeq:NP_414567 , RegulonDB:EG10492 , SMR:P00956 , String:511145.b0026 , UniProt:P00956

Relationship Links: InterPro:IN-FAMILY:IPR001412 , InterPro:IN-FAMILY:IPR002300 , InterPro:IN-FAMILY:IPR002301 , InterPro:IN-FAMILY:IPR009008 , InterPro:IN-FAMILY:IPR009080 , InterPro:IN-FAMILY:IPR010663 , InterPro:IN-FAMILY:IPR013155 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR023585 , Panther:IN-FAMILY:PTHR11946:SF9 , Pfam:IN-FAMILY:PF00133 , Pfam:IN-FAMILY:PF06827 , Pfam:IN-FAMILY:PF08264 , Prints:IN-FAMILY:PR00984 , Prosite:IN-FAMILY:PS00178

In Paralogous Gene Group: 7 (4 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006428 - isoleucyl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Durekovic73]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01a]
GO:0006450 - regulation of translational fidelity Inferred by computational analysis [GOA01a]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0002161 - aminoacyl-tRNA editing activity Inferred by computational analysis [GOA01a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004822 - isoleucine-tRNA ligase activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer protein related amino acid -activation

Essentiality data for ileS knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Credits:
Last-Curated ? 10-Jul-2006 by Keseler I , SRI International


Enzymatic reaction of: isoleucyl-tRNA synthetase

Synonyms: IleRS

EC Number: 6.1.1.5

tRNAile + L-isoleucine + ATP + H+ <=> L-isoleucyl-tRNAile + AMP + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA charging

Summary:
Pseudomonic acid (mupirocin) is a competitive inhibitor of IleRS from E. coli B [Hughes80].

Cofactors or Prosthetic Groups: Zn2+ [Schimmel93, Kayne72]

Inhibitors (Unknown Mechanism): 2-iodo-L-isoleucine-NHSO2-AMP [Lee03] , isoleucine tetrazole [Willshaw75]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-isoleucine
3.6
[Glasfeld96, BRENDA14]
L-isoleucine
5.69
[Fersht76]
L-isoleucine
5.2
27.7
[Landro94, BRENDA14]
L-isoleucine
1300.0
104.0
[Zhou95a, BRENDA14]
tRNAile
2.1
[Xu94]
tRNAile
3.1
[Zhou95a, BRENDA14]
ATP
0.54
[Landro94, BRENDA14]
ATP
700.0
[Zhou95a, BRENDA14]
ATP
30.0
[Fersht76]
ATP
4400.0
1.56
[Dulic10, BRENDA14]
ATP
0.28
80.4
[Glasfeld96, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Yanagisawa94, UniProt11]
UniProt: Removed.
Chain 2 -> 938
[UniProt09]
UniProt: Isoleucyl-tRNA synthetase;
Protein-Segment 58 -> 68
[UniProt10a]
UniProt: "HIGH" region; Sequence Annotation Type: short sequence motif;
Mutagenesis-Variant 94
[Clarke88, UniProt11]
Alternate sequence: G → R; UniProt: 6000-fold increase in Km for isoleucine and 4-fold increase in Km for ATP, with no effect on activity.
Mutagenesis-Variant 97
[Clarke88, UniProt11]
Alternate sequence: C → S; UniProt: No effect on activity.
Mutagenesis-Variant 102
[Clarke88, UniProt11]
Alternate sequence: I → N; UniProt: No significant effect on activity.
Mutagenesis-Variant 183
[Bishop03, UniProt11]
Alternate sequence: K → A; UniProt: Abolishes translocation from the aminoacylation site to the editing site, without effect on aminoacylation activity and posttransfer editing; when associated with A-421.
Acetylation-Modification 183
[Zhang09a, UniProt11]
UniProt: N6-acetyllysine.
Mutagenesis-Variant 241
[Nureki98, UniProt11]
Alternate sequence: T → A; UniProt: Nearly the same editing activity as the wild-type.
Mutagenesis-Variant 242
[Hendrickson00, UniProt11]
Alternate sequence: T → P; UniProt: Abolishes editing activity against valine, with little change in aminoacylation activity.
Alternate sequence: T → A; UniProt: Abolishes editing activity against valine, with little change in aminoacylation activity; when associated with A-250.
Mutagenesis-Variant 243
[Hendrickson02, Nureki98, UniProt11]
Alternate sequence: T → R; UniProt: Abolishes pretransfer editing.
Alternate sequence: T → A; UniProt: Abolishes editing activity against valine, with little change in aminoacylation activity.
Sequence-Conflict 243 -> 264
[Webster84, UniProt10a]
Alternate sequence: TPWTLPANRAISIAPDFDYALV → RRGLCLPTAQSLLHQISTMRWW; UniProt: (in Ref. 1; AA sequence);
Mutagenesis-Variant 246
[Nureki98, UniProt11]
Alternate sequence: T → A; UniProt: Nearly the same editing activity as the wild-type.
Mutagenesis-Variant 250
[Hendrickson00, Nureki98, UniProt11]
Alternate sequence: N → A; UniProt: Abolishes editing activity against valine, with little change in aminoacylation activity.
Sequence-Conflict 300 -> 301
[Webster84, UniProt10a]
Alternate sequence: EL → DV; UniProt: (in Ref. 1; AA sequence);
Mutagenesis-Variant 333
[Hendrickson02, UniProt11]
Alternate sequence: H → A; UniProt: Alters the specificity for hydrolysis of the aminoacyl tRNA ester, with no effect on pretransfer editing.
Mutagenesis-Variant 342
[Bishop02, UniProt11]
Alternate sequence: D → E; UniProt: Reduces 2- to 3-fold the total editing activity and 2-fold the deacylation activity. Moderately reduces translocation from the aminoacylation site to the editing site.
Alternate sequence: D → N; UniProt: Strong decrease in total editing and deacylation activities. Severely deficient in translocation from the aminoacylation site to the editing site.
Alternate sequence: D → A; UniProt: Strong decrease in total editing and deacylation activities. Severely deficient in translocation from the aminoacylation site to the editing site.
Mutagenesis-Variant 421
[Bishop03, UniProt11]
Alternate sequence: W → A; UniProt: Abolishes translocation from the aminoacylation site to the editing site, without effect on aminoacylation activity and posttransfer editing; when associated with A-183.
Amino-Acid-Sites-That-Bind 561
[UniProt10]
UniProt: Aminoacyl-adenylate; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 587
[Webster84, UniProt10a]
Alternate sequence: R → C; UniProt: (in Ref. 1; AA sequence);
Extrinsic-Sequence-Variant 594
[UniProt10a]
Alternate sequence: F → L; UniProt: (in strain: PS102);
Protein-Segment 602 -> 606
[UniProt10a]
UniProt: "KMSKS" region; Sequence Annotation Type: short sequence motif;
Amino-Acid-Sites-That-Bind 605
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 637
[Webster84, UniProt10a]
Alternate sequence: E → Q; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 724
[Webster84, UniProt10a]
Alternate sequence: G → V; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 738
[Webster84, UniProt10a]
Alternate sequence: A → P; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 740 -> 743
[Webster84, UniProt10a]
Alternate sequence: ADSV → RTVW; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 787
[Webster84, UniProt10a]
Alternate sequence: F → L; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 830
[Webster84, UniProt10a]
Alternate sequence: K → N; UniProt: (in Ref. 1; AA sequence);
Sequence-Conflict 867 -> 869
[Webster84, UniProt10a]
Alternate sequence: GAT → DRRY; UniProt: (in Ref. 1; AA sequence);
Metal-Binding-Site 901
[UniProt10]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 904
[UniProt10]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 921
[UniProt10]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 924
[UniProt10]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0026 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10492; confirmed by SwissProt match.


References

Auld96: Auld DS, Schmimmel P (1996). "Single sequence of a helix-loop peptide confers functional anticodon recognition on two tRNA synthetases." EMBO J 15(5);1142-8. PMID: 8605884

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

Bacher05: Bacher JM, de Crecy-Lagard V, Schimmel PR (2005). "Inhibited cell growth and protein functional changes from an editing-defective tRNA synthetase." Proc Natl Acad Sci U S A 102(5);1697-701. PMID: 15647356

Bishop02: Bishop AC, Nomanbhoy TK, Schimmel P (2002). "Blocking site-to-site translocation of a misactivated amino acid by mutation of a class I tRNA synthetase." Proc Natl Acad Sci U S A 99(2);585-90. PMID: 11782529

Bishop03: Bishop AC, Beebe K, Schimmel PR (2003). "Interstice mutations that block site-to-site translocation of a misactivated amino acid bound to a class I tRNA synthetase." Proc Natl Acad Sci U S A 100(2);490-4. PMID: 12515858

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

Brissette91: Brissette JL, Weiner L, Ripmaster TL, Model P (1991). "Characterization and sequence of the Escherichia coli stress-induced psp operon." J Mol Biol 220(1);35-48. PMID: 1712397

Burbaum90: Burbaum JJ, Starzyk RM, Schimmel P (1990). "Understanding structural relationships in proteins of unsolved three-dimensional structure." Proteins 7(2);99-111. PMID: 2183216

Clarke88: Clarke ND, Lien DC, Schimmel P (1988). "Evidence from cassette mutagenesis for a structure-function motif in a protein of unknown structure." Science 240(4851);521-3. PMID: 3282306

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Durekovic73: Durekovic A, Flossdorf J, Kula MR (1973). "Isolation and properties of isoleucyl-tRNA synthetase from Escherichia coli MRE 600." Eur J Biochem 36(2);528-33. PMID: 4581276

Eriani90: Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990). "Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs." Nature 347(6289);203-6. PMID: 2203971

Farrow01: Farrow MA, Schimmel P (2001). "Editing by a tRNA synthetase: DNA aptamer-induced translocation and hydrolysis of a misactivated amino acid." Biochemistry 40(14);4478-83. PMID: 11284704

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Flossdorf76: Flossdorf J, Pratorius HJ, Kula MR (1976). "Influence of side-chain structure of aliphatic amino acids on binding to isoleucyl-tRNA synthetase from Escherichia coli MRE 600." Eur J Biochem 66(1);147-55. PMID: 782880

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Freist82: Freist W, Sternbach H, Cramer F (1982). "Isoleucyl-tRNA synthetase from Escherichia coli MRE 600. Different pathways of the aminoacylation reaction depending on presence of pyrophosphatase, order of substrate addition in the pyrophosphate exchange, and substrate specificity with regard to ATP analogs." Eur J Biochem 128(2-3);315-29. PMID: 6129973

Freist87: Freist W, Sternbach H, Cramer F (1987). "Isoleucyl-tRNA synthetase from baker's yeast and from Escherichia coli MRE 600. Discrimination of 20 amino acids in aminoacylation of tRNA(Ile)-C-C-A(3'NH2)." Eur J Biochem 169(1);33-9. PMID: 3315663

Freist87a: Freist W, Cramer F (1987). "Isoleucyl-tRNA synthetase from Escherichia coli MRE 600: discrimination between isoleucine and valine with modulated accuracy." Biol Chem Hoppe Seyler 368(3);229-37. PMID: 3297096

Freist88: Freist W, Sternbach H, Cramer F (1988). "Isoleucyl-tRNA synthetase from baker's yeast and from Escherichia coli MRE 600. Discrimination of 20 amino acids in aminoacylation of tRNA(Ile)-C-C-A." Eur J Biochem 173(1);27-34. PMID: 3281834

Glasfeld96: Glasfeld E, Landro JA, Schimmel P (1996). "C-terminal zinc-containing peptide required for RNA recognition by a class I tRNA synthetase." Biochemistry 35(13);4139-45. PMID: 8672449

Glasfeld97: Glasfeld E, Schimmel P (1997). "Zinc-dependent tRNA binding by a peptide element within a tRNA synthetase." Biochemistry 36(22);6739-44. PMID: 9184155

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GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Hale96: Hale SP, Schimmel P (1996). "Protein synthesis editing by a DNA aptamer." Proc Natl Acad Sci U S A 93(7);2755-8. PMID: 8610114

Hendrickson00: Hendrickson TL, Nomanbhoy TK, Schimmel P (2000). "Errors from selective disruption of the editing center in a tRNA synthetase." Biochemistry 39(28);8180-6. PMID: 10889024

Hendrickson02: Hendrickson TL, Nomanbhoy TK, de Crecy-Lagard V, Fukai S, Nureki O, Yokoyama S, Schimmel P (2002). "Mutational separation of two pathways for editing by a class I tRNA synthetase." Mol Cell 9(2);353-62. PMID: 11864608

Hinz76: Hinz HJ, Weber K, Flossdorf J, Kula MR (1976). "Thermodynamic studies on the specificity of L-isoleucine-tRNA ligase of Escherichia coli MRE 600. Calorimetric investigations on binding of amino acids and isoleucinol to the enzyme." Eur J Biochem 71(2);437-42. PMID: 795668

Hughes05: Hughes RA, Ellington AD (2005). "Mistakes in translation don't translate into termination." Proc Natl Acad Sci U S A 102(5);1273-4. PMID: 15677335

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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

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Kamio85: Kamio Y, Lin CK, Regue M, Wu HC (1985). "Characterization of the ileS-lsp operon in Escherichia coli. Identification of an open reading frame upstream of the ileS gene and potential promoter(s) for the ileS-lsp operon." J Biol Chem 260(9);5616-20. PMID: 2985604

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Landes95: Landes C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL (1995). "A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases." Biochimie 77(3);194-203. PMID: 7647112

Landro94: Landro JA, Schmidt E, Schimmel P, Tierney DL, Penner-Hahn JE (1994). "Thiol ligation of two zinc atoms to a class I tRNA synthetase: evidence for unshared thiols and role in amino acid binding and utilization." Biochemistry 33(47);14213-20. PMID: 7947832

Landro94a: Landro JA, Schimmel P (1994). "Zinc-dependent cell growth conferred by mutant tRNA synthetase." J Biol Chem 269(32);20217-20. PMID: 8051111

Lee03: Lee J, Kim SE, Lee JY, Kim SY, Kang SU, Seo SH, Chun MW, Kang T, Choi SY, Kim HO (2003). "N-Alkoxysulfamide, N-hydroxysulfamide, and sulfamate analogues of methionyl and isoleucyl adenylates as inhibitors of methionyl-tRNA and isoleucyl-tRNA synthetases." Bioorg Med Chem Lett 13(6);1087-92. PMID: 12643918

Miller87: Miller KW, Wu HC (1987). "Cotranscription of the Escherichia coli isoleucyl-tRNA synthetase (ileS) and prolipoprotein signal peptidase (lsp) genes. Fine-structure mapping of the lsp internal promoter." J Biol Chem 262(1);389-93. PMID: 2432063

Miller87a: Miller KW, Bouvier J, Stragier P, Wu HC (1987). "Identification of the genes in the Escherichia coli ileS-lsp operon. Analysis of multiple polycistronic mRNAs made in vivo." J Biol Chem 262(15);7391-7. PMID: 3294831

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Other References Related to Gene Regulation

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Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608


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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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