Escherichia coli K-12 substr. MG1655 Protein: CytR DNA-binding transcriptional repressor

Gene: cytR Accession Numbers: EG10200 (EcoCyc), b3934, ECK3926

Synonyms: regulator for deo operon, udp, cdd, tsx, nupC, and nupG

Regulation Summary Diagram: ?

Regulation summary diagram for cytR

Component of: CytR-cytidine

Subunit composition of CytR DNA-binding transcriptional repressor = [CytR]2

CytR, "Cytidine Regulator," is a transcription factor required for transport and utilization of ribonucleosides and deoxyribonucleosides [NorregaardMadse94, Pedersen95, Craig94, Gerlach91, Jorgensen98, Kallipolitis98, Zolotukhina03].

The repressor CytR and the activator CRP, two dimeric proteins, interact to form a complex repressor nucleoprotein in the intergenic region. When only CRP is bound to this promoter, it functions as an activator, and then, when CytR binds to DNA and to CRP, the activation is repressed because CytR masks an activating region of CRP that otherwise would contact the RNA polymerase to activate transcription [ValentinHansen96, Meibom00, Kristensen97, Meibom99, Meibom00, Kristensen96, Rasmussen96].

The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP [SogaardAndersen90a, SogaardAndersen90, SogaardAndersen91b]. However, footprinting analyses showed that the dimers of CytR are flanked or "sandwiched" by two dimers of CRP [Pedersen91, Meibom00, Gavigan99, Perini96]. At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation [ValentinHansen96].

Gavigan et al. (1999) and Perini et al. (1996) showed that CytR binds in tandem in the regulated intergenic region [Gavigan99, Perini96]. On the other hand, in 1997, Pedersen and Valentin-Hanses showed that CytR binds to octamer repeats, GTTGCATT in either the direct or inverted orientation and preferably separated by 2 or 3 bp [Pedersen97, Kallipolitis04, Jorgensen98]. For this reason the length of the CytR DNA-binding site is variable.

Gene induction occurs when the physiological inducer, cytidine, binds to the CytR regulator and when cellular cAMP levels are high. CytR senses and binds cytidine, and when this happens the cooperativity of CytR and CRP is interrupted and the expression of genes is induced [Pedersen91, Gerlach91].

CytR belongs to the GalR/LacI family of transcriptional regulators [Weickert92a]. Like the other members of this family, it has an N-terminal domain that contains a helix-turn-helix (HTH) motif for DNA binding and a C-terminal domain for dimerization, inducer binding [Weickert92a], and protein contact with CRP [Kallipolitis97]. Between these two domains, CytR has a disordered sequence that provides the HTH motif with freedom of movement [Pedersen97, Jorgensen98], which would allow this protein to interact with octameric half DNA-binding sites that could be arranged as inverted or direct repeats and with different lengths of spacer regions [Jorgensen98, Pedersen97]. This interdomain linker is protected from proteolytic digestion in the presence of CRP [Kallipolitis04].

Based on nuclear magnetic resonance (NMR) spectroscopy, the structure of the CytR DNA-binding domain (DBD) bound to the udp half-site and characterization of the free state were obtained [Moody11].

The cytR gene is autorepressed and is activated by CRP [Gerlach90, Pedersen92].

Review: [ValentinHansen96, MullerHill98].

Citations: [ValentinHansen86a, Lee90, Plunkett93]

Locations: cytosol

Map Position: [4,121,454 <- 4,122,479] (88.83 centisomes, 320°)
Length: 1026 bp / 341 aa

Molecular Weight of Polypeptide: 37.82 kD (from nucleotide sequence)

pI: 6.25

Unification Links: ASAP:ABE-0012853 , CGSC:887 , DIP:DIP-9390N , EchoBASE:EB0196 , EcoGene:EG10200 , EcoliWiki:b3934 , ModBase:P0ACN7 , OU-Microarray:b3934 , PortEco:cytR , PR:PRO_000022391 , Pride:P0ACN7 , Protein Model Portal:P0ACN7 , RefSeq:NP_418369 , RegulonDB:EG10200 , SMR:P0ACN7 , String:511145.b3934 , UniProt:P0ACN7

Relationship Links: InterPro:IN-FAMILY:IPR000843 , InterPro:IN-FAMILY:IPR010982 , InterPro:IN-FAMILY:IPR028082 , PDB:Structure:2LCV , Pfam:IN-FAMILY:PF00356 , Prosite:IN-FAMILY:PS00356 , Prosite:IN-FAMILY:PS50932 , Smart:IN-FAMILY:SM00354

In Paralogous Gene Group: 30 (25 members)

In Reactions of unknown directionality:

Not in pathways:
CytR + cytidine = CytR-cytidine

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for cytR

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [NorregaardMadse94]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0000976 - transcription regulatory region sequence-specific DNA binding Inferred from experiment [NorregaardMadse94]
GO:0005515 - protein binding Inferred from experiment [Arifuzzaman06]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer RNA related Transcription related
metabolism central intermediary metabolism nucleotide and nucleoside conversions
regulation genetic unit regulated regulon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

DNA binding site length: 18 base-pairs

Symmetry: Inverted Repeat, Direct Repeat

Consensus DNA Binding Sequence: AATGcAACgcGTTGCATT , GTTGCATTnnGTTgCATt

Regulated Transcription Units (14 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Essentiality data for cytR 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]

Created 04-Nov-2008 by Gama-Castro S , UNAM
Last-Curated ? 09-Jan-2009 by Gama-Castro S , UNAM

Subunit of: CytR-cytidine

Subunit composition of CytR-cytidine = [(CytR)2][cytidine]
         CytR DNA-binding transcriptional repressor = (CytR)2 (extended summary available)

Sequence Length: 341 AAs

In Reactions of unknown directionality:

Not in pathways:
CytR + cytidine = CytR-cytidine

MultiFun Terms: information transfer RNA related Transcription related
metabolism central intermediary metabolism nucleotide and nucleoside conversions
regulation genetic unit regulated regulon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Sequence Features

Protein sequence of CytR with features indicated

Feature Class Location Citations Comment
Conserved-Region 10 -> 64
UniProt: HTH lacI-type;
DNA-Binding-Region 12 -> 31
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3934 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10200; confirmed by SwissProt match.


Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Craig94: Craig JE, Zhang Y, Gallagher MP (1994). "Cloning of the nupC gene of Escherichia coli encoding a nucleoside transport system, and identification of an adjacent insertion element, IS 186." Mol Microbiol 1994;11(6);1159-68. PMID: 8022285

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gavigan99: Gavigan SA, Nguyen T, Nguyen N, Senear DF (1999). "Role of multiple CytR binding sites on cooperativity, competition, and induction at the Escherichia coli udp promoter." J Biol Chem 1999;274(23);16010-9. PMID: 10347150

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

Gerlach90: Gerlach P, Valentin-Hansen P, Bremer E (1990). "Transcriptional regulation of the cytR repressor gene of Escherichia coli: autoregulation and positive control by the cAMP/CAP complex." Mol Microbiol 1990;4(3);479-88. PMID: 2162467

Gerlach91: Gerlach P, Sogaard-Andersen L, Pedersen H, Martinussen J, Valentin-Hansen P, Bremer E (1991). "The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli K-12." J Bacteriol 1991;173(17);5419-30. PMID: 1715855

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

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

Jorgensen98: Jorgensen CI, Kallipolitis BH, Valentin-Hansen P (1998). "DNA-binding characteristics of the Escherichia coli CytR regulator: a relaxed spacing requirement between operator half-sites is provided by a flexible, unstructured interdomain linker." Mol Microbiol 27(1);41-50. PMID: 9466254

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

Kallipolitis04: Kallipolitis BH, Valentin-Hansen P (2004). "A role for the interdomain linker region of the Escherichia coli CytR regulator in repression complex formation." J Mol Biol 342(1);1-7. PMID: 15313602

Kallipolitis97: Kallipolitis BH, Norregaard-Madsen M, Valentin-Hansen P (1997). "Protein-protein communication: structural model of the repression complex formed by CytR and the global regulator CRP." Cell 89(7);1101-9. PMID: 9215632

Kallipolitis98: Kallipolitis BH, Valentin-Hansen P (1998). "Transcription of rpoH, encoding the Escherichia coli heat-shock regulator sigma32, is negatively controlled by the cAMP-CRP/CytR nucleoprotein complex." Mol Microbiol 1998;29(4);1091-9. PMID: 9767576

Kristensen96: Kristensen HH, Valentin-Hansen P, Sogaard-Andersen L (1996). "CytR/cAMP-CRP nucleoprotein formation in E. coli: the CytR repressor binds its operator as a stable dimer in a ternary complex with cAMP-CRP." J Mol Biol 260(2);113-9. PMID: 8764393

Kristensen97: Kristensen HH, Valentin-Hansen P, Sogaard-Andersen L (1997). "Design of CytR regulated, cAMP-CRP dependent class II promoters in Escherichia coli: RNA polymerase-promoter interactions modulate the efficiency of CytR repression." J Mol Biol 266(5);866-76. PMID: 9086266

Lee90: Lee EH, Masai H, Allen GC, Kornberg A (1990). "The priA gene encoding the primosomal replicative n' protein of Escherichia coli." Proc Natl Acad Sci U S A 1990;87(12);4620-4. PMID: 2162050

Meibom00: Meibom KL, Kallipolitis BH, Ebright RH, Valentin-Hansen P (2000). "Identification of the subunit of cAMP receptor protein (CRP) that functionally interacts with CytR in CRP-CytR-mediated transcriptional repression." J Biol Chem 275(16);11951-6. PMID: 10766824

Meibom99: Meibom KL, Sogaard-Andersen L, Mironov AS, Valentin-Hansen P (1999). "Dissection of a surface-exposed portion of the cAMP-CRP complex that mediates transcription activation and repression." Mol Microbiol 32(3);497-504. PMID: 10320573

Moody11: Moody CL, Tretyachenko-Ladokhina V, Laue TM, Senear DF, Cocco MJ (2011). "Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One upon Recognition of a Specific DNA Surface." Biochemistry 50(31);6622-32. PMID: 21688840

MullerHill98: Muller-Hill B (1998). "Some repressors of bacterial transcription." Curr Opin Microbiol 1(2);145-51. PMID: 10066473

NorregaardMadse94: Norregaard-Madsen M, Mygind B, Pedersen R, Valentin-Hansen P, Sogaard-Andersen L (1994). "The gene encoding the periplasmic cyclophilin homologue, PPIase A, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP-CRP complex and negatively regulated by the CytR repressor." Mol Microbiol 1994;14(5);989-97. PMID: 7715459

Pedersen91: Pedersen H, Sogaard-Andersen L, Holst B, Valentin-Hansen P (1991). "Heterologous cooperativity in Escherichia coli. The CytR repressor both contacts DNA and the cAMP receptor protein when binding to the deoP2 promoter." J Biol Chem 266(27);17804-8. PMID: 1655726

Pedersen92: Pedersen H, Sogaard-Andersen L, Holst B, Gerlach P, Bremer E, Valentin-Hansen P (1992). "cAMP-CRP activator complex and the CytR repressor protein bind co-operatively to the cytRP promoter in Escherichia coli and CytR antagonizes the cAMP-CRP-induced DNA bend." J Mol Biol 1992;227(2);396-406. PMID: 1328649

Pedersen95: Pedersen H, Dall J, Dandanell G, Valentin-Hansen P (1995). "Gene-regulatory modules in Escherichia coli: nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter." Mol Microbiol 1995;17(5);843-53. PMID: 8596434

Pedersen97: Pedersen H, Valentin-Hansen P (1997). "Protein-induced fit: the CRP activator protein changes sequence-specific DNA recognition by the CytR repressor, a highly flexible LacI member." EMBO J 16(8);2108-18. PMID: 9155036

Perini96: Perini LT, Doherty EA, Werner E, Senear DF (1996). "Multiple specific CytR binding sites at the Escherichia coli deoP2 promoter mediate both cooperative and competitive interactions between CytR and cAMP receptor protein." J Biol Chem 271(52);33242-55. PMID: 8969182

Plunkett93: Plunkett G, Burland V, Daniels DL, Blattner FR (1993). "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Nucleic Acids Res 1993;21(15);3391-8. PMID: 8346018

Rasmussen96: Rasmussen PB, Holst B, Valentin-Hansen P (1996). "Dual-function regulators: the cAMP receptor protein and the CytR regulator can act either to repress or to activate transcription depending on the context." Proc Natl Acad Sci U S A 93(19);10151-5. PMID: 8816767

SogaardAndersen90: Sogaard-Andersen L, Martinussen J, Mollegaard NE, Douthwaite SR, Valentin-Hansen P (1990). "The CytR repressor antagonizes cyclic AMP-cyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12." J Bacteriol 1990;172(10);5706-13. PMID: 2170326

SogaardAndersen90a: Sogaard-Andersen L, Mollegaard NE, Douthwaite SR, Valentin-Hansen P (1990). "Tandem DNA-bound cAMP-CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli." Mol Microbiol 4(9);1595-601. PMID: 1962841

SogaardAndersen91b: Sogaard-Andersen L, Pedersen H, Holst B, Valentin-Hansen P (1991). "A novel function of the cAMP-CRP complex in Escherichia coli: cAMP-CRP functions as an adaptor for the CytR repressor in the deo operon." Mol Microbiol 5(4);969-75. PMID: 1649947

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

ValentinHansen86a: Valentin-Hansen P, Larsen JE, Hojrup P, Short SA, Barbier CS (1986). "Nucleotide sequence of the CytR regulatory gene of E. coli K-12." Nucleic Acids Res 1986;14(5);2215-28. PMID: 3515317

ValentinHansen96: Valentin-Hansen P, Sogaard-Andersen L, Pedersen H (1996). "A flexible partnership: the CytR anti-activator and the cAMP-CRP activator protein, comrades in transcription control." Mol Microbiol 20(3);461-6. PMID: 8736525

Weickert92a: Weickert MJ, Adhya S (1992). "A family of bacterial regulators homologous to Gal and Lac repressors." J Biol Chem 267(22);15869-74. PMID: 1639817

Zolotukhina03: Zolotukhina M, Ovcharova I, Eremina S, Errais Lopes L, Mironov AS (2003). "Comparison of the structure and regulation of the udp gene of Vibrio cholerae, Yersinia pseudotuberculosis, Salmonella typhimurium, and Escherichia coli." Res Microbiol 154(7);510-20. PMID: 14499937

Other References Related to Gene Regulation

Holst92: Holst B, Sogaard-Andersen L, Pedersen H, Valentin-Hansen P (1992). "The cAMP-CRP/CytR nucleoprotein complex in Escherichia coli: two pairs of closely linked binding sites for the cAMP-CRP activator complex are involved in combinatorial regulation of the cdd promoter." EMBO J 11(10);3635-43. PMID: 1327747

Holt10: Holt AK, Senear DF (2010). "An unusual pattern of CytR and CRP binding energetics at Escherichia coli cddP suggests a unique blend of class I and class II mediated activation." Biochemistry 49(3);432-42. PMID: 20000490

Zolotukhina02: Zolotukhina MA, Ovcharova IV, Eremina SIu, Errais LL, Mironov AS (2002). "[Functional interrelationship between elements of the Escherichia coli udp gene promotor responsible for binding regulatory proteins CytR, CRP, and RNA polymerase]." Genetika 38(9);1223-34. PMID: 12391883

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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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