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Pathway Description
Operon: Nucleotide and Deoxyribonucleotide Catabolism Inactivation
Escherichia coli
Category:
Protein Pathway
Sub-Categories:
Gene Regulatory
Cellular Response
Created: 2015-11-12
Last Updated: 2025-05-31
The nucleotide and deoxyribonucleotide operon is a polycistronic operon consisting of the genes DeoC, DeoA, DeoB and DeoD. DeoC encodes for a ribose-1,5-bisphosphate isomerase, DeoA encodes for a deoxyribose-5-phosphate aldolase, DeoB encodes for a ribose-5-phosphate isomerase and DeoD encodes for a deoxyribose-5-phosphate isomerase. This operon's transcription is activated by Fis DNA-binding transcriptional dual regulator binding to a -102 bp site off the promoter, thus enhancing RNA polymerase binding. This operon can also be activated by having CRP-cAMP DNA-binding transcriptional dual regulator binding either to -93.5 or -40.5. The repression of the operon's transcription can be controlled by multiple sites upsteam the promoter. DeoR (DeoR DNA-binding transcriptional repressor) which binds to -887, -309, -8 sites of the promoter deoP2, preventing RNA polymerase from initiating transcription. For promoter deoP1, DeoR binds at -609, -8, 269 sites, repressing transcription by blocking access to the promoter.
CRP-cAMP DNA-binding transcriptional dual regulator binds at -93.5 for promoter deop2, CytR (CytR DNA-binding transcriptional repressor) binds to -87.5, -70.5, -61 for promoter deop2 and ModE-MoO42- DNA-binding transcriptional dual regulator binds to -35 for promoter deop2
References
Operon: Nucleotide and Deoxyribonucleotide Catabolism Inactivation References
Albrechtsen H, Ahmad SI: Regulation of the synthesis of nucleoside catabolic enzymes in Escherichia coli: further analysis of a deo Oc mutant strain. Mol Gen Genet. 1980;179(2):457-60.
Pubmed: 6780756
Amouyal M, Mortensen L, Buc H, Hammer K: Single and double loop formation when deoR repressor binds to its natural operator sites. Cell. 1989 Aug 11;58(3):545-51.
Pubmed: 2667765
Brikun I, Suziedelis K, Stemmann O, Zhong R, Alikhanian L, Linkova E, Mironov A, Berg DE: Analysis of CRP-CytR interactions at the Escherichia coli udp promoter. J Bacteriol. 1996 Mar;178(6):1614-22.
Pubmed: 8626289
Chahla M, Wooll J, Laue TM, Nguyen N, Senear DF: Role of protein-protein bridging interactions on cooperative assembly of DNA-bound CRP-CytR-CRP complex and regulation of the Escherichia coli CytR regulon. Biochemistry. 2003 Apr 8;42(13):3812-25. doi: 10.1021/bi0271143.
Pubmed: 12667072
Gavigan SA, Nguyen T, Nguyen N, Senear DF: Role of multiple CytR binding sites on cooperativity, competition, and induction at the Escherichia coli udp promoter. J Biol Chem. 1999 Jun 4;274(23):16010-9.
Pubmed: 10347150
Gerlach P, Sogaard-Andersen L, Pedersen H, Martinussen J, Valentin-Hansen P, Bremer E: 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 Sep;173(17):5419-30.
Pubmed: 1715855
Gonzalez-Gil G, Bringmann P, Kahmann R: FIS is a regulator of metabolism in Escherichia coli. Mol Microbiol. 1996 Oct;22(1):21-9.
Pubmed: 8899705
Holst B, Sogaard-Andersen L, Pedersen H, Valentin-Hansen P: 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. 1992 Oct;11(10):3635-43.
Pubmed: 1327747
Holt AK, Senear DF: 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. 2010 Jan 26;49(3):432-42. doi: 10.1021/bi901583n.
Pubmed: 20000490
Huerta AM, Collado-Vides J: Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol. 2003 Oct 17;333(2):261-78.
Pubmed: 14529615
Jorgensen CI, Kallipolitis BH, Valentin-Hansen P: 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. 1998 Jan;27(1):41-50.
Pubmed: 9466254
Larsen JE, Albrechtsen B, Valentin-Hansen P: Analysis of the terminator region after the deoCABD operon of Escherichia coli K-12 using a new class of single copy number operon-fusion vectors. Nucleic Acids Res. 1987 Jul 10;15(13):5125-40.
Pubmed: 3299264
Mayes DG: A comparison of menstrual bleeding patterns associated with three IUD models: an example of reference period analysis. J Biosoc Sci. 1977 Jan;9(1):121-35.
Pubmed: 845188
Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J: Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res. 2011 Feb;39(3):808-24. doi: 10.1093/nar/gkq710. Epub 2010 Oct 4.
Pubmed: 20923783
Meibom KL, Kallipolitis BH, Ebright RH, Valentin-Hansen P: Identification of the subunit of cAMP receptor protein (CRP) that functionally interacts with CytR in CRP-CytR-mediated transcriptional repression. J Biol Chem. 2000 Apr 21;275(16):11951-6.
Pubmed: 10766824
Mollegaard NE, Rasmussen PB, Valentin-Hansen P, Nielsen PE: Characterization of promoter recognition complexes formed by CRP and CytR for repression and by CRP and RNA polymerase for activation of transcription on the Escherichia coli deoP2 promoter. J Biol Chem. 1993 Aug 15;268(23):17471-7.
Pubmed: 8394345
Pedersen H, Sogaard-Andersen L, Holst B, Valentin-Hansen P: 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. 1991 Sep 25;266(27):17804-8.
Pubmed: 1655726
Pedersen H, Valentin-Hansen P: Protein-induced fit: the CRP activator protein changes sequence-specific DNA recognition by the CytR repressor, a highly flexible LacI member. EMBO J. 1997 Apr 15;16(8):2108-18. doi: 10.1093/emboj/16.8.2108.
Pubmed: 9155036
Perini LT, Doherty EA, Werner E, Senear DF: 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. 1996 Dec 27;271(52):33242-55.
Pubmed: 8969182
Shin M, Kang S, Hyun SJ, Fujita N, Ishihama A, Valentin-Hansen P, Choy HE: Repression of deoP2 in Escherichia coli by CytR: conversion of a transcription activator into a repressor. EMBO J. 2001 Oct 1;20(19):5392-9. doi: 10.1093/emboj/20.19.5392.
Pubmed: 11574471
Sogaard-Andersen L, Mollegaard NE, Douthwaite SR, Valentin-Hansen P: Tandem DNA-bound cAMP-CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli. Mol Microbiol. 1990 Sep;4(9):1595-601.
Pubmed: 1962841
Sogaard-Andersen L, Martinussen J, Mollegaard NE, Douthwaite SR, Valentin-Hansen P: The CytR repressor antagonizes cyclic AMP-cyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12. J Bacteriol. 1990 Oct;172(10):5706-13.
Pubmed: 2170326
Sogaard-Andersen L, Pedersen H, Holst B, Valentin-Hansen P: 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. 1991 Apr;5(4):969-75.
Pubmed: 1649947
Sogaard-Andersen L, Valentin-Hansen P: Restored DNA-binding of the cAMP-CRP activator complex reestablishes negative regulation by the CytR repressor in the deoP2 promoter in Escherichia coli. Mol Gen Genet. 1991 Dec;231(1):76-80.
Pubmed: 1661372
Sogaard-Andersen L, Mironov AS, Pedersen H, Sukhodelets VV, Valentin-Hansen P: Single amino acid substitutions in the cAMP receptor protein specifically abolish regulation by the CytR repressor in Escherichia coli. Proc Natl Acad Sci U S A. 1991 Jun 1;88(11):4921-5.
Pubmed: 1647022
Sogaard-Andersen L, Valentin-Hansen P: Protein-protein interactions in gene regulation: the cAMP-CRP complex sets the specificity of a second DNA-binding protein, the CytR repressor. Cell. 1993 Nov 5;75(3):557-66.
Pubmed: 8221894
Svenningsen BA: Regulated in vitro synthesis of the enzymes of the deo operon of Escerichia coli. properties of the DNA directed system. Mol Gen Genet. 1975;137(4):289-304.
Pubmed: 810659
Tao H, Hasona A, Do PM, Ingram LO, Shanmugam KT: Global gene expression analysis revealed an unsuspected deo operon under the control of molybdate sensor, ModE protein, in Escherichia coli. Arch Microbiol. 2005 Dec;184(4):225-33. doi: 10.1007/s00203-005-0039-7. Epub 2005 Nov 15.
Pubmed: 16205910
Valentin-Hansen P, Aiba H, Schumperli D: The structure of tandem regulatory regions in the deo operon of Escherichia coli K12. EMBO J. 1982;1(3):317-22.
Pubmed: 16453417
Valentin-Hansen P: Tandem CRP binding sites in the deo operon of Escherichia coli K-12. EMBO J. 1982;1(9):1049-54.
Pubmed: 6329724
Valentin-Hansen P, Larsen JE, Hojrup P, Short SA, Barbier CS: Nucleotide sequence of the CytR regulatory gene of E. coli K-12. Nucleic Acids Res. 1986 Mar 11;14(5):2215-28.
Pubmed: 3515317
Valentin-Hansen P, Albrechtsen B, Love Larsen JE: DNA-protein recognition: demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor. EMBO J. 1986 Aug;5(8):2015-21.
Pubmed: 3019678
Valentin-Hansen P, Holst B, Josephsen J, Hammer K, Albrechtsen B: CRP/cAMP- and CytR-regulated promoters in Escherichia coli K12: the cdd promoter. Mol Microbiol. 1989 Oct;3(10):1385-90.
Pubmed: 2575702
Valentin-Hansen P, Sogaard-Andersen L, Pedersen H: A flexible partnership: the CytR anti-activator and the cAMP-CRP activator protein, comrades in transcription control. Mol Microbiol. 1996 May;20(3):461-6.
Pubmed: 8736525
Zheng D, Constantinidou C, Hobman JL, Minchin SD: Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res. 2004 Nov 1;32(19):5874-93. doi: 10.1093/nar/gkh908. Print 2004.
Pubmed: 15520470
Zolotukhina MA, Ovcharova IV, Eremina SIu, Errais LL, Mironov AS: [Functional interrelationship between elements of the Escherichia coli udp gene promotor responsible for binding regulatory proteins CytR, CRP, and RNA polymerase]. Genetika. 2002 Sep;38(9):1223-34.
Pubmed: 12391883
Ji XJ, Nie ZK, Huang H, Ren LJ, Peng C, Ouyang PK: Elimination of carbon catabolite repression in Klebsiella oxytoca for efficient 2,3-butanediol production from glucose-xylose mixtures. Appl Microbiol Biotechnol. 2011 Feb;89(4):1119-25. doi: 10.1007/s00253-010-2940-5. Epub 2010 Oct 19.
Pubmed: 20957355
Johnson RC, Ball CA, Pfeffer D, Simon MI: Isolation of the gene encoding the Hin recombinational enhancer binding protein. Proc Natl Acad Sci U S A. 1988 May;85(10):3484-8. doi: 10.1073/pnas.85.10.3484.
Pubmed: 2835774
Koch C, Vandekerckhove J, Kahmann R: Escherichia coli host factor for site-specific DNA inversion: cloning and characterization of the fis gene. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4237-41. doi: 10.1073/pnas.85.12.4237.
Pubmed: 2837762
Ball CA, Osuna R, Ferguson KC, Johnson RC: Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol. 1992 Dec;174(24):8043-56. doi: 10.1128/jb.174.24.8043-8056.1992.
Pubmed: 1459953
Valentin-Hansen P, Larsen JE, Hojrup P, Short SA, Barbier CS: Nucleotide sequence of the CytR regulatory gene of E. coli K-12. Nucleic Acids Res. 1986 Mar 11;14(5):2215-28. doi: 10.1093/nar/14.5.2215.
Pubmed: 3515317
Plunkett G 3rd, Burland V, Daniels DL, Blattner FR: Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res. 1993 Jul 25;21(15):3391-8. doi: 10.1093/nar/21.15.3391.
Pubmed: 8346018
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. doi: 10.1126/science.277.5331.1453.
Pubmed: 9278503
Ovchinnikov YA, Monastyrskaya GS, Gubanov VV, Guryev SO, Chertov OYu, Modyanov NN, Grinkevich VA, Makarova IA, Marchenko TV, Polovnikova IN, Lipkin VM, Sverdlov ED: The primary structure of Escherichia coli RNA polymerase. Nucleotide sequence of the rpoB gene and amino-acid sequence of the beta-subunit. Eur J Biochem. 1981 Jun 1;116(3):621-9. doi: 10.1111/j.1432-1033.1981.tb05381.x.
Pubmed: 6266829
Blattner FR, Burland V, Plunkett G 3rd, Sofia HJ, Daniels DL: Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov 25;21(23):5408-17. doi: 10.1093/nar/21.23.5408.
Pubmed: 8265357
Meek DW, Hayward RS: Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4? Nucleic Acids Res. 1984 Jul 25;12(14):5813-21. doi: 10.1093/nar/12.14.5813.
Pubmed: 6379605
Igarashi K, Fujita N, Ishihama A: Sequence analysis of two temperature-sensitive mutations in the alpha subunit gene (rpoA) of Escherichia coli RNA polymerase. Nucleic Acids Res. 1990 Oct 25;18(20):5945-8. doi: 10.1093/nar/18.20.5945.
Pubmed: 2235479
Ovchinnikov YA, Lipkin VM, Modyanov NN, Chertov OY, Smirnov YV: Primary structure of alpha-subunit of DNA-dependent RNA polymerase from Escherichia coli. FEBS Lett. 1977 Apr 1;76(1):108-11. doi: 10.1016/0014-5793(77)80131-2.
Pubmed: 323055
Ovchinnikov YuA, Monastyrskaya GS, Gubanov VV, Guryev SO, Salomatina IS, Shuvaeva TM, Lipkin VM, Sverdlov ED: The primary structure of E. coli RNA polymerase, Nucleotide sequence of the rpoC gene and amino acid sequence of the beta'-subunit. Nucleic Acids Res. 1982 Jul 10;10(13):4035-44. doi: 10.1093/nar/10.13.4035.
Pubmed: 6287430
Squires C, Krainer A, Barry G, Shen WF, Squires CL: Nucleotide sequence at the end of the gene for the RNA polymerase beta' subunit (rpoC). Nucleic Acids Res. 1981 Dec 21;9(24):6827-40. doi: 10.1093/nar/9.24.6827.
Pubmed: 6278450
Burton Z, Burgess RR, Lin J, Moore D, Holder S, Gross CA: The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12. Nucleic Acids Res. 1981 Jun 25;9(12):2889-903. doi: 10.1093/nar/9.12.2889.
Pubmed: 6269063
Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. doi: 10.1038/msb4100049. Epub 2006 Feb 21.
Pubmed: 16738553
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