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Escherichia coli K-12 substr. MG1655 Polypeptide: DNA damage-inducible protein I



Gene: dinI Accession Numbers: G6558 (EcoCyc), b1061, ECK1046

Regulation Summary Diagram: ?

Summary:
The dinI gene was first identified as a chromosomal locus containing a high affinity operator for the LexA repressor [Lewis94]. It encodes a small protein with 80 amino acids and a molecular weight of 8.818 KDa [Yasuda96a].

DinI is not detectable during normal growth of the bacteria, but is induced by DNA damage and is dependent on both LexA and RecA [Yasuda98, Voloshin01]. Its function depends on the concentration of the protein. At concentrations that are stoichimetric with those of RecA, DinI protein acts mainly as a positive modulator of RecA function [Lusetti04]. DinI stabilizes the RecA filament, reducing or preventing disassembly [Lusetti04a], which does not affect RecA-mediated ATP hydrolysis and LexA co-protease activities. DinI and RecX (a negative modulator of RecA, which blocks RecA filament extension and leads to net filament disassembly) constitute a regulatory network of RecA [Lusetti04].

When DinI is present at very high concentrations that are superstoichiometric relative to RecA in vivo, it has contradictory effects on RecA. Overexpression of dinI in E. coli mutant leads to increased UV sensitivity [Yasuda98]. DinI inhibits both the ability of RecA to induce cleavage of UmuD as well as its recombinase activity [Yasuda98]. DinI binds to active RecA filament and inhibits its coprotease activity, but not its ATPase activity [Yasuda01]. Nuclear magnetic resonance (NMR) spectroscopy show that DinI tightly binds to the central region of RecA (between the N- and C-terminal domains) and that this interaction is enhanced upon the oligomerisation of RecA [Yoshimasu03].

A solution structure of DinI has been determined [Ramirez00].

Locations: cytosol

Map Position: [1,120,465 <- 1,120,710] (24.15 centisomes)
Length: 246 bp / 81 aa

Molecular Weight of Polypeptide: 8.949 kD (from nucleotide sequence), 8.818 kD (experimental) [Yasuda96a ]

Unification Links: ASAP:ABE-0003599 , EchoBASE:EB2536 , EcoGene:EG12670 , EcoliWiki:b1061 , ModBase:P0ABR1 , OU-Microarray:b1061 , PortEco:dinI , PR:PRO_000022449 , Pride:P0ABR1 , Protein Model Portal:P0ABR1 , RefSeq:NP_415579 , RegulonDB:G6558 , SMR:P0ABR1 , String:511145.b1061 , UniProt:P0ABR1

Relationship Links: InterPro:IN-FAMILY:IPR010391 , PDB:Structure:1GHH , Pfam:IN-FAMILY:PF06183

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009432 - SOS response Inferred from experiment Inferred by computational analysis [UniProtGOA11, Lusetti04]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0019899 - enzyme binding Inferred from experiment [Voloshin01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes SOS response
information transfer DNA related DNA repair

Essentiality data for dinI 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]

Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

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

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

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

Lewis94: Lewis LK, Harlow GR, Gregg-Jolly LA, Mount DW (1994). "Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli." J Mol Biol 241(4);507-23. PMID: 8057377

Lusetti04: Lusetti SL, Drees JC, Stohl EA, Seifert HS, Cox MM (2004). "The DinI and RecX proteins are competing modulators of RecA function." J Biol Chem 279(53);55073-9. PMID: 15489505

Lusetti04a: Lusetti SL, Voloshin ON, Inman RB, Camerini-Otero RD, Cox MM (2004). "The DinI protein stabilizes RecA protein filaments." J Biol Chem 279(29);30037-46. PMID: 15138263

Ramirez00: Ramirez BE, Voloshin ON, Camerini-Otero RD, Bax A (2000). "Solution structure of DinI provides insight into its mode of RecA inactivation." Protein Sci 9(11);2161-9. PMID: 11152126

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

Voloshin01: Voloshin ON, Ramirez BE, Bax A, Camerini-Otero RD (2001). "A model for the abrogation of the SOS response by an SOS protein: a negatively charged helix in DinI mimics DNA in its interaction with RecA." Genes Dev 15(4);415-27. PMID: 11230150

Yasuda01: Yasuda T, Morimatsu K, Kato R, Usukura J, Takahashi M, Ohmori H (2001). "Physical interactions between DinI and RecA nucleoprotein filament for the regulation of SOS mutagenesis." EMBO J 20(5);1192-202. PMID: 11230142

Yasuda96a: Yasuda T, Nagata T, Ohmori H (1996). "Multicopy suppressors of the cold-sensitive phenotype of the pcsA68 (dinD68) mutation in Escherichia coli." J Bacteriol 178(13);3854-9. PMID: 8682790

Yasuda98: Yasuda T, Morimatsu K, Horii T, Nagata T, Ohmori H (1998). "Inhibition of Escherichia coli RecA coprotease activities by DinI." EMBO J 17(11);3207-16. PMID: 9606202

Yoshimasu03: Yoshimasu M, Aihara H, Ito Y, Rajesh S, Ishibe S, Mikawa T, Yokoyama S, Shibata T (2003). "An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes." Nucleic Acids Res 31(6);1735-43. PMID: 12626715

Other References Related to Gene Regulation

Fernandez00: Fernandez De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R (2000). "Identification of additional genes belonging to the LexA regulon in Escherichia coli." Mol Microbiol 35(6);1560-72. PMID: 10760155

Kaleta10: Kaleta C, Gohler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S (2010). "Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis." BMC Syst Biol 4;116. PMID: 20718955

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Oberto10: Oberto J (2010). "FITBAR: a web tool for the robust prediction of prokaryotic regulons." BMC Bioinformatics 11;554. PMID: 21070640

Wade05: Wade JT, Reppas NB, Church GM, Struhl K (2005). "Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites." Genes Dev 19(21);2619-30. PMID: 16264194


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, biocyc13.