Escherichia coli K-12 substr. MG1655 Polypeptide: transcription-repair coupling factor

Gene: mfd Accession Numbers: EG11619 (EcoCyc), b1114, ECK1100

Synonyms: TRCF

Regulation Summary Diagram: ?

Regulation summary diagram for mfd

The Mfd (mutation frequency decline) protein, also known as transcription-repair coupling factor [Selby91], is responsible for ATP-dependent removal of stalled RNA polymerase (RNAP) from DNA lesions [Selby93] by inducing forward movement of the RNA polymerase [Park02a] and subsequent recruitment of nucleotide excision repair machinery to the sites of the lesions [Selby93]. In this way Mfd is responsible for preferentially repairing template strand lesions [Selby91]. Mfd discriminates the stalled RNAP-DNA elongation complex and after ATP hydrolysis it disrupts the complex releasing RNAP from the site. Further ATP hydrolysis is required for dissociation of Mfd [Howan12]. Mfd remains bound to DNA in a relatively long-lived complex that may act as a marker for sites of damage [Howan12]. Mfd also rescues roadblocked and back-tracked RNA polymerases by catalyzing the restoration of the forward position [Park02a].

The Mfd-dependent transcription coupled repair pathway is able to repair template strand lesions downstream of a stalled RNAP complex. This repair is dependent on the presence of the Mfd protein. Once activated by binding to stalled RNAP, Mfd is able to translocate more than 100 bp along DNA suggesting that repair of downstream lesions is facilitated by the translocation activity of Mfd [Haines14].

Mfd contains helicase motifs with a region similar to RecG involved in binding DNA and ATP hydrolysis, a leucine zipper motif believed to allow binding to RNA polymerase, and a region similar to UvrB which contains a binding domain for UvrA2 [Selby93, Selby95]. The crystal structure of Mfd has been determined to a resolution of 3.2 Å [Deaconescu06, Deaconescu05]. The crystal structure of the N-terminal region of Mfd has been solved to a resolution of 2.1 Å [Assenmacher06]. In vitro repair assays [Selby91] and UV-induced mutations in vivo [Oller92] show that mfd mutants do not exhibit template strand-specific repair.

Reviews: [Selby94, Roberts04]
Comments: [Van14a]

Locations: cytosol

Map Position: [1,169,741 <- 1,173,187] (25.21 centisomes, 91°)
Length: 3447 bp / 1148 aa

Molecular Weight of Polypeptide: 129.98 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003763 , CGSC:35179 , DIP:DIP-10199N , EchoBASE:EB1576 , EcoGene:EG11619 , EcoliWiki:b1114 , Mint:MINT-1231460 , ModBase:P30958 , OU-Microarray:b1114 , PortEco:mfd , PR:PRO_000023221 , Pride:P30958 , Protein Model Portal:P30958 , RefSeq:NP_415632 , RegulonDB:EG11619 , SMR:P30958 , String:511145.b1114 , Swiss-Model:P30958 , UniProt:P30958

Relationship Links: InterPro:IN-FAMILY:IPR001650 , InterPro:IN-FAMILY:IPR003711 , InterPro:IN-FAMILY:IPR004576 , InterPro:IN-FAMILY:IPR005118 , InterPro:IN-FAMILY:IPR011545 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:2B2N , PDB:Structure:2EYQ , PDB:Structure:3HJH , PDB:Structure:4DFC , Pfam:IN-FAMILY:PF00270 , Pfam:IN-FAMILY:PF00271 , Pfam:IN-FAMILY:PF02559 , Pfam:IN-FAMILY:PF03461 , Prosite:IN-FAMILY:PS51192 , Prosite:IN-FAMILY:PS51194 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00490 , Smart:IN-FAMILY:SM00982 , Smart:IN-FAMILY:SM01058

In Paralogous Gene Group: 563 (2 members)

GO Terms:

Biological Process: GO:0000716 - transcription-coupled nucleotide-excision repair, DNA damage recognition Inferred from experiment Inferred by computational analysis [GOA06, Howan12, Selby93]
GO:0006281 - DNA repair Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Selby91]
GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [GOA06, Selby93]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment Inferred by computational analysis [UniProtGOA11, Selby93]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Selby95]
GO:0005515 - protein binding Inferred from experiment [Deaconescu12]
GO:0008026 - ATP-dependent helicase activity Inferred from experiment [Selby93]
GO:0015616 - DNA translocase activity Inferred from experiment [Haines14]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003684 - damaged DNA binding Inferred by computational analysis [GOA01]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: information transfer RNA related Transcription related

Essentiality data for mfd 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]

Sequence Features

Protein sequence of transcription-repair coupling factor with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 365
[Selby93, UniProt10a]
UniProt: (in Ref. 1);
Conserved-Region 615 -> 776
UniProt: Helicase ATP-binding;
Nucleotide-Phosphate-Binding-Region 628 -> 635
UniProt: ATP; Non-Experimental Qualifier: potential;
Protein-Segment 729 -> 732
UniProt: DEEH box; Sequence Annotation Type: short sequence motif.
Conserved-Region 798 -> 951
UniProt: Helicase C-terminal;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1114 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11619; confirmed by SwissProt match.


Assenmacher06: Assenmacher N, Wenig K, Lammens A, Hopfner KP (2006). "Structural Basis for Transcription-coupled Repair: the N Terminus of Mfd Resembles UvrB with Degenerate ATPase Motifs." J Mol Biol 355(4):675-83. PMID: 16309703

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

Deaconescu05: Deaconescu AM, Darst SA (2005). "Crystallization and preliminary structure determination of Escherichia coli Mfd, the transcription-repair coupling factor." Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 12);1062-4. PMID: 16511235

Deaconescu06: Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, Savery NJ, Darst SA (2006). "Structural basis for bacterial transcription-coupled DNA repair." Cell 124(3);507-20. PMID: 16469698

Deaconescu12: Deaconescu AM, Sevostyanova A, Artsimovitch I, Grigorieff N (2012). "Nucleotide excision repair (NER) machinery recruitment by the transcription-repair coupling factor involves unmasking of a conserved intramolecular interface." Proc Natl Acad Sci U S A 109(9);3353-8. PMID: 22331906

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

GOA01: 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."

Haines14: Haines NM, Kim YI, Smith AJ, Savery NJ (2014). "Stalled transcription complexes promote DNA repair at a distance." Proc Natl Acad Sci U S A 111(11);4037-42. PMID: 24554077

Howan12: Howan K, Smith AJ, Westblade LF, Joly N, Grange W, Zorman S, Darst SA, Savery NJ, Strick TR (2012). "Initiation of transcription-coupled repair characterized at single-molecule resolution." Nature 490(7420);431-4. PMID: 22960746

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

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

Oller92: Oller AR, Fijalkowska IJ, Dunn RL, Schaaper RM (1992). "Transcription-repair coupling determines the strandedness of ultraviolet mutagenesis in Escherichia coli." Proc Natl Acad Sci U S A 89(22);11036-40. PMID: 1438310

Park02a: Park JS, Marr MT, Roberts JW (2002). "E. coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation." Cell 109(6);757-67. PMID: 12086674

Roberts04: Roberts J, Park JS (2004). "Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination." Curr Opin Microbiol 7(2);120-5. PMID: 15063847

Selby91: Selby CP, Witkin EM, Sancar A (1991). "Escherichia coli mfd mutant deficient in "mutation frequency decline" lacks strand-specific repair: in vitro complementation with purified coupling factor." Proc Natl Acad Sci U S A 88(24);11574-8. PMID: 1763073

Selby93: Selby CP, Sancar A (1993). "Molecular mechanism of transcription-repair coupling." Science 260(5104);53-8. PMID: 8465200

Selby94: Selby CP, Sancar A (1994). "Mechanisms of transcription-repair coupling and mutation frequency decline." Microbiol Rev 58(3);317-29. PMID: 7968917

Selby95: Selby CP, Sancar A (1995). "Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties." J Biol Chem 270(9);4882-9. PMID: 7876261

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

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."

Van14a: Van Houten B, Kisker C (2014). "Transcriptional pausing to scout ahead for DNA damage." Proc Natl Acad Sci U S A 111(11);3905-6. PMID: 24599593

Other References Related to Gene Regulation

Ogasawara05: Ogasawara H, Teramoto J, Yamamoto S, Hirao K, Yamamoto K, Ishihama A, Utsumi R (2005). "Negative regulation of DNA repair gene (uvrA) expression by ArcA/ArcB two-component system in Escherichia coli." FEMS Microbiol Lett 251(2);243-9. PMID: 16140472

Stanley03: Stanley LK, Savery NJ (2003). "Characterisation of the Escherichia coli mfd promoter." Arch Microbiol 2003;179(5);381-5. PMID: 12658334

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065

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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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