Mfd

• Description: transcription-repair coupling factor, eliminates genetic damage from transcriptionally active genes during sporulation, required for increased mutagenesis of lagging strand genes
  
  

Gene name	mfd
Synonyms
Essential	no
Product	transcription-repair coupling factor
Function	promotes strand-specific DNA repair by displacing RNA polymerase stalled at a nucleotide lesion and directing the (A)BC excinuclease to the RNA damage site
Gene expression levels in SubtiExpress: mfd
Interactions involving this protein in SubtInteract: Mfd
MW, pI	133 kDa, 5.367
Gene length, protein length	3531 bp, 1177 aa
Immediate neighbours	fin, spoVT
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

DNA repair/ recombination, transcription

The gene

Basic information

• Locus tag: BSU00550

Phenotypes of a mutant

• in an mfd knock-out, the cell's ability to accumulate adaptive mutations in stationary phase is depressed. PubMed
• increased UV-induced mutagenesis via PolY1/ PolY2-mediated translesion synthesis PubMed
• the mutation suppresses the mucoid phenotype of motA or motB mutants PubMed

Database entries

• BsubCyc: BSU00550

• DBTBS entry: no entry

• SubtiList entry: [1]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity:
  • promotes strand-specific DNA repair by displacing RNA polymerase stalled at a nucleotide lesion and directing the (A)BC excinuclease to the RNA damage site
  • is required for roadblock transcription repression by transcription factors with binding sites downstream of the promoter (as for CcpA PubMed and CodY PubMed)
  • required for the processing of genetic damage during sporulation PubMed

• Protein family:

• Paralogous protein(s): RecG

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactors:

• Effectors of protein activity:

• Interactions:
  • Mfd interacts with the RNA polymerase PubMed
  • Mfd-UvrA PubMed
  • Mfd-RpoB PubMed

• Localization:

Database entries

• BsubCyc: BSU00550

• Structure:
  • 2EYQ (Mfd from E. coli) PubMed
  • 3MLQ (RNA polymerase interacting domain of Thermus thermophilus Mfd with the Thermus aquaticus RpoB beta1 domain) PubMed

• UniProt: P37474

• KEGG entry: [2]

• E.C. number:

Expression and regulation

• Operon:

• Expression browser: mfd PubMed

• Sigma factor:

• Regulation:
  • expressed throughout growth and sporulation, during sporulation both in the mother cell and the forespore PubMed

• Regulatory mechanism:

• Additional information:
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 103 PubMed
  • number of protein molecules per cell (complex medium with amino acids, without glucose): 611 PubMed

Biological materials

• Mutant: GP1167 (del ermC), available in Jörg Stülke's lab

• Expression vector:

• lacZ fusion:

• GFP fusion: GP1510 (spc, based on pGP1870, pGP1389-derivative ), available in Jörg Stülke's lab

• YFP fusion: GP1511 (spc, based on pGP1871, pGP1389-derivative ), available in Jörg Stülke's lab

• two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Fabian Commichau's lab

• Antibody:

• Strep-tag construct: GP890 (spc, based on pGP1389), available in the Stülke lab

References

Reviews

Georgiy A Belogurov, Irina Artsimovitch
Regulation of Transcript Elongation.
Annu Rev Microbiol: 2015, 69;49-69
[PubMed:26132790] [WorldCat.org] [DOI] (I p)

Justin S Lenhart, Jeremy W Schroeder, Brian W Walsh, Lyle A Simmons
DNA repair and genome maintenance in Bacillus subtilis.
Microbiol Mol Biol Rev: 2012, 76(3);530-64
[PubMed:22933559] [WorldCat.org] [DOI] (I p)

Ann Ganesan, Graciela Spivak, Philip C Hanawalt
Transcription-coupled DNA repair in prokaryotes.
Prog Mol Biol Transl Sci: 2012, 110;25-40
[PubMed:22749141] [WorldCat.org] [DOI] (I p)

Eduardo A Robleto, Holly A Martin, Mario Pedraza-Reyes
Mfd and transcriptional derepression cause genetic diversity in Bacillus subtilis.
Front Biosci (Elite Ed): 2012, 4(4);1246-54
[PubMed:22201950] [WorldCat.org] [DOI] (I e)

Philip C Hanawalt, Graciela Spivak
Transcription-coupled DNA repair: two decades of progress and surprises.
Nat Rev Mol Cell Biol: 2008, 9(12);958-70
[PubMed:19023283] [WorldCat.org] [DOI] (I p)

Rodrigo S Galhardo, P J Hastings, Susan M Rosenberg
Mutation as a stress response and the regulation of evolvability.
Crit Rev Biochem Mol Biol: 2007, 42(5);399-435
[PubMed:17917874] [WorldCat.org] [DOI] (P p)

Alexandra M Deaconescu, Nigel Savery, Seth A Darst
The bacterial transcription repair coupling factor.
Curr Opin Struct Biol: 2007, 17(1);96-102
[PubMed:17239578] [WorldCat.org] [DOI] (P p)

James J Truglio, Deborah L Croteau, Bennett Van Houten, Caroline Kisker
Prokaryotic nucleotide excision repair: the UvrABC system.
Chem Rev: 2006, 106(2);233-52
[PubMed:16464004] [WorldCat.org] [DOI] (P p)

Sergei Borukhov, Jookyung Lee, Oleg Laptenko
Bacterial transcription elongation factors: new insights into molecular mechanism of action.
Mol Microbiol: 2005, 55(5);1315-24
[PubMed:15720542] [WorldCat.org] [DOI] (P p)

Jeffrey Roberts, Joo-Seop Park
Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination.
Curr Opin Microbiol: 2004, 7(2);120-5
[PubMed:15063847] [WorldCat.org] [DOI] (P p)

E C Friedberg
Relationships between DNA repair and transcription.
Annu Rev Biochem: 1996, 65;15-42
[PubMed:8811173] [WorldCat.org] [DOI] (P p)

C P Selby, A Sancar
Mechanisms of transcription-repair coupling and mutation frequency decline.
Microbiol Rev: 1994, 58(3);317-29
[PubMed:7968917] [WorldCat.org] [DOI] (P p)

Original publications

Evan T Graves, Camille Duboc, Jun Fan, François Stransky, Mathieu Leroux-Coyau, Terence R Strick
A dynamic DNA-repair complex observed by correlative single-molecule nanomanipulation and fluorescence.
Nat Struct Mol Biol: 2015, 22(6);452-7
[PubMed:25961799] [WorldCat.org] [DOI] (I p)

Samuel Million-Weaver, Ariana N Samadpour, Daniela A Moreno-Habel, Patrick Nugent, Mitchell J Brittnacher, Eli Weiss, Hillary S Hayden, Samuel I Miller, Ivan Liachko, Houra Merrikh
An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2015, 112(10);E1096-105
[PubMed:25713353] [WorldCat.org] [DOI] (I p)

Hirokazu Suzuki, Jyumpei Kobayashi, Keisuke Wada, Megumi Furukawa, Katsumi Doi
Thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from Geobacillus kaustophilus HTA426.
Appl Environ Microbiol: 2015, 81(1);149-58
[PubMed:25326311] [WorldCat.org] [DOI] (I p)

Jia Mun Chan, Sarah B Guttenplan, Daniel B Kearns
Defects in the flagellar motor increase synthesis of poly-γ-glutamate in Bacillus subtilis.
J Bacteriol: 2014, 196(4);740-53
[PubMed:24296669] [WorldCat.org] [DOI] (I p)

Fernando H Ramírez-Guadiana, Rocío Del Carmen Barajas-Ornelas, Víctor M Ayala-García, Ronald E Yasbin, Eduardo Robleto, Mario Pedraza-Reyes
Transcriptional coupling of DNA repair in sporulating Bacillus subtilis cells.
Mol Microbiol: 2013, 90(5);1088-99
[PubMed:24118570] [WorldCat.org] [DOI] (I p)

Kévin Howan, Abigail J Smith, Lars F Westblade, Nicolas Joly, Wilfried Grange, Sylvain Zorman, Seth A Darst, Nigel J Savery, Terence R Strick
Initiation of transcription-coupled repair characterized at single-molecule resolution.
Nature: 2012, 490(7420);431-4
[PubMed:22960746] [WorldCat.org] [DOI] (I p)

Holly Anne Martin, Mario Pedraza-Reyes, Ronald E Yasbin, Eduardo A Robleto
Transcriptional de-repression and Mfd are mutagenic in stressed Bacillus subtilis cells.
J Mol Microbiol Biotechnol: 2011, 21(1-2);45-58
[PubMed:22248542] [WorldCat.org] [DOI] (I p)

Katrin Gunka, Stefan Tholen, Jan Gerwig, Christina Herzberg, Jörg Stülke, Fabian M Commichau
A high-frequency mutation in Bacillus subtilis: requirements for the decryptification of the gudB glutamate dehydrogenase gene.
J Bacteriol: 2012, 194(5);1036-44
[PubMed:22178973] [WorldCat.org] [DOI] (I p)

Olivier Delumeau, François Lecointe, Jan Muntel, Alain Guillot, Eric Guédon, Véronique Monnet, Michael Hecker, Dörte Becher, Patrice Polard, Philippe Noirot
The dynamic protein partnership of RNA polymerase in Bacillus subtilis.
Proteomics: 2011, 11(15);2992-3001
[PubMed:21710567] [WorldCat.org] [DOI] (I p)

Boris R Belitsky, Abraham L Sonenshein
Roadblock repression of transcription by Bacillus subtilis CodY.
J Mol Biol: 2011, 411(4);729-43
[PubMed:21699902] [WorldCat.org] [DOI] (I p)

Laura Manelyte, Young-In T Kim, Abigail J Smith, Rachel M Smith, Nigel J Savery
Regulation and rate enhancement during transcription-coupled DNA repair.
Mol Cell: 2010, 40(5);714-24
[PubMed:21145481] [WorldCat.org] [DOI] (I p)

Lars F Westblade, Elizabeth A Campbell, Chirangini Pukhrambam, Julio C Padovan, Bryce E Nickels, Valerie Lamour, Seth A Darst
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.
Nucleic Acids Res: 2010, 38(22);8357-69
[PubMed:20702425] [WorldCat.org] [DOI] (I p)

Christine Pybus, Mario Pedraza-Reyes, Christian A Ross, Holly Martin, Katherine Ona, Ronald E Yasbin, Eduardo Robleto
Transcription-associated mutation in Bacillus subtilis cells under stress.
J Bacteriol: 2010, 192(13);3321-8
[PubMed:20435731] [WorldCat.org] [DOI] (I p)

Christian Ross, Christine Pybus, Mario Pedraza-Reyes, Huang-Mo Sung, Ronald E Yasbin, Eduardo Robleto
Novel role of mfd: effects on stationary-phase mutagenesis in Bacillus subtilis.
J Bacteriol: 2006, 188(21);7512-20
[PubMed:16950921] [WorldCat.org] [DOI] (P p)

Alexandra M Deaconescu, Anna L Chambers, Abigail J Smith, Bryce E Nickels, Ann Hochschild, Nigel J Savery, Seth A Darst
Structural basis for bacterial transcription-coupled DNA repair.
Cell: 2006, 124(3);507-20
[PubMed:16469698] [WorldCat.org] [DOI] (P p)

J M Zalieckas, L V Wray, A E Ferson, S H Fisher
Transcription-repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons.
Mol Microbiol: 1998, 27(5);1031-8
[PubMed:9535092] [WorldCat.org] [DOI] (P p)

S Ayora, F Rojo, N Ogasawara, S Nakai, J C Alonso
The Mfd protein of Bacillus subtilis 168 is involved in both transcription-coupled DNA repair and DNA recombination.
J Mol Biol: 1996, 256(2);301-18
[PubMed:8594198] [WorldCat.org] [DOI] (P p)

V D Filippov, E E Zagoruiko
Study of MFD in Bacillus subtilis.
Mutat Res: 1978, 52(1);49-56
[PubMed:104170] [WorldCat.org] [DOI] (P p)