The C-Terminal Domain of the Bacterial SSB Protein Acts as a DNA Maintenance Hub at Active Chromosome Replication Forks

English version České info

We have investigated in vivo the role of the carboxy-terminal domain of the Bacillus subtilis Single-Stranded DNA Binding protein (SSB_Cter) as a recruitment platform at active chromosomal forks for many proteins of the genome maintenance machineries. We probed this SSB_Cter interactome using GFP fusions and by Tap-tag and biochemical analysis. It includes at least 12 proteins. The interactome was previously shown to include PriA, RecG, and RecQ and extended in this study by addition of DnaE, SbcC, RarA, RecJ, RecO, XseA, Ung, YpbB, and YrrC. Targeting of YpbB to active forks appears to depend on RecS, a RecQ paralogue, with which it forms a stable complex. Most of these SSB partners are conserved in bacteria, while others, such as the essential DNA polymerase DnaE, YrrC, and the YpbB/RecS complex, appear to be specific to B. subtilis. SSB_Cter deletion has a moderate impact on B. subtilis cell growth. However, it markedly affects the efficiency of repair of damaged genomic DNA and arrested replication forks. ssbΔCter mutant cells appear deficient in RecA loading on ssDNA, explaining their inefficiency in triggering the SOS response upon exposure to genotoxic agents. Together, our findings show that the bacterial SSB_Cter acts as a DNA maintenance hub at active chromosomal forks that secures their propagation along the genome.

Vyšlo v časopise: The C-Terminal Domain of the Bacterial SSB Protein Acts as a DNA Maintenance Hub at Active Chromosome Replication Forks. PLoS Genet 6(12): e32767. doi:10.1371/journal.pgen.1001238
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1001238

Souhrn

Zdroje

1. MichelB

GromponeG

FloresMJ

BidnenkoV

2004 Multiple pathways process stalled replication forks. Proc Natl Acad Sci U S A 101 12783 12788

2. MichelB

BoubakriH

BaharogluZ

LeMassonM

LestiniR

2007 Recombination proteins and rescue of arrested replication forks. DNA Repair (Amst) 6 967 980

3. HellerRC

MariansKJ

2006 Replisome assembly and the direct restart of stalled replication forks. Nat Rev Mol Cell Biol 7 932 943

4. KongXP

OnrustR

O'DonnellM

KuriyanJ

1992 Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell 69 425 437

5. Lopez de SaroF

2009 Regulation of interactions with sliding clamps during DNA replication and repair. Curr Genomics 10 206 215

6. SheredaRD

KozlovAG

LohmanTM

CoxMM

KeckJL

2008 SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol 43 289 318

7. LuD

KeckJL

2008 Structural basis of Escherichia coli single-stranded DNA-binding protein stimulation of exonuclease I. Proc Natl Acad Sci U S A 105 9169 9174

8. LecointeF

SerenaC

VeltenM

CostesA

McGovernS

2007 Anticipating chromosomal replication fork arrest: SSB targets repair DNA helicases to active forks. Embo J 26 4239 4251

9. CurthU

GenschelJ

UrbankeC

GreipelJ

1996 In vitro and in vivo function of the C-terminus of Escherichia coli single-stranded DNA binding protein. Nucleic Acids Res 24 2706 2711

10. MeileJC

WuLJ

EhrlichSD

ErringtonJ

NoirotP

2006 Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory. Proteomics 6 2135 2146

11. PossozC

FilipeSR

GraingeI

SherrattDJ

2006 Tracking of controlled Escherichia coli replication fork stalling and restart at repressor-bound DNA in vivo. Embo J 25 2596 2604

12. Reyes-LamotheR

PossozC

DanilovaO

SherrattDJ

2008 Independent positioning and action of Escherichia coli replisomes in live cells. Cell 133 90 102

13. LiuJ

MariansKJ

1999 PriA-directed assembly of a primosome on D loop DNA. J Biol Chem 274 25033 25041

14. BruandC

FaracheM

McGovernS

EhrlichSD

PolardP

2001 DnaB, DnaD and DnaI proteins are components of the Bacillus subtilis replication restart primosome. Mol Microbiol 42 245 255

15. PolardP

MarsinS

McGovernS

VeltenM

WigleyDB

2002 Restart of DNA replication in Gram-positive bacteria: functional characterisation of the Bacillus subtilis PriA initiator. Nucleic Acids Res 30 1593 1605

16. RudolphCJ

UptonAL

HarrisL

LloydRG

2009 Pathological replication in cells lacking RecG DNA translocase. Mol Microbiol 73 352 366

17. ZhangJ

MahdiAA

BriggsGS

LloydRG

2010 Promoting and avoiding recombination: contrasting activities of the Escherichia coli RuvABC Holliday junction resolvase and RecG DNA translocase. Genetics 185 23 37

18. RigautG

ShevchenkoA

RutzB

WilmM

MannM

1999 A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17 1030 1032

19. SanchezH

KidaneD

Castillo CozarM

GraumannPL

AlonsoJC

2006 Recruitment of Bacillus subtilis RecN to DNA double-strand breaks in the absence of DNA end processing. J Bacteriol 188 353 360

20. SheredaRD

BernsteinDA

KeckJL

2007 A central role for SSB in Escherichia coli RecQ DNA helicase function. J Biol Chem 282 19247 19258

21. SheredaRD

ReiterNJ

ButcherSE

KeckJL

2009 Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus. J Mol Biol 386 612 625

22. PetitMA

DervynE

RoseM

EntianKD

McGovernS

1998 PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication. Mol Microbiol 29 261 273

23. NoirotP

Noirot-GrosMF

2004 Protein interaction networks in bacteria. Curr Opin Microbiol 7 505 512

24. VeauteX

DelmasS

SelvaM

JeussetJ

Le CamE

2005 UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli. Embo J 24 180 189

25. AnandSP

ZhengH

BiancoPR

LeubaSH

KhanSA

2007 DNA helicase activity of PcrA is not required for the displacement of RecA protein from DNA or inhibition of RecA-mediated strand exchange. J Bacteriol 189 4502 4509

26. BoubakriH

de SeptenvilleAL

VigueraE

MichelB

2010 The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo. Embo J 29 145 157

27. PetitMA

EhrlichD

2002 Essential bacterial helicases that counteract the toxicity of recombination proteins. Embo J 21 3137 3147

28. DervynE

SuskiC

DanielR

BruandC

ChapuisJ

2001 Two essential DNA polymerases at the bacterial replication fork. Science 294 1716 1719

29. LemonKP

GrossmanAD

1998 Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science 282 1516 1519

30. ConnellyJC

KirkhamLA

LeachDR

1998 The SbcCD nuclease of Escherichia coli is a structural maintenance of chromosomes (SMC) family protein that cleaves hairpin DNA. Proc Natl Acad Sci U S A 95 7969 7974

31. Noirot-GrosMF

DervynE

WuLJ

MerveletP

ErringtonJ

2002 An expanded view of bacterial DNA replication. Proc Natl Acad Sci U S A 99 8342 8347

32. LestiniR

MichelB

2007 UvrD controls the access of recombination proteins to blocked replication forks. Embo J 26 3804 3814

33. Noirot-GrosMF

VeltenM

YoshimuraM

McGovernS

MorimotoT

2006 Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus subtilis. Proc Natl Acad Sci U S A 103 2368 2373

34. SimmonsLA

GrossmanAD

WalkerGC

2007 Replication is required for the RecA localization response to DNA damage in Bacillus subtilis. Proc Natl Acad Sci U S A 104 1360 1365

35. ButlandG

Peregrin-AlvarezJM

LiJ

YangW

YangX

2005 Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531 537

36. HandaP

AcharyaN

VarshneyU

2001 Chimeras between single-stranded DNA-binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C-terminal domains interact with uracil DNA glycosylases. J Biol Chem 276 16992 16997

37. DuigouS

EhrlichSD

NoirotP

Noirot-GrosMF

2004 Distinctive genetic features exhibited by the Y-family DNA polymerases in Bacillus subtilis. Mol Microbiol 54 439 451

38. HobbsMD

SakaiA

CoxMM

2007 SSB protein limits RecOR binding onto single-stranded DNA. J Biol Chem 282 11058 11067

39. MauelC

KaramataD

1984 Prophage induction in thermosensitive DNA mutants of Bacillus subtilis. Mol Gen Genet 194 451 456

40. KaguniJM

2006 DnaA: controlling the initiation of bacterial DNA replication and more. Annu Rev Microbiol 60 351 375

41. YuzhakovA

KelmanZ

O'DonnellM

1999 Trading places on DNA–a three-point switch underlies primer handoff from primase to the replicative DNA polymerase. Cell 96 153 163

42. SuskiC

MariansKJ

2008 Resolution of converging replication forks by RecQ and topoisomerase III. Mol Cell 30 779 789

43. GloverBP

McHenryCS

1998 The chi psi subunits of DNA polymerase III holoenzyme bind to single-stranded DNA-binding protein (SSB) and facilitate replication of an SSB-coated template. J Biol Chem 273 23476 23484

44. KelmanZ

YuzhakovA

AndjelkovicJ

O'DonnellM

1998 Devoted to the lagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. Embo J 17 2436 2449

45. SandersGM

DallmannHG

McHenryCS

2010 Reconstitution of the B. subtilis replisome with 13 proteins including two distinct replicases. Mol Cell 37 273 281

46. MolineuxIJ

GefterML

1974 Properties of the Escherichia coli in DNA binding (unwinding) protein: interaction with DNA polymerase and DNA. Proc Natl Acad Sci U S A 71 3858 3862

47. BonnerCA

RandallSK

RayssiguierC

RadmanM

EritjaR

1988 Purification and characterization of an inducible Escherichia coli DNA polymerase capable of insertion and bypass at abasic lesions in DNA. J Biol Chem 263 18946 18952

48. Le ChatelierE

BecherelOJ

d'AlenconE

CanceillD

EhrlichSD

2004 Involvement of DnaE, the second replicative DNA polymerase from Bacillus subtilis, in DNA mutagenesis. J Biol Chem 279 1757 1767

49. WebbBL

CoxMM

InmanRB

1997 Recombinational DNA repair: the RecF and RecR proteins limit the extension of RecA filaments beyond single-strand DNA gaps. Cell 91 347 356

50. FernandezS

AyoraS

AlonsoJC

2000 Bacillus subtilis homologous recombination: genes and products. Res Microbiol 151 481 486

51. AradG

HendelA

UrbankeC

CurthU

LivnehZ

2008 Single-stranded DNA-binding protein recruits DNA polymerase V to primer termini on RecA-coated DNA. J Biol Chem 283 8274 8282

52. ZeghoufM

LiJ

ButlandG

BorkowskaA

CanadienV

2004 Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J Proteome Res 3 463 468

53. MsadekT

KunstF

HennerD

KlierA

RapoportG

1990 Signal transduction pathway controlling synthesis of a class of degradative enzymes in Bacillus subtilis: expression of the regulatory genes and analysis of mutations in degS and degU. J Bacteriol 172 824 834

54. DavidsenT

BeckE

GanapathyA

MontgomeryR

ZafarN

2010 The comprehensive microbial resource. Nucleic Acids Res 38 D340 D345