#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element


Integrative and conjugative elements (ICEs) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT) by the ICE–encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP), encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability.


Vyšlo v časopise: A Conserved Helicase Processivity Factor Is Needed for Conjugation and Replication of an Integrative and Conjugative Element. PLoS Genet 9(1): e32767. doi:10.1371/journal.pgen.1003198
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003198

Souhrn

Integrative and conjugative elements (ICEs) are agents of horizontal gene transfer and have major roles in evolution and acquisition of new traits, including antibiotic resistances. ICEs are found integrated in a host chromosome and can excise and transfer to recipient bacteria via conjugation. Conjugation involves nicking of the ICE origin of transfer (oriT) by the ICE–encoded relaxase and transfer of the nicked single strand of ICE DNA. For ICEBs1 of Bacillus subtilis, nicking of oriT by the ICEBs1 relaxase NicK also initiates rolling circle replication. This autonomous replication of ICEBs1 is critical for stability of the excised element in growing cells. We found a conserved and previously uncharacterized ICE gene that is required for conjugation and replication of ICEBs1. Our results indicate that this gene, helP (formerly ydcP), encodes a helicase processivity factor that enables the host-encoded helicase PcrA to unwind the double-stranded ICEBs1 DNA. HelP was required for both conjugation and replication of ICEBs1, and HelP and NicK were the only ICEBs1 proteins needed for replication from ICEBs1 oriT. Using chromatin immunoprecipitation, we measured association of HelP, NicK, PcrA, and the host-encoded single-strand DNA binding protein Ssb with ICEBs1. We found that NicK was required for association of HelP and PcrA with ICEBs1 DNA. HelP was required for association of PcrA and Ssb with ICEBs1 regions distal, but not proximal, to oriT, indicating that PcrA needs HelP to progress beyond nicked oriT and unwind ICEBs1. In vitro, HelP directly stimulated the helicase activity of the PcrA homologue UvrD. Our findings demonstrate that HelP is a helicase processivity factor needed for efficient unwinding of ICEBs1 for conjugation and replication. Homologues of HelP and PcrA-type helicases are encoded on many known and putative ICEs. We propose that these factors are essential for ICE conjugation, replication, and genetic stability.


Zdroje

1. WozniakRA, WaldorMK (2010) Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8: 552–563.

2. GuglielminiJ, QuintaisL, Garcillan-BarciaMP, de la CruzF, RochaEP (2011) The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet 7: e1002222 doi:10.1371/journal.pgen.1002222.

3. Alvarez-MartinezCE, ChristiePJ (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73: 775–808.

4. ChristiePJ, VogelJP (2000) Bacterial type IV secretion: conjugation systems adapted to deliver effector molecules to host cells. Trends Microbiol 8: 354–360.

5. AbajyMY, KopecJ, SchiwonK, BurzynskiM, DoringM, et al. (2007) A type IV-secretion-like system is required for conjugative DNA transport of broad-host-range plasmid pIP501 in gram-positive bacteria. J Bacteriol 189: 2487–2496.

6. LeeCA, BabicA, GrossmanAD (2010) Autonomous plasmid-like replication of a conjugative transposon. Mol Microbiol 75: 268–279.

7. SitkiewiczI, GreenNM, GuoN, MereghettiL, MusserJM (2011) Lateral gene transfer of streptococcal ICE element RD2 (region of difference 2) encoding secreted proteins. BMC Microbiol 11: 65.

8. CarraroN, LibanteV, MorelC, DecarisB, Charron-BourgoinF, et al. (2011) Differential regulation of two closely related integrative and conjugative elements from Streptococcus thermophilus. BMC Microbiol 11: 238.

9. AuchtungJM, LeeCA, MonsonRE, LehmanAP, GrossmanAD (2005) Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci U S A 102: 12554–12559.

10. BurrusV, PavlovicG, DecarisB, GuedonG (2002) The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration. Plasmid 48: 77–97.

11. BaasPD (1985) DNA replication of single-stranded Escherichia coli DNA phages. Biochim Biophys Acta 825: 111–139.

12. KhanSA (2005) Plasmid rolling-circle replication: highlights of two decades of research. Plasmid 53: 126–136.

13. LohmanTM, TomkoEJ, WuCG (2008) Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nat Rev Mol Cell Biol 9: 391–401.

14. BensonAK, HaldenwangWG (1993) Regulation of sigma-B levels and activity in Bacillus subtilis. J Bacteriol 175: 2347–2356.

15. LeeCA, GrossmanAD (2007) Identification of the origin of transfer (oriT) and DNA relaxase required for conjugation of the integrative and conjugative element ICEBs1 of Bacillus subtilis. J Bacteriol 189: 7254–7261.

16. AuchtungJM, LeeCA, GarrisonKL, GrossmanAD (2007) Identification and characterization of the immunity repressor (ImmR) that controls the mobile genetic element ICEBs1 of Bacillus subtilis. Mol Microbiol 64: 1515–1528.

17. BerkmenMB, LeeCA, LovedayEK, GrossmanAD (2010) Polar positioning of a conjugation protein from the integrative and conjugative element ICEBs1 of Bacillus subtilis. J Bacteriol 192: 38–45.

18. LeeCA, ThomasJ, GrossmanAD (2012) The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions. J Bacteriol 194: 3165–3172.

19. Niedziela-MajkaA, ChesnikMA, TomkoEJ, LohmanTM (2007) Bacillus stearothermophilus PcrA monomer is a single-stranded DNA translocase but not a processive helicase in vitro. J Biol Chem 282: 27076–27085.

20. Aramini J, Rossi P, Zhao L, Foote E, Jiang M, et al.. Solution NMR structure of sag0934 from Streptococcus agalactiae. Northeast structural genomics target sar32[1–108]. (PDB entry only; no PUBMED entry available) http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=66235.

21. FlynnRL, ZouL (2010) Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians. Crit Rev Biochem Mol Biol 45: 266–275.

22. ZhangW, DillinghamMS, ThomasCD, AllenS, RobertsCJ, et al. (2007) Directional loading and stimulation of PcrA helicase by the replication initiator protein RepD. J Mol Biol 371: 336–348.

23. AnandSP, MitraP, NaqviA, KhanSA (2004) Bacillus anthracis and Bacillus cereus PcrA helicases can support DNA unwinding and in vitro rolling-circle replication of plasmid pT181 of Staphylococcus aureus. J Bacteriol 186: 2195–2199.

24. PetitMA, EhrlichD (2002) Essential bacterial helicases that counteract the toxicity of recombination proteins. EMBO J 21: 3137–3147.

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. DillinghamMS (2011) Superfamily I helicases as modular components of DNA-processing machines. Biochem Soc Trans 39: 413–423.

27. BruandC, EhrlichSD (2000) UvrD-dependent replication of rolling-circle plasmids in Escherichia coli. Mol Microbiol 35: 204–210.

28. LlosaM, Gomis-RuthFX, CollM, de la CruzF (2002) Bacterial conjugation: a two-step mechanism for DNA transport. Mol Microbiol 45: 1–8.

29. BiD, XuZ, HarrisonEM, TaiC, WeiY, et al. (2012) ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res 40: D621–626.

30. MerrikhH, ZhangY, GrossmanAD, WangJD (2012) Replication-trancription conflicts in bacteria. Nat Rev Microbiol 10: 449–458.

31. PetitMA, DervynE, RoseM, EntianKD, McGovernS, et al. (1998) PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication. Mol Microbiol 29: 261–273.

32. IordanescuS (1993) Characterization of the Staphylococcus aureus chromosomal gene pcrA, identified by mutations affecting plasmid pT181 replication. Mol Gen Genet 241: 185–192.

33. AnandSP, ChattopadhyayA, KhanSA (2005) The PcrA3 mutant binds DNA and interacts with the RepC initiator protein of plasmid pT181 but is defective in its DNA helicase and unwinding activities. Plasmid 54: 104–113.

34. HaT, RasnikI, ChengW, BabcockHP, GaussGH, et al. (2002) Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419: 638–641.

35. FischerCJ, MalufNK, LohmanTM (2004) Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA. J Mol Biol 344: 1287–1309.

36. MalufNK, FischerCJ, LohmanTM (2003) A dimer of Escherichia coli UvrD is the active form of the helicase in vitro. J Mol Biol 325: 913–935.

37. YangY, DouSX, RenH, WangPY, ZhangXD, et al. (2008) Evidence for a functional dimeric form of the PcrA helicase in DNA unwinding. Nucleic Acids Res 36: 1976–1989.

38. ChengW, HsiehJ, BrendzaKM, LohmanTM (2001) E. coli Rep oligomers are required to initiate DNA unwinding in vitro. J Mol Biol 310: 327–350.

39. MatsonSW, RobertsonAB (2006) The UvrD helicase and its modulation by the mismatch repair protein MutL. Nucleic Acids Res 34: 4089–4097.

40. SinhaKM, StephanouNC, GaoF, GlickmanMS, ShumanS (2007) Mycobacterial UvrD1 is a Ku-dependent DNA helicase that plays a role in multiple DNA repair events, including double-strand break repair. J Biol Chem 282: 15114–15125.

41. Noirot-GrosMF, SoultanasP, WigleyDB, EhrlichSD, NoirotP, et al. (2002) The beta-propeller protein YxaL increases the processivity of the PcrA helicase. Mol Genet Genomics 267: 391–400.

42. VeauteX, DelmasS, SelvaM, JeussetJ, Le CamE, et al. (2005) UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli. EMBO J 24: 180–189.

43. ChangTL, NaqviA, AnandSP, KramerMG, MunshiR, et al. (2002) Biochemical characterization of the Staphylococcus aureus PcrA helicase and its role in plasmid rolling circle replication. J Biol Chem 277: 45880–45886.

44. IordanescuS (1993) Plasmid pT181-linked suppressors of the Staphylococcus aureus pcrA3 chromosomal mutation. J Bacteriol 175: 3916–3917.

45. MachonC, LynchGP, ThomsonNH, ScottDJ, ThomasCD, et al. (2010) RepD-mediated recruitment of PcrA helicase at the Staphylococcus aureus pC221 plasmid replication origin, oriD. Nucleic Acids Res 38: 1874–1888.

46. SlatterAF, ThomasCD, WebbMR (2009) PcrA helicase tightly couples ATP hydrolysis to unwinding double-stranded DNA, modulated by the initiator protein for plasmid replication, RepD. Biochemistry 48: 6326–6334.

47. SoultanasP, DillinghamMS, PapadopoulosF, PhillipsSE, ThomasCD, et al. (1999) Plasmid replication initiator protein RepD increases the processivity of PcrA DNA helicase. Nucleic Acids Res 27: 1421–1428.

48. ToselandCP, Martinez-SenacMM, SlatterAF, WebbMR (2009) The ATPase cycle of PcrA helicase and its coupling to translocation on DNA. J Mol Biol 392: 1020–1032.

49. Abdel-MonemM, Taucher-ScholzG, KlinkertMQ (1983) Identification of Escherichia coli DNA helicase I as the traI gene product of the F sex factor. Proc Natl Acad Sci U S A 80: 4659–4663.

50. LlosaM, GrandosoG, HernandoMA, de la CruzF (1996) Functional domains in protein TrwC of plasmid R388: dissected DNA strand transferase and DNA helicase activities reconstitute protein function. J Mol Biol 264: 56–67.

51. MatsonSW, SampsonJK, ByrdDR (2001) F plasmid conjugative DNA transfer: the TraI helicase activity is essential for DNA strand transfer. J Biol Chem 276: 2372–2379.

52. de la CruzF, FrostLS, MeyerRJ, ZechnerEL (2010) Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev 34: 18–40.

53. BrittonRA, EichenbergerP, Gonzalez-PastorJE, FawcettP, MonsonR, et al. (2002) Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis. J Bacteriol 184: 4881–4890.

54. GibsonDG, YoungL, ChuangRY, VenterJC, HutchisonCA3rd, et al. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6: 343–345.

55. YansuraDG, HennerDJ (1984) Use of the Escherichia coli lac repressor and operator to control gene expression in Bacillus subtilis. Proc Natl Acad Sci U S A 81: 439–443.

56. BoseB, AuchtungJM, LeeCA, GrossmanAD (2008) A conserved anti-repressor controls horizontal gene transfer by proteolysis. Mol Microbiol 70: 570–582.

57. SmitsWK, GoranovAI, GrossmanAD (2010) Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo. Mol Microbiol 75: 452–461.

58. LarkinMA, BlackshieldsG, BrownNP, ChennaR, McGettiganPA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948.

59. LetunicI, BorkP (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475–478.

60. FinnRD, ClementsJ, EddySR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39: W29–37.

61. NeedlemanSB, WunschCD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443–453.

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2013 Číslo 1
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Získaná hemofilie - Povědomí o nemoci a její diagnostika
nový kurz

Eozinofilní granulomatóza s polyangiitidou
Autori: doc. MUDr. Martina Doubková, Ph.D.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#