Mobility of the Native Conjugative Plasmid pLS20 Is Regulated by Intercellular Signaling

English version České info

Horizontal gene transfer mediated by plasmid conjugation plays a significant role in the evolution of bacterial species, as well as in the dissemination of antibiotic resistance and pathogenicity determinants. Characterization of their regulation is important for gaining insights into these features. Relatively little is known about how conjugation of Gram-positive plasmids is regulated. We have characterized conjugation of the native Bacillus subtilis plasmid pLS20. Contrary to the enterococcal plasmids, conjugation of pLS20 is not activated by recipient-produced pheromones but by pLS20-encoded proteins that regulate expression of the conjugation genes. We show that conjugation is kept in the default “OFF” state and identified the master repressor responsible for this. Activation of the conjugation genes requires relief of repression, which is mediated by an anti-repressor that belongs to the Rap family of proteins. Using both RNA sequencing methodology and genetic approaches, we have determined the regulatory effects of the repressor and anti-repressor on expression of the pLS20 genes. We also show that the activity of the anti-repressor is in turn regulated by an intercellular signaling peptide. Ultimately, this peptide dictates the timing of conjugation. The implications of this regulatory mechanism and comparison with other mobile systems are discussed.

Vyšlo v časopise: Mobility of the Native Conjugative Plasmid pLS20 Is Regulated by Intercellular Signaling. PLoS Genet 9(10): e32767. doi:10.1371/journal.pgen.1003892
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003892

Souhrn

Zdroje

1. OchmanH, LawrenceJG, GroismanEA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304 10.1038/35012500 [doi].

2. FrostLS, LeplaeR, SummersAO, ToussaintA (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Micobiol 3: 722–732.

3. ThomasCM, NielsenKM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3: 711–721 nrmicro1234 [pii];10.1038/nrmicro1234 [doi].

4. NovickRP, ChristieGE, PenadesJR (2010) The phage-related chromosomal islands of Gram-positive bacteria. Nat Rev Microbiol 8: 541–551 nrmicro2393 [pii];10.1038/nrmicro2393 [doi].

5. FrostLS, KoraimannG (2010) Regulation of bacterial conjugation: balancing opportunity with adversity. Future Microbiol 5: 1057–1071 10.2217/fmb.10.70 [doi].

6. SmillieC, Garcillán-BarciaMP, FranciaMV, RochaEPC, De la CruzF (2010) Mobility of plasmids. Microbiol Mol Biol Rev 74: 434–452.

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

8. FronzesR, ChristiePJ, WaksmanG (2009) The structural biology of type IV secretion systems. Nat Rev Microbiol 7: 703–714 nrmicro2218 [pii];10.1038/nrmicro2218 [doi].

9. GrohmannE, MuthG, EspinosaM (2003) Conjugative plasmid transfer in gram-positive bacteria. Microbiol Mol Biol Rev 67: 277–301.

10. HorodniceanuT, BougueleretL, El-SolhN, BouanchaudDH, ChabbertYA (1979) Conjugative R plasmids in Streptococcus agalactiae (group B). Plasmid 2: 197–206.

11. Goessweiner-MohrN, GrumetL, ArendsK, Pavkov-KellerT, GruberCC, et al. (2013) The 2.5 A structure of the enterococcus conjugation protein TraM resembles VirB8 type IV secretion proteins. J Biol Chem 288: 2018–2028 M112.428847 [pii];10.1074/jbc.M112.428847 [doi].

12. LiJ, AdamsV, BannamTL, MiyamotoK, GarciaJP, et al. (2013) Toxin plasmids of Clostridium perfringens. Microbiol Mol Biol Rev 77: 208–233 77/2/208 [pii];10.1128/MMBR.00062-12 [doi].

13. LiuMA, KwongSM, JensenSO, BrzoskaAJ, FirthN (2013) Biology of the staphylococcal conjugative multiresistance plasmid pSK41. Plasmid 70: 42–51 S0147-619X(13)00022-X [pii];10.1016/j.plasmid.2013.02.001 [doi].

14. CarylJA, O'NeillAJ (2009) Complete nucleotide sequence of pGO1, the prototype conjugative plasmid from the Staphylococci. Plasmid 62: 35–38 S0147-619X(09)00027-4 [pii];10.1016/j.plasmid.2009.03.001 [doi].

15. ClewellDB (2011) Tales of conjugation and sex pheromones: A plasmid and enterococcal odyssey. Mob Genet Elements 1: 38–54 10.4161/mge.1.1.15409 [doi];2159-2543-1-1-6 [pii].

16. DunnyGM, JohnsonCM (2011) Regulatory circuits controlling enterococcal conjugation: lessons for functional genomics. Curr Opin Microbiol 14: 174–180 S1369-5274(11)00020-8 [pii];10.1016/j.mib.2011.01.008 [doi].

17. ChatterjeeA, CookLC, ShuCC, ChenY, ManiasDA, et al. (2013) Antagonistic self-sensing and mate-sensing signaling controls antibiotic-resistance transfer. Proc Natl Acad Sci U S A 110: 7086–7090 1212256110 [pii];10.1073/pnas.1212256110 [doi].

18. Sonenshein AL, Hoch JA, Losick R (1993) Bacillus subtilis and other Gram-positive bacteria; Biochemistry, physiology, and molecular genetics. Washington, D.C.: American Society for Microbiology. 987 p.

19. Sonenshein AL, Hoch JA, Losick R (2001) Bacillus subtilis and its closest relatives: from genes to cells. ASM Press.

20. TitokMA, ChapuisJ, SeleznevaYV, LagodichAV, ProkulevichVA, et al. (2003) Bacillus subtilis soil isolates: plasmid replicon analysis and construction of a new theta-replicating vector. Plasmid 49: 53–62.

21. CuttingSM (2011) Bacillus probiotics. Food Microbiol 28: 214–220 S0740-0020(10)00049-3 [pii];10.1016/j.fm.2010.03.007 [doi].

22. TanakaT, KoshikawaT (1977) Isolation and characterization of four types of plasmids from Bacillus subtilis (natto). J Bacteriol 131: 699–701.

23. KoehlerTM, ThorneCB (1987) Bacillus subtilis (natto) plasmid pLS20 mediates interspecies plasmid transfer. J Bacteriol 169: 5271–5278.

24. ItayaM, SakayaN, MatsunagaS, FujitaK, KanekoS (2006) Conjugational transfer kinetics of pLS20 between Bacillus subtilis in liquid medium. Biosci Biotechnol Biochem 70: 740–742 JST.JSTAGE/bbb/70.740 [pii].

25. MeijerWJJ, de BoerA, van TongerenS, VenemaG, BronS (1995) Characterization of the replication region of the Bacillus subtilis plasmid pLS20: a novel type of replicon. Nucleic Acids Res 23: 3214–3223.

26. DermanAI, BeckerEC, TruongBD, FujiokaA, TuceyTM, et al. (2009) Phylogenetic analysis identifies many uncharacterized actin-like proteins (Alps) in bacteria: regulated polymerization, dynamic instability and treadmilling in Alp7A. Mol Microbiol 73: 534–552.

27. SinghPK, RamachandranG, Duran-AlcaldeL, AlonsoC, WuLJ, et al. (2012) Inhibition of Bacillus subtilis natural competence by a native, conjugative plasmid-encoded comK repressor protein. Environ Microbiol 14: 2812–2825 10.1111/j.1462-2920.2012.02819.x [doi].

28. BauerT, RoschT, ItayaM, GraumannPL (2011) Localization pattern of conjugation machinery in a Gram-positive bacterium. J Bacteriol 193: 6244–6256 JB.00175-11 [pii];10.1128/JB.00175-11 [doi].

29. PeregoM, HansteinC, WelshKM, DjavakhishviliT, GlaserP, et al. (1994) Multiple protein aspartate phosphatases provide a mechanism for the integration of diverse signals in the control of development in Bacillus subtilis. Cell 79: 1047–1055.

30. SolomonJM, LazazzeraBA, GrossmanAD (1996) Purification and characterization of an extracellular peptide factor that affects different developmental pathways in Bacillus subtilis. Genes Develop 10: 2014–2024.

31. LazazzeraBA, SolomonJM, GrossmanAD (1997) An exported peptide functions intracellularly to contribute to cell density signaling in B. subtilis. . Cell 89: 917–925 S0092-8674(00)80277-9 [pii].

32. PeregoM, HochJA (1996) Cell-cell communication regulates the effects of protein aspartate phosphatases on the phosphorelay controlling development in Bacillus subtilis. Proc Natl Acad Sci USA 93: 1549–1553.

33. JiangM, ShaoW, PeregoM, HochJA (2000) Multiple histidine kinases regulate entry into stationary phase and sporulation in Bacillus subtilis. Mol Microbiol 38: 535–542.

34. Ogura M, Shimane K, Asai K, Ogasawara N, Tanaka T (2003) Binding of response regulator DegU to the aprE promoter is inhibited by RapG, which is counteracted by extracellular PhrG in Bacillus subtilis. Mol Microbiol 49: : 1685–1697. 3665 [pii].

35. SmitsWK, BongiorniC, VeeningJW, HamoenLW, KuipersOP, et al. (2007) Temporal separation of distinct differentiation pathwasys by a dual specificity Rap-Phr system in Bacillus subtilis. Mol Microbiol 65: 103–120.

36. MeijerWJJ, WismanGBA, TerpstraP, ThorstedPB, ThomasCM, et al. (1998) Rolling-circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram-positive bacteria. FEMS Microbiol Rev 21: 337–368.

37. SinghPK, Ballestero-BeltranS, RamachandranG, MeijerWJ (2010) Complete nucleotide sequence and determination of the replication region of the sporulation inhibiting plasmid p576 from Bacillus pumilus NRS576. Res Microbiol 161: 772–782 S0923-2508(10)00186-5 [pii];10.1016/j.resmic.2010.07.007 [doi].

38. BongiorniC, StoesselR, ShoemakerD, PeregoM (2006) Rap phosphatases of virulence plasmid pXO1 inhibits Bacillus anthracis sporulation. J Bacteriol 188: 487–498.

39. KoetjeEJ, Hajdo-MilasinovicA, KiewietR, BronS, TjalsmaH (2003) A plasmid-borne Rap-Phr system of Bacillus subtilis can mediate cell-density controlled production of extracellular proteases. Microbiology 149: 19–28.

40. ParasharV, KonkolMA, KearnsDB, NeiditchMB (2013) A plasmid-encoded phosphatase regulates Bacillus subtilis biofilm architecture, sporulation, and genetic competence. J Bacteriol 195: 2437–2448 JB.02030-12 [pii];10.1128/JB.02030-12 [doi].

41. Burrus V, Pavlovic G, Decaris B, Guedon G (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. S0147619X02001026 [pii].

42. 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 0505835102 [pii];10.1073/pnas.0505835102 [doi].

43. PottathilM, LazazzeraBA (2003) The extracellular Phr peptide-Rap phosphatase signaling circuit of Bacillus subtilis. Front Biosci 8: d32–d45.

44. ParasharV, MirouzeN, DubnauDA, NeiditchMB (2011) Structural basis of response regulator dephosphorylation by Rap phosphatases. PLoS Biol 9: e1000589 10.1371/journal.pbio.1000589 [doi].

45. BakerMD, NeiditchMB (2011) Structural basis of response regulator inhibition by a bacterial anti-activator protein. PLoS Biol 9: e1001226 10.1371/journal.pbio.1001226 [doi];PBIOLOGY-D-11-02308 [pii].

46. BurbulysD, TrachKA, HochJA (1991) Initiation of sporulation in B. subtilis is controlled by a multicomponent phosphorelay. Cell 64: 545–552.

47. BongiorniC, IshikawaS, StephensonS, OgasawaraN, PeregoM (2005) Synergistic regulation of competence development in Bacillus subtilis by two Rap-Phr systems. J Bacteriol 187: 4353–4361.

48. Core L, Perego M (2003) TPR-mediated interaction of RapC with ComA inhibits response regulator-DNA binding for competence development in Bacillus subtilis. Mol Microbiol 49: : 1509–1522. 3659 [pii].

49. WatersCM, BasslerBL (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21: 319–346 10.1146/annurev.cellbio.21.012704.131001 [doi].

50. ThoendelM, HorswillAR (2010) Biosynthesis of peptide signals in gram-positive bacteria. Adv Appl Microbiol 71: 91–112 S0065-2164(10)71004-2 [pii];10.1016/S0065-2164(10)71004-2 [doi].

51. ZhuJ, OgerPM, SchrammeijerB, HooykaasPJ, FarrandSK, et al. (2000) The bases of crown gall tumorigenesis. J Bacteriol 182: 3885–3895.

52. BoseB, AuchtungJM, LeeCA, GrossmanAD (2008) A conserved anti-repressor controls horizontal gene transfer by proteolysis. Mol Microbiol 70: 570–582 MMI6414 [pii];10.1111/j.1365-2958.2008.06414.x [doi].

53. BoseB, GrossmanAD (2011) Regulation of horizontal gene transfer in Bacillus subtilis by activation of a conserved site-specific protease. J Bacteriol 193: 22–29 JB.01143-10 [pii];10.1128/JB.01143-10 [doi].

54. 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 10.1371/journal.pgen.1002222 [doi];PGENETICS-D-11-00532 [pii].

55. StrauchMA, HochJA (1993) Transition state regulators: sentinels of Bacillus subtilis post-exponential gene expression. Mol Microbiol 7: 337–342.

56. ParasharV, JeffreyPD, NeiditchMB (2013) Conformational change-induced repeat domain expansion regulates rap phosphatase quorum-sensing signal receptors. PLoS Biol 11: e1001512 10.1371/journal.pbio.1001512 [doi];PBIOLOGY-D-12-03568 [pii].

57. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.

58. Bron S (1990) Plasmids. In: Harwood CR, Cutting SM, editors. Molecular Biological Methods for Bacillus. Chichester, UK: John Wiley & Sons Ltd. pp. 75–174.

59. SchaefferP, MilletI, AubertJ (1965) Catabolite repression of bacterial sporulation. Proc Natl Acad Sci USA 54: 704–711.

60. ZhangXZ, ZhangYH (2011) Simple, fast and high-efficiency transformation system for directed evolution of cellulase in Bacillus subtilis. Microb Biotechnol 4: 98–105 10.1111/j.1751-7915.2010.00230.x [doi].

61. ParkhomchukD, BorodinaT, AmstislavskiyV, BanaruM, HallenL, et al. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123 gkp596 [pii];10.1093/nar/gkp596 [doi].

62. LangmeadB, TrapnellC, PopM, SalzbergSL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25 gb-2009-10-3-r25 [pii];10.1186/gb-2009-10-3-r25 [doi].

63. EwingB, HillierL, WendlMC, GreenP (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175–185.

64. EwingB, GreenP (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186–194.

65. AltschulSF, GishW, MillerW, MyersEW, LipmanDJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410 10.1016/S0022-2836(05)80360-2 [doi];S0022-2836(05)80360-2 [pii].

66. HuangW, UmbachDM, VincentJN, AbellAN, JohnsonGL, et al. (2011) Efficiently identifying genome-wide changes with next-generation sequencing data. Nucleic Acids Res 39: e130 gkr592 [pii];10.1093/nar/gkr592 [doi].

67. PavlidisP, NobleWS (2003) Matrix2png: a utility for visualizing matrix data. Bioinformatics 19: 295–296.