A Complex Genetic Switch Involving Overlapping Divergent Promoters and DNA Looping Regulates Expression of Conjugation Genes of a Gram-positive Plasmid
Plasmids are extrachromosomal, autonomously replicating units that are harbored by many bacteria. Many plasmids encode transfer function allowing them to be transferred into plasmid-free bacteria by a process named conjugation. Since many of them also carry antibiotic resistance genes, plasmid-mediated conjugation is a major mechanism in the dissemination of antibiotic resistance. In depth knowledge on the regulation of conjugation genes is a prerequisite to design measures interfering with the spread of antibiotic resistance. pLS20 is a conjugative plasmid of the soil bacterium Bacillus subtilis, which is also a gut commensal in animals and humans. Here we describe in detail the molecular mechanism by which the key transcriptional regulator tightly represses the conjugation genes during conditions unfavorable to conjugation without compromising the ability to switch on accurately the conjugation genes when appropriate. We found that conjugation is subject to the control of a unique genetic switch where at least three levels of regulation are integrated. The first level involves overlapping divergent promoters of different strengths. The second layer involves a triple function of the transcriptional regulator. And the third level of regulation concerns formation of a DNA loop mediated by the transcriptional regulator.
Vyšlo v časopise:
A Complex Genetic Switch Involving Overlapping Divergent Promoters and DNA Looping Regulates Expression of Conjugation Genes of a Gram-positive Plasmid. PLoS Genet 10(10): e32767. doi:10.1371/journal.pgen.1004733
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004733
Souhrn
Plasmids are extrachromosomal, autonomously replicating units that are harbored by many bacteria. Many plasmids encode transfer function allowing them to be transferred into plasmid-free bacteria by a process named conjugation. Since many of them also carry antibiotic resistance genes, plasmid-mediated conjugation is a major mechanism in the dissemination of antibiotic resistance. In depth knowledge on the regulation of conjugation genes is a prerequisite to design measures interfering with the spread of antibiotic resistance. pLS20 is a conjugative plasmid of the soil bacterium Bacillus subtilis, which is also a gut commensal in animals and humans. Here we describe in detail the molecular mechanism by which the key transcriptional regulator tightly represses the conjugation genes during conditions unfavorable to conjugation without compromising the ability to switch on accurately the conjugation genes when appropriate. We found that conjugation is subject to the control of a unique genetic switch where at least three levels of regulation are integrated. The first level involves overlapping divergent promoters of different strengths. The second layer involves a triple function of the transcriptional regulator. And the third level of regulation concerns formation of a DNA loop mediated by the transcriptional regulator.
Zdroje
1. OchmanH, LawrenceJG, GroismanEA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304.
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.
4. NovickRP, ChristieGE, PenadesJR (2010) The phage-related chromosomal islands of Gram-positive bacteria. Nat Rev Microbiol 8: 541–551.
5. WozniakRA, WaldorMK (2010) Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8: 552–563.
6. 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.
7. FrostLS, KoraimannG (2010) Regulation of bacterial conjugation: balancing opportunity with adversity. Future Microbiol 5: 1057–1071.
8. SmillieC, Garcillán-BarciaMP, FranciaMV, RochaEPC, De la CruzF (2010) Mobility of plasmids. Microbiol Mol Biol Rev 74: 434–452.
9. Alvarez-MartinezCE, ChristiePJ (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73: 775–808.
10. FronzesR, ChristiePJ, WaksmanG (2009) The structural biology of type IV secretion systems. Nat Rev Microbiol 7: 703–714.
11. Goessweiner-MohrN, GrumetL, ArendsK, Pavkov-KellerT, GruberCC, GruberK, Birner-GruenbergerR, Kropec-HuebnerA, HuebnerJ, GrohmannE, KellerW (2013) The 2.5 A structure of the enterococcus conjugation protein TraM resembles VirB8 type IV secretion proteins. J Biol Chem 288: 2018–2028.
12. LiJ, AdamsV, BannamTL, MiyamotoK, GarciaJP, UzalFA, RoodJI, McClaneBA (2013) Toxin plasmids of Clostridium perfringens. Microbiol Mol Biol Rev 77: 208–233.
13. LiuMA, KwongSM, JensenSO, BrzoskaAJ, FirthN (2013) Biology of the staphylococcal conjugative multiresistance plasmid pSK41. Plasmid 70: 42–51.
14. CarylJA, O'NeillAJ (2009) Complete nucleotide sequence of pGO1, the prototype conjugative plasmid from the Staphylococci. Plasmid 62: 35–38 S.
15. ClewellDB (2011) Tales of conjugation and sex pheromones: A plasmid and enterococcal odyssey. Mob Genet Elements 1: 38–54.
16. DunnyGM, JohnsonCM (2011) Regulatory circuits controlling enterococcal conjugation: lessons for functional genomics. Curr Opin Microbiol 14: 174–180.
17. ChatterjeeA, CookLC, ShuCC, ChenY, ManiasDA, RamkrishnaD, DunnyGM, HuWS (2013) Antagonistic self-sensing and mate-sensing signaling controls antibiotic-resistance transfer. Proc Natl Acad Sci U S A 110: 7086–7090.
18. Sonenshein, A. L., Hoch, J. A., and 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, A. L., Hoch, J. A., and Losick, R. (2001) Bacillus subtilis and its closest relatives: from genes to cells. ASM Press.
20. CuttingSM (2011) Bacillus probiotics. Food Microbiol 28: 214–220.
21. TanakaT, KoshikawaT (1977) Isolation and characterization of four types of plasmids from Bacillus subtilis (natto). J Bacteriol 131: 699–701.
22. KoehlerTM, ThorneCB (1987) Bacillus subtilis (natto) plasmid pLS20 mediates interspecies plasmid transfer. J Bacteriol 169: 5271–5278.
23. ItayaM, SakayaN, MatsunagaS, FujitaK, KanekoS (2006) Conjugational transfer kinetics of pLS20 between Bacillus subtilis in liquid medium. Biosci Biotechnol Biochem 70: 740–742.
24. BauerT, RoschT, ItayaM, GraumannPL (2011) Localization pattern of conjugation machinery in a Gram-positive bacterium. J Bacteriol 193: 6244–6256.
25. RöschTC, GolmanW, HucklesbyL, Gonzalez-PastorJE, GraumannPL (2014) The presence of conjugative plasmid pLS20 affects global transcription of Its Bacillus subtilis host and confers beneficial stress resistance to cells. Appl Environ Microbiol 80: 1349–1358.
26. 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.
27. DermanAI, BeckerEC, TruongBD, FujiokaA, TuceyTM, ErbML, PattersonPC, PoglianoJ (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.
28. SinghPK, RamachandranG, Duran-AlcaldeL, AlonsoC, WuLJ, MeijerWJ (2012) Inhibition of Bacillus subtilis natural competence by a native, conjugative plasmid-encoded comK repressor protein. Environ Microbiol 14: 2812–2825.
29. SinghPK, RamachandranG, Ramos-RuizR, Peiro-PastorR, AbiaD, WuLJ, MeijerWJ (2013) Mobility of the Native Bacillus subtilis Conjugative Plasmid pLS20 Is Regulated by Intercellular Signaling. PLoS Genet 9: e1003892.
30. BaileyTL, ElkanC (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28–36.
31. LiuX, BrutlagDL, LiuJS (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 127–138.
32. HagermanPJ (1988) Flexibility of DNA. Annu Rev Biophys Biophys Chem 17: 265–286.
33. HaranTE, MohantyU (2009) The unique structure of A-tracts and intrinsic DNA bending. Q Rev Biophys 42: 41–81.
34. BeckCF, WarrenRA (1988) Divergent promoters, a common form of gene organization. Microbiol Rev 52: 318–326.
35. WangP, YangJ, LawleyB, PittardAJ (1997) Repression of the aroP gene of Escherichia coli involves activation of a divergent promoter. J Bacteriol 179: 4213–4218.
36. WangP, YangJ, IshihamaA, PittardAJ (1998) Demonstration that the TyrR protein and RNA polymerase complex formed at the divergent P3 promoter inhibits binding of RNA polymerase to the major promoter, P1, of the aroP gene of Escherichia coli. J Bacteriol 180: 5466–5472.
37. BendtsenKM, ErdossyJ, CsiszovszkiZ, SvenningsenSL, SneppenK, KrishnaS, SemseyS (2011) Direct and indirect effects in the regulation of overlapping promoters. Nucleic Acids Res 39: 6879–6885.
38. CournacA, PlumbridgeJ (2013) DNA looping in prokaryotes: experimental and theoretical approaches. J Bacteriol 195: 1109–1119.
39. DunnTM, HahnS, OgdenS, SchleifRF (1984) An operator at −280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression. Proc Natl Acad Sci U S A 81: 5017–5020.
40. AdhyaS (1989) Multipartite genetic control elements: communication by DNA loop. Annu Rev Genet 23: 227–250.
41. MatthewsKS (1992) DNA looping. Microbiol Rev 56: 123–136.
42. SchleifR (1992) DNA looping. Annu Rev Biochem 61: 199–223.
43. HochschildA, LewisM (2009) The bacteriophage lambda CI protein finds an asymmetric solution. Curr Opin Struct Biol 19: 79–86.
44. MukherjeeS, EricksonH, BastiaD (1988) Enhancer-origin interaction in plasmid R6K involves a DNA loop mediated by initiator protein. Cell 52: 375–383.
45. DunnyGM (2013) Enterococcal sex pheromones: signaling, social behavior, and evolution. Annu Rev Genet 47: 457–482.
46. 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.
47. ZatykaM, Jagura-BurdzyG, ThomasCM (1997) Transcriptional and translational control of the genes for the mating pair formation apparatus of promiscuous IncP plasmids. J Bacteriol 179: 7201–7209.
48. LangJ, FaureD (2014) Functions and regulation of quorum-sensing in Agrobacterium tumefaciens. Front Plant Sci 5: 14.
49. OehlerS, Muller-HillB (2010) High local concentration: a fundamental strategy of life. J Mol Biol 395: 242–253.
50. VilarJM, SaizL (2005) DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise. Curr Opin Genet Dev 15: 136–144.
51. SaizL, VilarJM (2006) DNA looping: the consequences and its control. Curr Opin Struct Biol 16: 344–350.
52. KorobkovaE, EmonetT, VilarJM, ShimizuTS, CluzelP (2004) From molecular noise to behavioural variability in a single bacterium. Nature 428: 574–578.
53. DubnauD, LosickR (2006) Bistability in bacteria. Mol Microbiol 61: 564–572.
54. VeeningJW, SmitsWK, KuipersOP (2008) Bistability, epigenetics, and bet-hedging in bacteria. Annu Rev Microbiol 62: 193–210.
55. DoddIB, ShearwinKE, EganJB (2005) Revisited gene regulation in bacteriophage lambda. Curr Opin Genet Dev 15: 145–152.
56. OppenheimAB, KobilerO, StavansJ, CourtDL, AdhyaS (2005) Switches in bacteriophage lambda development. Annu Rev Genet 39: 409–429.
57. LittleJW, ShepleyDP, WertDW (1999) Robustness of a gene regulatory circuit. EMBO J 18: 4299–4307.
58. DoddIB, PerkinsAJ, TsemitsidisD, EganJB (2001) Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogeny. Genes Dev 15: 3013–3022.
59. DoddIB, ShearwinKE, PerkinsAJ, BurrT, HochschildA, EganJB (2004) Cooperativity in long-range gene regulation by the lambda CI repressor. Genes Dev 18: 344–354.
60. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
61. 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.
62. Bron S (1990) Plasmids. In: Harwood CR, Cutting SM, editors. Molecular Biological Methods for Bacillus. Chichester, UK: John Wiley & Sons Ltd. pp. 75–174.
63. Miller, J. H. (1982) Experiments in molecular genetics. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
64. MorenoR, FonsecaP, RojoF (2012) Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression. Mol Microbiol 83: 24–40.
65. MaxamAM, GilbertW (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol 65: 499–560.
66. MeijerWJJ, Castilla-LlorenteV, VillarL, MurrayH, ErringtonJ, SalasM (2005) Molecular basis for the exploitation of spore formation as survival mechanism by virulent phage φ29. EMBO J 24: 3647–3657.
67. BolshoyA, McNamaraP, HarringtonRE, TrifonovEN (1991) Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci U S A 88: 2312–2316.
68. SchuckP (2000) Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys J 78: 1606–1609.
69. Laue TM, Shah BD, Ridgeway TM, Pelletier SL (1992) Interpretation of analytical sedimentation data for proteins. In: Harding SE, Rowe AJ, Horton JC, editors. Analytical ultracentrifugation in biochemistry and polymer science. Cambridge, UK: Royal Society of Chemistry. pp. 90–125.
70. ColeJL (2004) Analysis of heterogeneous interactions. Methods Enzymol 384: 212–232.
71. ShimomayeE, SalvatoM (1989) Use of avian myeloblastosis virus reverse transcriptase at high temperature for sequence analysis of highly structured RNA. Gene Anal Tech 6: 25–28.
72. LoreauN, BoiziauC, VerspierenP, ShireD, ToulmeJJ (1990) Blockage of AMV reverse transcriptase by antisense oligodeoxynucleotides. FEBS Lett 274: 53–56.
73. CrooksGE, HonG, ChandoniaJM, BrennerSE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188–1190.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2014 Číslo 10
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination
- A Splice Mutation in the Gene Causes High Glycogen Content and Low Meat Quality in Pig Skeletal Muscle
- Keratin 76 Is Required for Tight Junction Function and Maintenance of the Skin Barrier
- A Role for Taiman in Insect Metamorphosis