ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Cells
The DNA uptake of naturally competent bacteria has been attributed to the action of DNA uptake machineries resembling type IV pilus complexes. However, the protein(s) for pulling the DNA across the outer membrane of Gram-negative bacteria remain speculative. Here we show that the competence protein ComEA binds incoming DNA in the periplasm of naturally competent Vibrio cholerae cells thereby promoting DNA uptake, possibly through ratcheting and entropic forces associated with ComEA binding. Using comparative modeling and molecular simulations, we projected the 3D structure and DNA-binding site of ComEA. These in silico predictions, combined with in vivo and in vitro validations of wild-type and site-directed modified variants of ComEA, suggested that ComEA is not solely a DNA receptor protein but plays a direct role in the DNA uptake process. Furthermore, we uncovered that ComEA homologs of other bacteria (both Gram-positive and Gram-negative) efficiently compensated for the absence of ComEA in V. cholerae, suggesting that the contribution of ComEA in the DNA uptake process might be conserved among naturally competent bacteria.
Vyšlo v časopise:
ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Cells. PLoS Genet 10(1): e32767. doi:10.1371/journal.pgen.1004066
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004066
Souhrn
The DNA uptake of naturally competent bacteria has been attributed to the action of DNA uptake machineries resembling type IV pilus complexes. However, the protein(s) for pulling the DNA across the outer membrane of Gram-negative bacteria remain speculative. Here we show that the competence protein ComEA binds incoming DNA in the periplasm of naturally competent Vibrio cholerae cells thereby promoting DNA uptake, possibly through ratcheting and entropic forces associated with ComEA binding. Using comparative modeling and molecular simulations, we projected the 3D structure and DNA-binding site of ComEA. These in silico predictions, combined with in vivo and in vitro validations of wild-type and site-directed modified variants of ComEA, suggested that ComEA is not solely a DNA receptor protein but plays a direct role in the DNA uptake process. Furthermore, we uncovered that ComEA homologs of other bacteria (both Gram-positive and Gram-negative) efficiently compensated for the absence of ComEA in V. cholerae, suggesting that the contribution of ComEA in the DNA uptake process might be conserved among naturally competent bacteria.
Zdroje
1. ChenI, ChristiePJ, DubnauD (2005) The ins and outs of DNA transfer in bacteria. Science 310: 1456–1460.
2. ChenI, DubnauD (2004) DNA uptake during bacterial transformation. Nat Rev Microbiol 2: 241–249.
3. AllemandJF, MaierB (2009) Bacterial translocation motors investigated by single molecule techniques. FEMS Microbiol Rev 33: 593–610.
4. BurtonB, DubnauD (2010) Membrane-associated DNA transport machines. Cold Spring Harb Perspect Biol 2: a000406.
5. ClaverysJP, PrudhommeM, MartinB (2006) Induction of competence regulons as a general response to stress in gram-positive bacteria. Annu Rev Microbiol 60: 451–475.
6. SeitzP, BlokeschM (2013) Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria. FEMS Microbiol Rev 37: 336–363.
7. LorenzMG, WackernagelW (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 58: 563–602.
8. MeibomKL, BlokeschM, DolganovNA, WuC-Y (2005) Schoolnik GK (2005) Chitin induces natural competence in Vibrio cholerae. Science 310: 1824–1827.
9. LippEK, HuqA, ColwellRR (2002) Effects of global climate on infectious disease: the cholera model. Clin Microbiol Rev 15: 757–770.
10. BlokeschM (2012) Chitin colonization, chitin degradation and chitin-induced natural competence of Vibrio cholerae are subject to catabolite repression. Environ Microbiol 14: 1898–1912.
11. SeitzP, BlokeschM (2013) DNA-uptake machinery of naturally competent Vibrio cholerae. Proc Natl Acad Sci USA 110: 17987–17992.
12. PelicicV (2008) Type IV pili: e pluribus unum? Mol Microbiol 68: 827–837.
13. ClaverysJP, MartinB, PolardP (2009) The genetic transformation machinery: composition, localization, and mechanism. FEMS Microbiol Rev 33: 643–656.
14. KrügerNJ, StinglK (2011) Two steps away from novelty-principles of bacterial DNA uptake. Mol Microbiol 80: 860–867.
15. InamdarMM, GelbartWM, PhillipsR (2006) Dynamics of DNA ejection from bacteriophage. Biophys J 91: 411–420.
16. HahnJ, MaierB, HaijemaBJ, SheetzM, DubnauD (2005) Transformation proteins and DNA uptake localize to the cell poles in Bacillus subtilis. Cell 122: 59–71.
17. KidaneD, GraumannPL (2005) Intracellular protein and DNA dynamics in competent Bacillus subtilis cells. Cell 122: 73–84.
18. KramerN, HahnJ, DubnauD (2007) Multiple interactions among the competence proteins of Bacillus subtilis. Mol Microbiol 65: 454–464.
19. KaufensteinM, van der LaanM, GraumannPL (2011) The three-layered DNA uptake machinery at the cell pole in competent Bacillus subtilis cells is a stable complex. J Bacteriol 193: 1633–1642.
20. InamineGS, DubnauD (1995) ComEA, a Bacillus subtilis integral membrane protein required for genetic transformation, is needed for both DNA binding and transport. J Bacteriol 177: 3045–3051.
21. ProvvediR, DubnauD (1999) ComEA is a DNA receptor for transformation of competent Bacillus subtilis. Mol Microbiol 31: 271–280.
22. BergeM, MoscosoM, PrudhommeM, MartinB, ClaverysJP (2002) Uptake of transforming DNA in Gram-positive bacteria: a view from Streptococcus pneumoniae. Mol Microbiol 45: 411–421.
23. ChenI, GotschlichEC (2001) ComE, a competence protein from Neisseria gonorrhoeae with DNA-binding activity. J Bacteriol 183: 3160–3168.
24. SuckowG, SeitzP, BlokeschM (2011) Quorum sensing contributes to natural transformation of Vibrio cholerae in a species-specific manner. J Bacteriol 193: 4914–4924.
25. Lo ScrudatoM, BlokeschM (2012) The regulatory network of natural competence and transformation of Vibrio cholerae. PLoS Genet 8: e1002778.
26. BlokeschM (2012) A quorum sensing-mediated switch contributes to natural transformation of Vibrio cholerae. Mob Genet Elements 2: 224–227.
27. StinglK, MullerS, Scheidgen-KleyboldtG, ClausenM, MaierB (2010) Composite system mediates two-step DNA uptake into Helicobacter pylori. Proc Natl Acad Sci USA 107: 1184–1189.
28. WhiteJ, StelzerE (1999) Photobleaching GFP reveals protein dynamics inside live cells. Trends Cell Biol 9: 61–65.
29. Ishikawa-AnkerholdHC, AnkerholdR, DrummenGP (2012) Advanced fluorescence microscopy techniques–FRAP, FLIP, FLAP, FRET and FLIM. Molecules 17: 4047–4132.
30. MullenLM, BosseJT, NairSP, WardJM, RycroftAN, et al. (2008) Pasteurellaceae ComE1 proteins combine the properties of fibronectin adhesins and DNA binding competence proteins. PLoS One 3: e3991.
31. JeonB, ZhangQ (2007) Cj0011c, a periplasmic single- and double-stranded DNA-binding protein, contributes to natural transformation in Campylobacter jejuni. J Bacteriol 189: 7399–7407.
32. DohertyAJ, SerpellLC, PontingCP (1996) The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Res 24: 2488–2497.
33. ShaoX, GrishinNV (2000) Common fold in helix-hairpin-helix proteins. Nucleic Acids Res 28: 2643–2650.
34. FeilmeierBJ, IsemingerG, SchroederD, WebberH, PhillipsGJ (2000) Green fluorescent protein functions as a reporter for protein localization in Escherichia coli. J Bacteriol 182: 4068–4076.
35. LybargerSR, JohnsonTL, GrayMD, SikoraAE, SandkvistM (2009) Docking and assembly of the type II secretion complex of Vibrio cholerae. J Bacteriol 191: 3149–3161.
36. FocaretaT, ManningPA (1991) Distinguishing between the extracellular DNases of Vibrio cholerae and development of a transformation system. Mol Microbiol 5: 2547–2555.
37. FocaretaT, ManningPA (1991) Genetic analysis of the export of an extracellular DNase of Vibrio cholerae using DNase-beta-lactamase fusions. Gene 108: 31–37.
38. BlokeschM (2008) Schoolnik GK (2008) The extracellular nuclease Dns and its role in natural transformation of Vibrio cholerae. J Bacteriol 190: 7232–7240.
39. HolmL, RosenstromP (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545–549.
40. YangY, SassLE, DuC, HsiehP, ErieDA (2005) Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions. Nucleic Acids Res 33: 4322–4334.
41. Mortier-BarriereI, VeltenM, DupaigneP, MirouzeN, PietrementO, et al. (2007) A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Cell 130: 824–836.
42. GrangeW, DuckelyM, HusaleS, JacobS, EngelA, et al. (2008) VirE2: a unique ssDNA-compacting molecular machine. PLoS Biol 6: e44.
43. SinhaS, MellJC, RedfieldRJ (2012) Seventeen Sxy-dependent cyclic AMP receptor protein site-regulated genes are needed for natural transformation in Haemophilus influenzae. J Bacteriol 194: 5245–5254.
44. MatiasVR, BeveridgeTJ (2005) Cryo-electron microscopy reveals native polymeric cell wall structure in Bacillus subtilis 168 and the existence of a periplasmic space. Mol Microbiol 56: 240–251.
45. BergeMJ, KamgoueA, MartinB, PolardP, CampoN, et al. (2013) Midcell recruitment of the DNA uptake and virulence nuclease, EndA, for pneumococcal transformation. PLoS Pathog 9: e1003596.
46. SimonSM, PeskinCS, OsterGF (1992) What drives the translocation of proteins? Proc Natl Acad Sci U S A 89: 3770–3774.
47. PeskinCS, OdellGM, OsterGF (1993) Cellular motions and thermal fluctuations: the Brownian ratchet. Biophys J 65: 316–324.
48. AmbjörnssonT, MetzlerR (2004) Chaperone-assisted translocation. Phys Biol 1: 77–88.
49. SalmanH, ZbaidaD, RabinY, ChatenayD, ElbaumM (2001) Kinetics and mechanism of DNA uptake into the cell nucleus. Proc Natl Acad Sci U S A 98: 7247–7252.
50. Yanisch-PerronC, VieiraJ, MessingJ (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103–119.
51. StudierFW, MoffattBA (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189: 113–130.
52. SimonR, PrieferU, PühlerA (1983) A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria. Nat Biotechnol 1: 784–791.
53. YildizFH (1998) Schoolnik GK (1998) Role of rpoS in stress survival and virulence of Vibrio cholerae. J Bacteriol 180: 773–784.
54. MeibomKL, LiXB, NielsenAT, WuCY, RosemanS, et al. (2004) The Vibrio cholerae chitin utilization program. Proc Natl Acad Sci USA 101: 2524–2529.
55. De Souza SilvaO, BlokeschM (2010) Genetic manipulation of Vibrio cholerae by combining natural transformation with FLP recombination. Plasmid 64: 186–195.
56. BlokeschM (2012) TransFLP – a method to genetically modify V. cholerae based on natural transformation and FLP-recombination. J Vis Exp 68: e3761 doi:3710.3791/3761
57. BorgeaudS, BlokeschM (2013) Overexpression of the tcp gene cluster using the T7 RNA polymerase/promoter system and natural transformation-mediated genetic engineering of Vibrio cholerae. PLoS One 8: e53952.
58. MarvigRL, BlokeschM (2010) Natural transformation of Vibrio cholerae as a tool-optimizing the procedure. BMC Microbiol 10: 155.
59. R Development Core Team (2009) R: A language and environment for statistical computing. ViennaAustria: R Foundation for Statistical Computing. 409 p.
60. SanchezR, SaliA (2000) Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol 143: 97–129.
61. EvansRJ, DaviesDR, BullardJM, ChristensenJ, GreenLS, et al. (2008) Structure of PolC reveals unique DNA binding and fidelity determinants. Proc Natl Acad Sci USA 105: 20695–20700.
62. PettersenEF, GoddardTD, HuangCC, CouchGS, GreenblattDM, et al. (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 25: 1605–1612.
63. PhillipsJC, BraunR, WangW, GumbartJ, TajkhorshidE, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781–1802.
64. PerezA, MarchanI, SvozilD, SponerJ, CheathamTE3rd, et al. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J 92: 3817–3829.
65. JorgensenWL, ChandrasekharJ, MaduraJD, ImpeyRW, KleinML (1983) Comparison of Simple Potential Functions for Simulating Liquid Water. J Chem Phys 79: 926–935.
66. RyckaertJP, CiccottiG, BerendsenHJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23: 327–341.
67. DardenT, PereraL, LiL, PedersenL (1999) New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure 7: R55–60.
68. MartynaGJ, TobiasDJ, KleinML (1994) Constant-Pressure Molecular-Dynamics Algorithms. J Chem Phys 101: 4177–4189.
69. FellerSE, ZhangYH, PastorRW, BrooksBR (1995) Constant-Pressure Molecular-Dynamics Simulation - the Langevin Piston Method. J Chem Phys 103: 4613–4621.
70. MillerBR, McGeeTD, SwailsJM, HomeyerN, GohlkeH, et al. (2012) MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. J Chem Theory Comput 8: 3314–3321.
71. Lo ScrudatoM, BlokeschM (2013) A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable. Nucleic Acids Res 41: 3644–3658.
72. BradfordMM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248–254.
73. PetersenTN, BrunakS, von HeijneG, NielsenH (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785–786.
74. WolfgangM, van PuttenJP, HayesSF, DorwardD, KoomeyM (2000) Components and dynamics of fiber formation define a ubiquitous biogenesis pathway for bacterial pili. EMBO J 19: 6408–6418.
75. KorotkovKV, GonenT, HolWG (2011) Secretins: dynamic channels for protein transport across membranes. Trends Biochem Sci 36: 433–443.
76. DraskovicI, DubnauD (2005) Biogenesis of a putative channel protein, ComEC, required for DNA uptake: membrane topology, oligomerization and formation of disulphide bonds. Mol Microbiol 55: 881–896.
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