The CD27L and CTP1L Endolysins Targeting Contain a Built-in Trigger and Release Factor

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Clostridium difficile infection is a common cause of hospital-acquired diarrhea, following broad-spectrum antibiotic treatment particularly in elderly patients. Bacteriophage therapy could provide an alternative treatment, but a better understanding of the viral components that lyse the bacterial cell is necessary. Here, we report on the activation of two endolysins from bacteriophages that lyse Clostridia. The structures of autoproteolytic fragments of two endolysins were determined by X-ray crystallography. Based on the structures, we introduced mutations that affect the autolytic cleavage of the enzymatic portion of the endolysins, and we show that two oligomeric states have an effect on the cleavage mechanism. Moreover, the lysis activity is affected when autocleavage is inhibited for one endolysin. We propose that the cleavage and oligomerization are linked, and they provide the endolysin with a trigger and release mechanism that leads to activation. The identification of a trigger and release factor may not only be relevant to Clostridia endolysins, but could be an important factor in the triggering of many bacteriophage endolysins. A fuller understanding of this activation mechanism will help in the design of recombinant endolysins or bacteriophages with a more efficient therapeutic potential.

Vyšlo v časopise: The CD27L and CTP1L Endolysins Targeting Contain a Built-in Trigger and Release Factor. PLoS Pathog 10(7): e32767. doi:10.1371/journal.ppat.1004228
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004228

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Zdroje

1. HenryM, DebarbieuxL (2012) Tools from viruses: bacteriophage successes and beyond. Virology 434: 151–161 doi:10.1016/j.virol.2012.09.017

2. ReaMC, AlemayehuD, RossRP, HillC (2013) Gut solutions to a gut problem: bacteriocins, probiotics and bacteriophage for control of Clostridium difficile infection. J Med Microbiol 62: 1369–1378 doi:10.1099/jmm.0.058933-0

3. MeaderE, MayerMJ, SteverdingD, CardingSR, NarbadA (2013) Evaluation of bacteriophage therapy to control Clostridium difficile and toxin production in an in vitro human colon model system. Anaerobe 22: 25–30 doi:10.1016/j.anaerobe.2013.05.001

4. VenugopalAA, JohnsonS (2012) Current state of Clostridium difficile treatment options. Clin Infect Dis Off Publ Infect Dis Soc Am 55 Suppl 2S71–76 doi:10.1093/cid/cis355

5. MayerMJ, NarbadA, GassonMJ (2008) Molecular characterization of a Clostridium difficile bacteriophage and its cloned biologically active endolysin. J Bacteriol 190: 6734–6740 doi:10.1128/JB.00686-08

6. LoessnerMJ (2005) Bacteriophage endolysins—current state of research and applications. Curr Opin Microbiol 8: 480–487 doi:10.1016/j.mib.2005.06.002

7. MayerMJ, GarefalakiV, SpoerlR, NarbadA, MeijersR (2011) Structure-based modification of a Clostridium difficile-targeting endolysin affects activity and host range. J Bacteriol 193: 5477–5486 doi:10.1128/JB.00439-11

8. HermosoJA, GarcíaJL, GarcíaP (2007) Taking aim on bacterial pathogens: from phage therapy to enzybiotics. Curr Opin Microbiol 10: 461–472 doi:10.1016/j.mib.2007.08.002

9. WhiteR, ChibaS, PangT, DeweyJS, SavvaCG, et al. (2011) Holin triggering in real time. Proc Natl Acad Sci U S A 108: 798–803 doi:10.1073/pnas.1011921108

10. DeweyJS, SavvaCG, WhiteRL, VithaS, HolzenburgA, et al. (2010) Micron-scale holes terminate the phage infection cycle. Proc Natl Acad Sci U S A 107: 2219–2223 doi:10.1073/pnas.0914030107

11. HermosoJA, MonterrosoB, AlbertA, GalánB, AhrazemO, et al. (2003) Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1. Struct Lond Engl 1993 11: 1239–1249.

12. PorterCJ, SchuchR, PelzekAJ, BuckleAM, McGowanS, et al. (2007) The 1.6 A crystal structure of the catalytic domain of PlyB, a bacteriophage lysin active against Bacillus anthracis. J Mol Biol 366: 540–550 doi:10.1016/j.jmb.2006.11.056

13. LowLY, YangC, PeregoM, OstermanA, LiddingtonRC (2005) Structure and lytic activity of a Bacillus anthracis prophage endolysin. J Biol Chem 280: 35433–35439 doi:10.1074/jbc.M502723200

14. MayerMJ, PayneJ, GassonMJ, NarbadA (2010) Genomic sequence and characterization of the virulent bacteriophage phiCTP1 from Clostridium tyrobutyricum and heterologous expression of its endolysin. Appl Environ Microbiol 76: 5415–5422 doi:10.1128/AEM.00989-10

15. XuM, ArulanduA, StruckDK, SwansonS, SacchettiniJC, et al. (2005) Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme. Science 307: 113–117 doi:10.1126/science.1105143

16. McGowanS, BuckleAM, MitchellMS, HoopesJT, GallagherDT, et al. (2012) X-ray crystal structure of the streptococcal specific phage lysin PlyC. Proc Natl Acad Sci 109: 12752–7 doi:10.1073/pnas.1208424109 Available: http://www.pnas.org/content/early/2012/07/17/1208424109 Accessed 24 January 2013..

17. HolmL, SanderC (1999) Protein folds and families: sequence and structure alignments. Nucleic Acids Res 27: 244–247.

18. KorndörferIP, DanzerJ, SchmelcherM, ZimmerM, SkerraA, et al. (2006) The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls. J Mol Biol 364: 678–689 doi:10.1016/j.jmb.2006.08.069

19. Pérez-DoradoI, CampilloNE, MonterrosoB, HesekD, LeeM, et al. (2007) Elucidation of the molecular recognition of bacterial cell wall by modular pneumococcal phage endolysin CPL-1. J Biol Chem 282: 24990–24999 doi:10.1074/jbc.M704317200

20. EmsleyP, LohkampB, ScottWG, CowtanK (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486–501 doi:10.1107/S0907444910007493

21. KrissinelE (2011) Macromolecular complexes in crystals and solutions. Acta Crystallogr D Biol Crystallogr 67: 376–385 doi:10.1107/S0907444911007232

22. KabschW (1978) A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr Sect A 34: 827–828 doi:10.1107/S0567739478001680

23. SvergunD, BarberatoC, KochMHJ (1995) CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates. J Appl Crystallogr 28: 768–773 doi:10.1107/S0021889895007047

24. PetoukhovMV, FrankeD, ShkumatovAV, TriaG, KikhneyAG, et al. (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 45: 342–350 doi:10.1107/S0021889812007662

25. HinoN, OkazakiY, KobayashiT, HayashiA, SakamotoK, et al. (2005) Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nat Methods 2: 201–206 doi:10.1038/nmeth739

26. Fernández-TorneroC, GarcíaE, LópezR, Giménez-GallegoG, RomeroA (2002) Two new crystal forms of the choline-binding domain of the major pneumococcal autolysin: insights into the dynamics of the active homodimer. J Mol Biol 321: 163–173.

27. ReschG, MoreillonP, FischettiVA (2011) A stable phage lysin (Cpl-1) dimer with increased antipneumococcal activity and decreased plasma clearance. Int J Antimicrob Agents 38: 516–521 doi:10.1016/j.ijantimicag.2011.08.009

28. ChangeuxJ-P (2011) Allostery and the Monod-Wyman-Changeux Model After 50 Years. Annu Rev Biophys 41: 103–33 doi:10.1146/annurev-biophys-050511-102222 Available: http://www.ncbi.nlm.nih.gov/pubmed/22224598 Accessed 3 April 2012..

29. LowLY, YangC, Perego M OstermanA, LiddingtonR (2011) Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins. J Biol Chem 286: 34391–34403 doi:10.1074/jbc.M111.244160

30. XiangY, LeimanPG, LiL, GrimesS, AndersonDL, et al. (2009) Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Mol Cell 34: 375–386 doi:10.1016/j.molcel.2009.04.009

31. EgererM, GiesemannT, JankT, SatchellKJF, AktoriesK (2007) Auto-catalytic cleavage of Clostridium difficile toxins A and B depends on cysteine protease activity. J Biol Chem 282: 25314–25321 doi:10.1074/jbc.M703062200

32. ReinekeJ, TenzerS, RupnikM, KoschinskiA, HasselmayerO, et al. (2007) Autocatalytic cleavage of Clostridium difficile toxin B. Nature 446: 415–419 doi:10.1038/nature05622

33. MayerMJ, GassonMJ, NarbadA (2012) Genomic sequence of bacteriophage ATCC 8074-B1 and activity of its endolysin and engineered variants against Clostridium sporogenes. Appl Environ Microbiol 78: 3685–3692 doi:10.1128/AEM.07884-11

34. BullerAR, FreemanMF, WrightNT, SchildbachJF, TownsendCA (2012) Insights into cis-autoproteolysis reveal a reactive state formed through conformational rearrangement. Proc Natl Acad Sci U S A 109: 2308–2313 doi:10.1073/pnas.1113633109

35. PaulusH (2000) Protein splicing and related forms of protein autoprocessing. Annu Rev Biochem 69: 447–496 doi:10.1146/annurev.biochem.69.1.447

36. OtwinowskiZ, BorekD, MajewskiW, MinorW (2003) Multiparametric scaling of diffraction intensities. Acta Crystallogr A 59: 228–234.

37. SchneiderTR, SheldrickGM (2002) Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr 58: 1772–1779.

38. CowtanK (2012) Completion of autobuilt protein models using a database of protein fragments. Acta Crystallogr D Biol Crystallogr 68: 328–335 doi:10.1107/S0907444911039655

39. McCoyAJ, Grosse-KunstleveRW, AdamsPD, WinnMD, StoroniLC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658–674 doi:10.1107/S0021889807021206

40. VaginA, TeplyakovA (2010) Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 66: 22–25 doi:10.1107/S0907444909042589

41. MurshudovGN, SkubákP, LebedevAA, PannuNS, SteinerRA, et al. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67: 355–367 doi:10.1107/S0907444911001314

42. ChenVB, ArendallWB3rd, HeaddJJ, KeedyDA, ImmorminoRM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12–21 doi:10.1107/S0907444909042073

43. KonarevPV, VolkovVV, SokolovaAV, KochMHJ, SvergunDI (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J Appl Crystallogr 36: 1277–1282 doi:10.1107/S0021889803012779

44. Guinier A (n.d.) La diffraction des rayons X aux tres petits angles: applications a l'etude de phenomenes ultramicroscopiques. Available: http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/15232. Accessed 19 August 2013.

45. SemenyukAV, SvergunDI (1991) GNOM – a program package for small-angle scattering data processing. J Appl Crystallogr 24: 537–540 doi:10.1107/S002188989100081X

46. FrankeD, SvergunDI (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J Appl Crystallogr 42: 342–346 doi:10.1107/S0021889809000338

47. VolkovVV, SvergunDI (2003) Uniqueness of ab initio shape determination in small-angle scattering. J Appl Crystallogr 36: 860–864 doi:10.1107/S0021889803000268

48. FarrellIS, ToroneyR, HazenJL, MehlRA, ChinJW (2005) Photo-cross-linking interacting proteins with a genetically encoded benzophenone. Nat Methods 2: 377–384 doi:10.1038/nmeth0505-377

49. GouetP, RobertX, CourcelleE (2003) ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31: 3320–3323 doi:10.1093/nar/gkg556