Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Identification of a Second Type of AHL-Lactonase from Rhodococcus sp. BH4, belonging to the α/β Hydrolase Superfamily

  • Ryu, Du-Hwan (Department of Biomedicinal Science and Biotechnology, Paichai University) ;
  • Lee, Sang-Won (Department of Biomedicinal Science and Biotechnology, Paichai University) ;
  • Mikolaityte, Viktorija (Department of Biomedicinal Science and Biotechnology, Paichai University) ;
  • Kim, Yea-Won (Department of Biomedicinal Science and Biotechnology, Paichai University) ;
  • Jeong, Haeyoung (Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Lee, Sang Jun (Department of Systems Biotechnology, Chung-Ang University) ;
  • Lee, Chung-Hak (School of Chemical and Biological Engineering, Seoul National University) ;
  • Lee, Jung-Kee (Department of Biomedicinal Science and Biotechnology, Paichai University)
  • Received : 2020.01.03
  • Accepted : 2020.03.06
  • Published : 2020.06.28
Download PDF
⟨ Previous Next ⟩

Abstract

N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) plays a major role in development of biofilms, which contribute to rise in infections and biofouling in water-related industries. Interference in QS, called quorum quenching (QQ), has recieved a lot of attention in recent years. Rhodococcus spp. are known to have prominent quorum quenching activity and in previous reports it was suggested that this genus possesses multiple QQ enzymes, but only one gene, qsdA, which encodes an AHL-lactonase belonging to phosphotriesterase family, has been identified. Therefore, we conducted a whole genome sequencing and analysis of Rhodococcus sp. BH4 isolated from a wastewater treatment plant. The sequencing revealed another gene encoding a QQ enzyme (named jydB) that exhibited a high AHL degrading activity. This QQ enzyme had a 46% amino acid sequence similarity with the AHL-lactonase (AidH) of Ochrobactrum sp. T63. HPLC analysis and AHL restoration experiments by acidification revealed that the jydB gene encodes an AHL-lactonase which shares the known characteristics of the α/β hydrolase family. Purified recombinant JydB demonstrated a high hydrolytic activity against various AHLs. Kinetic analysis of JydB revealed a high catalytic efficiency (kcat/KM) against C4-HSL and 3-oxo-C6 HSL, ranging from 1.88 x 106 to 1.45 x 106 M-1 s-1, with distinctly low KM values (0.16-0.24 mM). This study affirms that the AHL degrading activity and biofilm inhibition ability of Rhodococcus sp. BH4 may be due to the presence of multiple quorum quenching enzymes, including two types of AHL-lactonases, in addition to AHL-acylase and oxidoreductase, for which the genes have yet to be described.

Keywords

References

  1. Miller M, Bassler B. 2001. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55: 165-199. https://doi.org/10.1146/annurev.micro.55.1.165
  2. Whitehead N, Barnard A, Slater H, Simpson N, Salmond G. 2001. Quorum-sensing in Gram-negative bacteria. FEMS Microbiol. Rev. 25: 365-404. https://doi.org/10.1111/j.1574-6976.2001.tb00583.x
  3. Davies D. 1998. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 280: 295-298. https://doi.org/10.1126/science.280.5361.295
  4. Dickschat J. 2010. Quorum sensing and bacterial biofilms. Nat. Prod. Rep. 27: 343. https://doi.org/10.1039/b804469b
  5. Grandclement C, Tannieres M, Morera S, Dessaux Y, Faure D. 2015. Quorum quenching: role in nature and applied developments. FEMS Microbiol. Rev. 40: 86-116. https://doi.org/10.1093/femsre/fuv038
  6. Yeon K, Cheong W, Oh H, Lee W, Hwang B, Lee C, et al. 2009. Quorum sensing: a new biofouling control paradigm in a membrane bioreactor for advanced wastewater treatment. Environ. Sci. Technol. 43: 380-385. https://doi.org/10.1021/es8019275
  7. Dong Y, Wang L, Xu J, Zhang H, Zhang X, Zhang L. 2001. Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature 411: 813-817. https://doi.org/10.1038/35081101
  8. Lee S, Park S, Lee, J, Yum D, Koo B, Lee J. 2002. Genes encoding the N-acyl homoserine lactone-degrading enzyme are widespread in many subspecies of Bacillus thuringiensis. Appl. Environ. Microbiol. 68: 3919-3924. https://doi.org/10.1128/AEM.68.8.3919-3924.2002
  9. Uroz S, Chhabra S, Camara M, Williams P, Oger P, Dessaux Y. 2005. N-Acylhomoserine lactone quorum-sensing molecules are modified and degraded by Rhodococcus erythropolis W2 by both amidolytic and novel oxidoreductase activities. Microbiology 151: 3313-3322. https://doi.org/10.1099/mic.0.27961-0
  10. Wang L, Dong Y, Zhang L. 2007. Quorum quenching: impact and mechanisms. Philos. Trans. R. Soc. 362: 1201-1211. https://doi.org/10.1098/rstb.2007.2045
  11. Lin Y, Xu J, Hu J, Wang L, Ong S, Leadbetter J, et al. 2003. Acyl-homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum-quenching enzymes. Mol. Microbiol. 47: 849-860. https://doi.org/10.1046/j.1365-2958.2003.03351.x
  12. Huang J, Petersen A, Whiteley M, Leadbetter J. 2006. Identification of QuiP, the product of gene PA1032, as the second acylhomoserine lactone acylase of Pseudomonas aeruginosa PAO1. Appl. Environ. Microbiol. 72: 1190-1197. https://doi.org/10.1128/AEM.72.2.1190-1197.2006
  13. Chowdhary P, Keshavan N, Nguyen H, Peterson J, Gonzalez J, Haines D. 2007. Bacillus megaterium CYP102A1 oxidation of acyl homoserine lactones and acyl homoserines. Biochemistry 46: 14429-14437. https://doi.org/10.1021/bi701945j
  14. Bijtenhoorn P, Schipper C, Hornung C, Quitschau M, Grond S, Weiland N, et al. 2011. BpiB05, a novel metagenome-derived hydrolase acting on N-acylhomoserine lactones. J. Biotechnol. 155: 86-94. https://doi.org/10.1016/j.jbiotec.2010.12.016
  15. Kalia V. 2013. Quorum sensing inhibitors: an overview. Biotechnol. Adv. 31: 224-245. https://doi.org/10.1016/j.biotechadv.2012.10.004
  16. Fetzner S. 2015. Quorum quenching enzymes. J. Biotechnol. 201: 2-14. https://doi.org/10.1016/j.jbiotec.2014.09.001
  17. Bzdrenga J, Daude D, Remy B, Jacquet P, Plener L, Elias M, et al. 2017. Biotechnological applications of quorum quenching enzymes. Chem. Biol. Interact. 267: 104-115. https://doi.org/10.1016/j.cbi.2016.05.028
  18. Dong Y, Xu J, Li X, Zhang L. 2000. AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc. Natl. Acad. Sci. USA 97: 3526-3531. https://doi.org/10.1073/pnas.97.7.3526
  19. Kim M, Choi W, Kang H, Lee J, Kang B, Kim K, et al. 2005. The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase. Proc. Natl. Acad. Sci. 102: 17606-17611 https://doi.org/10.1073/pnas.0504996102
  20. Uroz S, Oger P, Chapelle E, Adeline M, Faure D, Dessaux Y. 2008. A Rhodococcus qsdA-encoded enzyme defines a novel class of largespectrum quorum-quenching lactonases. Appl. Environ. Microbiol. 74: 1357-1366. https://doi.org/10.1128/AEM.02014-07
  21. Xue B, Chow J, Baldansuren A, Yap L, Gan Y, Dikanov S, et al. 2013. Structural evidence of a productive active site architecture for an evolved quorum-quenching GKL lactonase. Biochemistry 52: 2359-2370. https://doi.org/10.1021/bi4000904
  22. Mei G, Yan X, Turak A, Luo Z, Zhang L. 2010. AidH, an alpha/beta-hydrolase fold family member from an Ochrobactrum sp. strain, is a novel N-acylhomoserine lactonase. Appl. Environ. Microbiol. 76: 4933-4942. https://doi.org/10.1128/AEM.00477-10
  23. Wang W, Morohoshi T, Someya N, Ikeda T. 2012. Diversity and distribution of N-acylhomoserine lactone (AHL)-degrading activity and AHL-lactonase (AiiM) in genus Microbacterium. Microbes. Environ. 27: 330-333. https://doi.org/10.1264/jsme2.ME11341
  24. Kim D, Choi K, Yoo M, Zylstra G, Kim E. 2018. Biotechnological potential of Rhodococcus biodegradative pathways. J. Microbiol. Biotechnol. 28: 1037-1051. https://doi.org/10.4014/jmb.1712.12017
  25. de Carvalho C, da Fonseca M. 2005. The remarkable Rhodococcus erythropolis. Appl. Microbiol. Biotechnol. 67: 715-726. https://doi.org/10.1007/s00253-005-1932-3
  26. van der Geize R, Dijkhuizen L. 2004. Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr. Opin. In. Microbiol. 7: 255-261. https://doi.org/10.1016/j.mib.2004.04.001
  27. Oh H, Yeon K, Yang C, Kim S, Lee C, Park S, et al. 2012. Control of membrane biofouling in MBR for wastewater treatment by quorum quenching bacteria encapsulated in microporous membrane. Environ. Sci. Technol. 46: 4877-4884. https://doi.org/10.1021/es204312u
  28. Barbey C, Chane A, Burini J, Maillot O, Merieau A, Gallique M, et al. 2018. A rhodococcal transcriptional regulatory mechanism detects the common lactone ring of AHL quorum-sensing signals and triggers the quorum-quenching response. Front. Microbiol. 9: 2800. https://doi.org/10.3389/fmicb.2018.02800
  29. Park S, Hwang B, Shin M, Kim J, Kim H, Lee J. 2006. N-acylhomoserine lactonase producing Rhodococcus spp. with different AHLdegrading activities. FEMS Microbiol. Lett. 261: 102-108. https://doi.org/10.1111/j.1574-6968.2006.00336.x
  30. Latifi A, Winson M, Foglino M, Bycroft B, Stewart G, Lazdunski A, et al. 1995. Multiple homologues of LuxR and LuxI control expression of virulence determinants and secondary metabolites through quorum sensing in Pseudomonas aeruginosa PAO1. Mol. Microbiol. 17: 333-343. https://doi.org/10.1111/j.1365-2958.1995.mmi_17020333.x
  31. Cook D, Li P, Ruchaud F, Padden S, Farrand S. 1997. Ti plasmid conjugation is independent of vir: reconstitution of the tra functions from pTiC58 as a binary system. J. Bacteriol. 179: 1291-1297. https://doi.org/10.1128/JB.179.4.1291-1297.1997
  32. Zhu J, Winans S. 1998. Activity of the quorum-sensing regulator TraR of Agrobacterium tumefaciens is inhibited by a truncated, dominant defective TraR-like protein. Mol. Microbiol. 27: 289-297. https://doi.org/10.1046/j.1365-2958.1998.00672.x
  33. Tang K, Zhang Y, Yu M, Shi X, Coenye T, Bossier P, et al. 2013. Evaluation of a new high-throughput method for identifying quorum quenching bacteria. Sci. Rep. 3: 2935. https://doi.org/10.1038/srep02935
  34. Kim A, Park S, Lee C, Lee C, Lee J. 2014. Quorum quenching bacteria isolated from the sludge of a wastewater treatment plant and their application for controlling biofilm formation. J. Microbiol. Biotechnol. 24: 1574-1582. https://doi.org/10.4014/jmb.1407.07009
  35. Zhu B, Cai G, Hall EO, Freeman GJ. 2007. In-fusion assembly: seamless engineering of multidomain fusion proteins, modular vectors, and mutations. Biotechniques 43: 354-359. https://doi.org/10.2144/000112536
  36. McClean K, Winson M, Fish L, Taylor A, Chhabra S, Camara M, et al. 1997. Quorum sensing and Chromobacterium violaceum: exploitation of violacein production and inhibition for the detection of N-acylhomoserine lactones. Microbiology 143: 3703-3711. https://doi.org/10.1099/00221287-143-12-3703
  37. Shastry RP, Dolan SK, Abdelhamid Y, Vittal RR, Welch M. 2018. Purification and characterisation of a quorum quenching AHLlactonase from the endophytic bacterium Enterobacter sp. CS66. FEMS Microbiol. Lett. 365: fny054.
  38. Last D, Kruger G, Dorr M, Bornscheuer U. 2016. Fast, continuous, and high-throughput (bio)chemical activity assay for N-acyl-lhomoserine lactone quorum-quenching enzymes. Appl. Environ. Microbiol. 82: 4145-4154. https://doi.org/10.1128/AEM.00830-16
  39. Yates E, Philipp B, Buckley C, Atkinson S, Chhabra S, Sockett R, et al. 2002. N-acylhomoserine lactones undergo lactonolysis in a pH-, temperature-, and acyl chain length-dependent manner during growth of Yersinia pseudotuberculosis and Pseudomonas aeruginosa. Infect. Immun. 70: 5635-5646. https://doi.org/10.1128/IAI.70.10.5635-5646.2002
  40. O'Toole G, Kolter R. 1998. Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signaling pathways: a genetic analysis. Mol. Microbiol. 28: 449-461. https://doi.org/10.1046/j.1365-2958.1998.00797.x
  41. Fan X, Liang M, Wang L, Chen R, Li H, Liu X. 2017. Aii810, a novel cold-adapted N-acylhomoserine lactonase discovered in a metagenome, can strongly attenuate Pseudomonas aeruginosa virulence factors and biofilm formation. Front. Microbiol. 8: 1950. https://doi.org/10.3389/fmicb.2017.01950
  42. Holmquist M. 2000. Alpha beta-hydrolase fold enzymes structures, functions and mechanisms. Curr. Protein Pept. Sci. 1: 209-235. https://doi.org/10.2174/1389203003381405
  43. Gao A, Mei G, Liu S, Wang P, Tang Q, Liu Y, et al. 2012. High-resolution structures of AidH complexes provide insights into a novel catalytic mechanism forN-acyl homoserine lactonase. Acta. Crystallogr. Sect. D-Biol. Crystallogr. 69: 82-91. https://doi.org/10.1107/S0907444912042369
  44. Czajkowski R, Krzyzanowska D, Karczewska J, Atkinson S, Przysowa J, Lojkowska E, et al. 2011. Inactivation of AHLs by Ochrobactrum sp. A44 depends on the activity of a novel class of AHL acylase. Environ. Microbiol. Rep. 3: 59-68. https://doi.org/10.1111/j.1758-2229.2010.00188.x
  45. Mayer C, Muras A, Romero M, Lopez M, Tomas M, Otero A. 2018. Multiple quorum quenching enzymes are active in the nosocomial pathogen Acinetobacter baumannii ATCC17978. Front. Cell. Infect. Microbiol. 8: 310. https://doi.org/10.3389/fcimb.2018.00310
  46. Bokhove M, Jimenez P, Quax W, Dijkstra B. 2009. The quorum-quenching N-acyl homoserine lactone acylase PvdQ is an Ntnhydrolase with an unusual substrate-binding pocket. Proc. Natl. Acad. Sci. USA 107: 686-691. https://doi.org/10.1073/pnas.0911839107
  47. Schipper C, Hornung C, Bijtenhoorn P, Quitschau M, Grond S, Streit W. 2008. Metagenome-derived clones encoding two novel lactonase family proteins involved in biofilm inhibition in Pseudomonas aeruginosa. Appl. Environ. Microbiol. 75: 224-233. https://doi.org/10.1128/AEM.01389-08
  48. Fan X, Liu X, Liu Y. 2012. The cloning and characterization of one novel metagenome-derived thermostable esterase acting on Nacylhomoserine lactones. J. Mol. Catal. B-Enzym. 83:29-37. https://doi.org/10.1016/j.molcatb.2012.07.006
  49. Afriat L, Roodveldt C, Manco G, Tawfik D. 2006. The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase. Biochemistry 45: 13677-13686. https://doi.org/10.1021/bi061268r

Cited by

  1. Biocontrol of Biofilm Formation: Jamming of Sessile-Associated Rhizobial Communication by Rhodococcal Quorum-Quenching vol.22, pp.15, 2021, https://doi.org/10.3390/ijms22158241