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Comparative Genomic Analysis and BTEX Degradation Pathways of a Thermotolerant Cupriavidus cauae PHS1

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Volatile organic compounds such as benzene, toluene, ethylbenzene, and isomers of xylenes (BTEX) constitute a group of monoaromatic compounds that are found in petroleum and have been classified as priority pollutants. In this study, based on its newly sequenced genome, we reclassified the previously identified BTEX-degrading thermotolerant strain Ralstonia sp. PHS1 as Cupriavidus cauae PHS1. Also presented are the complete genome sequence of C. cauae PHS1, its annotation, species delineation, and a comparative analysis of the BTEX-degrading gene cluster. Moreover, we cloned and characterized the BTEX-degrading pathway genes in C. cauae PHS1, the BTEX-degrading gene cluster of which consists of two monooxygenases and meta-cleavage genes. A genome-wide investigation of the PHS1 coding sequence and the experimentally confirmed regioselectivity of the toluene monooxygenases and catechol 2,3-dioxygenase allowed us to reconstruct the BTEX degradation pathway. The degradation of BTEX begins with aromatic ring hydroxylation, followed by ring cleavage, and eventually enters the core carbon metabolism. The information provided here on the genome and BTEX-degrading pathway of the thermotolerant strain C. cauae PHS1 could be useful in constructing an efficient production host.

Abstract

Volatile organic compounds such as benzene, toluene, ethylbenzene, and isomers of xylenes (BTEX) constitute a group of monoaromatic compounds that are found in petroleum and have been classified as priority pollutants. In this study, based on its newly sequenced genome, we reclassified the previously identified BTEX-degrading thermotolerant strain Ralstonia sp. PHS1 as Cupriavidus cauae PHS1. Also presented are the complete genome sequence of C. cauae PHS1, its annotation, species delineation, and a comparative analysis of the BTEX-degrading gene cluster. Moreover, we cloned and characterized the BTEX-degrading pathway genes in C. cauae PHS1, the BTEX-degrading gene cluster of which consists of two monooxygenases and meta-cleavage genes. A genome-wide investigation of the PHS1 coding sequence and the experimentally confirmed regioselectivity of the toluene monooxygenases and catechol 2,3-dioxygenase allowed us to reconstruct the BTEX degradation pathway. The degradation of BTEX begins with aromatic ring hydroxylation, followed by ring cleavage, and eventually enters the core carbon metabolism. The information provided here on the genome and BTEX-degrading pathway of the thermotolerant strain C. cauae PHS1 could be useful in constructing an efficient production host.

참고문헌 (76)

  1. Adipah S, "Introduction of petroleum hydrocarbons contaminants and its human effects", J. Environ. Sci. Public Health, 3, pp.1~9 (2019)
  2. U.S. EPA, "Cleaning Up the Nation’s Waste Sites: Markets and Technology Trends, 2004 edition. 2004th Ed", Office of Solid Waste And Emergency Response, EPAU.S. EPA, 2004
  3. Scientific investigations report 2005-5104 Fate and Transport of petroleum hydrocarbons in soil and ground water at big south fork national river and recreation area, Tennessee and Kentucky, 2002-2003, "Williams S.", U.S. Geol. Surv, 29~, pp.U.S. Geol. Surv. Sci. Investig. Rep. 2005-5104 (2006)
  4. Somboon K, "Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion", Nat. Commun, 11, pp.6331~ (2020)
  5. You J, "BTEX degradation by a newly isolated bacterium: performance, kinetics, and mechanism", Int. Biodeterior. Biodegrad, 129, pp.202~208 (2018)
  6. Jiang B, "Biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and pxylenes by the newly isolated bacterium Comamonas sp. JB", Appl. Biochem. Biotechnol, 176, pp.1700~1708 (2015)
  7. Lee SH, "Complete genome sequence of the BTEX-degrading bacterium Pseudoxanthomonas spadix BD-a59", J. Bacteriol, 194, pp.544~ (2012)
  8. Lee SK, "Isolation and characterization of a thermotolerant bacterium Ralstonia sp. strain PHS1 that degrades benzene, toluene, ethylbenzene, and o-xylene", Appl. Microbiol. Biotechnol, 56, pp.270~275 (2001)
  9. Meyer-Cifuentes I, "Isolation and characterization of Magnetospirillum sp. strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model", PLoS One, 12, pp.e0174750~ (2017)
  10. Surendra SV, "Degradation of monoaromatics by Bacillus pumilus MVSV3", Braz. Arch. Biol. Technol, 60, pp.16160319~ (2017)
  11. Wongbunmak A, "BTEX- and naphthalene-degrading bacterium Microbacterium esteraromaticum strain SBS1-7 isolated from estuarine sediment", J. Hazard. Mater, 339, pp.82~90 (2017)
  12. Wongbunmak A, "BTEX biodegradation by Bacillus amyloliquefaciens subsp. plantarum W1 and its proposed BTEX biodegradation pathways", Sci. Rep, 10, pp.17408~ (2020)
  13. Yrjälä K, "Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4plasmid", FEMS Microbiol. Lett, 154, pp.403~408 (1997)
  14. Zhang S, "Current advances of VOCs degradation by bioelectrochemical systems:a review", Chem. Eng. J, 334, pp.2625~2637 (2018)
  15. Lee Y, "Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil", Sci. Rep, 9, pp.860~ (2019)
  16. El-Naas MH, "Aerobic biodegradation of BTEX: progresses and prospects", J. Environ. Chem. Eng, 2, pp.1104~1122 (2014)
  17. Lee K, "Toluene and ethylbenzene oxidation by purified naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4", Appl. Environ. Microbiol, 62, pp.3101~3106 (1996)
  18. Bühler B, "Characterization and application of xylene monooxygenase for multistep biocatalysis", Appl. Environ. Microbiol, 68, pp.560~568 (2002)
  19. Yu H, "The roles of intermediates in biodegradation of benzene, toluene, and p-xylene by Pseudomonas putida F1", Biodegradation, 12, pp.455~463 (2001)
  20. Bickerdike SR, "Evidence for metabolism of o-xylene by simultaneous ring and methyl group oxidation in a new soil isolate", Microbiology, 143, pp.2321~2329 (1997)
  21. 이성국, "Substrate Utilization Patterns During BTEX Biodegradation by an o-Xylene-Degrading Bacterium Ralstonia sp. PHS1", Journal of Microbiology and Biotechnology, 12(6), pp.909~915 (2002), 한국미생물·생명공학회
  22. Jeong E, "Removal of O-xylene using biofilter inoculated with Rhodococcus sp. BTO62", J. Hazard. Mater, 152, pp.140~147 (2008)
  23. Taki H, "Identification and characterization of o-xylene-degrading Rhodococcus spp. which were dominant species in the remediation of o-xylene-contaminated soils", Biodegradation, 18, pp.17~26 (2007)
  24. Bertoni G, "Cloning of the genes for and characterization of the early stages of toluene and oxylene catabolism in Pseudomonas stutzeri OX1", Appl. Environ. Microbiol, 62, pp.3704~3711 (1996)
  25. Boeckmann B, "The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003", Nucleic Acids Res, 31, pp.365~370 (2003)
  26. Buchfink B, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nat. Methods, 18, pp.366~368 (2021)
  27. Galperin MY, "COG database update: focus on microbial diversity, model organisms, and widespread pathogens", Nucleic Acids Res, 49, pp.D274~D281 (2021)
  28. Jeske L, "BRENDA in 2019: a European ELIXIR core data resource", Nucleic Acids Res, 47, pp.D542~D549 (2019)
  29. Kanehisa M, "KEGG as a reference resource for gene and protein annotation", Nucleic Acids Res, 44, pp.D457~D462 (2016)
  30. Bertelli C, "IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets", Nucleic Acids Res, 45, pp.W30~W35 (2017)
  31. Tamura K, "MEGA11: molecular evolutionary genetics analysis version 11", Mol. Biol. Evol, 38, pp.3022~3027 (2021)
  32. Kim Jihyeon, "UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis", The Journal of Microbiology, 59(6), pp.609~615 (2021), 한국미생물학회[DOI]
  33. Lee I, "OrthoANI: an improved algorithm and software for calculating average nucleotide identity", Int. J. Syst. Evol. Microbiol, 66, pp.1100~1103 (2016)
  34. Meier-Kolthoff JP, "Genome sequence-based species delimitation with confidence intervals and improved distance functions", BMC Bioinformatics, 14, pp.60~ (2013)
  35. Chun J, "Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes", Int. J. Syst. Evol. Microbiol, 68, pp.461~466 (2018)
  36. Wang X, "Genome sequence analysis of the naphthenic acid degrading and metal resistant bacterium Cupriavidus gilardii CR3", PLoS One, 10, pp.e0132881~ (2015)
  37. Ensley BD, "Expression of naphthalene oxidation genes in Escherichia coli results in the biosynthesis of indigo", Science, 222, pp.167~169 (1983)
  38. Arenghi FLG, "Organization and Regulation of meta cleavage pathway genes for toluene and o-xylene derivative degradation in Pseudomonas stutzeri OX1", Appl. Environ. Microbiol, 67, pp.3304~3308 (2001)
  39. Kaschabek SR, "Degradation of chloroaromatics: purification and characterization of a novel type of chlorocatechol 2,3-dioxygenase of Pseudomonas putida GJ31", J. Bacteriol, 180, pp.296~302 (1998)
  40. Choi EJ, "Comparative genomic analysis and benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) degradation pathways of Pseudoxanthomonas spadix BD-a59", Appl. Environ. Microbiol, 79, pp.663~671 (2013)
  41. Espinoza Tofalos A, "Toluene degradation by Cupriavidus metallidurans CH34 in nitrate-reducing conditions and in bioelectrochemical systems", FEMS Microbiol. Lett, 365, pp.fny119~ (2018)
  42. Kumar A, "Continuous operation of membrane bioreactor treating toluene vapors by Burkholderia vietnamiensis G4", Chem. Eng. J, 140, pp.193~200 (2008)
  43. Perez-Pantoja D, "Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134", FEMS Microbiol. Rev, 32, pp.736~794 (2008)
  44. Shingler V, "Nucleotide-sequence and functional-analysis of the complete phenol", 3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain-Cf600, 1992, pp.174, 711~724
  45. Tinberg CE, "Multiple roles of component proteins in bacterial multicomponent monooxygenases:phenol hydroxylase and toluene", o-xylene monooxygenase from Pseudomonas sp. OX1, 2011, pp.50, 1788~1798
  46. Hou YJ, "Structural and biochemical analysis reveals a distinct catalytic site of salicylate 5-monooxygenase NagGH from Rieske dioxygenases", Appl. Environ. Microbiol, 87, pp.e01629-20~ (2021)
  47. Karlsson A, "Crystal structure of naphthalene dioxygenase: sideon binding of dioxygen to iron", Science, 299, pp.1039~1042 (2003)
  48. Xu JR, "How significant is a protein structure similarity with TM-score=0.5?", Bioinformatics, 26, pp.889~895 (2010)
  49. Kim M, "Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes", Int. J. Syst. Evol. Microbiol, 64, pp.346~351 (2014)
  50. Moreno-Hagelsieb G, "Choosing BLAST options for better detection of orthologs as reciprocal best hits", Bioinformatics, 24, pp.319~324 (2008)
  51. Burbank LP, "Conjugative plasmid transfer in Xylella fastidiosa is dependent on tra and trb operon functions", J. Bacteriol, 199, pp.e00388-17~ (2017)
  52. Newman LM, "Purification and characterization of toluene 2-monooxygenase from Burkholderia cepacia G4", Biochemistry, 34, pp.14066~14076 (1995)
  53. Cafaro V, "Phenol hydroxylase and toluene", o-xylene monooxygenase from Pseudomonas stutzeri OX1: interplay between two enzymes, 2004, pp.70, 2211~2219
  54. Arai H, "Adaptation of Comamonas testosteroni TA441 to utilize phenol: organization and regulation of the genes involved in phenol degradation", Microbiology, 144, pp.2895~2903 (1998)
  55. Nordlund I, "Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600", J. Bacteriol, 172, pp.6826~6833 (1990)
  56. Shields MS, "TOM, a new aromatic degradative plasmid from Burkholderia (Pseudomonas) cepacia G4", Appl. Environ. Microbiol, 61, pp.1352~1356 (1995)
  57. Fox BG, "Stearoyl-acyl carrier protein delta 9 desaturase from Ricinus communis is a diironoxo protein", Proc. Natl. Acad. Sci. USA, 90, pp.2486~ (1993)
  58. Johnson GR, "Multiple pathways for toluene degradation in Burkholderia sp. strain JS150", Appl. Environ. Microbiol, 63, pp.4047~ (1997)
  59. Harayama S, "Divergent evolution of chloroplast-type ferredoxins", FEBS Lett, 285, pp.85~88 (1991)
  60. Laurie AD, "Conserved and hybrid meta-cleavage operons from PAH-degrading Burkholderia RP007", Biochem. Biophys. Res. Commun, 262, pp.308~314 (1999)
  61. Arai H, "Arrangement and regulation of the genes for meta-pathway enzymes required for degradation of phenol in Comamonas testosteroni TA441", Microbiology, 146(Pt 7), pp.1707~1715 (2000)
  62. Pérez-Pantoja D, "Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales", Environ. Microbiol, 14, pp.1091~1117 (2012)
  63. Romine MF, "Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199", J. Bacteriol, 181, pp.1585~ (1999)
  64. Erickson BD, "Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400", J. Bacteriol, 174, pp.2903~ (1992)
  65. Froland WA, "Methane monooxygenase component B and reductase alter the regioselectivity of the hydroxylase component-catalyzed reactions. A novel role for protein-protein interactions in an oxygenase mechanism", J. Biol. Chem, 267, pp.17588~17597 (1992)
  66. Mason JR, "The electron-transport proteins of hydroxylating bacterial dioxygenases", Annu. Rev. Microbiol, 46, pp.277~305 (1992)
  67. Kitayama A, "Gene organization and low regiospecificity in aromatic-ring hydroxylation of a benzene monooxygenase of Pseudomonas aeruginosa JI104", J. Ferment. Bioeng, 82, pp.421~425 (1996)
  68. Olsen RH, "A novel toluene-3-monooxygenase pathway cloned from Pseudomonas pickettii PKO1", J. Bacteriol, 176, pp.3749~3756 (1994)
  69. Mitchell KH, "Combined participation of hydroxylase active site residues and effector protein binding in a para to ortho modulation of toluene 4-monooxygenase regiospecificity", Biochemistry, 41, pp.3176~3188 (2002)
  70. Bertoni G, "Analysis of the gene cluster encoding toluene", o-xylene monooxygenase from Pseudomonas stutzeri OX1, 1998, pp.64, 3626~3632
  71. Jiang T, "Catalytic hydroxylation of benzene to phenol with hydrogen peroxide using catalysts based on molecular sieves", New J. Chem, 37, pp.1654~1664 (2013)
  72. Barbieri P, "Alternative pathways for o-xylene or m-xylene and p-xylene degradation in a Pseudomonas stutzeri strain", Biodegrad, 4, pp.71~80 (1993)
  73. Fowler SJ, "Identification of toluene degraders in a methanogenic enrichment culture", FEMS Microbiol. Ecol, 89, pp.625~636 (2014)
  74. Kahng HY, "Genetic and functional analysis of the tbc operons for catabolism of alkyl- and chloroaromatic compounds in Burkholderia sp. strain JS150", Appl. Environ. Microbiol, 67, pp.4805~4816 (2001)
  75. Siani L, "The role of residue Thr249 in modulating the catalytic efficiency and substrate specificity of catechol-2,3-dioxygenase from Pseudomonas stutzeri OX1", FEBS J, 273, pp.2963~2976 (2006)
  76. Krzywinski M, "Circos: an information aesthetic for comparative genomics", Genome Res, 19, pp.1639~1645 (2009)

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