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A novel Bacillus ligniniphilus catechol 2,3-dioxygenase shows unique substrate preference and metal requirement

  • 1.

    Lee, S., Kang, M., Bae, J.-H., Sohn, J.-H. & Sung, B. H. Bacterial valorization of lignin: strains, enzymes, conversion pathways, biosensors, and perspectives. Front. Bioeng. Biotechnol. https://doi.org/10.3389/fbioe.2019.00209 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 2.

    Kamimura, N., Sakamoto, S., Mitsuda, N., Masai, E. & Kajita, S. Advances in microbial lignin degradation and its applications. Curr. Opin. Biotechnol. 56, 179–186. https://doi.org/10.1016/j.copbio.2018.11.011 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 3.

    Ponnusamy, V. K. et al. A review on lignin structure, pretreatments, fermentation reactions and biorefinery potential. Biores. Technol. 271, 462–472. https://doi.org/10.1016/j.biortech.2018.09.070 (2019).

    CAS 
    Article 

    Google Scholar 

  • 4.

    Wei, Z. et al. Characterization of thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase enzymes from Rhodococcus jostii RHA1 and Pseudomonas fluorescens Pf-5 involved in degradation of Aryl C2 lignin degradation fragments. Biochemistry 58, 5281–5293. https://doi.org/10.1021/acs.biochem.9b00177 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 5.

    Saito, Y. et al. Screening of fungi for decomposition of lignin-derived products from Japanese cedar. J. Biosci. Bioeng. 126, 573–579. https://doi.org/10.1016/j.jbiosc.2018.05.001 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 6.

    Wang, Y., Shao, Y., Zou, X., Yang, M. & Guo, L. Synergistic action between extracellular products from white-rot fungus and cellulase significantly improves enzymatic hydrolysis. Bioengineered 9, 178–185. https://doi.org/10.1080/21655979.2017.1308991 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 7.

    Voběrková, S., Solčány, V., Vršanská, M. & Adam, V. Immobilization of ligninolytic enzymes from white-rot fungi in cross-linked aggregates. Chemosphere 202, 694–707. https://doi.org/10.1016/j.chemosphere.2018.03.088 (2018).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 8.

    Jha, H. In Mycodegradation of Lignocelluloses (ed. Naraian, R.) 35–49 (Springer International Publishing, 2019).

    Chapter 

    Google Scholar 

  • 9.

    Bouacem, K. et al. Purification and characterization of two novel peroxidases from the dye-decolorizing fungus Bjerkandera adusta strain CX-9. Int. J. Biol. Macromol. 106, 636–646. https://doi.org/10.1016/j.ijbiomac.2017.08.061 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 10.

    Xu, R. et al. Lignin depolymerization and utilization by bacteria. Biores. Technol. 269, 557–566. https://doi.org/10.1016/j.biortech.2018.08.118 (2018).

    CAS 
    Article 

    Google Scholar 

  • 11.

    Tian, J.-H., Pourcher, A.-M., Bouchez, T., Gelhaye, E. & Peu, P. Occurrence of lignin degradation genotypes and phenotypes among prokaryotes. Appl. Microbiol. Biotechnol. 98, 9527–9544. https://doi.org/10.1007/s00253-014-6142-4 (2014).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 12.

    Barton, N. et al. Enabling the valorization of guaiacol-based lignin: Integrated chemical and biochemical production of cis, cis-muconic acid using metabolically engineered Amycolatopsis sp ATCC 39116. Metab. Eng. 45, 200–210. https://doi.org/10.1016/j.ymben.2017.12.001 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 13.

    Chatterjee, A., DeLorenzo, D. M., Carr, R. & Moon, T. S. Bioconversion of renewable feedstocks by Rhodococcus opacus. Curr. Opin. Biotechnol. 64, 10–16. https://doi.org/10.1016/j.copbio.2019.08.013 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 14.

    Roell, G. W. et al. A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630. Metab. Eng. 55, 120–130. https://doi.org/10.1016/j.ymben.2019.06.013 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 15.

    Bhatia, S. K. et al. Bioconversion of barley straw lignin into biodiesel using Rhodococcus sp. YHY01. Bioresource Technol. 289, 121704. https://doi.org/10.1016/j.biortech.2019.121704 (2019).

    CAS 
    Article 

    Google Scholar 

  • 16.

    Xu, Z., Qin, L., Cai, M., Hua, W. & Jin, M. Biodegradation of kraft lignin by newly isolated Klebsiella pneumoniae, Pseudomonas putida, and Ochrobactrum tritici strains. Environ. Sci. Pollut. Res. 25, 14171–14181. https://doi.org/10.1007/s11356-018-1633-y (2018).

    CAS 
    Article 

    Google Scholar 

  • 17.

    Ravi, K., García-Hidalgo, J., Gorwa-Grauslund, M. F. & Lidén, G. Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost. Appl. Microbiol. Biotechnol. 101, 5059–5070. https://doi.org/10.1007/s00253-017-8211-y (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 18.

    Ravi, K., García-Hidalgo, J., Nöbel, M., Gorwa-Grauslund, M. F. & Lidén, G. Biological conversion of aromatic monolignol compounds by a Pseudomonas isolate from sediments of the Baltic Sea. AMB Express 8, 32. https://doi.org/10.1186/s13568-018-0563-x (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 19.

    Li, Y.-Y., Liu, H., Xu, Y. & Zhou, N.-Y. A two-component monooxygenase initiates a novel 2-bromo-4-nitrophenol catabolic pathway in newly isolated Cupriavidus sp. strain NyZ375. Int. Biodeter. Biodegrad. 140, 99–105. https://doi.org/10.1016/j.ibiod.2019.03.013 (2019).

    CAS 
    Article 

    Google Scholar 

  • 20.

    Li, C. et al. Siderophore-mediated iron acquisition enhances resistance to oxidative and aromatic compound stress in cupriavidus necator JMP134. Appl. Environ. Microbiol. 85, e01938-e11918. https://doi.org/10.1128/aem.01938-18 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 21.

    Ihssen, J. et al. Engineered Bacillus pumilus laccase-like multi-copper oxidase for enhanced oxidation of the lignin model compound guaiacol. Protein Eng. Des. Sel. 30, 449–453. https://doi.org/10.1093/protein/gzx026 (2017).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 22.

    Huang, X.-F. et al. Isolation and characterization of lignin-degrading bacteria from rainforest soils. Biotechnol. Bioeng. 110, 1616–1626. https://doi.org/10.1002/bit.24833 (2013).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 23.

    Narnoliya, L. K., Agarwal, N., Patel, S. N. & Singh, S. P. Kinetic characterization of laccase from Bacillus atrophaeus, and its potential in juice clarification in free and immobilized forms. J. Microbiol. 57, 900–909. https://doi.org/10.1007/s12275-019-9170-z (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 24.

    Li, L., Long, L. & Ding, S. Bioproduction of high-concentration 4-vinylguaiacol using whole-cell catalysis harboring an organic solvent-tolerant phenolic acid decarboxylase from Bacillus atrophaeus. Front. Microbiol. https://doi.org/10.3389/fmicb.2019.01798 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 25.

    Zhu, D. et al. Biodegradation of alkaline lignin by Bacillus ligniniphilus L1. Biotechnol. Biofuels 10, 44. https://doi.org/10.1186/s13068-017-0735-y (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 26.

    Patel, S. & Gupta, R. S. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.. Int. J. Syst. Evolut. Microbiol. 70, 406–438. https://doi.org/10.1099/ijsem.0.003775 (2020).

    CAS 
    Article 

    Google Scholar 

  • 27.

    Hayaishi, O., Nozaki, M. & Abbott, M. T. In The Enzymes Vol. 12 (ed. Boyer, P. D.) 119–189 (Academic Press, 1975).

    Google Scholar 

  • 28.

    Kojima, Y., Itada, N. & Hayaishi, O. Metapyrocatechase: a new catechol-cleaving enzyme. J. Biol. Chem. 236, 2223–2228 (1961).

    CAS 
    Article 

    Google Scholar 

  • 29.

    Li, C. et al. Recent advancement in lignin biorefinery: With special focus on enzymatic degradation and valorization. Biores. Technol. 291, 121898. https://doi.org/10.1016/j.biortech.2019.121898 (2019).

    CAS 
    Article 

    Google Scholar 

  • 30.

    Bugg, T. D. & Lin, G. Solving the riddle of the intradiol and extradiol catechol dioxygenases: How do enzymes control hydroperoxide rearrangements?. Chem. Commun. 37, 941–952 (2001).

    Article 

    Google Scholar 

  • 31.

    Guengerich, F. P. & Yoshimoto, F. K. Formation and cleavage of C-C bonds by enzymatic oxidation-reduction reactions. Chem. Rev. 118, 6573–6655. https://doi.org/10.1021/acs.chemrev.8b00031 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 32.

    Wang, Y., Li, J. & Liu, A. Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics. J. Biol. Inorg. Chem. 22, 395–405. https://doi.org/10.1007/s00775-017-1436-5 (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 33.

    Sahu, S. & Goldberg, D. P. Activation of dioxygen by iron and manganese complexes: A heme and nonheme perspective. J. Am. Chem. Soc. 138, 11410–11428. https://doi.org/10.1021/jacs.6b05251 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 34.

    Hassan, H. A. & Aly, A. A. Isolation and characterization of three novel catechol 2,3-dioxygenase from three novel haloalkaliphilic BTEX-degrading Pseudomonas strains. Int. J. Biol. Macromol. 106, 1107–1114. https://doi.org/10.1016/j.ijbiomac.2017.08.113 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 35.

    Liu, Z. et al. Highly sensitive microbial biosensor based on recombinant Escherichia coli overexpressing catechol 2,3-dioxygenase for reliable detection of catechol. Biosens. Bioelectron. 126, 51–58. https://doi.org/10.1016/j.bios.2018.10.050 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 36.

    Kotake, T. et al. Purification and partial characterization of the extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase, in the fluorene degradation pathway from Rhodococcus sp strain DFA3. Biosci. Biotechnol. Biochem. 80, 719–725. https://doi.org/10.1080/09168451.2015.1123605 (2016).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 37.

    Zhu, D. et al. Insight into Depolymerization Mechanism of Bacterial Laccase for Lignin. ACS Sustain. Chem. Eng. 8, 12920–12933. https://doi.org/10.1021/acssuschemeng.0c03457 (2020).

    CAS 
    Article 

    Google Scholar 

  • 38.

    Bugg, T. D., Ahmad, M., Hardiman, E. M. & Singh, R. The emerging role for bacteria in lignin degradation and bio-product formation. Curr. Opin. Biotechnol. 22, 394–400 (2011).

    CAS 
    Article 

    Google Scholar 

  • 39.

    Bugg, T. D. & Winfield, C. J. Enzymatic cleavage of aromatic rings: mechanistic aspects of the catechol dioxygenases and later enzymes of bacterial oxidative cleavage pathways. Nat. Prod. Rep. 15, 513–530 (1998).

    CAS 
    Article 

    Google Scholar 

  • 40.

    Gao, J., Ellis, L. B. & Wackett, L. P. The University of Minnesota biocatalysis/biodegradation database: improving public access. Nucleic Acids Res. 38, D488–D491 (2010).

    CAS 
    Article 

    Google Scholar 

  • 41.

    Hupert-Kocurek, K., Guzik, U. & Wojcieszyńska, D. Characterization of catechol 2, 3-dioxygenase from Planococcus sp. strain S5 induced by high phenol concentration. Acta Biochim. Pol. 59, 345–351 (2012).

    CAS 
    Article 

    Google Scholar 

  • 42.

    Kim, Y., Choi, B., Lee, J., Chang, H. & Rak Min, K. Characterization of catechol 2,3-dioxygenases. Biochem. Biophys. Res. Commun. 183, 77–82. https://doi.org/10.1016/0006-291X(92)91611-S (1992).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 43.

    Takeo, M., Nishimura, M., Shirai, M., Takahashi, H. & Negoro, S. Purification and characterization of catechol 2, 3-dioxygenase from the aniline degradation pathway of Acinetobacter sp. YAA and its mutant enzyme, which resists substrate inhibition. Biosci. Biotechnol. Biochem. 0706060442–0706060442 (2007).

  • 44.

    Ravi, K. et al. Physiological characterization and sequence analysis of a syringate-consuming Actinobacterium. Biores. Technol. 285, 121327. https://doi.org/10.1016/j.biortech.2019.121327 (2019).

    CAS 
    Article 

    Google Scholar 

  • 45.

    Hupert-Kocurek, K., Wojcieszyńska, D. & Guzik, U. Activity of a carboxyl-terminal truncated form of catechol 2,3-dioxygenase from Planococcus sp. S5. ScientificWorldJournal 2015, 598518. https://doi.org/10.1155/2014/598518 (2014).

    Article 

    Google Scholar 

  • 46.

    Bayly, R. C., Dagley, S. & Gibson, D. T. The metabolism of cresols by species of Pseudomonas. Biochem. J. 101, 293–301. https://doi.org/10.1042/bj1010293 (1966).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 47.

    Guo, G. et al. Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium. Sci. Rep. 5, 17603. https://doi.org/10.1038/srep17603 (2015).

    ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 48.

    Tai, H. H. & Sih, C. J. 3,4-Dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-Dioxygenase from Nocardia restrictus: II. KINETIC STUDIES. J. Biol. Chem. 245, 5072–5078. https://doi.org/10.1016/S0021-9258(18)62819-4 (1970).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 49.

    Kunz, D. A. & Chapman, P. J. Catabolism of pseudocumene and 3-ethyltoluene by Pseudomonas putida (arvilla) mt-2: evidence for new functions of the TOL (pWWO) plasmid. J. Bacteriol. 146, 179–191 (1981).

    CAS 
    Article 

    Google Scholar 

  • 50.

    Velupillaimani, D. & Muthaiyan, A. Potential of Bacillus subtilis from marine environment to degrade aromatic hydrocarbons. Environ. Sustain. 2, 381–389. https://doi.org/10.1007/s42398-019-00080-2 (2019).

    CAS 
    Article 

    Google Scholar 

  • 51.

    Woo, H. L. & Hazen, T. C. Enrichment of bacteria from Eastern Mediterranean Sea involved in lignin degradation via the phenylacetyl-CoA pathway. Front. Microbiol. 9, 922 (2018).

    Article 

    Google Scholar 

  • 52.

    Silva, A. S. et al. Enzymatic activity of catechol 1, 2-dioxygenase and catechol 2, 3-dioxygenase produced by Gordonia polyisoprenivorans. Quim. Nova 35, 1587–1592 (2012).

    CAS 
    Article 

    Google Scholar 

  • 53.

    Wojcieszyńska, D., Hupert-Kocurek, K. & Guzik, U. Factors affecting activity of catechol 2, 3-dioxygenase from 2-chlorophenol-degrading Stenotrophomonas maltophilia strain KB2. Biocatal. Biotransform. 31, 141–147 (2013).

    Article 

    Google Scholar 

  • 54.

    Xi, L., Liu, D., Wang, L., Qiao, N. & Liu, J. Catechol 2,3-dioxygenase from a new phenolic compound degrader Thauera sp. K11: purification and biochemical characterization. J. Basic Microbiol. 58, 255–262. https://doi.org/10.1002/jobm.201700566 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 55.

    Boldt, Y. R., Sadowsky, M. J., Ellis, L. B., Que, L. & Wackett, L. P. A manganese-dependent dioxygenase from Arthrobacter globiformis CM-2 belongs to the major extradiol dioxygenase family. J. Bacteriol. 177, 1225–1232 (1995).

    CAS 
    Article 

    Google Scholar 

  • 56.

    Hatta, T., Mukerjee-Dhar, G., Damborsky, J., Kiyohara, H. & Kimbara, K. Characterization of a novel thermostable Mn (II)-dependent 2, 3-dihydroxybiphenyl 1, 2-dioxygenase from a polychlorinated biphenyl-and naphthalene-degrading Bacillus sp. JF8. J. Biol. Chem. 278, 21483–21492 (2003).

    CAS 
    Article 

    Google Scholar 

  • 57.

    Que, L., Widom, J. & Crawford, R. 3, 4-Dihydroxyphenylacetate 2, 3-dioxygenase. A manganese (II) dioxygenase from Bacillus brevis. J. Biol. Chem. 256, 10941–10944 (1981).

    CAS 
    Article 

    Google Scholar 

  • 58.

    Whiting, A. K., Boldt, Y. R., Hendrich, M. P., Wackett, L. P. & Que, L. Manganese (II)-dependent extradiol-cleaving catechol dioxygenase from Arthrobacter globiformis CM-2. Biochemistry 35, 160–170 (1996).

    CAS 
    Article 

    Google Scholar 

  • 59.

    Vetting, M. W., Wackett, L. P., Que, L., Lipscomb, J. D. & Ohlendorf, D. H. Crystallographic comparison of manganese-and iron-dependent homoprotocatechuate 2, 3-dioxygenases. J. Bacteriol. 186, 1945–1958 (2004).

    CAS 
    Article 

    Google Scholar 

  • 60.

    Cho, H. J. et al. Substrate binding mechanism of a type I extradiol dioxygenase. J. Biol. Chem. 285, 34643–34652 (2010).

    CAS 
    Article 

    Google Scholar 

  • 61.

    Tam, N. K. et al. The intestinal life cycle of Bacillus subtilis and close relatives. J. Bacteriol. 188, 2692–2700 (2006).

    CAS 
    Article 

    Google Scholar 

  • 62.

    Happe, B., Eltis, L., Poth, H., Hedderich, R. & Timmis, K. Characterization of 2, 2’, 3-trihydroxybiphenyl dioxygenase, an extradiol dioxygenase from the dibenzofuran-and dibenzo-p-dioxin-degrading bacterium Sphingomonas sp. strain RW1. J. Bacteriol. 175, 7313–7320 (1993).

    CAS 
    Article 

    Google Scholar 

  • 63.

    Yang, X., Xie, F., Zhang, G., Shi, Y. & Qian, S. Purification, characterization, and substrate specificity of two 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus sp. R04, showing their distinct stability at various temperature. Biochimie 90, 1530–1538. https://doi.org/10.1016/j.biochi.2008.05.020 (2008).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 64.

    Asturias, J. A., Eltis, L. D., Prucha, M. & Timmis, K. N. Analysis of three 2,3-dihydroxybiphenyl 1,2-dioxygenases found in Rhodococcus globerulus. P6 Identification of a new family of extradiol dioxygenases. J. Biol. Chem. 269, 7807–7815. https://doi.org/10.1016/S0021-9258(17)37358-1 (1994).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 65.

    Eltis, L. D., Hofmann, B., Hecht, H. J., Lünsdorf, H. & Timmis, K. N. Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase. J. Biol. Chem. 268, 2727–2732. https://doi.org/10.1016/S0021-9258(18)53834-5 (1993).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 66.

    Taira, K. et al. Cloning and nucleotide sequence of the 2, 3-dihydroxybiphenyl dioxygenase gene from the PCB-degrading strain of Pseudomonas paucimobilis Q1. Biochemistry 27, 3990–3996 (1988).

    CAS 
    Article 

    Google Scholar 

  • 67.

    Furukawa, K. & Arimura, N. Purification and properties of 2, 3-dihydroxybiphenyl dioxygenase from polychlorinated biphenyl-degrading Pseudomonas pseudoalcaligenes and Pseudomonas aeruginosa carrying the cloned bphC gene. J. Bacteriol. 169, 924–927 (1987).

    CAS 
    Article 

    Google Scholar 

  • 68.

    Kita, A. et al. An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2, 3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2. Structure 7, 25–34 (1999).

    CAS 
    Article 

    Google Scholar 

  • 69.

    Okuta, A., Ohnishi, K., Yagame, S. & Harayama, S. Intersubunit interaction and catalytic activity of catechol 2,3-dioxygenases. Biochem. J. 371, 557–564. https://doi.org/10.1042/BJ20021657 (2003).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 70.

    Torshin, I. Activating oligomerization as intermediate level of signal transduction: analysis of protein-protein contacts and active sites in several glycolytic enzymes. Front. Biosci. 4, D557-570 (1999).

    CAS 
    PubMed 

    Google Scholar 

  • 71.

    Taguchi, K., Motoyama, M., Iida, T. & Kudo, T. Polychlorinated biphenyl/biphenyl degrading gene clusters in Rhodococcus sp. K37, HA99, and TA431 are different from well-known bph gene clusters of Rhodococci. Biosci. Biotechnol. Biochem. 71, 1136–1144 (2007).

    CAS 
    Article 

    Google Scholar 

  • 72.

    Kirk, T. K. & Farrell, R. L. Enzymatic” combustion”: the microbial degradation of lignin. Annu. Rev. Microbiol. 41, 465–501 (1987).

    CAS 
    Article 

    Google Scholar 

  • 73.

    Floudas, D. et al. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336, 1715–1719 (2012).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 74.

    Bugg, T. D., Ahmad, M., Hardiman, E. M. & Rahmanpour, R. Pathways for degradation of lignin in bacteria and fungi. Nat. Prod. Rep. 28, 1883–1896 (2011).

    CAS 
    Article 

    Google Scholar 

  • 75.

    Linger, J. G. et al. Lignin valorization through integrated biological funneling and chemical catalysis. Proc. Natl. Acad. Sci. 111, 12013–12018 (2014).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 76.

    Xu, Z., Lei, P., Zhai, R., Wen, Z. & Jin, M. Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products. Biotechnol. Biofuels 12, 32 (2019).

    CAS 
    Article 

    Google Scholar 

  • 77.

    Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 78.

    Zuckerkandl, E. & Pauling, L. In Evolving Genes and Proteins (eds Bryson, V. & Vogel, H. J.) 97–166 (Academic Press, 1965).

    Chapter 

    Google Scholar 

  • 79.

    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 80.

    Mevarech, M., Frolow, F. & Gloss, L. M. Halophilic enzymes: Proteins with a grain of salt. Biophys. Chem. 86, 155–164 (2000).

    CAS 
    Article 

    Google Scholar 

  • 81.

    Lee, J., Min, K. R. & Kim, Y. Cloning and overexpression of methylcatechol 2, 3-dioxygenase gene from toluene-degradingPseudomonas putida mt-2 (pWWO). Arch. Pharmacal Res. 15, 360–364 (1992).

    CAS 
    Article 

    Google Scholar 

  • 82.

    Baggi, G., Barbieri, P., Galli, E. & Tollari, S. Isolation of a Pseudomonas stutzeri strain that degrades o-xylene. Appl. Environ. Microbiol. 53, 2129–2132 (1987).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • 83.

    Cerdan, P., Wasserfallen, A., Rekik, M., Timmis, K. N. & Harayama, S. Substrate specificity of catechol 2, 3-dioxygenase encoded by TOL plasmid pWW0 of Pseudomonas putida and its relationship to cell growth. J. Bacteriol. 176, 6074–6081 (1994).

    CAS 
    Article 

    Google Scholar 

  • 84.

    Cerdan, P., Rekik, M. & Harayama, S. Substrate specificity differences between two catechol 2,3-dioxygenases encoded by the TOL and NAH Plasmids from Pseudomonas putida. Eur. J. Biochem. 229, 113–118. https://doi.org/10.1111/j.1432-1033.1995.0113l.x (1995).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 85.

    Junca, H., Plumeier, I., Hecht, H.-J. & Pieper, D. H. Difference in kinetic behaviour of catechol 2, 3-dioxygenase variants from a polluted environment. Microbiology 150, 4181–4187 (2004).

    CAS 
    Article 

    Google Scholar 

  • 86.

    Kobayashi, T. et al. Overexpression of Pseudomonas putida catechol 2,3-dioxygenase with high specific activity by genetically engineered Escherichia coli. The Journal of Biochemistry 117, 614–622. https://doi.org/10.1093/oxfordjournals.jbchem.a124753 (1995).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 87.

    Zhang, X. et al. A new thermophilic extradiol dioxygenase promises biodegradation of catecholic pollutants. J. Hazard. Mater. 422, 126860. https://doi.org/10.1016/j.jhazmat.2021.126860 (2022).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 88.

    Ishida, T., Tanaka, H. & Horiike, K. Quantitative structure-activity relationship for the cleavage of C3/C4-substituted catechols by a prototypal extradiol catechol dioxygenase with broad substrate specificity. J. Biochem. 135, 721–730 (2004).

    CAS 
    Article 

    Google Scholar 

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