Boerjan W, Ralph J, Baucher M. Lignin biosynthesis. Annu Rev Plant Biol. 2003;54:519–46. https://doi.org/10.1146/annurev.arplant.54.031902.134938.
Google Scholar
Ragauskas AJ, Beckham GT, Biddy MJ, Chandra R, Chen F, Davis MF, et al. Lignin valorization: improving lignin processing in the biorefinery. Science. 2014;344:1246843. https://doi.org/10.1126/science.1246843.
Google Scholar
Hildén K, Hakala TK, Lundell T. Thermotolerant and thermostable laccases. Biotechnol Lett. 2009;31:1117. https://doi.org/10.1007/s10529-009-9998-0.
Google Scholar
Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME J. 2018;1. https://doi.org/10.1038/s41396-018-0279-6.
Bugg TDH, Ahmad M, Hardiman EM, Singh R. The emerging role for bacteria in lignin degradation and bio-product formation. Curr Opin Biotechnol. 2011;22:394–400. https://doi.org/10.1016/j.copbio.2010.10.009.
Google Scholar
Kamimura N, Takahashi K, Mori K, Araki T, Fujita M, Higuchi Y, et al. Bacterial catabolism of lignin-derived aromatics: new findings in a recent decade: update on bacterial lignin catabolism. Environ Microbiol Rep. 2017;9:679–705. https://doi.org/10.1111/1758-2229.12597.
Google Scholar
Singh R, Hu J, Regner MR, Round JW, Ralph J, Saddler JN, et al. Enhanced delignification of steam-pretreated poplar by a bacterial laccase. Sci Rep. 2017;7:42121. https://doi.org/10.1038/srep42121.
Google Scholar
Perna V, Meyer AS, Holck J, Eltis LD, Eijsink VGH, Wittrup Agger J. Laccase-catalyzed oxidation of lignin induces production of H2O2. ACS Sustain Chem Eng. 2020;8:831–41. https://doi.org/10.1021/acssuschemeng.9b04912.
Google Scholar
Johnson CW, Salvachúa D, Rorrer NA, Black BA, Vardon DR, St. John PC, et al. Innovative chemicals and materials from bacterial aromatic catabolic pathways. Joule. 2019;3:1523–37. https://doi.org/10.1016/j.joule.2019.05.011.
Google Scholar
Brady AL, Sharp CE, Grasby SE, Dunfield PF. Anaerobic carboxydotrophic bacteria in geothermal springs identified using stable isotope probing. Front Microbiol. 2015;6. https://doi.org/10.3389/fmicb.2015.00897.
Grasby SE, Hutcheon I, Krouse HR. The influence of water–rock interaction on the chemistry of thermal springs in western Canada. Appl Geochem. 2000;15:439–54. https://doi.org/10.1016/S0883-2927(99)00066-9.
Google Scholar
Bauchop T, Elsden SR. The growth of micro-organisms in relation to their energy supply. Microbiology. 1960;23:457–69. https://doi.org/10.1099/00221287-23-3-457.
Google Scholar
Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, et al. DNA stable-isotope probing. Nat Protoc. 2007;2:860–6. https://doi.org/10.1038/nprot.2007.109.
Google Scholar
Wilhelm RC, Singh R, Eltis LD, Mohn WW. Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing. ISME J. 2019;13:413–29. https://doi.org/10.1038/s41396-018-0279-6.
Google Scholar
Wilhelm R, Szeitz A, Klassen TL, Mohn WW. Sensitive, efficient quantitation of 13C-enriched nucleic acids via ultrahigh-performance liquid chromatography-tandem mass spectrometry for applications in stable isotope probing. Appl Environ Microbiol. 2014;80:7206–11. https://doi.org/10.1128/AEM.02223-14.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinforma Oxf Engl. 2014;30:2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77. https://doi.org/10.1089/cmb.2012.0021.
Google Scholar
Lin H-H, Liao Y-C. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Sci Rep. 2016;6:24175. https://doi.org/10.1038/srep24175.
Google Scholar
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359. https://doi.org/10.7717/peerj.7359.
Google Scholar
Alneberg J, Bjarnason BS, Bruijn ID, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11:1144–6. https://doi.org/10.1038/nmeth.3103.
Google Scholar
Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinforma Oxf Engl. 2016;32:605–7. https://doi.org/10.1093/bioinformatics/btv638.
Google Scholar
Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol. 2018;3:836–43. https://doi.org/10.1038/s41564-018-0171-1.
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55. https://doi.org/10.1101/gr.186072.114.
Google Scholar
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119. https://doi.org/10.1186/1471-2105-11-119.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60. https://doi.org/10.1038/nmeth.3176.
Google Scholar
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–5. https://doi.org/10.1093/nar/gkt1178.
Google Scholar
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95–101. https://doi.org/10.1093/nar/gky418.
Google Scholar
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47:D427–32. https://doi.org/10.1093/nar/gky995.
Google Scholar
Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, et al. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 2001;29:41–3.
Google Scholar
Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020. https://doi.org/10.1093/bioinformatics/btz859.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15. https://doi.org/10.1186/s13059-014-0550-8.
R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2018. https://www.R-project.org.
Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–5. https://doi.org/10.1093/nar/gkw290.
Google Scholar
Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28–36. https://doi.org/10.1111/2041-210X.12628.
Google Scholar
Brenner AJ, Harris ED. A quantitative test for copper using bicinchoninic acid. Anal Biochem. 1995;226:80–4. https://doi.org/10.1006/abio.1995.1194.
Google Scholar
Brown ME, Barros T, Chang MCY. Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium. ACS Chem Biol. 2012;7:2074–81. https://doi.org/10.1021/cb300383y.
Google Scholar
Levy-Booth DJ, Hashimi A, Roccor R, Liu L-Y, Renneckar S, Eltis LD, et al. Genomics and metatranscriptomics of biogeochemical cycling and degradation of lignin-derived aromatic compounds in thermal swamp sediment. ISME J. 2021;15:879–93. https://doi.org/10.1038/s41396-020-00820-x.
Google Scholar
Aston JE, Apel WA, Lee BD, Thompson DN, Lacey JA, Newby DT, et al. Degradation of phenolic compounds by the lignocellulose deconstructing thermoacidophilic bacterium Alicyclobacillus Acidocaldarius. J Ind Microbiol Biotechnol. 2016;43:13–23. https://doi.org/10.1007/s10295-015-1700-z.
Google Scholar
Morgan-Lang C, McLaughlin R, Armstrong Z, Zhang G, Chan K, Hallam SJ. TreeSAPP: the tree-based sensitive and accurate phylogenetic profiler. Bioinformatics. 2020. https://doi.org/10.1093/bioinformatics/btaa588.
Machczynski MC, Vijgenboom E, Samyn B, Canters GW. Characterization of SLAC: a small laccase from streptomyces coelicolor with unprecedented activity. Protein Sci Publ Protein Soc. 2004;13:2388–97. https://doi.org/10.1110/ps.04759104.
Google Scholar
Berini F, Verce M, Ausec L, Rosini E, Tonin F, Pollegioni L, et al. Isolation and characterization of a heterologously expressed bacterial laccase from the anaerobe Geobacter metallireducens. Appl Microbiol Biotechnol. 2018;102:2425–39. https://doi.org/10.1007/s00253-018-8785-z.
Google Scholar
Yin Q, Zhou G, Peng C, Zhang Y, Kües U, Liu J, et al. The first fungal laccase with an alkaline pH optimum obtained by directed evolution and its application in indigo dye decolorization. AMB Express. 2019;9:151. https://doi.org/10.1186/s13568-019-0878-2.
Google Scholar
Kumar D, Kumar A, Sondhi S, Sharma P, Gupta N. An alkaline bacterial laccase for polymerization of natural precursors for hair dye synthesis. 3 Biotech. 2018;8:182. https://doi.org/10.1007/s13205-018-1181-7.
Google Scholar
Hilgers R, Vincken J-P, Gruppen H, Kabel MA. Laccase/mediator systems: their reactivity toward phenolic lignin structures. ACS Sustain Chem Eng. 2018;6:2037–46. https://doi.org/10.1021/acssuschemeng.7b03451.
Google Scholar
Wu S, Argyropoulos D. An improved method for isolating lignin in high yield and purity. J Pulp Pap Sci. 2003;29:235–40.
Google Scholar
Gao R, Li Y, Kim H, Mobley JK, Ralph J. Selective oxidation of lignin model compounds. ChemSusChem. 2018;11:2045–50. https://doi.org/10.1002/cssc.201800598.
Google Scholar
Rahimi A, Azarpira A, Kim H, Ralph J, Stahl SS. Chemoselective metal-free aerobic alcohol oxidation in lignin. J Am Chem Soc. 2013;135:6415–8. https://doi.org/10.1021/ja401793n.
Google Scholar
Schutyser W, Renders T, Bosch SV, den, Koelewijn S-F, Beckham GT, Sels BF. Chemicals from lignin: an interplay of lignocellulose fractionation, depolymerisation, and upgrading. Chem Soc Rev. 2018;47:852–908. https://doi.org/10.1039/C7CS00566K.
Google Scholar
Sun X, Bai R, Zhang Y, Wang Q, Fan X, Yuan J, et al. Laccase-catalyzed oxidative polymerization of phenolic compounds. Appl Biochem Biotechnol. 2013;171:1673–80. https://doi.org/10.1007/s12010-013-0463-0.
Google Scholar
Hu D, Zang Y, Mao Y, Gao B. Identification of molecular markers that are specific to the class Thermoleophilia. Front Microbiol. 2019;10. https://doi.org/10.3389/fmicb.2019.01185.
Chen M-Y, Wu S-H, Lin G-H, Lu C-P, Lin Y-T, Chang W-C, et al. Rubrobacter taiwanensis sp. nov., a novel thermophilic, radiation-resistant species isolated from hot springs. Int J Syst Evol Microbiol. 2004;54:1849–55. https://doi.org/10.1099/ijs.0.63109-0.
Google Scholar
Tomariguchi N, Miyazaki K. Complete genome sequence of Rubrobacter xylanophilus strain AA3-22, isolated from Arima Onsen in Japan. Microbiol Resour Announc. 2019;8. https://doi.org/10.1128/MRA.00818-19.
Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, et al. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem. 2017;63:193–203. https://doi.org/10.1016/j.procbio.2017.08.018.
Google Scholar
Clark Mason J, Richards M, Zimmermann W, Broda P. Identification of extracellular proteins from actinomycetes responsible for the solubilisation of lignocellulose. Appl Microbiol Biotechnol. 1988;28:276–80. https://doi.org/10.1007/BF00250455.
Google Scholar
Yin Y-R, Sang P, Xian W-D, Li X, Jiao J-Y, Liu L, et al. Expression and characteristics of two glucose-tolerant GH1 β-glucosidases from Actinomadura amylolytica YIM 77502T for promoting cellulose degradation. Front Microbiol. 2018;9. https://doi.org/10.3389/fmicb.2018.03149.
Zimmermann W, Broda P. Utilization of lignocellulose from barley straw by actinomycetes. Appl Microbiol Biotechnol. 1989;30:103–9. https://doi.org/10.1007/BF00256005.
Google Scholar
Abe T, Masai E, Miyauchi K, Katayama Y, Fukuda M. A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6. J Bacteriol. 2005;187:2030–7. https://doi.org/10.1128/JB.187.6.2030-2037.2005.
Google Scholar
Varman AM, He L, Follenfant R, Wu W, Wemmer S, Wrobel SA, et al. Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization. Proc Natl Acad Sci USA. 2016;113:E5802–11. https://doi.org/10.1073/pnas.1606043113.
Google Scholar
Studenik S, Vogel M, Diekert G. Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2. J Bacteriol. 2012;194:3317–26. https://doi.org/10.1128/JB.00146-12.
Google Scholar
Fahrbach M, Kuever J, Remesch M, Huber BE, Kämpfer P, Dott W, et al. Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium. Int J Syst Evol Microbiol. 2008;58:2215–23. https://doi.org/10.1099/ijs.0.65342-0.
Google Scholar
Nogi Y, Yoshizumi M, Hamana K, Miyazaki M, Horikoshi K. Povalibacter uvarum gen. nov., sp. nov., a polyvinyl-alcohol-degrading bacterium isolated from grapes. Int J Syst Evol Microbiol. 2014;64:2712–7. https://doi.org/10.1099/ijs.0.062620-0.
Google Scholar
Sharma V, Siedenburg G, Birke J, Mobeen F, Jendrossek D, Prakash T. Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y. PLoS ONE. 2018;13:e0197448. https://doi.org/10.1371/journal.pone.0197448.
Google Scholar
Reiss R, Ihssen J, Richter M, Eichhorn E, Schilling B, Thöny-Meyer L. Laccase versus laccase-like multi-copper oxidase: a comparative study of similar enzymes with diverse substrate spectra. PLoS ONE. 2013;8:e65633. https://doi.org/10.1371/journal.pone.0065633.
Google Scholar
Christopher LP, Yao B, Ji Y. Lignin biodegradation with laccase-mediator systems. Front Energy Res. 2014;2. https://doi.org/10.3389/fenrg.2014.00012.
Mate DM, Alcalde M. Laccase: a multi‐purpose biocatalyst at the forefront of biotechnology. Micro Biotechnol. 2016;10:1457–67. https://doi.org/10.1111/1751-7915.12422.
Google Scholar
Sirim D, Wagner F, Wang L, Schmid RD, Pleiss J. The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases. Database J Biol Databases Curation. 2011;2011. https://doi.org/10.1093/database/bar006.
Fang Z, Li T, Wang Q, Zhang X, Peng H, Fang W, et al. A bacterial laccase from marine microbial metagenome exhibiting chloride tolerance and dye decolorization ability. Appl Microbiol Biotechnol. 2011;89:1103–10. https://doi.org/10.1007/s00253-010-2934-3.
Google Scholar
Komori H, Miyazaki K, Higuchi Y. X-ray structure of a two-domain type laccase: a missing link in the evolution of multi-copper proteins. FEBS Lett. 2009;583:1189–95. https://doi.org/10.1016/j.febslet.2009.03.008.
Google Scholar
Sherif M, Waung D, Korbeci B, Mavisakalyan V, Flick R, Brown G, et al. Biochemical studies of the multicopper oxidase (small laccase) from Streptomyces coelicolor using bioactive phytochemicals and site-directed mutagenesis. Microb Biotechnol. 2013;6:588–97. https://doi.org/10.1111/1751-7915.12068
Google Scholar
Gunne M, Urlacher VB. Characterization of the alkaline laccase Ssl1 from Streptomyces sviceus with unusual properties discovered by genome mining. PLOS ONE. 2012;7:e52360 https://doi.org/10.1371/journal.pone.0052360
Google Scholar
Dubé E, Shareck F, Hurtubise Y, Beauregard M, Daneault C. Decolourization of recalcitrant dyes with a laccase from Streptomyces coelicolor under alkaline conditions. J Ind Microbiol Biotechnol. 2008;35:1123–9. https://doi.org/10.1007/s10295-008-0391-0
Google Scholar
Koschorreck K, Richter SM, Ene AB, Roduner E, Schmid RD, Urlacher VB. Cloning and characterization of a new laccase from Bacillus licheniformis catalyzing dimerization of phenolic acids. Appl Microbiol Biotechnol. 2008;79:217–24. https://doi.org/10.1007/s00253-008-1417-2
Google Scholar
Mohammadian M, Fathi-Roudsari M, Mollania N, Badoei-Dalfard A, Khajeh K. Enhanced expression of a recombinant bacterial laccase at low temperature and microaerobic conditions: purification and biochemical characterization. J Ind Microbiol Biotechnol. 2010;37:863–9. https://doi.org/10.1007/s10295-010-0734-5
Google Scholar
Ausec L, Berini F, Casciello C, Cretoiu MS, van Elsas JD, Marinelli F, et al. The first acidobacterial laccase-like multicopper oxidase revealed by metagenomics shows high salt and thermo-tolerance. Appl Microbiol Biotechnol. 2017;101:6261–76. https://doi.org/10.1007/s00253-017-8345-y
Google Scholar
Ausec L, Črnigoj M, Šnajder M, Ulrih NP, Mandic-Mulec I. Characterization of a novel high-pH-tolerant laccase-like multicopper oxidase and its sequence diversity in Thioalkalivibrio sp. Appl Microbiol Biotechnol. 2015;99:9987–99. https://doi.org/10.1007/s00253-015-6843-3
Google Scholar
Source: Ecology - nature.com