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      Dye-decolorizing peroxidases in Irpex lacteus combining the catalytic properties of heme peroxidases and laccase play important roles in ligninolytic system

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          Abstract

          Background

          The white rot fungus Irpex lacteus exhibits a great potential in biopretreatment of lignocellulose as well as in biodegradation of xenobiotic compounds by extracellular ligninolytic enzymes. Among these enzymes, the possible involvement of dye-decolorizing peroxidase (DyP) in lignin degradation is not clear yet.

          Results

          Based on the extracellular enzyme activities and secretome analysis, I. lacteus CD2 produced DyPs as the main ligninolytic enzymes when grown in Kirk’s medium supplemented with lignin. Further transcriptome analysis revealed that induced transcription of genes encoding DyPs was accompanied by the increased expression of transcripts for H 2O 2-generating enzymes such as alcohol oxidase, pyranose 2-oxidase, and glyoxal oxidases. Meanwhile, accumulation of transcripts for glycoside hydrolase and protease was observed, in agreement with abundant proteins. Moreover, the biochemical analysis of IlDyP2 and IlDyP1 confirmed that DyPs were able to catalyze the oxidation of typical peroxidases substrates ABTS, phenolic lignin compounds DMP, and guaiacol as well as non-phenolic lignin compound, veratryl alcohol. More importantly, IlDyP1 enhanced catalytic activity for veratryl alcohol oxidation in the presence of mediator 1-hydroxybenzotriazole, which was similar to the laccase/1-hydroxybenzotriazole system.

          Conclusions

          The results proved for the first time that DyPs depolymerized lignin individually, combining catalytic features of different peroxidases on the functional level. Therefore, DyPs may be considered an important part of ligninolytic system in wood-decaying fungi.

          Electronic supplementary material

          The online version of this article (10.1186/s13068-018-1303-9) contains supplementary material, which is available to authorized users.

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          Most cited references38

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          Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

          Background Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. Results Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name “Auxiliary Activities” in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). Conclusions The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.
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            PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.

            A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins. Copyright 2003 John Wiley & Sons, Ltd.
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              Liquid fuels, hydrogen and chemicals from lignin: A critical review

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                Author and article information

                Contributors
                xingqin@hust.edu.cn
                luohuiying@caas.cn
                zhangxiaoyu@hust.edu.cn
                binyao@caas.cn
                +86-27-87792108 , mafuying@hust.edu.cn
                +86-10-82106094 , suxiaoyun@caas.cn
                Journal
                Biotechnol Biofuels
                Biotechnol Biofuels
                Biotechnology for Biofuels
                BioMed Central (London )
                1754-6834
                8 November 2018
                8 November 2018
                2018
                : 11
                : 302
                Affiliations
                [1 ]ISNI 0000 0004 0368 7223, GRID grid.33199.31, Department of Biotechnology, College of Life Science and Technology, , Huazhong University of Science and Technology, ; Wuhan, 430074 China
                [2 ]ISNI 0000 0001 0526 1937, GRID grid.410727.7, Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, , Chinese Academy of Agricultural Sciences, ; No. 12 South Zhongguancun Street, Beijing, 100081 China
                Author information
                http://orcid.org/0000-0002-7891-8124
                Article
                1303
                10.1186/s13068-018-1303-9
                6223037
                9649b379-25e6-4047-8019-6b36f88e7c4f
                © The Author(s) 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 3 September 2018
                : 26 October 2018
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31570577
                Award ID: 31672458
                Award Recipient :
                Funded by: National Key Research and Development Program of China
                Award ID: 2016YFD0501409-02
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100005153, China National Funds for Distinguished Young Scientists;
                Award ID: 31225026
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2018

                Biotechnology
                dye-decolorizing peroxidase,white rot fungi,irpex lacteus,lignin biodegradation,mediator

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