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Molecular characterization and overexpression of mnp6 and vp3 from Pleurotus ostreatus revealed their involvement in biodegradation of cotton stalk lignin

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      ABSTRACT

      Fungal secretory heme peroxidase (Class II POD) plays a significant role in biomass conversion due to its lignin-degrading activity. In this study, genome-wide identification and bioinformatics were performed to analyze Pleurotus ostreatus peroxidases (PoPODs). A total of six manganese peroxidases (MnPs) and three versatile peroxidases (VPs) were obtained. Bioinformatics analysis and qRT-PCR showed that P. ostreatus mnp6 (Pomnp6) and P. ostreatus vp3 (Povp3) could be involved in lignin degradation. Both Pomnp6 and Povp3 transgenetic fungi showed significantly increased lignin degradation of cotton stalks. 1H-NMR revealed that Pomnp6 and Povp3 may preferentially degrade S-lignin in cotton stalks and mainly break β-O-4′ bond linkages and hydroxyl. These results support the possible utility of Pomnp6 and Povp3 in natural straw resources and development of sustainable energy.

      Abstract

      Summary: Pleurotus ostreatus mnp6 and vp3 could degrade cotton stalk lignin and may preferentially degrade S-lignin.

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      Most cited references 39

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      Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

       K Livak,  T Schmittgen (2001)
      The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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        MEME Suite: tools for motif discovery and searching

        The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms—MAST, FIMO and GLAM2SCAN—allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm Tomtom. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and Tomtom), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.
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          Assaying chimeric genes in plants: The GUS gene fusion system

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            Author and article information

            Affiliations
            [1 ]School of Life Sciences, Anhui Agricultural University , Hefei 230036, China
            [2 ]Horticultural Research Institute, Anhui Academy of Agricultural Sciences , Hefei 230031, China
            Author notes
            [*]

            These authors contributed equally to this work.

            []Author for correspondence ( swkx12@ 123456ahau.edu.cn ; fan.n@ 123456163.com )
            Journal
            Biol Open
            Biol Open
            BIO
            biolopen
            Biology Open
            The Company of Biologists Ltd
            2046-6390
            15 February 2019
            24 December 2018
            24 December 2018
            : 8
            : 2
            30584069
            6398461
            10.1242/bio.036483
            BIO036483
            © 2019. Published by The Company of Biologists Ltd

            This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.

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            Funding
            Funded by: Anhui Academy of Agricultural Sciences Youth Innovation Fund Project;
            Award ID: 14B0322
            Funded by: Technical System of Anhui Vegetable Industry;
            Award ID: AHCYJSTX-09-05
            Categories
            Research Article

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