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      Distinct laccase expression and activity profiles of Trametes versicolor facilitate degradation of benzo[a]pyrene

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          Abstract

          A Trametes versicolor isolate from the Changbai Mountain showed promising activity in degrading benzo[a]pyrene (BaP), which is a high molecular weight (HMW) polycyclic aromatic hydrocarbon (PAH) compound. It was hypothesized that the T. versicolor isolate encode BaP-degrading enzymes, among which laccase is mostly sought after due to significant commercial potential. Genome of the T. versicolor isolate was sequenced and assembled, and seven laccase homologues were identified ( TvLac1-7) as candidate genes potentially contributing to BaP degradation. In order to further identify the BaP responsive laccases, time-course transcriptomic and proteomic analyses were conducted in parallel on the T. versicolor isolate upon BaP treatment. Homologous laccases showed distinct expression patterns. Most strikingly, TvLac5 was rapidly induced in the secreted proteomes (secretomes), while TvLac2 was repressed. Recombinant laccase expression and biochemical characterization further showed corresponding enzymatic activity profiles, where TvLac5 was 21-fold more effective in BaP degradation compared to TvLac2. Moreover, TvLac5 also showed 3.6-fold higher BaP degrading activity compared to a commercial laccase product of T. versicolor origin. Therefore, TvLac5 was concluded to be a BaP-responsive enzyme from T. versicolor showing effective BaP degradation activity.

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          AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

          T.J White, T. Bruns, S. Lee … (1990)
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            Correlation between protein and mRNA abundance in yeast.

            S P Gygi, Y Rochon, B R Franza … (1999)
            We have determined the relationship between mRNA and protein expression levels for selected genes expressed in the yeast Saccharomyces cerevisiae growing at mid-log phase. The proteins contained in total yeast cell lysate were separated by high-resolution two-dimensional (2D) gel electrophoresis. Over 150 protein spots were excised and identified by capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein spots were quantified by metabolic labeling and scintillation counting. Corresponding mRNA levels were calculated from serial analysis of gene expression (SAGE) frequency tables (V. E. Velculescu, L. Zhang, W. Zhou, J. Vogelstein, M. A. Basrai, D. E. Bassett, Jr., P. Hieter, B. Vogelstein, and K. W. Kinzler, Cell 88:243-251, 1997). We found that the correlation between mRNA and protein levels was insufficient to predict protein expression levels from quantitative mRNA data. Indeed, for some genes, while the mRNA levels were of the same value the protein levels varied by more than 20-fold. Conversely, invariant steady-state levels of certain proteins were observed with respective mRNA transcript levels that varied by as much as 30-fold. Another interesting observation is that codon bias is not a predictor of either protein or mRNA levels. Our results clearly delineate the technical boundaries of current approaches for quantitative analysis of protein expression and reveal that simple deduction from mRNA transcript analysis is insufficient.
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              Scaffolding pre-assembled contigs using SSPACE.

              Marten Boetzer, Christiaan Henkel, Hans J Jansen … (2011)
              De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield a number of contigs. Using paired-read sequencing data it is possible to assess the order, distance and orientation of contigs and combine them into so-called scaffolds. Although the latter process is a crucial step in finishing genomes, scaffolding algorithms are often built-in functions in de novo assembly tools and cannot be independently controlled. We here present a new tool, called SSPACE, which is a stand-alone scaffolder of pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. SSPACE shows promising results on both prokaryote and eukaryote genomic testsets where the amount of initial contigs was reduced by at least 75%.
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                Author and article information

                Contributors
                Yueming Sun: URI : https://loop.frontiersin.org/people/2421977/overviewRole: Role: Role: Role:
                Ying Li: URI : https://loop.frontiersin.org/people/2386660/overviewRole: Role:
                Hong Liang: Role:
                Ming Li: URI : https://loop.frontiersin.org/people/2387110/overviewRole: Role: Role:
                Ye Liu: Role: Role: Role:
                Litao Wang: Role: Role:
                Weijian Lai: Role: Role: Role:
                Teng Tang: Role:
                Yongzhao Diao: Role: Role: Role:
                Yuhong Bai: Role:
                Christian Isak Jørgensen: Role: Role: Role:
                Wanghui Xu: URI : https://loop.frontiersin.org/people/2384393/overviewRole: Role: Role: Role: Role:
                Dawen Gao: URI : https://loop.frontiersin.org/people/1627580/overviewRole: Role: Role: Role: Role:
                Journal
                Journal ID (nlm-ta): Front Bioeng Biotechnol
                Journal ID (iso-abbrev): Front Bioeng Biotechnol
                Journal ID (publisher-id): Front. Bioeng. Biotechnol.
                Title: Frontiers in Bioengineering and Biotechnology
                Publisher: Frontiers Media S.A.
                ISSN (Electronic): 2296-4185
                Publication date (Electronic): 21 September 2023
                Publication date Collection: 2023
                Volume: 11
                Electronic Location Identifier: 1264135
                Affiliations
                [1] 1 Novozymes (China) Investment Co., Ltd. , Beijing, China
                [2] 2 Centre for Urban Environmental Remediation , Beijing University of Civil Engineering and Architecture , Beijing, China
                [3] 3 Beijing Energy Conservation and Sustainable Urban and Rural Development Provincial and Ministry Co-construction Collaboration Innovation Center , Beijing University of Civil Engineering and Architecture , Beijing, China
                [4] 4 Novozymes A/S , Lyngby, Denmark
                Author notes

                Edited by: Andrea Zille, University of Minho, Portugal

                Reviewed by: Federica Spina, University of Turin, Italy

                Dirk Tischler, Ruhr University Bochum, Germany

                *Correspondence: Wanghui Xu, wnx@ 123456novozymes.com ; Dawen Gao, gaodawen@ 123456bucea.edu.cn
                [ † ]

                These authors have contributed equally to this work and share first authorship

                Article
                Publisher ID: 1264135
                DOI: 10.3389/fbioe.2023.1264135
                PMC ID: 10551628
                PubMed ID: 37811380
                SO-VID: f39a4fc1-35bc-47c7-96f5-bdce4eb2109a
                Copyright © Copyright © 2023 Sun, Li, Liang, Li, Liu, Wang, Lai, Tang, Diao, Bai, Jørgensen, Xu and Gao.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                Date received : 20 July 2023
                Date accepted : 05 September 2023
                Funding
                The authors declare financial support was received for the research, authorship, and/or publication of this article.The authors gratefully acknowledge the financial support by the National Key R&D Program of the Science and Technology of China (2020YFC1808801).
                Categories
                Subject: Bioengineering and Biotechnology
                Subject: Brief Research Report
                Custom metadata
                section-at-acceptance Industrial Biotechnology

                Keywords: polycyclic aromatic hydrocarbon (pah),benzo[a]pyrene (bap),trametes versicolor,laccase,multi-omics,soil remediation
                Data availability:
                Keywords: polycyclic aromatic hydrocarbon (pah), benzo[a]pyrene (bap), trametes versicolor, laccase, multi-omics, soil remediation

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