6
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      High Potential for Biomass-Degrading Enzymes Revealed by Hot Spring Metagenomics

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Enzyme stability and activity at elevated temperatures are important aspects in biotechnological industries, such as the conversion of plant biomass into biofuels. In order to reduce the costs and increase the efficiency of biomass conversion, better enzymatic processing must be developed. Hot springs represent a treasure trove of underexplored microbiological and protein chemistry diversity. Herein, we conduct an exploratory study into the diversity of hot spring biomass-degrading potential. We describe the taxonomic diversity and carbohydrate active enzyme (CAZyme) coding potential in 71 publicly available metagenomic datasets from 58 globally distributed terrestrial geothermal features. Through taxonomic profiling, we detected a wide diversity of microbes unique to varying temperature and pH ranges. Biomass-degrading enzyme potential included all five classes of CAZymes and we described the presence or absence of genes encoding 19 glycosyl hydrolases hypothesized to be involved with cellulose, hemicellulose, and oligosaccharide degradation. Our results highlight hot springs as a promising system for the further discovery and development of thermo-stable biomass-degrading enzymes that can be applied toward generation of renewable biofuels. This study lays a foundation for future research to further investigate the functional diversity of hot spring biomass-degrading enzymes and their potential utility in biotechnological processing.

          Related collections

          Most cited references99

          • Record: found
          • Abstract: not found
          • Article: not found

          Fitting Linear Mixed-Effects Models Usinglme4

            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            The carbohydrate-active enzymes database (CAZy) in 2013

            The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3D structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides. Functional and 3D structural information is added and curated on a regular basis based on the available literature. In addition to the use of the database by enzymologists seeking curated information on CAZymes, the dissemination of a stable nomenclature for these enzymes is probably a major contribution of CAZy. The past few years have seen the expansion of the CAZy classification scheme to new families, the development of subfamilies in several families and the power of CAZy for the analysis of genomes and metagenomes. This article outlines the changes that have occurred in CAZy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

              Abstract Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes. Here, dbCAN2 (http://cys.bios.niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database. Combining the three outputs and removing CAZymes found by only one tool can significantly improve the CAZome annotation accuracy. In addition, dbCAN2 now also accepts nucleotide sequence submission, and offers the service to predict physically linked CAZyme gene clusters (CGCs), which will be a very useful online tool for identifying putative polysaccharide utilization loci (PULs) in microbial genomes or metagenomes.
                Bookmark

                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                21 April 2021
                2021
                : 12
                : 668238
                Affiliations
                [1] 1Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT, United States
                [2] 2Thermal Biology Institute, Montana State University , Bozeman, MT, United States
                [3] 3Center for Biofilm Engineering, Montana State University , Bozeman, MT, United States
                [4] 4Department of Energy, Joint Genome Institute , Berkeley, CA, United States
                Author notes

                Edited by: Sara E. Blumer-Schuette, Oakland University, United States

                Reviewed by: Mircea Podar, Oak Ridge National Laboratory (DOE), United States; Yanbin Yin, University of Nebraska-Lincoln, United States

                *Correspondence: Roland Hatzenpichler, roland.hatzenpichler@ 123456montana.edu

                ORCID: Nicholas J. Reichart, 0000-0002-3901-2039; Robert M. Bowers, 0000-0002-0028-0407; Tanja Woyke, 0000-0002-9485-5637; Roland Hatzenpichler, 0000-0002-5489-3444

                This article was submitted to Extreme Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2021.668238
                8098120
                33968004
                aedb9451-3228-4568-b1f5-1eab98ed11e4
                Copyright © 2021 Reichart, Bowers, Woyke and Hatzenpichler.

                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
                : 15 February 2021
                : 29 March 2021
                Page count
                Figures: 4, Tables: 0, Equations: 0, References: 103, Pages: 13, Words: 0
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                bioprospecting,thermophilic enzymes,biotechnology,cazyme,cellulases
                Microbiology & Virology
                bioprospecting, thermophilic enzymes, biotechnology, cazyme, cellulases

                Comments

                Comment on this article