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      The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena

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          Summary

          Marine habitats represent a prolific source for molecules of biotechnological interest. In particular, marine bacteria have attracted attention and were successfully exploited for industrial applications. Recently, a group of Pseudomonas species isolated from extreme habitats or living in association with algae or sponges were clustered in the newly established Pseudomonas pertucinogena lineage. Remarkably for the predominantly terrestrial genus Pseudomonas, more than half (9) of currently 16 species within this lineage were isolated from marine or saline habitats. Unlike other Pseudomonas species, they seem to have in common a highly specialized metabolism. Furthermore, the marine members apparently possess the capacity to produce biomolecules of biotechnological interest (e.g. dehalogenases, polyester hydrolases, transaminases). Here, we summarize the knowledge regarding the enzymatic endowment of the marine Pseudomonas pertucinogena bacteria and report on a genomic analysis focusing on the presence of genes encoding esterases, dehalogenases, transaminases and secondary metabolites including carbon storage compounds.

          Abstract

          The newly established Pseudomonas pertucinogena lineage consists of several marine bacterial species which possess the capacity to produce biomolecules of biotechnological interest. Beside biocatalysts including dehalogenases, polyester hydrolases, and transaminases they produce several secondary metabolites and carbon storage compounds.

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          antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

          Abstract Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.
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            Role of Biocatalysis in Sustainable Chemistry.

            Based on the principles and metrics of green chemistry and sustainable development, biocatalysis is both a green and sustainable technology. This is largely a result of the spectacular advances in molecular biology and biotechnology achieved in the past two decades. Protein engineering has enabled the optimization of existing enzymes and the invention of entirely new biocatalytic reactions that were previously unknown in Nature. It is now eminently feasible to develop enzymatic transformations to fit predefined parameters, resulting in processes that are truly sustainable by design. This approach has successfully been applied, for example, in the industrial synthesis of active pharmaceutical ingredients. In addition to the use of protein engineering, other aspects of biocatalysis engineering, such as substrate, medium, and reactor engineering, can be utilized to improve the efficiency and cost-effectiveness and, hence, the sustainability of biocatalytic reactions. Furthermore, immobilization of an enzyme can improve its stability and enable its reuse multiple times, resulting in better performance and commercial viability. Consequently, biocatalysis is being widely applied in the production of pharmaceuticals and some commodity chemicals. Moreover, its broader application will be further stimulated in the future by the emerging biobased economy.
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              Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

              Plastics, including poly(ethylene terephthalate) (PET), possess many desirable characteristics and thus are widely used in daily life. However, non-biodegradability, once thought to be an advantage offered by plastics, is causing major environmental problem. Recently, a PET-degrading bacterium, Ideonella sakaiensis, was identified and suggested for possible use in degradation and/or recycling of PET. However, the molecular mechanism of PET degradation is not known. Here we report the crystal structure of I. sakaiensis PETase (IsPETase) at 1.5 Å resolution. IsPETase has a Ser–His-Asp catalytic triad at its active site and contains an optimal substrate binding site to accommodate four monohydroxyethyl terephthalate (MHET) moieties of PET. Based on structural and site-directed mutagenesis experiments, the detailed process of PET degradation into MHET, terephthalic acid, and ethylene glycol is suggested. Moreover, other PETase candidates potentially having high PET-degrading activities are suggested based on phylogenetic tree analysis of 69 PETase-like proteins.
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                Author and article information

                Contributors
                karl-erich.jaeger@fz-juelich.de
                Journal
                Microb Biotechnol
                Microb Biotechnol
                10.1111/(ISSN)1751-7915
                MBT2
                Microbial Biotechnology
                John Wiley and Sons Inc. (Hoboken )
                1751-7915
                25 June 2018
                January 2020
                : 13
                : 1 , Special Issue on Pseudomonas Applications ( doiID: 10.1111/mbt2.v13.1 )
                : 19-31
                Affiliations
                [ 1 ] Institute of Molecular Enzyme Technology Heinrich‐Heine‐University Düsseldorf Forschungszentrum Jülich D‐52425 Jülich Germany
                [ 2 ] Institute of Bio‐ and Geosciences IBG‐1: Biotechnology Forschungszentrum Jülich GmbH D‐52425 Jülich Germany
                Author notes
                [*] [* ]For correspondence. E‐mail karl-erich.jaeger@ 123456fz-juelich.de ; Tel. +49 2461 613716; Fax +49 2461 612490.
                Author information
                http://orcid.org/0000-0002-1349-7381
                http://orcid.org/0000-0003-4240-9149
                http://orcid.org/0000-0002-5535-2236
                http://orcid.org/0000-0002-6036-0708
                Article
                MBT213288
                10.1111/1751-7915.13288
                6922532
                29943398
                dcd6cf65-4d77-4795-bbaf-9973d955a701
                © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 10 May 2018
                : 24 May 2018
                : 25 May 2018
                Page count
                Figures: 1, Tables: 3, Pages: 13, Words: 9498
                Funding
                Funded by: European Union's Horizon 2020 research and innovation program
                Award ID: 634486
                Award ID: ERA‐IB 5 ‘METACAT’
                Funded by: Ministry of Culture and Science of the German State of North Rhine‐Westphalia
                Award ID: 313/323‐400‐00213
                Categories
                Minireview
                Minireviews
                Custom metadata
                2.0
                January 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.7.3 mode:remove_FC converted:19.12.2019

                Biotechnology
                Biotechnology

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