DOCSLIB.ORG

Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes Dissertation for obtaining the degree of Doctor rerum naturalium (Dr. rer. nat.) at the Department of Biology Subdivision at the Faculty of Mathematics, Informatics and Natural Sciences of the Universität Hamburg submitted by Dominik Danso from Hamburg Hamburg 2018 Genehmigt vom Fachbereich Biologie der Universität Hamburg auf Antrag von Prof. Dr. W. Streit Weiterer Gutachter der Dissertation: Prof. Dr. Bodo Saake Tag der Disputation: 25.01.2019 Eidesstattliche Versicherung Hiermit erkläre ich an Eides statt, dass ich die vorliegende Dissertationsschrift selbst verfasst und keine anderen als die angegebenen Quellen und Hilfsmittel benutzt habe. Declaration on oath I hereby declare, on oath, that I have written the present dissertation by my own and have not used any other than the acknowledged resources and aids. Hamburg, 08.02.2019 Dominik Danso Table of Contents I Table of Contents List of Figures ............................................................................................................................ I List of Tables ............................................................................................................................. II Abstract .................................................................................................................................... III 1 Introduction ........................................................................................................................ 1 1.1 Plastic as an environmental pollutant ............................................................................ 2 1.2 Degradation processes of plastic................................................................................... 2 1.2.1 Depletion of PET by enzymatic hydrolysis .............................................................. 3 1.2.2 Polyethylene terephthalate (PET) degrading α/β hydrolases .................................. 4 1.3 Metagenome screening for novel biocatalysts ............................................................... 6 1.4 Intention of this work ..................................................................................................... 7 2 Material and Methods ......................................................................................................... 9 2.1 Bacterial strains, plasmids and respective cultivation conditions ................................... 9 2.1.1 Bacterial strains ...................................................................................................... 9 2.1.2 Cultivating D. maricopensis, P. brachysporum and V. gazogenes .......................... 9 2.1.3 Cultivating E. coli strains ........................................................................................ 9 2.1.4 Enrichment of environmental samples containing PET degrading organisms ....... 10 2.2 Vectors, primers and Constructs used in this work ...................................................... 10 2.3 Transmission electron microscopy (TEM) and Scanning electron microscopy (SEM) .. 11 2.4 Function based screening of metagenome libraries .................................................... 12 2.4.1 Preparation of indicator plates .............................................................................. 12 2.4.2 Subcloning of potential PET hydrolase ORF’s from fosmid clones ....................... 13 2.5 Sequence based screening of metagenome libraries and databases .......................... 14 2.5.1 Construction of a Hidden Markov model ............................................................... 15 2.6 PET hydrolase expression in E. coli ............................................................................ 15 2.6.1 Cloning of PET2, PET5, PET6 and PET12 in E.coli ............................................. 15 2.6.2 Expression and purification .................................................................................. 16 Table of Contents II 2.7 Characterization of PET2, PET5, PET6 and PET12 .................................................... 17 2.7.1 para-nitrophenol (pNP) ester assay ...................................................................... 17 2.7.2 High-performance liquid chromatography (HPLC) measurements ........................ 18 2.8 Bioinformatic software ................................................................................................. 19 3 Results .............................................................................................................................. 21 3.1 Enrichment of PET degrading organisms .................................................................... 21 3.2 Function based screening of metagenomic libraries with indicator-plates .................... 22 3.3 Sequence based screening via a self-constructed HMM ............................................. 23 3.3.1 Alignment of known PET hydrolase sequences and construction of the HMM ...... 23 3.3.2 Seeking and classification of potential PET hydrolases from databases ............... 24 3.3.3 Seeking PET hydrolases within metagenomic datasets ........................................ 24 3.4 Characterization of the potential PET hydrolases PET2, PET5, PET6 and PET12 ...... 28 3.4.1 Plate assay .......................................................................................................... 29 3.4.2 Substrate specificity, temperature optimum and temperature stability .................. 30 3.4.3 Optimum pH ......................................................................................................... 32 3.4.4 Effect of metal ions, inhibitors detergents and solvents ........................................ 33 3.4.5 HPLC measurement of PET degradation products ............................................... 37 3.5 in silico analysis of functional tested PET hydrolases from this work ........................... 38 4 Discussion ........................................................................................................................ 41 4.1 Enrichment of a PET adhering Comamonas sp. strain ................................................ 41 4.2 Function vs. sequence based screening of novel PET hydrolyzing enzymes from metagenomes and databases ................................................................................................ 42 4.2.1 Analysis of database-derived sequence data and unraveling the taxonomic diversity of PET hydrolases ................................................................................................ 44 4.2.2 Worldwide distribution of PET hydrolases within terrestrial and marine metagenomes .................................................................................................................... 45 4.3 Biochemical characterization of PET hydrolases found by sequence mining ............... 46 4.3.1 Cloning and expression of highly toxic PET hydrolases ........................................ 47 Table of Contents III 4.3.2 Functional analysis revealing highly promiscuous and stable hydrolases ............. 47 4.4 in silico analysis of the new PET hydrolase PET2 ....................................................... 49 5 Conclusions and outlook ................................................................................................. 50 6 Appendix ........................................................................................................................... 52 7 References ........................................................................................................................ 84 8 Acknowledgments ............................................................................................................ 95 List of Figures I List of Figures Figure 1: Polycondensation of terephthalic acid (TPA) and ethylene glycole (EG) ....................... 1 Figure 2: Schematic overview of the partial PET degradation by bacteria ................................... 4 Figure 3: The canonical structure of α/β‑hydrolases ................................................................... 5 Figure 4: Schematic workflow of this study .................................................................................. 8 Figure 5: General procedure of constructing/refining the HMM .................................................. 14 Figure 6: Overlaid HPLC chromatogram from isocratic separation of TPA and BHET ............... 19 Figure 7: Microscopic imaging of Comamonas sp. .................................................................... 21 Figure 8: DEP hydrolase from the fosmid AL103_F12 ............................................................... 22 Figure 9: HMM logos of PET hydrolysis relevant motifs ............................................................. 23 Figure 10: Combined phylogenetic assignment of metagenomic PET hydrolase hits ................ 25 Figure 11: Taxonomical distribution on phylum level of PET hydrolase hits from metagenome records ...................................................................................................................................... 27 Figure 12: Geographical distribution of all used metagenomic datasets containing significant PET hydrolase hits .................................................................................................................... 28 Figure 13: Western blot analysis of partially purified PET hydrolases found in this study ........... 29 Figure 14: Plate
Load more

Recommended publications
  • Battistuzzi2009chap07.Pdf
    Eubacteria Fabia U. Battistuzzia,b,* and S. Blair Hedgesa shown increasing support for lower-level phylogenetic Department of Biology, 208 Mueller Laboratory, The Pennsylvania clusters (e.g., classes and below), they have also shown the State University, University Park, PA 16802-5301, USA; bCurrent susceptibility of eubacterial phylogeny to biases such as address: Center for Evolutionary Functional Genomics, The Biodesign horizontal gene transfer (HGT) (20, 21). Institute, Arizona State University, Tempe, AZ 85287-5301, USA In recent years, three major approaches have been used *To whom correspondence should be addressed (Fabia.Battistuzzi@ asu.edu) for studying prokaryote phylogeny with data from com- plete genomes: (i) combining gene sequences in a single analysis of multiple genes (e.g., 7, 9, 10), (ii) combining Abstract trees from individual gene analyses into a single “super- tree” (e.g., 22, 23), and (iii) using the presence or absence The ~9400 recognized species of prokaryotes in the of genes (“gene content”) as the raw data to investigate Superkingdom Eubacteria are placed in 25 phyla. Their relationships (e.g., 17, 18). While the results of these dif- relationships have been diffi cult to establish, although ferent approaches have not agreed on many details of some major groups are emerging from genome analyses. relationships, there have been some points of agreement, A molecular timetree, estimated here, indicates that most such as support for the monophyly of all major classes (85%) of the phyla and classes arose in the Archean Eon and some phyla (e.g., Proteobacteria and Firmicutes). (4000−2500 million years ago, Ma) whereas most (95%) of 7 ese A ndings, although criticized by some (e.g., 24, 25), the families arose in the Proterozoic Eon (2500−542 Ma).
    [Show full text]
  • Recent Advances in Biocatalysts Engineering for Polyethylene Terephthalate Plastic Waste Green Recycling
    Environment International 145 (2020) 106144 Contents lists available at ScienceDirect Environment International journal homepage: www.elsevier.com/locate/envint Review article Recent advances in biocatalysts engineering for polyethylene terephthalate plastic waste green recycling Nadia A. Samak a,b,c,1, Yunpu Jia a,b,1, Moustafa M. Sharshar a,b, Tingzhen Mu a, Maohua Yang a, Sumit Peh a,b, Jianmin Xing a,b,* a CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China b College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China c Processes Design and Development Department, Egyptian Petroleum Research Institute, Nasr City, 11727 Cairo, Egypt ARTICLE INFO ABSTRACT Handling Editor: Guo-ping Sheng The massive waste of poly(ethylene terephthalate) (PET) that ends up in the landfills and oceans and needs hundreds of years for degradation has attracted global concern. The poor stability and productivity of the Keywords: available PET biocatalysts hinder their industrial applications. Active PET biocatalysts can provide a promising Plastic waste avenue for PET bioconversion and recycling. Therefore, there is an urgent need to develop new strategies that Poly(ethylene terephthalate) could enhance the stability, catalytic activity, solubility, productivity, and re-usability of these PET biocatalysts Recycling under harsh conditions such as high temperatures, pH, and salinity. This has raised great attention in using Biocatalysts ’ Bioengineering bioengineering strategies to improve PET biocatalysts robustness and catalytic behavior. Herein, historical and forecasting data of plastic production and disposal were critically reviewed.
    [Show full text]
  • Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis
    International Journal of Molecular Sciences Review Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis David Johane Machate 1, Priscila Silva Figueiredo 2 , Gabriela Marcelino 2 , Rita de Cássia Avellaneda Guimarães 2,*, Priscila Aiko Hiane 2 , Danielle Bogo 2, Verônica Assalin Zorgetto Pinheiro 2, Lincoln Carlos Silva de Oliveira 3 and Arnildo Pott 1 1 Graduate Program in Biotechnology and Biodiversity in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] (D.J.M.); [email protected] (A.P.) 2 Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; pri.fi[email protected] (P.S.F.); [email protected] (G.M.); [email protected] (P.A.H.); [email protected] (D.B.); [email protected] (V.A.Z.P.) 3 Chemistry Institute, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-67-3345-7416 Received: 9 March 2020; Accepted: 27 March 2020; Published: 8 June 2020 Abstract: Long-term high-fat dietary intake plays a crucial role in the composition of gut microbiota in animal models and human subjects, which affect directly short-chain fatty acid (SCFA) production and host health. This review aims to highlight the interplay of fatty acid (FA) intake and gut microbiota composition and its interaction with hosts in health promotion and obesity prevention and its related metabolic dysbiosis.
    [Show full text]
  • World Journal of Clinical Cases
    World Journal of W J C C Clinical Cases Submit a Manuscript: http://www.f6publishing.com World J Clin Cases 2018 April 16; 6(4): 54-63 DOI: 10.12998/wjcc.v6.i4.54 ISSN 2307-8960 (online) ORIGINAL ARTICLE Observational Study Correlations between microbial communities in stool and clinical indicators in patients with metabolic syndrome Lang Lin, Zai-Bo Wen, Dong-Jiao Lin, Jiang-Ting Dong, Jie Jin, Fei Meng Lang Lin, Zai-Bo Wen, Dong-Jiao Lin, Jiang-Ting Dong, the use is non-commercial. See: http://creativecommons.org/ Department of Gastroenterology, Cangnan People’s Hospital, licenses/by-nc/4.0/ Cangnan 325800, Zhejiang Province, China Manuscript source: Unsolicited manuscript Jie Jin, Fei Meng, Department of Research Service, Zhiyuan Medical Inspection Institute CO., LTD, Hangzhou 310030, Correspondence to: Lang Lin, MSc, Chief Doctor, Department Zhejiang Province, China of Gastroenterology, Cangnan People’s Hospital, Lingxi Town, Yucang Road No.195, Cangnan 325800, Zhejiang Province, ORCID number: Lang Lin (0000-0001-5879-7487); Zai-Bo Wen China. [email protected] (0000-0003-1290-0404); Dong-Jiao Lin (0000-0001-5186-8182); Jiang- Telephone: +86-577-64767351 Ting Dong (0000-0002-6433-0143); Jie Jin (0000-0003-1481-5107); Fei Fax: +86-577-64767351 Meng (0000-0003-1233-4270). Received: January 2, 2018 Author contributions: Lin L formulated the problem; Wen ZB, Peer-review started: January 2, 2018 Lin DJ and Dong JT collected samples; Meng F performed 16S First decision: January 18, 2018 rDNA sequencing; Jin J analyzed the data; Lin L and Jin J wrote Revised: February 2, 2018 the paper.
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • 2019 Abstracts
    We are delighted EDITORIAL to welcome the worldwide yeast community in Gothenburg for ICYGMB2019! The “International Yeast Conferences” started in the 1960s with a handful of delegates and since then have become THE most important event in yeast research. Now the yeast meeting to returns to Gothenburg. Many yeast researchers still remember the meeting in 2003 with over 1,100 delegates, a truly memorable event. The Life Sciences are changing, and yeast research remains at their forefront. Advancements in genome sequencing and genome editing just make yeast more exciting as model organism in basic cell biological research, genome evolution and as a tool for synthetic biology and biotechnology. One of the most important reasons for the enormous success of yeast research lies in the unique character of the international yeast research community. No other community employs such a free exchange and access to information and research tools. Nor has any other community had the ability to build – even intercontinental – consortia of critical mass to tackle large‐scale projects, such as in sequencing the first eukaryotic genome or the first comprehensive yeast knockout library. Yeast2019 is the meeting of the international yeast research community where the latest, and even unpublished results are exchanged, and new projects, alliances, and collaborations are founded. A do‐not‐miss‐event. We attempt to incorporate the present excitement in yeast research in the programme of yeast2019. We are confident that this conference will contain important news and information for all yeast researchers. Taken together, yeast2019 will provide an up‐ to‐date overview in yeast research and it will set the scene for years to come.
    [Show full text]
  • A Genomic Timescale of Prokaryote Evolution: Insights Into the Origin of Methanogenesis, Phototrophy, and the Colonization of Land
    BMC Evolutionary Biology BioMed Central Research article Open Access A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land Fabia U Battistuzzi1, Andreia Feijao2 and S Blair Hedges*1 Address: 1NASA Astrobiology Institute and Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA and 2European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany Email: Fabia U Battistuzzi - [email protected]; Andreia Feijao - [email protected]; S Blair Hedges* - [email protected] * Corresponding author Published: 09 November 2004 Received: 07 August 2004 Accepted: 09 November 2004 BMC Evolutionary Biology 2004, 4:44 doi:10.1186/1471-2148-4-44 This article is available from: http://www.biomedcentral.com/1471-2148/4/44 © 2004 Battistuzzi et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (~7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. Results: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes.
    [Show full text]
  • Teaching About the Unintended Consequences of Plastics Tamara
    From Disposable Culture to Disposable People: Teaching About the Unintended Consequences of Plastics Tamara "Sasha" Adkins, MPH Dissertation Committee Dr. Alesia Maltz, Committee Chair Core Faculty, Environmental Studies, Antioch University New England Dr. Abigail Abrash Walton, Teaching Faculty, Environmental Studies, Antioch University New England Dr. Janaki Natarajan Tschannerl, Director, SPARK Teacher Education / Educational Praxis & Director, Bapagrama Educational Center, Bangalore, India From Disposable Culture to Disposable People: Teaching About the Unintended Consequences of Plastics By Tamara "Sasha" Adkins, DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Ph.D. in the Department of Environmental Studies Antioch University New England Keene, New Hampshire November 2017 Copyright 2017 Tamara “Sasha” Adkins All Rights Reserved Dedication Zendaya, To you I dedicate not only this dissertation but all my work to shape a world where no one is disposable. i Acknowledgments Alesia, my adviser and mentor for the past decade, sets a high bar for wisdom, compassion, and kindness. I will always remember you saying, "Oh, sweetie, too many sighs! If you are not having fun (with the dissertation research) then something is wrong." Thank you for not only patiently drawing out my best work, but for making the process a delightful one. Janaki, thank you for all I am learning from you in Spark and through this process. Abi joined my committee officially in my final semester, but had already been giving me encouragement and support for many years. It is much appreciated. I'd like to thank Charles Curtin, who served on my committee for a time, but due to extenuating circumstances, was not able to continue in that role.
    [Show full text]
  • Genes Preferring Non-AUG Start Codons in Bacteria Abstract
    Genes Preferring Non-AUG Start Codons in Bacteria 1,2 2,3,4 Anne Gvozdjak ​ and Manoj P. Samanta ​ ​ 1. Bellevue High School, 10416 SE Wolverine Way, Bellevue, WA 98004 2. Coding for Life Science, Redmond, WA 98053 3. Systemix Institute, Redmond, WA 98053 4. [email protected] Abstract Here we investigate translational regulation in bacteria by analyzing the distribution of start codons in fully assembled genomes. We report 36 genes (infC, rpoC, rnpA, etc.) showing a preference for non-AUG start codons in evolutionarily diverse phyla (“non-AUG genes”). Most of the non-AUG genes are functionally associated with translation, transcription or replication. In E. ​ coli, the percentage of essential genes among these 36 is significantly higher than among all ​ genes. Furthermore, the functional distribution of these genes suggests that non-AUG start codons may be used to reduce gene expression during starvation conditions, possibly through translational autoregulation or IF3-mediated regulation. Introduction Understanding the regulation of gene expression at the transcriptional and translational levels is a key step in deciphering the information contained by genomes. Whereas inexpensive, high-throughput technologies (ChIP-seq, RNAseq) are helping in extensive experimental investigation of transcriptional regulation [1,2], the measurement of translational regulation using ​ ​ high-throughput mass spectroscopy [3] is less widely adopted. Bioinformatics provides another ​ avenue to leverage the rapidly falling cost of DNA sequencing to explore translational regulation. Prior to 2000, computational researchers identified a number of relevant patterns through the comparative analysis of gene sequences [4,5] . With the availability of ~250,000 ​ prokaryotic genomes, thousands of eukaryotic genomes, and additional metagenomic sequences, those patterns can now be studied at a significantly larger scale, and new patterns may also be identified.
    [Show full text]
  • Studies with PET-Hydrolyzing Enzymes
    MASTERARBEIT / MASTER’S THESIS Titel der Masterarbeit / Title of the Master‘s Thesis „Investigating the properties of PET-hydrolase and PBS- depolymerase“ verfasst von / submitted by Christoph Clemens Hinterberger, BSc angestrebter akademischer Grad / in partial fulfilment of the requirements for the degree of Master of Science (MSc) Wien, 2018/ Vienna 2018 Studienkennzahl lt. Studienblatt / A 066 830 degree programme code as it appears on the student record sheet: Studienrichtung lt. Studienblatt / Masterstudium Molekulare degree programme as it appears on Mikrobiologie, Mikrobielle Ökologie und the student record sheet: Immunbiologie Betreut von / Supervisor: Univ.-Prof. Dr. Udo Bläsi Declaration I hereby declare that this thesis was composed by myself, that the work contained herein is my own except where explicitly stated otherwise in the text, and that this work has not been submitted for any other degree or processional qualification except as specified. Acknowledgements First and foremost, I have to thank Prof. Uwe T. Bornscheuer, who gave me the opportunity of working on this topic, and Dr. Dominique Böttcher, for supervising my work. My thanks also go out to everyone in Dr. Bornscheuer’s group, who helped me along the way, especially to the ever smiling Lukas. Furthermore I have to thank people in my life which made all of this possible: My parents who support me on every step on the road, my siblings, Paul, Max, Tao Su and everyone else in the hard core, Nils and everyone else from the Pack, Linda and Michelle and finally Julia. You’ve all done more than you think. Table of Contents Declaration .............................................................................................................................................. 2 Acknowledgements ................................................................................................................................
    [Show full text]
  • Enzymatic PET Degradation
    GREEN AND SUSTAINABLE CHEMISTRY CHIMIA 2019, 73, No. 9 743 doi:10.2533/chimia.2019.743 Chimia 73 (2019) 743–749 © Swiss Chemical Society Enzymatic PET Degradation Athena Papadopoulou§, Katrin Hecht§, and Rebecca Buller* Abstract: Plastic, in the form of packaging material, disposables, clothing and other articles with a short lifespan, has become an indispensable part of our everyday life. The increased production and use of plastic, however, accelerates the accumulation of plastic waste and poses an increasing burden on the environment with negative effects on biodiversity and human health. PET, a common thermoplastic, is recycled in many countries via ther- mal, mechanical and chemical means. Recently, several enzymes have been identified capable of degrading this recalcitrant plastic, opening possibilities for the biological recycling of the omnipresent material. In this review, we analyze the current knowledge of enzymatic PET degradation and discuss advances in improving the involved enzymes via protein engineering. Looking forward, the use of plastic degrading enzymes may facilitate sustain- able plastic waste management and become an important tool for the realization of a circular plastic economy. Keywords: Biocatalysis · Biodegradation · Enzyme engineering · Plastic recycling · PET Dr. Athena Papadopoulou studied Biology 1. Introduction and received her BSc from the University Plastic has become an omnipresent material in our daily life of Ioannina. She completed her MSc in and, as a consequence, the plastic industry has become the seventh Chemistry with a focus on Chemical and most important industry in Europe, employing more than 1.5 mil- Biochemical Technologies. In 2013 she lion people with a turnover of 355 billion Euros in 2017.[1] Plastic moved to Biotechnology group at the production is cheap and the generated plastic items are durable University of Ioannina to pursue her PhD and versatile.
    [Show full text]
  • Prokaryotic Gene Start Prediction: Algorithms for Genomes and Metagenomes
    PROKARYOTIC GENE START PREDICTION: ALGORITHMS FOR GENOMES AND METAGENOMES A Dissertation Presented to The Academic Faculty By Karl Gemayel In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Computational Science and Engineering Georgia Institute of Technology December 2020 © Karl Gemayel 2020 PROKARYOTIC GENE START PREDICTION: ALGORITHMS FOR GENOMES AND METAGENOMES Thesis committee: Dr. Mark Borodovsky Dr. Polo Chau School of Computational Science and En- School of Computational Science and En- gineering and Department of Biomedical gineering Engineering Georgia Institute of Technology Georgia Institute of Technology Dr. Umit¨ C¸atalyurek¨ Dr. King Jordan School of Computational Science and En- School of Biological Sciences gineering Georgia Institute of Technology Georgia Institute of Technology Dr. Pen Qui Department of Biomedical Engineering Georgia Institute of Technology Date approved: October 31, 2020 Wooster: “There are moments, Jeeves, when one asks oneself, ‘Do trousers matter?’” Jeeves: “The mood will pass, sir.” P.G. Wodehouse, The Code Of The Woosters To Mom and Dad, all my ancestors, and the first self-replicating molecule. Without you, this work would literally not have been possible. ACKNOWLEDGMENTS I am bound to forget someone or something and so, in fairness to all, I will forget most things and keep this vague and terse, though not necessarily short. I was very much at the right place at the right time to do this work, a time where these problems had not yet been solved. To the driven students who graduated early enough before such ideas came to them, thank you for being considerate. To my advisor Mark Borodovsky, who insisted that a lack of community funding for prokaryotic gene finding does not mean that the problem has actually been solved, thank you for continuously pushing for rigorous science that questions accepted beliefs.
    [Show full text]