skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes

Abstract

ABSTRACT Polyethylene terephthalate (PET) is one of the most important synthetic polymers used today. Unfortunately, the polymers accumulate in nature and to date no highly active enzymes are known that can degrade it at high velocity. Enzymes involved in PET degradation are mainly α- and β-hydrolases, like cutinases and related enzymes (EC 3.1.1). Currently, only a small number of such enzymes are well characterized. In this work, a search algorithm was developed that identified 504 possible PET hydrolase candidate genes from various databases. A further global search that comprised more than 16 Gb of sequence information within 108 marine and 25 terrestrial metagenomes obtained from the Integrated Microbial Genome (IMG) database detected 349 putative PET hydrolases. Heterologous expression of four such candidate enzymes verified the function of these enzymes and confirmed the usefulness of the developed search algorithm. In this way, two novel and thermostable enzymes with high potential for downstream application were partially characterized. Clustering of 504 novel enzyme candidates based on amino acid similarities indicated that PET hydrolases mainly occur in the phyla ofActinobacteria,Proteobacteria, andBacteroidetes. Within theProteobacteria, theBetaproteobacteria,Deltaproteobacteria, andGammaproteobacteriawere the main hosts. Remarkably enough, in the marine environment, bacteria affiliated with the phylumBacteroidetesappear to be the main hostsmore » of PET hydrolase genes, rather thanActinobacteriaorProteobacteria, as observed for the terrestrial metagenomes. Our data further imply that PET hydrolases are truly rare enzymes. The highest occurrence of 1.5 hits/Mb was observed in sequences from a sample site containing crude oil. IMPORTANCEPolyethylene terephthalate (PET) accumulates in our environment without significant microbial conversion. Although a few PET hydrolases are already known, it is still unknown how frequently they appear and with which main bacterial phyla they are affiliated. In this study, deep sequence mining of protein databases and metagenomes demonstrated that PET hydrolases indeed occur at very low frequencies in the environment. Furthermore, it was possible to link them to phyla that were previously not known to harbor such enzymes. This work contributes novel knowledge on the phylogenetic relationships, the recent evolution, and the global distribution of PET hydrolases. Finally, we describe the biochemical traits of four novel PET hydrolases.« less

Authors:
 [1];  [1];  [1]; ORCiD logo [2];  [2];  [3];  [4]; ORCiD logo [5];  [1]
  1. University of Hamburg (Germany). Department of Microbiology and Biotechnology, Biocenter Klein Flottbek
  2. Leipzig University (Germany). Institute of Biochemistry, Department of Microbiology and Bioprocess Technology
  3. evoxx technologies GmbH, Monheim am Rhein (Germany)
  4. Chengdu Institute of Biology, Chengdu (China)
  5. Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1468057
Alternate Identifier(s):
OSTI ID: 1479396
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 84; Journal Issue: 8; Journal ID: ISSN 0099-2240
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Danso, Dominik, Schmeisser, Christel, Chow, Jennifer, Zimmermann, Wolfgang, Wei, Ren, Leggewie, Christian, Li, Xiangzhen, Hazen, Terry C., and Streit, Wolfgang R. New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes. United States: N. p., 2018. Web. https://doi.org/10.1128/AEM.02773-17.
Danso, Dominik, Schmeisser, Christel, Chow, Jennifer, Zimmermann, Wolfgang, Wei, Ren, Leggewie, Christian, Li, Xiangzhen, Hazen, Terry C., & Streit, Wolfgang R. New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes. United States. https://doi.org/10.1128/AEM.02773-17
Danso, Dominik, Schmeisser, Christel, Chow, Jennifer, Zimmermann, Wolfgang, Wei, Ren, Leggewie, Christian, Li, Xiangzhen, Hazen, Terry C., and Streit, Wolfgang R. Mon . "New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes". United States. https://doi.org/10.1128/AEM.02773-17. https://www.osti.gov/servlets/purl/1468057.
@article{osti_1468057,
title = {New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes},
author = {Danso, Dominik and Schmeisser, Christel and Chow, Jennifer and Zimmermann, Wolfgang and Wei, Ren and Leggewie, Christian and Li, Xiangzhen and Hazen, Terry C. and Streit, Wolfgang R.},
abstractNote = {ABSTRACT Polyethylene terephthalate (PET) is one of the most important synthetic polymers used today. Unfortunately, the polymers accumulate in nature and to date no highly active enzymes are known that can degrade it at high velocity. Enzymes involved in PET degradation are mainly α- and β-hydrolases, like cutinases and related enzymes (EC 3.1.1). Currently, only a small number of such enzymes are well characterized. In this work, a search algorithm was developed that identified 504 possible PET hydrolase candidate genes from various databases. A further global search that comprised more than 16 Gb of sequence information within 108 marine and 25 terrestrial metagenomes obtained from the Integrated Microbial Genome (IMG) database detected 349 putative PET hydrolases. Heterologous expression of four such candidate enzymes verified the function of these enzymes and confirmed the usefulness of the developed search algorithm. In this way, two novel and thermostable enzymes with high potential for downstream application were partially characterized. Clustering of 504 novel enzyme candidates based on amino acid similarities indicated that PET hydrolases mainly occur in the phyla ofActinobacteria,Proteobacteria, andBacteroidetes. Within theProteobacteria, theBetaproteobacteria,Deltaproteobacteria, andGammaproteobacteriawere the main hosts. Remarkably enough, in the marine environment, bacteria affiliated with the phylumBacteroidetesappear to be the main hosts of PET hydrolase genes, rather thanActinobacteriaorProteobacteria, as observed for the terrestrial metagenomes. Our data further imply that PET hydrolases are truly rare enzymes. The highest occurrence of 1.5 hits/Mb was observed in sequences from a sample site containing crude oil. IMPORTANCEPolyethylene terephthalate (PET) accumulates in our environment without significant microbial conversion. Although a few PET hydrolases are already known, it is still unknown how frequently they appear and with which main bacterial phyla they are affiliated. In this study, deep sequence mining of protein databases and metagenomes demonstrated that PET hydrolases indeed occur at very low frequencies in the environment. Furthermore, it was possible to link them to phyla that were previously not known to harbor such enzymes. This work contributes novel knowledge on the phylogenetic relationships, the recent evolution, and the global distribution of PET hydrolases. Finally, we describe the biochemical traits of four novel PET hydrolases.},
doi = {10.1128/AEM.02773-17},
journal = {Applied and Environmental Microbiology},
number = 8,
volume = 84,
place = {United States},
year = {2018},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Identification and Characterization of Bacterial Cutinase
journal, July 2008

  • Chen, Sheng; Tong, Xing; Woodard, Ronald W.
  • Journal of Biological Chemistry, Vol. 283, Issue 38
  • DOI: 10.1074/jbc.M800848200

Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca
journal, April 2014

  • Roth, Christian; Wei, Ren; Oeser, Thorsten
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 18
  • DOI: 10.1007/s00253-014-5672-0

Production of a recombinant polyester-cleaving hydrolase from Thermobifida fusca in Escherichia coli
journal, June 2006

  • Dresler, Karolin; van den Heuvel, Joop; Müller, Rolf-Joachim
  • Bioprocess and Biosystems Engineering, Vol. 29, Issue 3
  • DOI: 10.1007/s00449-006-0069-9

Isolation and characterization of a new alkali-thermostable lipase cloned from a metagenomic library
journal, March 2009

  • Meilleur, Catherine; Hupé, Jean-François; Juteau, Pierre
  • Journal of Industrial Microbiology & Biotechnology, Vol. 36, Issue 6
  • DOI: 10.1007/s10295-009-0562-7

Evidence of Polyethylene Biodegradation by Bacterial Strains from the Guts of Plastic-Eating Waxworms
journal, November 2014

  • Yang, Jun; Yang, Yu; Wu, Wei-Min
  • Environmental Science & Technology, Vol. 48, Issue 23
  • DOI: 10.1021/es504038a

UniProt: the universal protein knowledgebase
journal, November 2016


Polyethylene Terephthalate May Yield Endocrine Disruptors
journal, April 2010


Plant biomass degradation by gut microbiomes: more of the same or something new?
journal, June 2009


A New Esterase from Thermobifida halotolerans Hydrolyses Polyethylene Terephthalate (PET) and Polylactic Acid (PLA)
journal, February 2012

  • Ribitsch, Doris; Herrero Acero, Enrique; Greimel, Katrin
  • Polymers, Vol. 4, Issue 1
  • DOI: 10.3390/polym4010617

Microbial enzymes for the recycling of recalcitrant petroleum‐based plastics: how far are we?
journal, March 2017


Enzymatic Surface Hydrolysis of PET: Effect of Structural Diversity on Kinetic Properties of Cutinases from Thermobifida
journal, June 2011

  • Herrero Acero, Enrique; Ribitsch, Doris; Steinkellner, Georg
  • Macromolecules, Vol. 44, Issue 12
  • DOI: 10.1021/ma200949p

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
journal, June 2016


IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011

  • Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1044

Biodegradation and Mineralization of Polystyrene by Plastic-Eating Mealworms: Part 1. Chemical and Physical Characterization and Isotopic Tests
journal, October 2015

  • Yang, Yu; Yang, Jun; Wu, Wei-Min
  • Environmental Science & Technology, Vol. 49, Issue 20
  • DOI: 10.1021/acs.est.5b02661

Fast and sensitive protein alignment using DIAMOND
journal, November 2014

  • Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3176

A bacterium that degrades and assimilates poly(ethylene terephthalate)
journal, March 2016


Diversity of polyester-degrading bacteria in compost and molecular analysis of a thermoactive esterase from Thermobifida alba AHK119
journal, April 2010

  • Hu, Xiaoping; Thumarat, Uschara; Zhang, Xian
  • Applied Microbiology and Biotechnology, Vol. 87, Issue 2
  • DOI: 10.1007/s00253-010-2555-x

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes
journal, May 2016

  • Foley, Matthew H.; Cockburn, Darrell W.; Koropatkin, Nicole M.
  • Cellular and Molecular Life Sciences, Vol. 73, Issue 14
  • DOI: 10.1007/s00018-016-2242-x

Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes: Xylan degradation by gut Bacteroidetes
journal, December 2010


Crystal structure of cutinase Est119 from Thermobifida alba AHK119 that can degrade modified polyethylene terephthalate at 1.76Å resolution
journal, May 2012


Plastic Degradation and Its Environmental Implications with Special Reference to Poly(ethylene terephthalate)
journal, December 2012

  • Webb, Hayden; Arnott, Jaimys; Crawford, Russell
  • Polymers, Vol. 5, Issue 1
  • DOI: 10.3390/polym5010001

Studies on transformation of Escherichia coli with plasmids
journal, June 1983


Biochemical and genetic analysis of a cutinase-type polyesterase from a thermophilic Thermobifida alba AHK119
journal, December 2011

  • Thumarat, Uschara; Nakamura, Ryota; Kawabata, Takeshi
  • Applied Microbiology and Biotechnology, Vol. 95, Issue 2
  • DOI: 10.1007/s00253-011-3781-6

The α / β hydrolase fold
journal, January 1992

  • Ollis, David L.; Cheah, Eong; Cygler, Miroslaw
  • "Protein Engineering, Design and Selection", Vol. 5, Issue 3
  • DOI: 10.1093/protein/5.3.197

Protein production by auto-induction in high-density shaking cultures
journal, May 2005


Insights into the Phylogeny and Metabolic Potential of a Primary Tropical Peat Swamp Forest Microbial Community by Metagenomic Analysis
journal, November 2010

  • Kanokratana, Pattanop; Uengwetwanit, Tanaporn; Rattanachomsri, Ukrit
  • Microbial Ecology, Vol. 61, Issue 3
  • DOI: 10.1007/s00248-010-9766-7

Engineered bacterial polyester hydrolases efficiently degrade polyethylene terephthalate due to relieved product inhibition: Engineered Polyester Hydrolases
journal, February 2016

  • Wei, Ren; Oeser, Thorsten; Schmidt, Juliane
  • Biotechnology and Bioengineering, Vol. 113, Issue 8
  • DOI: 10.1002/bit.25941

Environmental implications of plastic debris in marine settings—entanglement, ingestion, smothering, hangers-on, hitch-hiking and alien invasions
journal, July 2009

  • Gregory, Murray R.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 364, Issue 1526
  • DOI: 10.1098/rstb.2008.0265

Environmental and Gut Bacteroidetes: The Food Connection
journal, January 2011

  • Thomas, François; Hehemann, Jan-Hendrik; Rebuffet, Etienne
  • Frontiers in Microbiology, Vol. 2
  • DOI: 10.3389/fmicb.2011.00093

Reevaluation of the taxonomy ofVibrio, beneckea, andPhotobacterium: Abolition of the genusBeneckea
journal, May 1980

  • Baumann, Paul; Baumann, Linda; Bang, Sookie S.
  • Current Microbiology, Vol. 4, Issue 3
  • DOI: 10.1007/BF02602814

Turbidimetric analysis of the enzymatic hydrolysis of polyethylene terephthalate nanoparticles
journal, May 2014


The Protein Data Bank
journal, January 2000


Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach
journal, December 2011

  • Sulaiman, Sintawee; Yamato, Saya; Kanaya, Eiko
  • Applied and Environmental Microbiology, Vol. 78, Issue 5
  • DOI: 10.1128/AEM.06725-11

T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
journal, September 2000

  • Notredame, Cédric; Higgins, Desmond G.; Heringa, Jaap
  • Journal of Molecular Biology, Vol. 302, Issue 1
  • DOI: 10.1006/jmbi.2000.4042

A novel Ca2+-activated, thermostabilized polyesterase capable of hydrolyzing polyethylene terephthalate from Saccharomonospora viridis AHK190
journal, June 2014

  • Kawai, Fusako; Oda, Masayuki; Tamashiro, Tomonari
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 24
  • DOI: 10.1007/s00253-014-5860-y

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
journal, October 2013

  • Tamura, Koichiro; Stecher, Glen; Peterson, Daniel
  • Molecular Biology and Evolution, Vol. 30, Issue 12
  • DOI: 10.1093/molbev/mst197

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models
journal, January 2014

  • Wheeler, Travis J.; Clements, Jody; Finn, Robert D.
  • BMC Bioinformatics, Vol. 15, Issue 1
  • DOI: 10.1186/1471-2105-15-7

Biodegradation of Aliphatic-Aromatic Copolyesters by Thermomonospora fusca and Other Thermophilic Compost Isolates
journal, May 1998

  • Kleeberg, Ilona; Hetz, Claudia; Kroppenstedt, Reiner Michael
  • Applied and Environmental Microbiology, Vol. 64, Issue 5
  • DOI: 10.1128/AEM.64.5.1731-1735.1998

    Works referencing / citing this record:

    Cyclohexane, naphthalene, and diesel fuel increase oxidative stress, CYP153 , sodA, and recA gene expression in Rhodococcus erythropolis
    journal, March 2019

    • Sazykin, Ivan; Makarenko, Maksim; Khmelevtsova, Ludmila
    • MicrobiologyOpen, Vol. 8, Issue 9
    • DOI: 10.1002/mbo3.855

    Ecology of the plastisphere
    journal, January 2020

    • Amaral-Zettler, Linda A.; Zettler, Erik R.; Mincer, Tracy J.
    • Nature Reviews Microbiology, Vol. 18, Issue 3
    • DOI: 10.1038/s41579-019-0308-0

    The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena
    journal, January 2020

    • Bollinger, Alexander; Thies, Stephan; Katzke, Nadine
    • Microbial Biotechnology, Vol. 13, Issue 1
    • DOI: 10.1111/1751-7915.13288

    Agar plate‐based screening methods for the identification of polyester hydrolysis by Pseudomonas species
    journal, January 2020

    • Molitor, Rebecka; Bollinger, Alexander; Kubicki, Sonja
    • Microbial Biotechnology, Vol. 13, Issue 1
    • DOI: 10.1111/1751-7915.13418

    Structural studies reveal the molecular mechanism of PET ase
    journal, August 2018

    • Chen, Chun‐Chi; Han, Xu; Ko, Tzu‐Ping
    • The FEBS Journal, Vol. 285, Issue 20
    • DOI: 10.1111/febs.14612

    Plastics: Environmental and Biotechnological Perspectives on Microbial Degradation
    journal, July 2019

    • Danso, Dominik; Chow, Jennifer; Streit, Wolfgang R.
    • Applied and Environmental Microbiology, Vol. 85, Issue 19
    • DOI: 10.1128/aem.01095-19

    Microbial Ecotoxicology of Marine Plastic Debris: A Review on Colonization and Biodegradation by the “Plastisphere”
    journal, April 2019

    • Jacquin, Justine; Cheng, Jingguang; Odobel, Charlène
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.00865

    Metagenomic Insights Into the Taxonomic and Functional Features of Kinema, a Traditional Fermented Soybean Product of Sikkim Himalaya
    journal, August 2019


    A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri – Structural and Functional Insights
    journal, February 2020

    • Bollinger, Alexander; Thies, Stephan; Knieps-Grünhagen, Esther
    • Frontiers in Microbiology, Vol. 11
    • DOI: 10.3389/fmicb.2020.00114

    Microbial Genes for a Circular and Sustainable Bio-PET Economy
    journal, May 2019

    • Salvador, Manuel; Abdulmutalib, Umar; Gonzalez, Jaime
    • Genes, Vol. 10, Issue 5
    • DOI: 10.3390/genes10050373