Plastics degradation by hydrolytic enzymes: The plastics‐active enzymes database—PAZy

Abstract

Petroleum-based plastics are durable and accumulate in all ecological niches. Knowledge on enzymatic degradation is sparse. Today, less than 50 verified plastics-active enzymes are known. First examples of enzymes acting on the polymers polyethylene terephthalate (PET) and polyurethane (PUR) have been reported together with a detailed biochemical and structural description. Furthermore, very few polyamide (PA) oligomer active enzymes are known. In this article, the current known enzymes acting on the synthetic polymers PET and PUR are briefly summarized, their published activity data were collected and integrated into a comprehensive open access database. The Plastics-Active Enzymes Database (PAZy) represents an inventory of known and experimentally verified enzymes that act on synthetic fossil fuel-based polymers. Almost 3000 homologs of PET-active enzymes were identified by profile hidden Markov models. Over 2000 homologs of PUR-active enzymes were identified by BLAST. Based on multiple sequence alignments, conservation analysis identified the most conserved amino acids, and sequence motifs for PET-and PUR-active enzymes were derived.

Merging Plastics, Microbes, and Enzymes: Highlights from an International Workshop

“…Unfortunately, most of these labeled substrates are not yet commercially available. Finally, yet importantly, the development of bioinformatics tools and novel databases (e.g., PlasticDB, PMBD, and PAZy) ( 41 – 43 ) is crucial to identifying PDE from global metagenome/proteome data sets ( 20 ).…”

The first archaeal PET-degrading enzyme belongs to the feruloyl-esterase family

“…An HMM constructed from all PET-degrading enzymes listed in the PAZy database 16 was used to search against NCBI's non-redundant protein database (ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz) filtered for sequences of archaeal origin (tax ID: 2157) as described previously 13,23,32 .…”

“…Nevertheless, in recent years, several studies have identified microbial enzymes that are able to degrade some of these synthetic polymers, including PET, polyurethane (PUR), PA, and a few others from mainly renewable sources 13,15 . To date, approximately 120 enzymes have been described to act on these polymers (PAZy database 16 ), most of them being esterases, amidases, and oxygenases. Many of these proteins have relatively low conversion rates, show promiscuous activity or are only active on oligomers.…”

Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation

“…Quantification of plastic degradation and metaomics (metagenomics, metatranscriptomics, metaproteomics, and metabolomics) could be determined for these cultures in time-serial analysis for following microbial dynamics over polymer degradation. Through Hidden Markov Models (HMMs) and Basic Local Alignment Search Tools (BLAST), homology-based metagenomics identify putative degrading pathways or enzymes according to the similarity between query sequences and known sequences deposited in databases such as: MetaCyc and BioCyc ( Caspi et al, 2016 ), CAZy ( Cantarel et al, 2009 ), the University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (UM-BBD/PPS; Gao et al, 2010 ), Biochemical Network Integrated Computational Explorer (BNICE.ch; Hatzimanikatis et al, 2005 ), KEGG ( Kanehisa et al, 2014 ), Plastics Microbial Biodegradation Database (PMBD; Gan and Zhang, 2019 ), and Plastics-Active Enzymes Database (PAZy; Buchholz et al, 2022 ). Such powerful method could reveal the phylogenetic distribution of plastic degraders across the microbial tree of life, highlighting the diversity and evolution of these traits ( Gambarini et al, 2021 ).…”