Gene_locus Report for: 9bact-c3ryl0

A thermostable enzyme PET2, found in a metagenome library, has been engineered to improve its hydrolytic activity against polyethylene terephthalate (PET). The PET2 wild-type (WT) showed a melting temperature of 69.0 C and produced water-soluble reaction products at a rate of 0.40 min-1 (2.4 microM products from 0.1 microM enzyme after 60 min reaction) from an amorphous PET film at 60 C. Mutations for surface charge modification, backbone stabilization, and formation of additional disulfide bond were introduced into the PET2 WT, and the best mutant (PET2 7M) showed a melting temperature of 75.7 C and hydrolytic activity of 1.3 min-1 (7.8 micrM products from 0.1 microM enzyme after 60 min reaction at 60 C). X-ray crystal structures of PET2 mutants showed that introduced arginine and lysine residues oriented to the solvent, similar to a PET hydrolase from Ideonella sakaiensis 201-F6. Single-molecule fluorescence imaging revealed that these positively charged surface residues increased binding rate constant of PET2 7M to PET surface 2.7 times, compared with PET2 WT, and resulted in higher activity. Optimal temperature for amorphous PET hydrolysis by PET2 7M (68 C) was 8 C higher than that by PET2 WT (60 C), and hydrolytic activity of PET2 7M at the optimal temperature (2.7 min-1, 16.2 microM products from 0.1 microM enzyme after 60 min reaction) was 6.8 times higher than that of PET2 WT (0.40 min-1). Furthermore, PET2 7M generated reaction products with a constant rate for at least 24 h at 68 C, indicating long-term thermal stability at the optimal temperature.

Polyethylene terephthalate (PET) is one of the most important synthetic polymers used nowadays. Unfortunately, the polymers accumulate in nature and until now, no highly active enzymes are known that can degrade it at high velocity. Enzymes involved in PET degradation are mainly alpha/beta-hydrolases like cutinases and related enzymes (E.C. 3.1.-). Currently, only a small number of such enzymes are well characterized. Within 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 IMG data base 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. Thereby, two novel and thermostable enzymes with high potential for downstream application were in part characterized. Clustering of 504 novel enzyme candidates based on amino acid similarities indicated that PET hydrolases mainly occur in the phylum of Actinobacteria, Proteobacteria and Bacteroidetes Within the Proteobacteria, the Beta-, Delta- and Gammaproteobacteria were the main hosts. Remarkably enough, in the marine environment, bacteria affiliated with the phylum of the Bacteroidetes appear to be the main host of PET hydrolase genes rather than Actinobacteria or Proteobacteria 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 a sample site containing crude oil.IMPORTANCE Polyethylene terephthalate (PET) accumulates in our environment without significant microbial conversion. Although few PET hydrolases are already known it is still unknown how frequent they appear and which main bacterial phyla they are affiliated with. In this study, deep sequence mining of protein databases and metagenomes demonstrated that PET hydrolases indeed are occurring at very low frequencies in the environment. Further it was possible to link them to phyla which were previously unknown to harbor such enzymes. This work contributes novel knowledge to the phylogenetic relationship, the recent evolution and the global distribution of PET hydrolases. Finally, we describe biochemical traits of four novel PET hydrolases.

The construction of a cosmid library from the biomass produced in an enriched Sequencing Fed-Batch Reactor allowed the isolation of a new lipase by functional screening. The open reading frame of 928 bp encoded a polypeptide of 308 amino acids with a molecular mass of 32.6 kDa. The amino acid sequence analysis revealed the presence of the conserved pentapeptide GXSXG essential for lipase activity. Alignment with known sequences of proteins showed no more than 52% identity with different lipases, confirming the discovery of a novel gene sequence. The lipase was cloned and expressed in Streptomyces lividans and further purified by a combination of hydrophobic interaction and size-exclusion chromatography. Spectrophotometric assays with different p-nitrophenyl esters demonstrated a preference for long-length acyl chains, especially p-nitrophenylmyristate (C14). Moreover, the enzyme presented an optimal activity at 60 degrees C and at alkaline pH of 10.5.

Enzymatic deconstruction of poly(ethylene terephthalate) (PET) is under intense investigation, given the ability of hydrolase enzymes to depolymerize PET to its constituent monomers near the polymer glass transition temperature. To date, reported PET hydrolases have been sourced from a relatively narrow sequence space. Here, we identify additional PET-active biocatalysts from natural diversity by using bioinformatics and machine learning to mine 74 putative thermotolerant PET hydrolases. We successfully express, purify, and assay 51 enzymes from seven distinct phylogenetic groups; observing PET hydrolysis activity on amorphous PET film from 37 enzymes in reactions spanning pH from 4.5-9.0 and temperatures from 30-70 degreesC. We conduct PET hydrolysis time-course reactions with the best-performing enzymes, where we observe differences in substrate selectivity as function of PET morphology. We employed X-ray crystallography and AlphaFold to examine the enzyme architectures of all 74 candidates, revealing protein folds and accessory domains not previously associated with PET deconstruction. Overall, this study expands the number and diversity of thermotolerant scaffolds for enzymatic PET deconstruction.

A thermostable enzyme PET2, found in a metagenome library, has been engineered to improve its hydrolytic activity against polyethylene terephthalate (PET). The PET2 wild-type (WT) showed a melting temperature of 69.0 C and produced water-soluble reaction products at a rate of 0.40 min-1 (2.4 microM products from 0.1 microM enzyme after 60 min reaction) from an amorphous PET film at 60 C. Mutations for surface charge modification, backbone stabilization, and formation of additional disulfide bond were introduced into the PET2 WT, and the best mutant (PET2 7M) showed a melting temperature of 75.7 C and hydrolytic activity of 1.3 min-1 (7.8 micrM products from 0.1 microM enzyme after 60 min reaction at 60 C). X-ray crystal structures of PET2 mutants showed that introduced arginine and lysine residues oriented to the solvent, similar to a PET hydrolase from Ideonella sakaiensis 201-F6. Single-molecule fluorescence imaging revealed that these positively charged surface residues increased binding rate constant of PET2 7M to PET surface 2.7 times, compared with PET2 WT, and resulted in higher activity. Optimal temperature for amorphous PET hydrolysis by PET2 7M (68 C) was 8 C higher than that by PET2 WT (60 C), and hydrolytic activity of PET2 7M at the optimal temperature (2.7 min-1, 16.2 microM products from 0.1 microM enzyme after 60 min reaction) was 6.8 times higher than that of PET2 WT (0.40 min-1). Furthermore, PET2 7M generated reaction products with a constant rate for at least 24 h at 68 C, indicating long-term thermal stability at the optimal temperature.

Polyethylene terephthalate (PET) is one of the most important synthetic polymers used nowadays. Unfortunately, the polymers accumulate in nature and until now, no highly active enzymes are known that can degrade it at high velocity. Enzymes involved in PET degradation are mainly alpha/beta-hydrolases like cutinases and related enzymes (E.C. 3.1.-). Currently, only a small number of such enzymes are well characterized. Within 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 IMG data base 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. Thereby, two novel and thermostable enzymes with high potential for downstream application were in part characterized. Clustering of 504 novel enzyme candidates based on amino acid similarities indicated that PET hydrolases mainly occur in the phylum of Actinobacteria, Proteobacteria and Bacteroidetes Within the Proteobacteria, the Beta-, Delta- and Gammaproteobacteria were the main hosts. Remarkably enough, in the marine environment, bacteria affiliated with the phylum of the Bacteroidetes appear to be the main host of PET hydrolase genes rather than Actinobacteria or Proteobacteria 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 a sample site containing crude oil.IMPORTANCE Polyethylene terephthalate (PET) accumulates in our environment without significant microbial conversion. Although few PET hydrolases are already known it is still unknown how frequent they appear and which main bacterial phyla they are affiliated with. In this study, deep sequence mining of protein databases and metagenomes demonstrated that PET hydrolases indeed are occurring at very low frequencies in the environment. Further it was possible to link them to phyla which were previously unknown to harbor such enzymes. This work contributes novel knowledge to the phylogenetic relationship, the recent evolution and the global distribution of PET hydrolases. Finally, we describe biochemical traits of four novel PET hydrolases.

The construction of a cosmid library from the biomass produced in an enriched Sequencing Fed-Batch Reactor allowed the isolation of a new lipase by functional screening. The open reading frame of 928 bp encoded a polypeptide of 308 amino acids with a molecular mass of 32.6 kDa. The amino acid sequence analysis revealed the presence of the conserved pentapeptide GXSXG essential for lipase activity. Alignment with known sequences of proteins showed no more than 52% identity with different lipases, confirming the discovery of a novel gene sequence. The lipase was cloned and expressed in Streptomyces lividans and further purified by a combination of hydrophobic interaction and size-exclusion chromatography. Spectrophotometric assays with different p-nitrophenyl esters demonstrated a preference for long-length acyl chains, especially p-nitrophenylmyristate (C14). Moreover, the enzyme presented an optimal activity at 60 degrees C and at alkaline pH of 10.5.