Resources for Annotation of PolyHydroxyAlkanoate Synthases

Resources for Annotation of PolyHydroxyAlkanoate Synthases

Abstrakt

Current annotation of specific groups of enzymes is still limited by a lack of focused resources resulting in annotation with very general terms. This also applies to PolyHydroxyAlkanoates (PHA) synthases, enzymes capable of synthesizing microbial polyesters in various prokaryotic microorganisms that are often annotated simply as hydrolases. Therefore, we overlook the enormous biosynthetic capacity for novel green technologies because PHA themselves offer a solution to current challenges in the circular economy. Unlike petrochemical-based synthetic polymers, PHA are suitable for biological recycling offering sustainable, selective, and environmentally friendly plastic end-of-life options. PHA synthases are further divided into four different classes. While classes I and II are represented by monomers coded by phaC genes, classes III and IV are heterodimers coded beside phaC also phaE and phaR genes, respectively. As our recent results showed, while general resources like KEGG or COG contain entries on PHA synthases, they are mainly built around class I and II synthases and do not represent the actual division of PHA synthases. Here, we present our custom-made, manually curated, dataset of sequences coding PHA synthases considering all available current knowledge on their classification. Furthermore, we demonstrate the use of this dataset for annotation of PHA synthases in genomes of non-model bacteria using standard approaches based on sequence similarity and alignment like BLAST or Hidden Markov Models. Additionally, we show the limitation of their primary structure comparison and discuss the possible improvement based on predicted tertiary structure comparison.

Current annotation of specific groups of enzymes is still limited by a lack of focused resources resulting in annotation with very general terms. This also applies to PolyHydroxyAlkanoates (PHA) synthases, enzymes capable of synthesizing microbial polyesters in various prokaryotic microorganisms that are often annotated simply as hydrolases. Therefore, we overlook the enormous biosynthetic capacity for novel green technologies because PHA themselves offer a solution to current challenges in the circular economy. Unlike petrochemical-based synthetic polymers, PHA are suitable for biological recycling offering sustainable, selective, and environmentally friendly plastic end-of-life options. PHA synthases are further divided into four different classes. While classes I and II are represented by monomers coded by phaC genes, classes III and IV are heterodimers coded beside phaC also phaE and phaR genes, respectively. As our recent results showed, while general resources like KEGG or COG contain entries on PHA synthases, they are mainly built around class I and II synthases and do not represent the actual division of PHA synthases. Here, we present our custom-made, manually curated, dataset of sequences coding PHA synthases considering all available current knowledge on their classification. Furthermore, we demonstrate the use of this dataset for annotation of PHA synthases in genomes of non-model bacteria using standard approaches based on sequence similarity and alignment like BLAST or Hidden Markov Models. Additionally, we show the limitation of their primary structure comparison and discuss the possible improvement based on predicted tertiary structure comparison.

SEDLÁŘ, K.; HEŘMÁNKOVÁ, K.; UMAIR, M.; ŠABATOVÁ, K.

20.07.2025

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