Decoding Polyhydroxyalkanoate Synthase Genes: Insights from Database Searches

Decoding Polyhydroxyalkanoate Synthase Genes: Insights from Database Searches

Abstract

Polyhydroxyalkanoates (PHAs) are biodegradable polyesters synthesized and accumulated by prokaryotic microorganisms. The ability of these organisms to produce PHAs is encoded in their genomes. The current drawback is the hidden biosynthetic potential of prokaryotes which does not lie in the unavailability of genome sequencing and assembly, but rather in the following annotation processes. A major gap is related to PHA synthases, the enzymes responsible for PHA biosynthesis. This key enzyme in the formation of PHAs in the form of intracellular granules is being usually annotated as phaC or phbC gene. However, the recent review of PHA synthases shows that many genes are annotated as hypothetical protein coding. The first step to address this gap, is using the database searches for the overview of currently available PHA synthase gene sequences. We will utilize full-text searches based on gene abbreviations and enzyme identifiers. This includes searches in Kyoto Encyclopedia of Genes and Genomes (KEGG). The number of phaC genes in the KEGG GENES database is currently 4320 available under the EC 2.3.1.304. Another database including phaC genes is Clusters of Orthologous Genes (COG) currently with 1299 genes under identifier COG3243. Our work attempts to give an insight into the primary structure of PHA synthases by a combination of bioinformatics approaches to identify PHA synthase coding genes across annotated prokaryotic genomes.

Polyhydroxyalkanoates (PHAs) are biodegradable polyesters synthesized and accumulated by prokaryotic microorganisms. The ability of these organisms to produce PHAs is encoded in their genomes. The current drawback is the hidden biosynthetic potential of prokaryotes which does not lie in the unavailability of genome sequencing and assembly, but rather in the following annotation processes. A major gap is related to PHA synthases, the enzymes responsible for PHA biosynthesis. This key enzyme in the formation of PHAs in the form of intracellular granules is being usually annotated as phaC or phbC gene. However, the recent review of PHA synthases shows that many genes are annotated as hypothetical protein coding. The first step to address this gap, is using the database searches for the overview of currently available PHA synthase gene sequences. We will utilize full-text searches based on gene abbreviations and enzyme identifiers. This includes searches in Kyoto Encyclopedia of Genes and Genomes (KEGG). The number of phaC genes in the KEGG GENES database is currently 4320 available under the EC 2.3.1.304. Another database including phaC genes is Clusters of Orthologous Genes (COG) currently with 1299 genes under identifier COG3243. Our work attempts to give an insight into the primary structure of PHA synthases by a combination of bioinformatics approaches to identify PHA synthase coding genes across annotated prokaryotic genomes.

polyhydroxyalkanoates;bacteria;genes;COG;KEGG

polyhydroxyalkanoates;bacteria;genes;COG;KEGG

HEŘMÁNKOVÁ, K.; SEDLÁŘ, K.

14.04.2025

AMCA, spol. s.r.o.

Praha

978-80-88307-24

Book of abstracts of the 12th International Conference on Chemical Technology

152

153

172

https://www.icct.cz/cs/Amca-ICCT/media/content/2025/Program/Book_of_abstracts_-ICCT2025.pdf