Tracking polyhydroxyalkanoate biosynthesis in thermophilic microorganisms

Polyhydroxyalkanoates are biopolyesters synthesized and stored in intracellular granules by diverse prokaryotes. Despite intense research efforts and prior evidence of a rather widespread phylogenetic occurrence of the related genetic machinery, reports on extreme thermophilic and hyperthermophilic polyhydroxyalkanoates producers remain scarce. However, thermophilic cell factories for bioplastic production would serve as an excellent example of Next-Generation Industrial Biotechnology. In this study, we aim to address this research gap by establishing a bioinformatics pipeline to mine genomes of extremely and moderately thermophilic microorganisms for signatures of potential polyhydroxyalkanoate production. Based on a collection of verified protein sequences of polyhydroxyalkanoate polymerase PhaC, the key biosynthetic enzyme, carefully curated sets of thermophilic bacterial and archaeal genomes were screened. This revealed that although PhaC-encoding genes are prevalent in diverse moderately thermophilic bacteria, they are absent in the considered extreme thermophilic bacteria. In contrast, a few limited examples of extreme thermophilic archaea were found to encode putative phaC genes embedded within a typical polyhydroxyalkanoate synthesis operon in their genomes, namely within the genera Ferroglobus, Geoglobus and Archaeoglobus, while no hits were found in extreme thermophilic bacteria. The latter included Thermus thermophilus, which was previously reported as a polyhydroxyalkanoates producer. This was refuted in our bioinformatics analysis and moreover, the predicted absence of polyhydroxyalkanoates synthesis in T. thermophilus was experimentally confirmed by employing various extraction and analytical methods. Based on the findings in this study, we conclude that polyhydroxyalkanoate production is very scarce in extreme thermophiles and hyperthermophiles, for reasons that remain to be elucidated. HighlightsO_LIA bioinformatics pipeline was constructed to screen thermophilic genomes for PhaC. C_LIO_LIPHA production is widespread in moderate thermophiles but rare in extreme thermophiles. C_LIO_LIExtreme thermophilic archaea belonging to specific genera exceptionally harbor PHA synthesis genes. C_LIO_LINo PHA synthesis genes were found in extreme thermophilic bacteria like Thermus spp. C_LIO_LIExperimental work confirmed the absence of PHAs in Thermus thermophilus. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/652502v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@11fafe3org.highwire.dtl.DTLVardef@1548075org.highwire.dtl.DTLVardef@bd9ebaorg.highwire.dtl.DTLVardef@fff3e0_HPS_FORMAT_FIGEXP M_FIG C_FIG