Understanding the Role of Epigenetics in Bacterial Bioplastic Production 

In the last decade, global annual plastics production doubled to 359 million tonnes,placing enormous strains on non-renewable fossil fuel supply and the environment.Enhancing bacterial production of environmental-friendly bioplastic medium-chain-lengthpolyhydroxyalkanoate (hereinafter referred to as “PHA”) would make it morecost-competitive, and help decrease mankind’s reliance on plastics while ushering in anew era of innovative applications in biomedical/pharmaceutical products. Key to thisgoal realization is the comprehensive understanding of PHA production regulatorymechanism. Here, we propose research to gain new and holistic insights on theepigenetic regulation of PHA production. PHA has attracted great attention due to its biodegradable and biocompatible properties.Its “plastic-like” and elastomeric properties meant that PHA is a strong contender tosubstitute conventional plastics. More importantly, PHA could be developed intocommercial-valuable and high-end products such as, drug matrix encapsulation, softtissue regeneration, bioartificial organs design, stem cell engineering. PHA production istypically triggered by an environmental stress signal such as nitrogen limitation. Uponsensing this signal, bacteria will switch its metabolism from active growth state to PHAproduction state. However, the low to mediocre levels of PHA accumulation (20-40% celldry mass [CDM]) continues to hinder PHA commercialization. Incidentally, stress signals are also known to alter the bacterial epigenome. Epigenome isthe chemical modifications of DNA (e.g., methylation) which plays an important role ingene expression regulation. Epigenetic modifications can transform the global cellularmetabolism state and ultimately, phenotypes. However, the epigenetic effect on PHAproduction is currently unknown. This proposed research aims to delineate the role of epigenetics in PHA productionregulation. With this knowledge, we could design strategies for more effective andprolonged activation of PHA synthesis. Our preliminary data prove that nitrogen stressresulted in differences in epigenome, gene and protein expression profiles for a modelbacterium Pseudomonas putida NBUS12. Epigenetic modifications, which could altergene transcription, were also observed. Building upon these findings, this project plans to(1) identify the multi-omics features (using epigenomics, transcriptomics and proteomicsdata) that are unique to growth state and PHA production state, (2) deploy a multi-omicsclustering approach to identify the potential methyltransferase responsible forregulating PHA synthesis and (3) verify the epigenetic regulation and network usingmethyltransferase gene knockout mutant. The outcome of this project is expected toyield new possibilities for enhanced bacterial PHA production, and on the broader level,generate new interesting research topics regarding bacterial epigenetics and aromaticsbioremediation.