Systems biology-guided biodesign of lignin to PHA production

Pseudomonas putida are of interest in value-added chemicals production from renewable biological polymer, due to their diverse spectrum of carbon catabolic metabolism and great potential in biosynthesis of biodegradable plastics (polyhydroxyalkanoate, PHA). In this study, we firstly isolated and characterized fifteen P. putida strains from various soil environments, which exhibit diverse spectrums of carbon catabolic metabolism. From these fifteen strains, P. putida A514 was employed as the model, for its ability to utilize a wide range of carbon sources, including hexose, pentose, aromatic compounds and lignin. In order to unravel the potential catabolic pathways for various lignin-derived aromatic compounds, whole genome of A514 was sequenced via the PacBio sequencing platform. Moreover, the global proteome profiles at late-log phase were measured via shot-gun proteomics approaches, when culturing A514 in glucose, vanillic acid and lignin as sole carbon sources. Approximately 250 to 500 uniquely expressed proteins were identified for each state, indicating different metabolism pathways among these three substrates. Furthermore, different expression levels of enzymes involved in β-ketoadipate pathway, ferulate catabolic pathway, TCA cycle, aromatic amino acid metabolism and β-oxidation were detected. In addition, putative aromatic compounds specific transporters were identified. Based on the systems biology analysis, the functional modules for lignin-to-PHA production are being designed and implemented. The initial synthetic strains showed significantly improved growth rate and yield on aromatic compounds and lignin substrates. Our finding paved path for a new biorefinery stream to convert lignin to a higher value chemical, which could improve the economics and sustainability of lignocellulsic biofuels.