(368bj) Dissecting Lignin Degradation Mechanisms of Rhodopseudomonas Palustris

Research Interests: Microbiology, Metabolic Engineering, Synthetic Biology, Systems Biology, Molecular Cloning, Bioremediation, Chemical Engineering, Biotechnology, Bioinformatics

Lignin is a complex and abundant biopolymer that constitutes a significant proportion of the structural material of many plants. Roughly 30% of global plant biomass is composed of lignin, however, the phenolic and crosslinked structure of lignin biopolymer and lignin breakdown products prevent the efficient and cost-effective conversion to more valuable products. As a result, most lignin valorization reaction schemes are economically infeasible, and most produced lignin is instead burned as fuel. To effectively utilize lignin as a carbon substrate for bioreactors, lignin catabolism requires complex biochemistry for its degradation, which is typically supplied from a community of microorganisms and fungi. Rhodopsuedomonas palustris (hereafter, R. palustris), a non-model, gram-negative soil bacterium with a wide array of unique metabolic features, has demonstrated its ability to catabolize many lignin (Alsiyabi et al., 2021; Brown et al., 2020, 2022; Immethun et al., 2022). With its unique biochemistry that allows it to produce many sought-after chemicals such as bioplastic and biofuels, it has the potential to become a metabolic engineering chassis. From analysis of growth data collected in this study, R. palustris can catabolize multiple lignin breakdown products (LBPs), including p-coumarate, sodium ferulate, p-coumaryl, coniferyl, and sinapyl alcohols aerobically and anaerobically. Following from the study reported in literature on the catabolism of p-coumarate, this work elucidates the pathways in which other major breakdown products of lignin are catabolized by R. palustris. In this study, we investigate these pathways through an analogous “multi-omics” perspective by combining both proteomic and transcriptomic profiles of R. palustris cultured with several LBPs. A supplemental metabolomics and CRISPRi study are then used to confirm the metabolites and reactions present in these pathways. Overall, this study will advance the understanding of the complex carbon metabolism of R. palustris and assist in enabling sustainable biochemical production through lignin valorization.

Alsiyabi, A., Brown, B., Immethun, C., Long, D., Wilkins, M., & Saha, R. (2021). Synergistic experimental and computational approach identifies novel strategies for polyhydroxybutyrate overproduction. Metabolic Engineering, 68, 1–13. https://doi.org/10.1016/j.ymben.2021.08.008

Brown, B., Immethun, C., Wilkins, M., & Saha, R. (2020). Rhodopseudomonas palustris CGA009 polyhydroxybutyrate production from a lignin aromatic and quantification via flow cytometry. Bioresource Technology Reports, 11. https://doi.org/10.1016/j.biteb.2020.100474

Brown, B., Wilkins, M., & Saha, R. (2022). Rhodopseudomonas palustris: A biotechnology chassis. In Biotechnology Advances (Vol. 60). Elsevier Inc. https://doi.org/10.1016/j.biotechadv.2022.108001

Immethun, C. M., Kathol, M., Changa, T., & Saha, R. (2022). Synthetic Biology Tool Development Advances Predictable Gene Expression in the Metabolically Versatile Soil Bacterium Rhodopseudomonas palustris. Frontiers in Bioengineering and Biotechnology, 10. https://doi.org/10.3389/fbioe.2022.800734