Project description:To address the question of how photosynthetic bacterium Rhodopseudomonas palustris metabolize lignin derived compound p-coumarate, transcriptomics and quantitative proteomics were combined to characterize gene expression profiles at both the mRNA level and protein level in Rhodopseudomonas palustris grown with succinate, benzoate, and p-coumarate as the carbon source. Keywords: Comparison of transcriptome profiles
Project description:Lignin is a universal waste product of the agricultural industry and is currently seen as a potential feedstock for more sustainable manufacturing. While it is the second most abundant biopolymer in the world, most of it is currently burned as it is a very recalcitrant material. Many recent studies, however, have demonstrated the viability of biocatalysis to improve the value of this feedstock and convert it into more useful chemicals, such as polyhydroxybutyrate, and clean fuels like hydrogen and n-butanol. Rhodopseudomonas palustris is a gram-negative bacterium which demonstrates a plethora of desirable metabolic capabilities, including aromatic catabolism useful for lignin degradation. This study uses a multi-omics approach, including the first usage of CRISPRi in R. palustris, to investigate the lignin consumption mechanisms of R. palustris, the essentiality of redox homeostasis to lignin consumption, elucidate a potential lignin catabolic superpathway, and enable more economically viable sustainable lignin valorization processes.
Project description:To address the question of how photosynthetic bacterium Rhodopseudomonas palustris metabolize lignin derived compound p-coumarate, transcriptomics and quantitative proteomics were combined to characterize gene expression profiles at both the mRNA level and protein level in Rhodopseudomonas palustris grown with succinate, benzoate, and p-coumarate as the carbon source. Transcriptome profiles among Rhodopseudomonas palustris cells grown with succinate, benzoate, and p-coumarate as the carbon source were compared.
Project description:Convergent microbial biocatalysis has emerged as a promising approach for the conversion of lignin side-streams into value-added chemicals in recent decades. However, the current knowledge of metabolic pathways directing the bioconversion of lignin-related aromatics is still limited to a few microbial species and unavailable for some of these compounds. Thus, the aim of this study was to identify the genes involved in the bioconversion of aromatic compounds in Xanthomonas citri subsp. citri 306 (X. citri 306), a bacterium belonging to a compelling yet untapped genus for studies on lignin-related aromatics metabolism. For this purpose, we used an integrative approach including genome data mining, RNA-seq, enzymology and gene knockout studies. The RNA-seq analysis revealed a total of 278 to 1464 differentially expressed genes (DEGs) in the aromatic-containing conditions compared to the control XVM2m-glucose, evidencing the importance of these compounds in modulating various physiological processes of X. citri 306 beyond the pathways related to their metabolism. Moreover, this work revealed the operon molRKAB, which plays a role in the first catabolic steps of the three main monolignols (p-coumaryl, coniferyl and sinapyl alcohols), besides showing all the enzymatic steps funneling them up to the tricarboxylic acid cycle. Additionally, the study uncovered aryl aldehyde reductases and efflux strategies that likely function to protect the pathogen from aromatics toxicity. Together, these findings enhance the current understanding of Xanthomonas metabolism and transcriptional responses to lignin-related aromatic compounds, shedding light on the diverse metabolic pathways available to enable the engineering of microbial chassis dedicated to lignin valorization.
