Programmable marine bacteria catalyze the valorization of lignin monomers

Abstract

Efficiently converting lignin, the second most abundant biopolymer on Earth, into valuable chemicals is pivotal for a circular economy and net-zero future. However, lignin is recalcitrant to bio-upcycling, demanding innovative solutions. We report here the biological valorization of lignin-derived aromatic carbon to value-added chemicals without requesting extra organic carbon and freshwater via reprogramming the marine Roseobacter clade bacterium Roseovarius nubinhibens. We discovered the unusual catalytic advantages of this strain for the oxidation of lignin monomers and implemented a CRISPR interference (CRISPRi) system with the lacI-Ptrc inducible module, nuclease-deactivated Cas9, and programmable gRNAs. This enabled precise and efficient repression of target genes. By deploying the customized CRISPRi, we reprogrammed the carbon flux from a lignin monomer, 4-hydroxybenzoate, to achieve maximum production of protocatechuate, a pharmaceutical compound, while maintaining essential carbon for cell growth and biocatalysis. As a result, we achieved a 4.89-fold increase in protocatechuate yield with a dual-targeting CRISPRi system. Our study introduces a new-to-the-field lineage of marine bacteria and underscores the potential of blue biotechnology leveraging resources from the ocean for simultaneous carbon and water conservation.