English (United States)
The reality of global climate change and strain on fossil fuel reserves make the need for sustainable sources of fuel increasingly urgent. Second generation biofuels produced from lignocellulosic biomass offers a sustainable and efficient alternative resource for energy. With over 200 billion tons of lignin being produced as waste by the paper production industry, lignin is an untapped resource. A bacterium called Sphingobium sp. SYK-6 has the ability to degrade lignin using three dioxygenases from the Protocatechuate Dioxygenase Superfamily, LigAB, DesB, and DesZ. These dioxygenases are essential to the metabolism of lignin because they can cleave certain lignin derived aromatic compounds which allows their conversion into the metabolites necessary for entrance into the TCA cycle. DesB and LigAB were found to have a 30% sequence similarity, with nearly identical active site residues and Fe (II) centers. However, while LigAB is substrate promiscuous, being able to catalyze the ring opening for several compounds, DesB exhibits strict substrate specificity, only catalyzing the ring opening of its natural substrate, gallate. Furthermore, previous studies in the Taylor Lab demonstrated that DesB was inhibited by several lignin-derived compounds. This project explored the extent of DesB’s inhibition with these compounds through Ki determination. Moreover, DesB was thought to have an allosteric site that was analogous to the known allosteric site of LigAB. Additional kinetic studies with PCA, the strongest inhibitor of DesB, syringate, and vanillin, showed that these inhibitors exhibited mixed inhibition. It is possible that the putative allosteric site in DesB could influence the nature of inhibition of these compounds. Future studies will explore this allosteric site through mutagenesis and kinetic assays.
Uchendu, Stacy Ndidi, "Characterizing Protocatechuate Dioxygenase Superfamily Members: DesB Inhibition and Allosterism" (2017). Honors Theses - All. 1864.
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