Genomic analysis, identification and characterization of lignin degradation pathway and biofuel production by the Gram-positive bacterium Paenibacillus polymyxa CR1.

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Biofuels derived from lignocellulosic biomass hold promise as alternative sources of cleaner and renewable energy and chemicals. However, delignification or lignin decomposition is a bottleneck for biofuel and biorefinery. Therefore, it is very important to understand lignin degrading pathways, biofuel production and their regulatory mechanisms in bacteria. As part of my research program aiming at developing novel strategies for sustainable agriculture and environment, my lab recently characterized Paenibacilluspolymyxa CR1, a Gram-positive, sporulating, facultative anaerobe that we isolated from degrading corn roots in southern Ontario. We found P. polymyxa CR1 had a strong capacity to degrade and utilize lignin, cellulose and hemi-cellulose as a sole carbon source, and is able to ferment these plant-derived compounds directly to produce valuable biofuels including butanol (Weselowski et al., submitted and in revision). To better understand P. polymyxa CR1 metabolic pathways and regulatory mechanisms implicated in lignin degradation and biofuel production, my lab recently sequenced and annotated its complete genome which is approximately 6.02Mbp (Eastman et al., 2014. Genome Announcements). Our recent research also suggests P. polymyxa CR1 likely utilizes a yet to be identified lignin and aromatic degradation pathway, since it is incapable of degrading protocatechuate, a key nodal metabolite of currently characterized bacterial lignin degradation pathways. This is consistent with the lack of identified homologs for the protocatechuate cleavage pathway in all sequenced P. polymyxa genomes (Eastman et al., BMC Genomics. 2014). In this proposal, based on the wealth of genomic and genetic information we recently generated and our expertise of microbial genetics, we will use multiple “omics” techniques – including functional genomics, transcriptomics and metabolomics, to elucidate how P. polymyxa CR1 recognizes and metabolizes lignin at the system and molecular levels.  In particular, we aim to uncover bacterial genes, metabolic pathways and regulatory networks directly implicated in lignin degradation and biofuel production, which is a prerequisite and will provide a sound foundation for our long term goal of engineering P. polymyxa CR1 genetically to enhance the efficiency of lignin degradation and improve the production of biofuels and value-added chemicals directly from lignocellulosic biomass, thereby making biorefinery cost-efficient and biofuels economically viable.  Knowledge generated from the proposed study, once being translated, will significantly contribute to biofuel industry and bio-economy in several ways including reduced biorefinery cost, increased quantity and purity of biofuels, development of new supply chains and a new marketplace for otherwise low value lignocellulose feedstock such as forestry/crop residues, biosolids and etc.