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

从木质纤维生物质中提取的生物燃料有望成为更清洁和可再生的能源和化学品的替代来源。然而，脱木素或木质素分解是生物燃料和生物炼油的瓶颈。因此，了解木质素在细菌中的降解途径、生物燃料的产生及其调控机制是非常重要的。作为我旨在开发可持续农业和环境新战略的研究计划的一部分，我的实验室最近对多粘拟青霉CR1进行了鉴定，这是一种革兰氏阳性、产孢量大、兼性厌氧菌，我们从安大略省南部降解的玉米根部分离到了多粘拟青霉CR1。我们发现多粘拟青霉CR1具有很强的降解和利用木质素、纤维素和半纤维素作为唯一碳源的能力，并能够直接发酵这些植物衍生的化合物来生产有价值的生物燃料，包括丁醇(Weselowski等人提交并正在修订中)。为了更好地了解多粘菌CR1参与木质素降解和生物燃料生产的代谢途径和调控机制，我的实验室最近对其完整基因组进行了测序和注释，该基因组约为6.02Mbp(Eastman等人，2014年)。基因组公告)。我们最近的研究还表明，P.polymyxa CR1可能利用了一条尚未确定的木质素和芳香族降解途径，因为它不能降解原儿茶酸盐，原儿茶酸盐是目前已确定的细菌木质素降解途径的关键节点代谢物。这与在所有测序的多粘菌基因组中缺乏原儿茶酸裂解途径的同源物是一致的(Eastman等人，BMC基因组学。2014年)。 在这项计划中，基于我们最近产生的丰富的基因组和遗传信息以及我们在微生物遗传学方面的专业知识，我们将利用包括功能基因组学、转录组学和代谢组学在内的多种组学技术，在系统和分子水平上阐明多粘菌CR1是如何识别和代谢木质素的。尤其是，我们的目标是揭示与木质素降解和生物燃料生产直接相关的细菌基因、代谢途径和调控网络，这是前提条件，并将为我们通过基因工程改造多粘菌CR1以提高木质素降解效率、直接从木质纤维生物质中生产生物燃料和增值化学品的长期目标奠定坚实的基础。这项拟议研究产生的知识一旦被转化，将在几个方面对生物燃料工业和生物经济作出重大贡献，包括降低生物炼油成本、增加生物燃料的数量和纯度、开发新的供应链以及建立一个原本价值较低的木质纤维素原料的新市场，如林业/作物残渣、生物固体等。

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.