Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, Tucson, 85739, USA.
BMC Genomics. 2012 Oct 30;13:576. doi: 10.1186/1471-2164-13-576.
Microalgae hold promise for yielding a biofuel feedstock that is sustainable, carbon-neutral, distributed, and only minimally disruptive for the production of food and feed by traditional agriculture. Amongst oleaginous eukaryotic algae, the B race of Botryococcus braunii is unique in that it produces large amounts of liquid hydrocarbons of terpenoid origin. These are comparable to fossil crude oil, and are sequestered outside the cells in a communal extracellular polymeric matrix material. Biosynthetic engineering of terpenoid bio-crude production requires identification of genes and reconstruction of metabolic pathways responsible for production of both hydrocarbons and other metabolites of the alga that compete for photosynthetic carbon and energy.
A de novo assembly of 1,334,609 next-generation pyrosequencing reads form the Showa strain of the B race of B. braunii yielded a transcriptomic database of 46,422 contigs with an average length of 756 bp. Contigs were annotated with pathway, ontology, and protein domain identifiers. Manual curation allowed the reconstruction of pathways that produce terpenoid liquid hydrocarbons from primary metabolites, and pathways that divert photosynthetic carbon into tetraterpenoid carotenoids, diterpenoids, and the prenyl chains of meroterpenoid quinones and chlorophyll. Inventories of machine-assembled contigs are also presented for reconstructed pathways for the biosynthesis of competing storage compounds including triacylglycerol and starch. Regeneration of S-adenosylmethionine, and the extracellular localization of the hydrocarbon oils by active transport and possibly autophagy are also investigated.
The construction of an annotated transcriptomic database, publicly available in a web-based data depository and annotation tool, provides a foundation for metabolic pathway and network reconstruction, and facilitates further omics studies in the absence of a genome sequence for the Showa strain of B. braunii, race B. Further, the transcriptome database empowers future biosynthetic engineering approaches for strain improvement and the transfer of desirable traits to heterologous hosts.
微藻有望成为一种生物燃料原料，它具有可持续性、碳中和、分散性，并且对传统农业生产食物和饲料的影响最小。在产油真核藻类中，B 群 Botryococcus braunii 是独特的，因为它产生大量萜类来源的液体烃类。这些与化石原油相当，并且被隔离在细胞外的公共细胞外多聚物基质材料中。萜类生物原油生产的生物合成工程需要确定基因并重建负责生产烃类以及与藻类中争夺光合作用碳和能量的其他代谢物的代谢途径。
Showa 株 B 群 B. braunii 的 1,334,609 个新一代焦磷酸测序读取的从头组装产生了一个 46,422 个连续序列的转录组数据库，平均长度为 756bp。连续序列被赋予了途径、本体和蛋白质结构域标识符。手动注释允许重建从初级代谢物产生萜类液体烃的途径，以及将光合作用碳分流到四萜类类胡萝卜素、二萜类和倍半萜类醌和叶绿素的 prenyl 链的途径。还展示了用于重建包括三酰基甘油和淀粉在内的竞争储存化合物生物合成的途径的机器组装连续序列的清单。S-腺苷甲硫氨酸的再生，以及通过主动运输和可能的自噬将烃油细胞外定位也进行了研究。
构建一个带注释的转录组数据库，在基于网络的数据存储库和注释工具中公开提供，为代谢途径和网络重建提供了基础，并促进了在没有 Showa 株 B. braunii，B 群基因组序列的情况下进行进一步的组学研究。此外，转录组数据库为未来的生物合成工程方法提供了支持，以改善菌株和将理想性状转移到异源宿主。
