TY - JOUR
T1 - Bio-crude transcriptomics
T2 - Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)
AU - Molnár, István
AU - Lopez, David
AU - Wisecaver, Jennifer H.
AU - Devarenne, Timothy P.
AU - Weiss, Taylor L.
AU - Pellegrini, Matteo
AU - Hackett, Jeremiah D.
N1 - Funding Information:
The work in the authors’ laboratories is supported by the Department of Energy (contract DE-EE0003046 to the NAABB consortium). We are thankful to Andrew Koppisch (Northern Arizona Unviersity), Joe Chappell and Tom D. Niehaus (University of Kentucky), and Shigeru Okada (University of Tokyo) for their expertise and their efforts of initiating the B. braunii sequencing project as part of JGI Program CSP 2009, and to the scientists at the JGI who carried out the sequencing and publicly released their data into the NCBI Sequence Reads Archive. We are also grateful to the three anonymous reviewers for their comprehensive and constructive comments that strenghthened this manuscript.
PY - 2012/10/30
Y1 - 2012/10/30
N2 - Background: 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.Results: 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.Conclusions: 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.
AB - Background: 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.Results: 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.Conclusions: 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.
KW - ABC transporter
KW - Autophagy
KW - Biofuel
KW - Botryococcene
KW - Botryococcus braunii
KW - Fatty acid biosynthesis
KW - Starch biosynthesis
KW - Terpene biosynthesis
KW - Transcriptome
KW - Triacylglycerol biosynthesis
UR - http://www.scopus.com/inward/record.url?scp=84867896016&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-13-576
DO - 10.1186/1471-2164-13-576
M3 - Article
C2 - 23110428
AN - SCOPUS:84867896016
SN - 1471-2164
VL - 13
JO - BMC Genomics
JF - BMC Genomics
IS - 1
M1 - 576
ER -
