Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)*
AffiliationNatural Products Center, School of Natural Resources and the Environment, The University of Arizona, 250 E. Valencia Rd, Tucson, AZ, 85739, USA
Bio5 Institute, The University of Arizona, 1657 E. Helen St, Tucson, AZ, 85721, USA
Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, P. O. Box 951606, Los Angeles, CA, 90095, USA
Department of Ecology and Evolutionary Biology, The University of Arizona, 1041 E. Lowell St, Tucson, AZ, 85721, USA
Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
Fatty acid biosynthesis
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CitationMolnár et al. BMC Genomics 2012, 13:576 http://www.biomedcentral.com/1471-2164/13/576
Rights© 2012 Molnár et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection InformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at firstname.lastname@example.org.
AbstractBACKGROUND: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.
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Biosynthesis of gold and silver nanoparticles using Parkinsonia florida leaf extract and antimicrobial activity of silver nanoparticlesLópez-Millán, Alejandra; Del Toro-Sánchez, Carmen Lizette; Ramos-Enríquez, José Rogelio; Carrillo-Torres, Roberto Carlos; Zavala-Rivera, Paul; Esquivel, Reynaldo; Álvarez-Ramos, Enrique; Moreno-Corral, Ramón; Guzmán-Zamudio, Roberto; Lucero-Acuña, Armando; et al. (IOP PUBLISHING LTD, 2019-09)In this work, the biosynthesis of gold and silver nanoparticles from a leaf extract of Parkinsonia florida (P. florida) is reported. The P. florida leaf extract was analyzed by a phytochemical screening, by measuring the DPPH radical scavenging activity, and by Fourier-transform infrared spectroscopy (FT-IR). The phytochemical screening results indicated that biomolecules like carbohydrates, phenols, proteins, aminoacids, saponins, and flavonoids present in P. florida leaf extract might have participated in the chemical reduction of the metallic salts and further colloidal stabilization. The FT-IR results from leaf extract functional groups support the role of surface modification with the presence of residues of phenols, proteins, aminoacids, saponins, and flavonoids. The formation of metallic nanoparticles was confirmed by optical absorption spectroscopy with characteristic absorption bands at 550 nm and 430 nm, for gold and silver nanoparticles, respectively. Zeta potential for gold nanoparticles presents negative values in the range of 10 +/- 1 to 16 +/- 1 mV, depending on the amount of leaf extract used during the synthesis reaction. Similarly, zeta potential values for silver nanoparticles were in the range of -5 +/- 1 to 16 +/- 1 mV. STEM images revealed the average particles sizes in the range from 10 to 15 nm, and 10 to 57 nm, for gold and silver nanoparticles respectively. The silver nanoparticles presented good antibacterial activity, inhibiting the growth of Staphylococcus aureus and Escherichia coli.