Background: Up to now, there have been three published versions of a yeast genome-scale metabolic model: iFF708, iND750 and iLL672. All three models, however, lack a detailed description of lipid metabolism and thus are unable to be used as integrated scaffolds for gaining insights into lipid metabolism from multilevel omic measurement technologies (e.g. genome-wide mRNA levels). To overcome this limitation, we reconstructed a new version of the Saccharomyces cerevisiae genome-scale model, iIN800 that includes a more rigorous and detailed description of lipid metabolism.

For a bio-based economy, microbial lipids offer a potential solution as alternative feedstocks in the oleochemical industry. The existing genome data for the promising strains, oleaginous yeasts and fungi, allowed us to investigate candidate orthologous sequences that participate in their oleaginicity. Comparative genome analysis of the non-oleaginous (Saccharomyces cerevisiae, Candida albicans and Ashbya gossypii ) and oleaginous strains (Yarrowia lipolytica, Rhizopus oryzae, Aspergillus oryzae and Mucor circinelloides) showed that 209 orthologous protein sequences of the oleaginous microbes were distributed over several processes of the cells. Based on the 41 sequences categorized by metabolism, putative routes potentially involved in the generation of precursors for fatty acid and lipid synthesis, particularly acetyl-CoA, were then identified that were not present in the non-oleaginous strains. We found a set of the orthologous oleaginous proteins that was responsible for the biosynthesis of this key two-carbon metabolite through citrate catabolism, fatty acid b-oxidation, leucine metabolism and lysine degradation. Our findings suggest a relationship between carbohydrate, lipid and amino acid metabolism in the biosynthesis of acetyl-CoA, which contributes to the lipid production of oleaginous microbes. INTRODUCTIONLipids are dynamically bioactive molecules that contribute to the regulation of several complex systems of living cells. Besides the medical perspective, the remarkable growth of the lipid field is undoubtedly driven by the demand for feedstock for the oleochemical industry. In addition to the production of n-3 and n-6 polyunsaturated fatty acids that are beneficial to human health, extensive attention is being directed to biodiesel production from micro-organisms to replace non-sustainable petroleum (Liu & Zhao, 2007; Vicente et al., 2010). Certain strains, such as Rhodosporidiun toruloides, Lipomyces starkeyi, Yarrowia lipolytica and Mucor circinelloides, are known to accumulate substantial amounts of lipids, accounting for more than 20 % of their biomass, and are thus called oleaginous strains (Ageitos et al., 2011;Beopoulos et al., 2009;Meng et al. 2009;Ratledge, 2004). Due to their short cultivation time, their high level of intracellular lipids that are predominantly triacylglycerol (TAG) and their utilization of various substrates, oleaginous yeasts and fungi have become important model systems for alternatives to traditional sources of lipids derived from fossil, animal and plant origins (Beopoulos et al., 2009;Ratledge, 2004). Therefore, an understanding of lipid physiology is required to improve the efficient production of lipids of commercial interest. An integrated approach has been implemented using recent developments for studying the lipid metabolism of these promising micro-organisms. It has been reported that the lipid production of these oleaginous species is enhanced by controlling cultivation or nutritional conditions (Certik et al., 1999;Ruenwai et al., 2010). Based on the bioc...

Arthrospira platensis is a cyanobacterium that is extensively cultivated outdoors on a large commercial scale for consumption as a food for humans and animals. It can be grown in monoculture under highly alkaline conditions, making it attractive for industrial production. Here we describe the complete genome sequence of A. platensis C1 strain and its annotation. The A. platensis C1 genome contains 6,089,210 bp including 6,108 protein-coding genes and 45 RNA genes, and no plasmids. The genome information has been used for further comparative analysis, particularly of metabolic pathways, photosynthetic efficiency and barriers to gene transfer.

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BackgroundCassava is a well-known starchy root crop utilized for food, feed and biofuel production. However, the comprehension underlying the process of starch production in cassava is not yet available.ResultsIn this work, we exploited the recently released genome information and utilized the post-genomic approaches to reconstruct the metabolic pathway of starch biosynthesis in cassava using multiple plant templates. The quality of pathway reconstruction was assured by the employed parsimonious reconstruction framework and the collective validation steps. Our reconstructed pathway is presented in the form of an informative map, which describes all important information of the pathway, and an interactive map, which facilitates the integration of omics data into the metabolic pathway. Additionally, to demonstrate the advantage of the reconstructed pathways beyond just the schematic presentation, the pathway could be used for incorporating the gene expression data obtained from various developmental stages of cassava roots. Our results exhibited the distinct activities of the starch biosynthesis pathway in different stages of root development at the transcriptional level whereby the activity of the pathway is higher toward the development of mature storage roots.ConclusionsTo expand its applications, the interactive map of the reconstructed starch biosynthesis pathway is available for download at the SBI group’s website (http://sbi.pdti.kmutt.ac.th/?page_id=33). This work is considered a big step in the quantitative modeling pipeline aiming to investigate the dynamic regulation of starch biosynthesis in cassava roots.