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Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana.

Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC - Nat Commun (2012)

Bottom Line: The potential use of algae in biofuels applications is receiving significant attention.We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis.Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado 80401, USA.

ABSTRACT
The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.

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N. gaditana metabolic pathway map.Light grey background traces indicate KEGG pathways not encoded by the N. gaditana genome. KEGG pathways in green, magenta or blue are present in the N. gaditana genome. Genes that are up- or down-regulated during nitrogen deprivation are labelled in magenta and blue, respectively.
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f4: N. gaditana metabolic pathway map.Light grey background traces indicate KEGG pathways not encoded by the N. gaditana genome. KEGG pathways in green, magenta or blue are present in the N. gaditana genome. Genes that are up- or down-regulated during nitrogen deprivation are labelled in magenta and blue, respectively.

Mentions: To investigate metabolic pathways of interest for biofuel production, functional annotations were assigned to N. gaditana gene models. Gene ontology terms (GO-terms) were assigned to 3,838 gene models, from which 2,766 genes were identified as performing enzyme-catalysed reactions representing 700 unique EC numbers that were in turn used to populate metabolic pathway maps (Fig. 4). Some of the most frequent GO-terms, aside from housekeeping functions, are terms involved in auxin biosynthesis, photosynthesis, and lipid biosynthesis (Supplementary Fig. S5). Because of the exemplary lipid production by N. gaditana cultures, we focused on characterizing lipid metabolic pathway genes, including those involved in fatty acid biosynthesis, TAG assembly and lipid activation/degradation (Supplementary Table S5). BLASTp was used to identify homologues of the N. gaditana lipid metabolic genes in red/green/brown algae and diatoms. Comparison of the number of genes in each step of the lipid metabolic pathways suggests that N. gaditana has an expanded repertoire of genes involved in both TAG assembly and lipid degradation, including glycerol 3-phosphate dehydrogenase, glycerol 3-phosphate acyltransferase, diacylglycerol acyltransferase, long-chain acyl-CoA ligase and acyl-CoA oxidase (Fig. 5 and Supplementary Table S6). This increased number of lipid metabolic pathway genes is probably significant considering that N. gaditana has fewer total genes than all other algae used for this comparison, with the exception of C. merolae. To further examine the expansion of gene families in N. gaditana, we compared the prevalence of GO-terms with P. tricornutum and C. reinhardtii using the Fisher's exact test. A selected list of over- and under-represented terms is shown in Supplementary Table S7. This analysis confirms the overrepresentation of the GO-term for acyl-carrier protein biosynthetic processes and also indicates the expansion of several other gene families that may be of importance for the biomass production phenotype of N. gaditana. These include genes involved in auxin biosynthetic processes, carbon utilization, response to stress (including chemical, temperature and salt), and pyruvate metabolic processes. See Supplementary Note 3 for a more detailed analysis of these gene expansions/reductions.


Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana.

Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC - Nat Commun (2012)

N. gaditana metabolic pathway map.Light grey background traces indicate KEGG pathways not encoded by the N. gaditana genome. KEGG pathways in green, magenta or blue are present in the N. gaditana genome. Genes that are up- or down-regulated during nitrogen deprivation are labelled in magenta and blue, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3293424&req=5

f4: N. gaditana metabolic pathway map.Light grey background traces indicate KEGG pathways not encoded by the N. gaditana genome. KEGG pathways in green, magenta or blue are present in the N. gaditana genome. Genes that are up- or down-regulated during nitrogen deprivation are labelled in magenta and blue, respectively.
Mentions: To investigate metabolic pathways of interest for biofuel production, functional annotations were assigned to N. gaditana gene models. Gene ontology terms (GO-terms) were assigned to 3,838 gene models, from which 2,766 genes were identified as performing enzyme-catalysed reactions representing 700 unique EC numbers that were in turn used to populate metabolic pathway maps (Fig. 4). Some of the most frequent GO-terms, aside from housekeeping functions, are terms involved in auxin biosynthesis, photosynthesis, and lipid biosynthesis (Supplementary Fig. S5). Because of the exemplary lipid production by N. gaditana cultures, we focused on characterizing lipid metabolic pathway genes, including those involved in fatty acid biosynthesis, TAG assembly and lipid activation/degradation (Supplementary Table S5). BLASTp was used to identify homologues of the N. gaditana lipid metabolic genes in red/green/brown algae and diatoms. Comparison of the number of genes in each step of the lipid metabolic pathways suggests that N. gaditana has an expanded repertoire of genes involved in both TAG assembly and lipid degradation, including glycerol 3-phosphate dehydrogenase, glycerol 3-phosphate acyltransferase, diacylglycerol acyltransferase, long-chain acyl-CoA ligase and acyl-CoA oxidase (Fig. 5 and Supplementary Table S6). This increased number of lipid metabolic pathway genes is probably significant considering that N. gaditana has fewer total genes than all other algae used for this comparison, with the exception of C. merolae. To further examine the expansion of gene families in N. gaditana, we compared the prevalence of GO-terms with P. tricornutum and C. reinhardtii using the Fisher's exact test. A selected list of over- and under-represented terms is shown in Supplementary Table S7. This analysis confirms the overrepresentation of the GO-term for acyl-carrier protein biosynthetic processes and also indicates the expansion of several other gene families that may be of importance for the biomass production phenotype of N. gaditana. These include genes involved in auxin biosynthetic processes, carbon utilization, response to stress (including chemical, temperature and salt), and pyruvate metabolic processes. See Supplementary Note 3 for a more detailed analysis of these gene expansions/reductions.

Bottom Line: The potential use of algae in biofuels applications is receiving significant attention.We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis.Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, Colorado 80401, USA.

ABSTRACT
The potential use of algae in biofuels applications is receiving significant attention. However, none of the current algal model species are competitive production strains. Here we present a draft genome sequence and a genetic transformation method for the marine microalga Nannochloropsis gaditana CCMP526. We show that N. gaditana has highly favourable lipid yields, and is a promising production organism. The genome assembly includes nuclear (~29 Mb) and organellar genomes, and contains 9,052 gene models. We define the genes required for glycerolipid biogenesis and detail the differential regulation of genes during nitrogen-limited lipid biosynthesis. Phylogenomic analysis identifies genetic attributes of this organism, including unique stramenopile photosynthesis genes and gene expansions that may explain the distinguishing photoautotrophic phenotypes observed. The availability of a genome sequence and transformation methods will facilitate investigations into N. gaditana lipid biosynthesis and permit genetic engineering strategies to further improve this naturally productive alga.

Show MeSH
Related in: MedlinePlus