The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes

Abstract

The repertoire of biosynthetic enzymes found in an organism is an important clue for elucidating the chemical structural variations of various compounds. In the case of fatty acids, it is essential to examine key enzymes that are desaturases and elongases, whose combination determine the range of fatty acid structures. We systematically investigated 56 eukaryotic genomes to obtain 275 desaturase and 265 elongase homologs. Phylogenetic and motif analysis indicated that the desaturases consisted of four functionally distinct subfamilies and the elongases consisted of two subfamilies. From the combination of the subfamilies, we then predicted the ability to synthesize six types of fatty acids. Consequently, we found that the ranges of synthesizable fatty acids were often different even between closely related organisms. The reason is that, as well as diverging into subfamilies, the enzymes have functionally diverged within the individual subfamilies. Finally, we discuss how the adaptation to individual environments and the ability to synthesize specific metabolites provides some explanation for the diversity of enzyme functions. This study provides an example of a potent strategy to bridge the gap from genomic knowledge to chemical

Mono- and digalactosyldiacylglycerol composition of dinoflagellates. VI. Biochemical and genomic comparison of galactolipid biosynthesis betweenChromera velia(Chromerida), a photosynthetic alveolate with red algal plastid ancestry, and the dinoflagellate,Lingulodinium polyedrum

“…Thus we hypothesize that 16:0 is transported out of the plastid and incorporated into phospholipid(s), such as phosphatidylcholine, and subsequently elongated and desaturated within the ER. A number of elongases and desaturases identified in L. polyedrum and those annotated in this study would likely be involved in medium-chain fatty acids to produce 20:5 (Hashimoto et al, 2008). A homologue of a Δ15 desaturase used in the conversion to 16:0 or 18:0 to 20:5 in L. polyedrum was not found.…”

“…Evidence for this model also derives from previous observations by Leblond & Chapman (2000), who observed 18:4 and 18:5 in the phospholipid fraction of a number of peridinin-containing dinoflagellates, albeit in low amounts. It should be noted that Leblond & Chapman (2000) did not find 20:4 in their survey of phospholipid-associated fatty acids in peridinin-containing dinoflagellates; therefore, it is likely that 20:5 results from an elongation of 18:5, rather than elongation of 18:4 to 20:4 followed by desaturation to 20:5 (Hashimoto et al, 2008). Further radiolabelling studies using [1-14 C] linoleic acid will better elucidate how fatty acids are modified from medium chain fatty acids to long chain polyunsaturated fatty acids in the ER in a dinoflagellate such as L. polyedrum (KhozinGoldberg et al, 2002).…”

Genetics of cuticular hydrocarbon differences between males of the parasitoid wasps Nasonia giraulti and Nasonia vitripennis

“…First, eloF has only a marginal impact on the biosynthesis of alkenes in Drosophila (Chertemps et al, 2007), which could mean that it is specific for alkadienes, a CHC compound class that has not even been found in traces in the CHC profiles of Nasonia males. Second, to the best of our knowledge there is no single report of an elongase that has been shown to elongate hydrocarbons beyond the length of C30 (Hashimoto et al, 2008). For these two reasons, we think that LOC100118619 is not a promising candidate for being functionally involved in the biosynthesis of the alkenes 9-C31ene and 9-C33ene.…”

“…have not yet been functionally characterized (Hashimoto et al, 2008), but could occur in insects (Blomquist and Bagneres, 2010). Thus, the data allow prioritizing experiments when considering reverse genetic approaches.…”

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

“…To further enrich the KEGG pathway information, KEGG ortholog prediction tool is offered to categorize orthologous and paralogous gene groups from evolutionarily related organisms. Recent genome-wide studies have employed KEGG pathway database to identify genes and reconstruct major lipid biosynthetic pathways in various oleaginous microalgal species (Hashimoto et al, 2008;Misra et al, 2012;Rismani-Yazdi et al, 2011;Smith et al, 2012). MetaCyc (http://metacyc.org) is also a popular database that contains experimentally verified metabolic pathway information for more than 600 organisms including species ranging from lower microorganisms, to plants and human (Caspi et al, 2008).…”