Construction of Global Acyl Lipid Metabolic Map by Comparative Genomics and Subcellular Localization Analysis in the Red Alga Cyanidioschyzon merolae

Abstract

Pathways of lipid metabolism have been established in land plants, such as Arabidopsis thaliana, but the information on exact pathways is still under study in microalgae. In contrast with Chlamydomonas reinhardtii, which is currently studied extensively, the pathway information in red algae is still in the state in which enzymes and pathways are estimated by analogy with the knowledge in plants. Here we attempt to construct the entire acyl lipid metabolic pathways in a model red alga, Cyanidioschyzon merolae, as an initial basis for future genetic and biochemical studies, by exploiting comparative genomics and localization analysis. First, the data of whole genome clustering by Gclust were used to identify 121 acyl lipid-related enzymes. Then, the localization of 113 of these enzymes was analyzed by GFP-based techniques. We found that most of the predictions on the subcellular localization by existing tools gave erroneous results, probably because these tools had been tuned for plants or green algae. The experimental data in the present study as well as the data reported before in our laboratory will constitute a good training set for tuning these tools. The lipid metabolic map thus constructed show that the lipid metabolic pathways in the red alga are essentially similar to those in A. thaliana, except that the number of enzymes catalyzing individual reactions is quite limited. The absence of fatty acid desaturation to produce oleic and linoleic acids within the plastid, however, highlights the central importance of desaturation and acyl editing in the endoplasmic reticulum, for the synthesis of plastid lipids as well as other cellular lipids. Additionally, some notable characteristics of lipid metabolism in C. merolae were found. For example, phosphatidylcholine is synthesized by the methylation of phosphatidylethanolamine as in yeasts. It is possible that a single 3-ketoacyl-acyl carrier protein synthase is involved in the condensation reactions of fatty acid synthesis in the plastid. We will also discuss on the redundant β-oxidation enzymes, which are characteristic to red algae.

The lipid biochemistry of eukaryotic algae

“…Nevertheless, for now it can be assumed that the pathways identified in higher plants [239][240][241] are on the whole followed in eukaryotic algae though, perhaps, in a simpler form with less genetic redundancy [31] (Figure 4). In an overall survey by comparative genomics and subcellular localisation, it was concluded that the pathways for acyl lipid metabolism in the unicellular red alga Cyanidioschyzon merolae were essentially similar to Arabidopsis [242].…”

Complex origins of chloroplast membranes with photosynthetic machineries: multiple transfers of genes from divergent organisms at different times or a single endosymbiotic event?

“…The chloroplast is the sole site of fatty acid synthesis in plants and algal cells (Mori et al 2016;Ohlrogge et al 1979;Somerville and Browse 1991), and this was considered a result of cyanobacterial endosymbiosis. Indeed, the accD gene encoding a subunit of prokaryotic acetyl-CoA carboxylase is encoded by the chloroplast genome of many plants and algae.…”

Uncommon properties of lipid biosynthesis of isolated plastids in the unicellular red alga Cyanidioschyzon merolae

“…These results suggest that the desaturation of 18:0 does not take place in the plastid of C. merolae , as expected from the lack of stearoyl‐ACP desaturase. A previous study reported that a single KAS might be involved in the fatty acid synthesis in C. merolae plastid . In land plants, fatty acid synthesis involves three isoforms of KAS (KAS I/II/III) having different substrate specificities .…”

“…We then presented a hypothesis that Abbreviations ACP, acyl carrier protein; DAG, diacylglycerol; DGDG, digalactosyldiacylglycerol; ER, endoplasmic reticulum; FAME, fatty acid methyl ester; FFA, free fatty acid; G3P, glycerol 3-phosphate; the apparent differences in fatty acid composition in this alga and macrophytes could be understood in a common framework focusing on the role of plastid [1].Plastids are one of the major compartments of lipid metabolism in plants and algae, in which fatty acids and plastid membrane lipids are synthesized, such as monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), sulfoquinovosyldiacylglycerol (SQDG), and phosphatidylglycerol (PG) [8][9][10]. In plants, plastid is the sole site of long-chain fatty acid synthesis [11], and this is believed to be true for most algae [5,12,13]. The site of desaturation is, however, variable depending on fatty acids and double-bond position to be inserted.…”

“…In any way, there are two distinct pathways in plants and probably green algae. The situation in red algae, however, might be different.We previously found in C. merolae 'coupled pathway' for the synthesis of linoleoyl/palmitoyl species of MGDG [3,5], in which palmitic acid (16:0) is supplied from the inside of plastids whereas linoleic acid (18:2) is provided from outside (probably from ER) after desaturation. This molecular species was not synthesized by sequential desaturation from stearoyl/ palmitoyl species through oleoyl/palmitoyl species (in the following, stearic and oleic acids are abbreviated as 18:0 and 18:1, respectively).…”