61
subunits of acetyl CoA carboxylase complex (accA through accD) on the plastid
genome of Pyropia sp., except for the biotin carboxylase gene (accC) that was located
on the nuclear transcriptome data of Pyropia sp. Moreover, no KAS II gene was identified in Pyropia sp., suggesting that 16:0-ACP (rather than 18:0-ACP) is the final
product of fatty acid synthesis, or this last elongation step can alternatively be accomplished by KAS I. This indicated that 16:0-ACP is the main fatty acid conjugate
exported from the plastid and/or the elongation rate of C18-fatty acids is high. Besides
this “plant-type” FAS complex, orthologs of the fungal enzymes were also identified
in Pyropia spp. (Chan et al. 2012). Furthermore, these authors reported that Pyropia
spp. lack plastid desaturation pathway including the soluble acyl-ACP-desaturase
FAB2. Therefore, they hypothesized that possibly, saturated FAs (16:0 and possibly
18:0) are exported from the plastid to the ER for desaturation in contrast to higher
plants, where oleic acid (18:1) is the major fatty acid that is synthesized in chloroplasts and exported to the ER. It has been found that KAS II, one of the key enzymes
involved in FA biosynthesis in higher plants and microalgae, is not found in Pyropia
sp., and its role is played by another isoform, KAS I. The whole genomes of brown
seaweed Ectocarpus (Cock et al. 2010) and red seaweed Chondrus (Collén et al.
2013), Pyropia (Nakamura et al. 2013), Saccharina (Ye et al. 2015), and Cladosiphon
(Nishitsuji et al. 2016) have identified the genes/enzymes involved in seaweed lipid
metabolism but have also mentioned many unidentified loops such as in fatty acid,
oxylipin (especially methyl jasmonate), and sphingolipid pathways. The need is to
apply integrated approach of genomics, proteomics, and lipidomics to completely
understand the unresolved riddle of seaweed lipid metabolism.
4.4 Tools and Techniques in Seaweed Lipidomics
The detection, identification, and precise quantification of lipid compounds are
prerequisite for their potential utilization and exploration. Lipidomics aims at
characterization and functional annotation of a broad range of lipid molecular
species in organisms. As seaweed lipids are highly complex and diverse, full
characterization of all of its structural diversity and quantification is quite a
challenge. An overview of key factors involved in seaweed lipidomics is presented here.
4.4.1 Sampling and Lipid Extraction
For lipidomics, sample preparation is one of the crucial steps, and utmost care
should be taken while sample harvesting, and the samples should be immediately
quenched after harvest by snap freezing in liquid nitrogen to disrupt the cell metabolism and inactivate all the endogenous hydrolytic enzymes. The frozen samples
4 Seaweed Lipidomics in the Era of ‘Omics’ Biology: A Contemporary Perspective
subunits of acetyl CoA carboxylase complex (accA through accD) on the plastid
genome of Pyropia sp., except for the biotin carboxylase gene (accC) that was located
on the nuclear transcriptome data of Pyropia sp. Moreover, no KAS II gene was identified in Pyropia sp., suggesting that 16:0-ACP (rather than 18:0-ACP) is the final
product of fatty acid synthesis, or this last elongation step can alternatively be accomplished by KAS I. This indicated that 16:0-ACP is the main fatty acid conjugate
exported from the plastid and/or the elongation rate of C18-fatty acids is high. Besides
this “plant-type” FAS complex, orthologs of the fungal enzymes were also identified
in Pyropia spp. (Chan et al. 2012). Furthermore, these authors reported that Pyropia
spp. lack plastid desaturation pathway including the soluble acyl-ACP-desaturase
FAB2. Therefore, they hypothesized that possibly, saturated FAs (16:0 and possibly
18:0) are exported from the plastid to the ER for desaturation in contrast to higher
plants, where oleic acid (18:1) is the major fatty acid that is synthesized in chloroplasts and exported to the ER. It has been found that KAS II, one of the key enzymes
involved in FA biosynthesis in higher plants and microalgae, is not found in Pyropia
sp., and its role is played by another isoform, KAS I. The whole genomes of brown
seaweed Ectocarpus (Cock et al. 2010) and red seaweed Chondrus (Collén et al.
2013), Pyropia (Nakamura et al. 2013), Saccharina (Ye et al. 2015), and Cladosiphon
(Nishitsuji et al. 2016) have identified the genes/enzymes involved in seaweed lipid
metabolism but have also mentioned many unidentified loops such as in fatty acid,
oxylipin (especially methyl jasmonate), and sphingolipid pathways. The need is to
apply integrated approach of genomics, proteomics, and lipidomics to completely
understand the unresolved riddle of seaweed lipid metabolism.
4.4 Tools and Techniques in Seaweed Lipidomics
The detection, identification, and precise quantification of lipid compounds are
prerequisite for their potential utilization and exploration. Lipidomics aims at
characterization and functional annotation of a broad range of lipid molecular
species in organisms. As seaweed lipids are highly complex and diverse, full
characterization of all of its structural diversity and quantification is quite a
challenge. An overview of key factors involved in seaweed lipidomics is presented here.
4.4.1 Sampling and Lipid Extraction
For lipidomics, sample preparation is one of the crucial steps, and utmost care
should be taken while sample harvesting, and the samples should be immediately
quenched after harvest by snap freezing in liquid nitrogen to disrupt the cell metabolism and inactivate all the endogenous hydrolytic enzymes. The frozen samples
4 Seaweed Lipidomics in the Era of ‘Omics’ Biology: A Contemporary Perspective