Flatfishes colonised freshwater environments by acquisition of various DHA biosynthetic pathways

A complete biosynthetic pathway of the long-chain polyunsaturated fatty acids in an amphidromous fish, ayu sweetfish Plecoglossus altivelis (Stomiati; Osmeriformes)

The biosynthetic capability of the long-chain polyunsaturated fatty acids (LC-PUFA) in teleosts are highly diversified due to evolutionary events such as gene loss and subsequent neo- and/or sub-functionalisation of enzymes encoded by existing genes. In the present study, we have comprehensively characterised genes potentially involved in LC-PUFA biosynthesis, namely one front-end desaturase (fads2) and eight fatty acid elongases (elovl1a, elovl1b, elovl4a, elovl4b, elovl5, elovl7, elovl8a and elovl8b) from an amphidromous teleost, Ayu sweetfish, Plecoglossus altivelis. Functional analysis confirmed Fads2 with Δ6, Δ5 and Δ8 desaturase activities towards multiple PUFA substrates and several Elovl enzymes exhibited elongation capacities towards C18-20 or C18-22 PUFA substrates. Consequently, P. altivelis possesses a complete enzymatic capability to synthesise physiologically important LC-PUFA including arachidonic acid (ARA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3) from their C18 precursors. Interestingly, the loss of elovl2 gene in P. altivelis was corroborated by genomic and phylogenetic analyses. However, this constraint would possibly be overcome by the function of alternative Elovl enzymes, such as Elovl1b, which has not hitherto been functionally characterised in teleosts. The present study contributes novel insights into LC-PUFA biosynthesis in the relatively understudied teleost group, Osmeriformes (Stomiati), thereby enhancing our understanding of the complement of LC-PUFA biosynthetic genes within teleosts.

Effects of ocean warming on the fatty acid and epigenetic profile of Acartia tonsa: A multigenerational approach

The effects of climate change are becoming more prevalent, and it is important to know how copepods, the most abundant class in zooplankton, will react to changing temperatures as they are the main food source for secondary consumers. They act as key transferers of nutrients from primary producers to organisms higher up the food chain. Little is known about the effects of temperature changes on copepods on the long term, i.e., over several generations. Especially the epigenetic domain seems to be understudied and the question remains whether the nutritional value of copepods will permanently change with rising water temperatures. In this research, the effects of temperature on the fatty acid and epigenetic profiles of the abundant planktonic copepod Acartia tonsa were investigated, since we expect to see a link between these two. Indeed, changing methylation patterns helped copepods to deal with higher temperatures, which is in line with the relative abundance of the most important fatty acids, e.g., DHA. However, this pattern was only observed when temperature increased slowly. A sudden increase in temperature showed the opposite effect; Acartia tonsa did not show deviant methylation patterns and the relative abundance of DHA and other important fatty acids dropped significantly after several generations. These results suggest that local fluctuations in temperature have a greater effect on Acartia tonsa than an elevation of the global mean.

Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species

Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.

Diet effects on longevity, heat tolerance, lipid peroxidation and mitochondrial membrane potential in Daphnia

The dietary supply of polyunsaturated fatty acids (PUFA) crucially affects animals' performance at different temperatures. However, the underlying physiological mechanisms are still insufficiently understood. Here, we analyzed lifespan and heat tolerance of four genotypes of Daphnia magna reared on either the green alga Scenedesmus obliquus that lacks long-chain (> C18) PUFA, or the heterokont alga Nannochloropsis limnetica that contains C20 PUFA, both either at saturating and near-starvation levels. A significant genotype-by-diet interaction in lifespan was observed at saturating diets. The C20 PUFA-rich diet eliminated differences in lifespan among genotypes on the PUFA-deficient diet. Corrected for body length, acute heat tolerance was higher at low than at high food concentration, at least in the older of the two age groups analyzed. Genotypes differed significantly in heat tolerance, but there were no genotype-by-diet interactions. As predicted, the C20 PUFA-rich diet resulted in higher lipid peroxidation (LPO) and a lower mitochondrial membrane potential (ΔΨ_m). LPO levels averaged across clones and rearing conditions were inversely related to acute heat tolerance. Yet, heat tolerance was higher on the PUFA-rich diet than on the PUFA-deficient diet, particularly in older Daphnia, indicating that the C20 PUFA-rich diet allowed Daphnia to compensate for higher LPO. In contrast, Daphnia with intermediate levels of ΔΨ_m showed the lowest heat tolerance. Neither LPO nor ΔΨ_m explained the diet effects on lifespan. We hypothesize that antioxidants present in the PUFA-rich diet may have enabled higher heat tolerance of Daphnia despite higher LPO, which may also explain the lifespan expansion of otherwise short-lived genotypes.

Determination of dietary essential fatty acids in a deep-sea fish, the splendid alfonsino Beryx splendens: functional characterization of enzymes involved in long-chain polyunsaturated fatty acid biosynthesis

The splendid alfonsino Beryx splendens is a commercially important deep-sea fish in East Asian countries. Because the wild stock of this species has been declining, there is an urgent need to develop aquaculture systems. In the present study, we investigated the long-chain polyunsaturated fatty acid (LC-PUFA) requirements of B. splendens, which are known as essential dietary components in many carnivorous marine fish species. The fatty acid profiles of the muscles, liver, and stomach contents of B. splendens suggested that it acquires substantial levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) from its natural diet. The functional characterization of a fatty acid desaturase (Fads2) and three elongases (Elovl5, Elovl4a, and Elovl4b) from B. splendens confirmed their enzymatic capabilities in LC-PUFA biosynthesis. Fads2 showed Δ6 and Δ8 bifunctional desaturase activities. Elovl5 showed preferential elongase activities toward C₁₈ and C₂₀ PUFA substrates, whereas Elovl4a and Elovl4b showed activities toward various C_18-22 substrates. Given that Fads2 showed no Δ5 desaturase activity and no other fads-like sequence was found in the B. splendens genome, EPA and arachidonic acid cannot be synthesized from C₁₈ precursors; hence, they can be categorized as dietary essential fatty acids in B. splendens. EPA can be converted into DHA in B. splendens via the so-called Sprecher pathway. However, given that fads2 is only expressed in the brain, it is unlikely that the capacity of B. splendens to biosynthesize DHA from EPA can fulfill its physiological requirements. These results will be useful to researchers developing B. splendens aquaculture methods.

The role of vital dietary biomolecules in eco-evo-devo dynamics

The physiological dependence of animals on dietary intake of vitamins, amino acids, and fatty acids is ubiquitous. Sharp differences in the availability of these vital dietary biomolecules among different resources mean that consumers must adopt a range of strategies to meet their physiological needs. We review the emerging work on omega-3 long-chain polyunsaturated fatty acids, focusing predominantly on predator-prey interactions, to illustrate that trade-off between capacities to consume resources rich in vital biomolecules and internal synthesis capacity drives differences in phenotype and fitness of consumers. This can then feedback to impact ecosystem functioning. We outline how focus on vital dietary biomolecules in eco-eco-devo dynamics can improve our understanding of anthropogenic changes across multiple levels of biological organization.

Phylogenetic relationships and the origin of New World soles (Teleostei: Pleuronectiformes: Achiridae): The role of estuarine habitats

Even though the monophyletic status of Achiridae has been supported by morphological and molecular data, the interrelationships within the representatives of this family are poorly resolved. In the present study, we carried out the most complete molecular phylogenetic analysis of this group, encompassing all genera and employing both nuclear (Rhodopsin, Recombination activator [Rag 1], Mixed - lineage Leukemia [MLL] and Early Growth Response Protein 3 [EGR3]) and mitochondrial (Cytochrome C Oxidase Subunit I [COI], Cytochrome B [CytB], ATPase 6.8, 16S and 12S RNAr) genes. All topologies based on Maximum Likelihood, Bayesian inferences and Bayesian Inference of the Multispecies Coalescent confirmed the monophyletism of Achiridae, in spite of some incongruences in relation to Achirus mucuri, A. lineatus, Apionichthys finis and Trinectes microphthalmus. In fact, Achirus and Trinectes proved to be non-monophyletic genera while Hypoclinemus mentalis was closely related to A. achirus, suggesting this species should be reevaluated. We provided evidence that Achiridae has first arisen in estuaries (about 23.5 million years ago) and some lineages have evolved independently to either marine or freshwater habitats. Furthermore, we propose a diversification scenario of New World soles involving at least two events of marine incursions during Miocene and Pliocene - Pleistocene associated with natural geographic barriers (Victoria-Trindade chain), the width and exposure of continental shelf and headwater capture along the Amazon basin. Finally, the evolutionary dependence of Achirid soles on estuaries, characterized as highly dynamic environments, has probably driven the recent divergence of many species of Achiridae.

A complete inventory of long-chain polyunsaturated fatty acid biosynthesis pathway enzymes in the miniaturized cyprinid Paedocypris micromegethes

The capacity for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis activity in a species depends on the enzymatic activities of fatty acyl desaturase (Fads) and elongation of very long-chain fatty acid (Elovl). The miniaturized fish Paedocypris micromegethes is a developmentally truncated cyprinid living in highly acidic water conditions in tropical peat swamps. The capacity for LC-PUFA biosynthesis in this species, which has a reduced genome size, is unknown. A high-quality de novo transcriptome assembly enabled the identification of a putative Fads2 and four Elovl. The Fads2 was verified as a P. micromegethes Fads2 ortholog with in vitro Δ5 and Δ6 activities. The Elovl sequences were established as an Elovl5, Elovl2, and two Elovl4 paralogs, namely Elovl4a and Elovl4b. These Elovl enzymes, mainly Elovl5 and Elovl2, fulfill the necessary C18, C20, and C22 PUFA elongation steps for LC-PUFA biosynthesis. Collectively, these results validate the presence of a complete repertoire of LC-PUFA biosynthesis enzymes in a peat swamp miniatured freshwater fish.

Long-chain polyunsaturated fatty acid biosynthesis in a land-crab with advanced terrestrial adaptations: Molecular cloning and functional characterization of two fatty acyl elongases

Depending on the presence and activities of the front-end fatty acyl desaturases and elongation of very long-chain fatty acid (Elovl) enzymes, animals have different capacities for long-chain (≥C₂₀) polyunsaturated fatty acids (LC-PUFA) biosynthesis. Successful land colonisation in brachyuran crabs requires a shift towards terrestrial food chain with limited LC-PUFA availability. We cloned and functionally characterised two elovl genes from the purple land crab Gecarcoidea lalandii. The two Elovl contained all the necessary motifs of a typical polyunsaturated fatty acids (PUFA) Elovl and phylogenetically clustered in the Elovl1 and Elovl6 clades, respectively. The G. lalandii Elovl1 elongated saturated fatty acids, with low activities towards C20 and C22 PUFA substrates. Moreover, the G. lalandii Elovl6 was particularly active in the elongation of C18 PUFA, although it also recognised monounsaturated fatty acids as substrates for elongation. Collectively, the herein characterised G. lalandii elovl paralogues fulfil all the elongation steps involved in the LC-PUFA biosynthetic pathways. Tissue distribution of the G. lalandii elovl genes, along with the FA composition analyses, suggest the hepatopancreas and gill as key metabolic sites for fatty acid elongation. However, current data suggest that G. lalandii is unable to rely solely on biosynthesis to fulfil LC-PUFA requirements, since front-end desaturase appears to be absent in this species and other decapods.

Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis

Although numerous studies in aquatic organisms have linked lipid metabolism with intestinal bacterial structure, the possibility of the gut microbiota participating in the biosynthesis of beneficial long-chain polyunsaturated fatty acid (LC-PUFA) remains vague. We profiled the gut microbiota of the mud crab Scylla olivacea fed with either a LC-PUFA rich (FO) or a LC-PUFA-poor but C18-PUFA substrate-rich (LOCO) diet. Additionally, a diet with a similar profile as LOCO but with the inclusion of an antibiotic, oxolinic acid (LOCOAB), was also used to further demarcate the possibility of LC-PUFA biosynthesis in gut microbiota. Compared to diet FO treatment, crabs fed diet LOCO contained a higher proportion of Proteobacteria, notably two known taxonomy groups with PUFA biosynthesis capacity, Vibrio and Shewanella. Annotation of metagenomic datasets also revealed enrichment in the KEGG pathway of unsaturated fatty acid biosynthesis and polyketide synthase-like system sequences with this diet. Intriguingly, diet LOCOAB impeded the presence of Vibrio and Shewanella and with it, the function of unsaturated fatty acid biosynthesis. However, there was an increase in the function of short-chain fatty acid production, accompanied by a shift towards the abundance of phyla Bacteroidota and Spirochaetota. Collectively, these results exemplified bacterial communities and their corresponding PUFA biosynthesis pathways in the microbiota of an aquatic crustacean species.

Quantitative lipidomics and spatial MS-Imaging uncovered neurological and systemic lipid metabolic pathways underlying troglomorphic adaptations in cave-dwelling fish

The Sinocyclocheilus represents a rare, freshwater teleost genus endemic to China that comprises the river-dwelling surface fish and the cave-dwelling cavefish. Using a combinatorial approach of quantitative lipidomics and mass-spectrometry imaging (MSI), we demonstrated that neural compartmentalization of lipid distribution and lipid metabolism are associated with the evolution of troglomorphic traits in Sinocyclocheilus. Attenuated DHA biosynthesis via the Δ4 desaturase pathway led to reductions in docosahexaenoic acid (DHA)-phospholipids in cavefish cerebellum. Instead, cavefish accumulates arachidonic acid (ARA)-phospholipids that may disfavor retinotectal arbor growth. Importantly, MSI of sulfatides, coupled with immunostaining of myelin basic protein and transmission electron microscopy images of hindbrain axons revealed demyelination in cavefish raphe serotonergic neurons. Demyelination in cavefish parallels the loss of neuroplasticity governing social behavior such as aggressive dominance. Outside the brain, quantitative lipidomics and qRT-PCR revealed systemic reductions in membrane esterified DHAs in the liver, attributed to suppression of genes along the Sprecher pathway (elovl2, elovl5, acox1). Development of fatty livers was observed in cavefish, likely mediated by an impeded mobilization of storage lipids, as evident in the diminished expressions of pnpla2, lipea, lipeb, dagla and mgll; and suppressed β-oxidation of fatty acyls via both mitochondria and peroxisomes, reflected in the reduced expressions of cpt1ab, hadhaa, cpt2, decr1 and acox1. These neurological and systemic metabolic adaptations serve to reduce energy expenditure, forming the basis of recessive evolution that eliminates non-essential morphological and behavioral traits, giving cavefish a selective advantage to thrive in caves where proper resource allocation becomes a major determinant of survival.

Copy number variation of a fatty acid desaturase gene Fads2 associated with ecological divergence in freshwater stickleback populations

Fitness of aquatic animals can be limited by the scarcity of nutrients such as long-chain polyunsaturated fatty acids, especially docosahexaenoic acid (DHA). DHA availability from diet varies among aquatic habitats, imposing different selective pressures on resident animals to optimize DHA acquisition and synthesis. For example, DHA is generally poor in freshwater ecosystems compared to marine ecosystems. Our previous work revealed that, relative to marine fishes, several freshwater fishes evolved higher copy numbers of the fatty acid desaturase2 (Fads2) gene, which encodes essential enzymes for DHA biosynthesis, likely compensating for the limited availability of DHA in freshwater. Here, we demonstrate that Fads2 copy number also varies between freshwater sticklebacks inhabiting lakes and streams with stream fish having higher Fads2 copy number. Additionally, populations with benthic-like morphology possessed higher Fads2 copy number than those with planktivore-like morphology. This may be because benthic-like fish mainly feed on DHA-deficient prey such as macroinvertebrates whereas planktivore-like fish forage more regularly on DHA-rich prey, like copepods. Our results suggest that Fads2 copy number variation arises from ecological divergence not only between organisms exploiting marine and freshwater habitats but also between freshwater organisms exploiting divergent resources.

The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification

The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.

Lack of ∆5 Desaturase Activity Impairs EPA and DHA Synthesis in Fish Cells from Red Sea Bream and Japanese Flounder

Long-chain (≥ C₂₀) polyunsaturated fatty acids (LC-PUFA), such as eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA), are necessary for human health and are obtained from marine fish-derived oils. Marine fish are LC-PUFA-rich animals; however, many of them require LC-PUFA for growth. Therefore, it is suggested that they do not have sufficient ability to biosynthesize LC-PUFA. To evaluate in vivo LC-PUFA synthetic activity in fish cells, fish-derived cell lines from red sea bream (Pagrus major, PMS and PMF), Japanese flounder (Paralichthys olivaceus, HINAE), and zebrafish (Danio rerio, BRF41) were incubated with n-3 fatty acids labeled by radioisotopes or stable isotopes, and then, n-3 PUFA were analyzed by thin-layer chromatography or liquid chromatography-mass spectrometry. Labeled EPA and DHA were biosynthesized from labeled α-linolenic acid (18:3n-3) in BRF41, whereas they were not detected in PMS, PMF, or HINAE cells. We next cloned the fatty acid desaturase 2 (Fads2) cDNAs from PMF cells and zebrafish, expressed in budding yeasts, and then analyzed the substrate specificities of enzymes. As a result, we found that Fads2 from PMF cells was a ∆6/∆8 desaturase. Collectively, our study indicates that cell lines from red sea bream and Japanese flounder were not able to synthesize EPA or DHA by themselves, possibly due to the lack of ∆5 desaturase activity. Furthermore, this study provides a sensitive and reproducible non-radioactive method for evaluating LC-PUFA synthesis in fish cells using a stable isotope and liquid chromatography-mass spectrometry.

Influence of Dietary Lipids and Environmental Salinity on the n-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis Capacity of the Marine Teleost Solea senegalensis

Fish vary in their ability to biosynthesise long-chain polyunsaturated fatty acids (LC-PUFA) depending upon the complement and function of key enzymes commonly known as fatty acyl desaturases and elongases. It has been reported in Solea senegalensis the existence of a Δ4 desaturase, enabling the biosynthesis of docosahexaenoic acid (DHA) from eicosapentaenoic acid (EPA), which can be modulated by the diet. The present study aims to evaluate the combined effects of the partial replacement of fish oil (FO) with vegetable oils and reduced environmental salinity in the fatty acid composition of relevant body compartments (muscle, hepatocytes and enterocytes), the enzymatic activity over α-linolenic acid (ALA) to form n-3 LC-PUFA through the incubation of isolated hepatocytes and enterocytes with [1-¹⁴C] 18:3 n-3, and the regulation of the S. senegalensis fads2 and elovl5 in the liver and intestine. The presence of radiolabelled products, including 18:4n-3, 20:4n-3 and EPA, provided compelling evidence that a complete pathway enabling the biosynthesis of EPA from ALA, establishing S. senegalensis, has at least one Fads2 with ∆6 activity. Dietary composition prevailed over salinity in regulating the expression of fads2, while salinity did so over dietary composition for elovl5. FO replacement enhanced the proportion of DHA in S. senegalensis muscle and the combination with 20 ppt salinity increased the amount of n-3 LC-PUFA in hepatocytes.

Regulation of long-chain polyunsaturated fatty acid biosynthesis in teleost fish

Omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA, C_20-24), including eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3), are involved in numerous biological processes and have a range of health benefits. Fish have long been considered as the main source of n-3 LC-PUFA in human diets. However, the capacity for endogenous biosynthesis of LC-PUFA from C₁₈ PUFA varies in fish species based on the presence, expression and activity of key enzymes including fatty acyl desaturases (Fads) and elongation of very long-chain fatty acids (Elovl) proteins. In this article, we review progress on the identified Fads and Elovl, as well as the regulatory mechanisms of LC-PUFA biosynthesis both at transcriptional and post-transcriptional levels in teleosts. The most comprehensive advances have been obtained in rabbitfish Siganus canaliculatus, a marine teleost demonstrated to have the entire pathway for LC-PUFA biosynthesis, including the roles of transcription factors hepatocyte nuclear factor 4α (Hnf4α), liver X receptor alpha (Lxrα), sterol regulatory element-binding protein 1 (Srebp-1), peroxisome proliferator-activated receptor gamma (Pparγ) and stimulatory protein 1 (Sp1), as well as post-transcriptional regulation by individual microRNA (miRNA) or clusters. This research has, for the first time, demonstrated the involvement of Hnf4α, Pparγ and miRNA in the regulation of LC-PUFA biosynthesis in vertebrates. The present review provides readers with a relatively comprehensive overview of the progress made into understanding LC-PUFA biosynthetic systems in teleosts, and some insights into improving endogenous LC-PUFA biosynthesis capacity aimed at reducing the dependence of aquafeeds on fish oil while maintaining or increasing flesh LC-PUFA content and the nutritional quality of farmed fish.