Molecular Mechanism of Interaction Between Fatty Acid Delta 6 Desaturase and Acyl-CoA by Computational Prediction

Enzyme catalyzed desaturation of intracellular fatty acids plays an important role in various physiological and pathological processes related to lipids. Limited to the multiple transmembrane domains, it is difficult to obtain their three-dimensional structure of fatty acid desaturases. So how they interact with their substrates is unclear. Here, we predicted the complex of Micromonas pusilla delta 6 desaturase (MpFADS6) with the substrate linoleinyl-CoA (ALA-CoA) by trRosetta software and docking poses by Dock 6 software. The potential enzyme-substrate binding sites were anchored by analysis of the complex. Then, site-directed mutagenesis and activity verification clarified that W290, W224, and F352 were critical residues of the substrate tunnel and directly bonded to ALA-CoA. H94 and H69 were indispensable for transporting electrons with heme. H452, N445, and H358 significantly influenced the recognition and attraction of MpFADS6 to the substrate. These findings provide new insights and methods to determine the structure, mechanisms and directed transformation of membrane-bound desaturases.

The Arctic picoeukaryote <i>Micromonas pusilla</i> benefits from ocean acidification under constant and dynamic light

Compared to the rest of the globe, the Arctic Ocean is affected disproportionately by climate change. Despite these fast environmental changes, we currently know little about the effects of ocean acidification (OA) on marine key species in this area. Moreover, the existing studies typically test the effects of OA under constant, hence artificial, light fields. In this study, the abundant Arctic picoeukaryote Micromonas pusilla was acclimated to current (400 µatm) and future (1000 µatm) pCO2 levels under a constant as well as a dynamic light, simulating more realistic light fields as experienced in the upper mixed layer. To describe and understand the responses to these drivers, growth, particulate organic carbon (POC) production, elemental composition, photophysiology and reactive oxygen species (ROS) production were analysed. M. pusilla was able to benefit from OA on various scales, ranging from an increase in growth rates to enhanced photosynthetic capacity, irrespective of the light regime. These beneficial effects were, however, not reflected in the POC production rates, which can be explained by energy partitioning towards cell division rather than biomass build-up. In the dynamic light regime, M. pusilla was able to optimize its photophysiology for effective light usage during both low- and high-light periods. This photoacclimative response, which was achieved by modifications to photosystem II (PSII), imposed high metabolic costs leading to a reduction in growth and POC production rates when compared to constant light. There were no significant interactions observed between dynamic light and OA, indicating that M. pusilla is able to maintain effective photoacclimation without increased photoinactivation under high pCO2. Based on these findings, M. pusilla is likely to cope well with future conditions in the Arctic Ocean.

Consensus mutagenesis and ancestral reconstruction provide insight into the substrate specificity and evolution of the front-end Δ6-desaturase family

ABSTRACTMarine algae are a major source of omega (ω)-3 long-chain polyunsaturated fatty acids (ω3-LCPUFAs), which are conditionally essential nutrients in humans and a target for industrial production. The biosynthesis of these molecules in marine algae begins with the desaturation of fatty acids by Δ6-desaturases and enzymes from different species display a range of specificities towards ω3 and ω6 LCPUFAs. In the absence of a molecular structure, the structural basis for the variable substrate specificity of Δ6-desaturases is poorly understood. Here we have conducted a consensus mutagenesis and ancestral protein reconstruction-based analysis of the Δ6-desaturase family, focusing on the ω3-specific Δ6-desaturase from Micromonas pusilla (MpΔ6des) and the bispecific (ω3/ω6) Δ6-desaturase from Ostreococcus tauri (OtΔ6des). Our characterization of consensus amino acid substitutions in MpΔ6des revealed that residues in diverse regions of the protein, such as the N-terminal cytochrome b5 domain, can make important contributions to determining substrate specificity. Ancestral protein reconstruction also suggests that some extant Δ6-desaturases, such as OtΔ6des, could have adapted to different environmental conditions by losing specificity for ω3-LCPUFAs. This dataset provides a map of regions within Δ6-desaturases that contribute to substrate specificity and could facilitate future attempts to engineer these proteins for use in biotechnology.

Genome Resolved Biogeography of Mamiellales

Among marine phytoplankton, Mamiellales encompass several species from the genera Micromonas, Ostreococcus and Bathycoccus, which are important contributors to primary production. Previous studies based on single gene markers described their wide geographical distribution but led to discussion because of the uneven taxonomic resolution of the method. Here, we leverage genome sequences for six Mamiellales species, two from each genus Micromonas, Ostreococcus and Bathycoccus, to investigate their distribution across 133 stations sampled during the Tara Oceans expedition. Our study confirms the cosmopolitan distribution of Mamiellales and further suggests non-random distribution of species, with two triplets of co-occurring genomes associated with different temperatures: Ostreococcus lucimarinus, Bathycoccus prasinos and Micromonas pusilla were found in colder waters, whereas Ostreococcus spp. RCC809, Bathycoccus spp. TOSAG39-1 and Micromonas commoda were more abundant in warmer conditions. We also report the distribution of the two candidate mating-types of Ostreococcus for which the frequency of sexual reproduction was previously assumed to be very low. Indeed, both mating types were systematically detected together in agreement with either frequent sexual reproduction or the high prevalence of a diploid stage. Altogether, these analyses provide novel insights into Mamiellales’ biogeography and raise novel testable hypotheses about their life cycle and ecology.

The Arctic picoeukaryote <i>Micromonas pusilla</i> benefits from Ocean Acidification under constant and dynamic light

Compared to the rest of the globe, the Arctic Ocean is affected disproportionately by climate change. Despite these fast environmental changes, we currently know little about the effects of ocean acidification (OA) on marine key species in this area. Moreover, the existing studies typically test the effects of OA under constant, hence artificial light fields. In this study, the abundant Arctic picoeukaryote Micromonas pusilla was acclimated to current (400 μatm) and future (1000 μatm) pCO2 levels under a constant as well as dynamic light, simulating natural light fields as experienced in the upper mixed layer. To describe and understand the responses to these drivers, growth, particulate organic carbon (POC) production, elemental composition, photophysiology and reactive oxygen species (ROS) production were analysed. M. pusilla was able to benefit from OA on various scales, ranging from an increase in growth rates to enhanced photosynthetic capacity, irrespective of the light regime. These beneficial effects were, however, not reflected in the POC production rates, which can be explained by energy partitioning towards cell division rather than biomass build-up. In the dynamic light regime, M. pusilla was able to optimise its photophysiology for effective light usage during both low and high light periods. This effective photoacclimation, which was achieved by modifications to photosystem II (PSII), imposed high metabolic costs leading to a reduction in growth and POC production rates when compared to constant light. There were no significant interactions observed between dynamic light and OA, indicating that M. pusilla was able maintain effective photoacclimation without increased photoinactivation under high pCO2. Based on these findings, physiologically plastic M. pusilla may exhibit a robust positive response to future Arctic Ocean conditions.

Cell explosions: single cell death triggers an avoidance response in local populations of the ecologically prominent phytoplankton genus Micromonas

The global phytoplankton community, comprised of aquatic photosynthetic organisms, is acknowledged for being responsible for half of the global oxygen production Prominent among these is the pico-eukaryote Micromonas commoda (formally Micromonas pusilla of the genus Micromonas), which can be found in marine and coastal environments across the globe. Cell death of phytoplankton has been identified as contributing to the largest carbon transfers on the planet moving 109 tonnes of carbon in the oceans every day. During a cell death organic matter is released into the local environment which can act as both a food source and a warning signal for nearby organisms. Here we present a novel motility response to single cell death in populations of Micromonas sp., where the death of a single cell releases a chemical patch triggers surrounding cells to escape the immediate affected area. These so-called “burst events” are then modelled and compared with a spherically symmetric diffusing patch which is found to faithfully reproduce the observed behaviour. Finally, laser ablation of single cells reproduces the observed avoidance response, confirming that Micromonas sp. has evolved a specific motility response in order to escape harmful environments for example nearby predator-prey interactions or virus lysis induced cell death.

Phototaxis of the dominant marine pico-eukaryote Micromonas sp.: from population to single cell

Micromonas commoda (previously Micromonas pusilla, a unicellular photosynthetic picoeukaryote globally dominant in marine ecosystems, has previously been qualified as being strongly phototactic. To date, no detailed quantitative or qualitative description of this behaviour has been reported, nor have thorough studies of its motility been undertaken. This primary producer has only been qualitatively described as utilizing run-and-tumble motion, but such motility strategy is incompatible with its morphology comprising only one propelling flagellum. Moreover, it is still unclear as to how Micromonas sp. detects a light direction due to the lack of a dedicated eyespot; the organism is essentially blind. Here we first perform population-scale phototactic experiments to show that this organism actively responds to a wide range of light wavelengths and intensities. These population responses are well accounted for within a simple drift-diffusion framework. Based on single-cell tracking experiments, we then detail thoroughly Micromonas sp.’s motility which resembles run-and-reverse styles of motion commonly observed in marine prokaryotes and that we name stop-run or reverse. The associated peculiar microscopic changes upon photo-stimulation are finally described and integrating those into jump-diffusion simulations appears to produce phototactic drifts that are quantitatively compatible with those obtained experimentally at the population level.