Evolution and expression of core SWI/SNF genes in red algae

Red algae are the oldest identifiable multicellular eukaryotes, with a fossil record dating back more than a billion years. During that time two major rhodophyte lineages, bangiophytes and florideophytes, have evolved varied levels of morphological complexity. These two groups are distinguished, in part, by different patterns of multicellular development, with florideophytes exhibiting a far greater diversity of morphologies. Interestingly, during their long evolutionary history, there is no record of a rhodophyte achieving the kinds of cellular and tissue‐specific differentiation present in other multicellular algal lineages. To date, the genetic underpinnings of unique aspects of red algal development are largely unexplored; however, they must reflect the complements and patterns of expression of key regulatory genes. Here we report comparative evolutionary and gene expression analyses of core subunits of the SWI/SNF chromatin‐remodeling complex, which is implicated in cell differentiation and developmental regulation in more well studied multicellular groups. Our results suggest that a single, canonical SWI/SNF complex was present in the rhodophyte ancestor, with gene duplications and evolutionary diversification of SWI/SNF subunits accompanying the evolution of multicellularity in the common ancestor of bangiophytes and florideophytes. Differences in how SWI/SNF chromatin remodeling evolved subsequently, in particular gene losses and more rapid divergence of SWI3 and SNF5 in bangiophytes, could help to explain why they exhibit a more limited range of morphological complexity than their florideophyte cousins

Chlorophyll-binding proteins revisited - a multigenic family of light-harvesting and stress proteins from a brown algal perspective

<p>Abstract</p> <p>Background</p> <p>Chlorophyll-binding proteins (CBPs) constitute a large family of proteins with diverse functions in both light-harvesting and photoprotection. The evolution of CBPs has been debated, especially with respect to the origin of the LI818 subfamily, members of which function in non-photochemical quenching and have been found in chlorophyll a/c-containing algae and several organisms of the green lineage, but not in red algae so far. The recent publication of the <it>Ectocarpus siliculosus </it>genome represents an opportunity to expand on previous work carried out on the origin and function of CBPs.</p> <p>Results</p> <p>The <it>Ectocarpus </it>genome codes for 53 CBPs falling into all major families except the exclusively green family of chlorophyll a/b binding proteins. Most stress-induced CBPs belong to the LI818 family. However, we highlight a few stress-induced CBPs from <it>Phaeodactylum tricornutum </it>and <it>Chondrus crispus </it>that belong to different sub-families and are promising targets for future functional studies. Three-dimensional modeling of two LI818 proteins revealed features common to all LI818 proteins that are likely to interfere with their capacity to bind chlorophyll b and lutein, but may enable binding of chlorophyll c and fucoxanthin. In the light of this finding, we examined the possibility that LI818 proteins may have originated in a chlorophyll c/fucoxanthin containing organism and compared this scenario to three alternatives: an independent evolution of LI818 proteins in different lineages, an ancient origin together with the first CBPs, before the separation of the red and the green lineage, or an origin in the green lineage and a transfer to an ancestor of haptophytes and heterokonts during a cryptic endosymbiosis event.</p> <p>Conclusions</p> <p>Our findings reinforce the idea that the LI818 family of CBPs has a role in stress response. In addition, statistical analyses of phylogenetic trees show an independent origin in different eukaryotic lineages or a green algal origin of LI818 proteins to be highly unlikely. Instead, our data favor an origin in an ancestral chlorophyll a/c-containing organism and a subsequent lateral transfer to some green algae, although an origin of LI818 proteins in a common ancestor of red and green algae cannot be ruled out.</p

Photosynthesis in Chondrus crispus: The contribution of energy spill-over in the regulation of excitonic flux

AbstractChondrus crispus is a species of red algae that grows on rocks from the middle intertidal into the subtidal zones of the North Atlantic coasts. As such, it has to cope with strongly variable abiotic conditions. Here we studied the response of the photosynthetic apparatus of this red alga to illumination. We found that, as previously described in the case of the unicellular alga Rhodella violacea (E. Delphin et al., Plant Physiol. 118 (1998) 103–113), a single multi-turnover saturating pulse of light is sufficient to induce a strong quenching of fluorescence. To elucidate the mechanisms underlying this fluorescence quenching, we combined room temperature and 77K fluorescence measurements with absorption spectroscopy to monitor the redox state of the different electron carriers in the chain. In addition, we studied the dependence of these various observables upon the excitation wavelength. This led us to identify energy spill-over from Photosystem II to Photosystem I rather than a qE-type non-photochemical quenching as the major source of fluorescence quenching that develops upon a series of 200ms pulses of saturating light results, in line with the conclusion of Ley and Butler (Biochim. Biophys. Acta 592 (1980) 349–363) from their studies of the unicellular red alga Porphyridium cruentum. In addition, we show that the onset of this spill-over is triggered by the reduction of the plastoquinone pool

Is geographical variation driving the transcriptomic responses to multiple stressors in the kelp Saccharina latissima

Background: Kelps (Laminariales, Phaeophyceae) are brown macroalgae of utmost ecological, and increasingly economic, importance on temperate to polar rocky shores. Omics approaches in brown algae are still scarce and knowledge of their acclimation mechanisms to the changing conditions experienced in coastal environments can benefit from the application of RNA-sequencing. Despite evidence of ecotypic differentiation, transcriptomic responses from distinct geographical locations have, to our knowledge, never been studied in the sugar kelp Saccharina latissima so far. Results: In this study we investigated gene expression responses using RNA-sequencing of S. latissima from environments with contrasting temperature and salinity conditions – Roscoff, in temperate eastern Atlantic, and Spitsbergen in the Arctic. Juvenile sporophytes derived from uniparental stock cultures from both locations were pre-cultivated at 8 °C and SA 30. Sporophytes acclimated to 0 °C, 8 °C and 15 °C were exposed to a low salinity treatment (SA 20) for 24 h. Hyposalinity had a greater impact at the transcriptomic level than the temperature alone, and its effects were modulated by temperature. Namely, photosynthesis and pigment synthesis were extensively repressed by low salinity at low temperatures. Although some responses were shared among sporophytes from the different sites, marked differences were revealed by principal component analysis, differential expression and GO enrichment. The interaction between low temperature and low salinity drove the largest changes in gene expression in sporophytes from Roscoff while specimens from Spitsbergen required more metabolic adjustment at higher temperatures. Moreover, genes related to cell wall adjustment were differentially expressed between Spitsbergen and Roscoff control samples. Conclusions: Our study reveals interactive effects of temperature and salinity on transcriptomic profiles in S. latissima. Moreover, our data suggest that under identical culture conditions sporophytes from different locations diverge in their transcriptomic responses. This is probably connected to variations in temperature and salinity in their respective environment of origin. The current transcriptomic results support the plastic response pattern in sugar kelp which is a species with several reported ecotypes. Our data provide the baseline for a better understanding of the underlying processes of physiological plasticity and may help in the future to identify strains adapted to specific environments and its genetic control

In Silico Survey of the Mitochondrial Protein Uptake and Maturation Systems in the Brown Alga Ectocarpus siliculosus

The acquisition of mitochondria was a key event in eukaryote evolution. The aim of this study was to identify homologues of the components of the mitochondrial protein import machinery in the brown alga Ectocarpus and to use this information to investigate the evolutionary history of this fundamental cellular process. Detailed searches were carried out both for components of the protein import system and for related peptidases. Comparative and phylogenetic analyses were used to investigate the evolution of mitochondrial proteins during eukaryote diversification. Key observations include phylogenetic evidence for very ancient origins for many protein import components (Tim21, Tim50, for example) and indications of differences between the outer membrane receptors that recognize the mitochondrial targeting signals, suggesting replacement, rearrangement and/or emergence of new components across the major eukaryotic lineages. Overall, the mitochondrial protein import components analysed in this study confirmed a high level of conservation during evolution, indicating that most are derived from very ancient, ancestral proteins. Several of the protein import components identified in Ectocarpus, such as Tim21, Tim50 and metaxin, have also been found in other stramenopiles and this study suggests an early origin during the evolution of the eukaryotes

Infection of the brown alga Ectocarpus siliculosus by the oomycete Eurychasma dicksonii induces oxidative stress and halogen metabolism

Acknowledgments We would like to thank the Aberdeen Proteome Facility, especially Phil Cash, David Stead and Evelyn Argo for assistance with 2D electrophoresis and mass spectrometry. M.S. gratefully acknowledges a Marie Curie PhD fellowship from the European Commission (ECOSUMMER, MEST-CT-2005-20501), a joint FEMS/ESCMID Research Fellowship and the Genomia Fund. C.M.M.G. is supported by a Marie Curie postdoctoral fellowship (MEIF-CT-2006-022837), a Marie Curie Re-Integration Grant (PERG03-GA-2008-230865) and a New Investigator grant from the UK Natural Environment Research Council (NERC, grant NE/J00460X/1). F.C.K. would like to thank NERC for funding (grants NE/D521522/1, NE/F012705/1 and Oceans 2025 / WP 4.5). L.J.G.-B., C.M.M.G., F.C.K. and P.W. would like to acknowledge funding from NERC for a Strategic Ocean Funding Initiative award (NE/F012578/1). Funding from the MASTS pooling initiative (Marine Alliance for Science and Technology for Scotland, funded by the Scottish Funding Council and contributing institutions; grant reference HR09011) and from the TOTAL Foundation (Paris) to F.C.K. is gratefully acknowledged. Finally, we would like to thank the two anonymous referees for constructive suggestions to improve our manuscript.Peer reviewedPublisher PD

Polar lipids of commercial Ulva spp. of different origins: profiling and relevance for seaweed valorization

Macroalgae of the genus Ulva have long been used as human food. Local environmental conditions, among other factors, can have an impact on their nutrient and phytochemical composition, as well as on the value of the seaweed for food and non-food applications. This study is the first to initiate a comparison between commercial Ulva spp. from different European origins, France (FR, wild-harvested Ulva spp.), and Portugal (PT, farm-raised Ulva rigida), in terms of proximate composition, esterified fatty acids (FA), and polar lipids. The ash content was higher in PT samples, while FR samples had higher levels of proteins, lipids, and carbohydrates and other compounds. The profile of esterified FA, as well as FA-containing polar lipids at the class and species levels were also significantly different. The FR samples showed about three-fold higher amount of n-3 polyunsaturated FA, while PT samples showed two-fold higher content of monounsaturated FA. Quantification of glycolipids and phospholipids revealed, respectively, two-fold and three-fold higher levels in PT samples. Despite the differences found, the polar lipids identified in both batches included some lipid species with recognized bioactivity, valuing Ulva biomass with functional properties, increasing their added value, and promoting new applications, namely in nutraceutical and food markets.UIDB/50011/2020+UIDP/50011/2020, UID/QUI/00062/2019, UIDB/50006/2020, UIDB/50017/2020+UIDP/50017/2020, LISBOA-01-0145-FEDER-402-022125, POCI-01-0145-FEDER-030962, BPD/UI51/5041/2017, BPD/UI51/5042/2018; EC/H2020/727892/EUinfo:eu-repo/semantics/publishedVersio

Ulvan Activates Chicken Heterophils and Monocytes Through Toll-Like Receptor 2 and Toll-Like Receptor 4

Responsiveness to invasive pathogens, clearance via the inflammatory response, and activation of appropriate acquired responses are all coordinated by innate host defenses. Toll-like receptor (TLR) ligands are potent immune-modulators with profound effects on the generation of adaptive immune responses. This property is being exploited in TLR-based vaccines and therapeutic agents in chickens. However, for administering the TLR agonist, all previous studies used in ovo, intra-muscular or intra-venous routes that cannot be performed in usual farming conditions, thus highlighting the need for TLR ligands that display systemic immune effects when given orally (per os). Here we have demonstrated that an ulvan extract of Ulva armoricana is able to activate avian heterophils and monocytes in vitro. Using specific inhibitors, we have evidenced that ulvan may be a new ligand for TLR2 and TLR4; and that they regulate heterophil activation in slightly different manner. Moreover, activation of heterophils as well as of monocytes leads to release pro-inflammatory cytokines, including interleukin1-β, interferon α and interferon γ, through pathways that we partly identified. Finally, when given per os to animals ulvan induces heterophils and monocytes to be activated in vivo thus leading to a transient release of pro-inflammatory cytokines with plasma concentrations returning toward baseline levels at day 3

Novel endosomolytic compounds enable highly potent delivery of antisense oligonucleotides

The therapeutic and research potentials of oligonucleotides (ONs) have been hampered in part by their inability to effectively escape endosomal compartments to reach their cytosolic and nuclear targets. Splice-switching ONs (SSOs) can be used with endosomolytic small molecule compounds to increase functional delivery. So far, development of these compounds has been hindered by a lack of high-resolution methods that can correlate SSO trafficking with SSO activity. Here we present in-depth characterization of two novel endosomolytic compounds by using a combination of microscopic and functional assays with high spatiotemporal resolution. This system allows the visualization of SSO trafficking, evaluation of endosomal membrane rupture, and quantitates SSO functional activity on a protein level in the presence of endosomolytic compounds. We confirm that the leakage of SSO into the cytosol occurs in parallel with the physical engorgement of LAMP1-positive late endosomes and lysosomes. We conclude that the new compounds interfere with SSO trafficking to the LAMP1-positive endosomal compartments while inducing endosomal membrane rupture and concurrent ON escape into the cytosol. The efficacy of these compounds advocates their use as novel, potent, and quick-acting transfection reagents for antisense ONs