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

MOLECULAR TOOLS FOR MONITORING HARMFUL ALGAL BLOOMS GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays

Abstract Monitoring of marine microalgae is important to predict and manage harmful algae blooms. It currently relies mainly on light-microscopic identification and enumeration of algal cells, yet several molecular tools are currently being developed to complement traditional methods. MIcroarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a hierarchical multispecies microarray as one of these tools. Prototype arrays are currently being tested with field samples, yet the analysis of the large quantities of data generated by these arrays presents a challenge as suitable analysis tools or protocols are scarce. This paper proposes a two-part protocol for the analysis of the MIDTAL and other hierarchical multispecies arrays: Signal-to-noise ratios can be used to determine the presence or absence of signals and to identify potential false-positives considering parallel and hierarchical probes. In addition, normalized total signal intensities are recommended for comparisons between microarrays and in order to relate signals for specific probes to cell concentrations using external calibration curves. Hybridization-and probe-specific detection limits can be calculated to help evaluate negative results. The suggested analyses were implemented in &quot;GPRAnalyzer&quot;, a platform-independent and graphical user interface-based application, enabling non-specialist users to quickly and quantitatively analyze hierarchical multispecies microarrays. It is available online at http://folk.uio.no/ edvardse/gpranalyzer

Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

<p/> <p>Background</p> <p>Brown algae of the genus <it>Ectocarpus </it>exhibit high levels of genetic diversity and variability in morphological and physiological characteristics. With the establishment of <it>E. siliculosus </it>as a model and the availability of a complete genome sequence, it is now of interest to analyze variability among different species, ecotypes, and strains of the genus <it>Ectocarpus </it>both at the genome and the transcriptome level.</p> <p>Results</p> <p>We used an <it>E. siliculosus </it>gene expression microarray based on EST sequences from the genome-sequenced strain (reference strain) to carry out comparative genome hybridizations for five <it>Ectocarpus </it>strains: four <it>E. siliculosus </it>isolates (the male genome strain, a female strain used for outcrosses with the genome strain, a strain isolated from freshwater, and a highly copper-tolerant strain), as well as one strain of the sister species <it>E. fasciculatus</it>. Our results revealed significant genomic differences between ecotypes of the same species, and enable the selection of conserved probes for future microarray experiments with these strains. In the two closely related strains (a male and a female strain used for crosses), genomic differences were also detected, but concentrated in two smaller genomic regions, one of which corresponds to a viral insertion site.</p> <p>Conclusion</p> <p>The high variability between strains supports the concept of <it>E. siliculosus </it>as a complex of cryptic species. Moreover, our data suggest that several parts of the <it>Ectocarpus </it>genome may have evolved at different rates: high variability was detected particularly in transposable elements and fucoxanthin chlorophyll a/c binding proteins.</p

No downregulation of immune function during breeding in two year-round breeding bird species in an equatorial East African environment

Some equatorial environments exhibit substantial within-location variation in environmental conditions throughout the year and yet have year-round breeding birds. This implies that breeding in such systems are potentially unrelated to the variable environmental conditions. By breeding not being influenced by environmental conditions, we become sure that any differences in immune function between breeding and non-breeding birds do not result from environmental variation, therefore allowing for exclusion of the confounding effect of variation in environmental conditions. This create a unique opportunity to test if immune function is down-regulated during reproduction compared to non-breeding periods. We compared the immune function of sympatric male and female chick-feeding and non-breeding red-capped Calandrella cinerea and rufous-naped larks Mirafra africana in equatorial East Africa. These closely-related species occupy different niches and have different breeding strategies in the same grassland habitat. Red-capped larks prefer areas with short grass or almost bare ground, and breed during low rainfall periods. Rufous-naped larks prefer areas of tall grass and scattered shrubs and breed during high rainfall. We measured the following immune indices: nitric oxide, haptoglobin, agglutination and lysis, and measured total monthly rain, monthly average minimum (T-min) and maximum (T-max) temperatures. Contrary to our predictions, we found no down-regulation of immune function during breeding; breeding birds had higher nitric oxide than non-breeding ones in both species, while the other three immune indices did not differ between breeding phases. Red-capped larks had higher nitric oxide concentrations than Rufous-naped larks, which in turn had higher haptoglobin levels than red-capped larks. T-max was higher during breeding than during non-breeding for red-capped larks only, suggesting potential confounding effect of T-max on the comparison of immune function between breeding and non-breeding birds for this species. Overall, we conclude that in the two year-round breeding equatorial larks, immune function is not down-regulated during breeding

Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus

<p>Abstract</p> <p>Background</p> <p>Brown algae are plant multi-cellular organisms occupying most of the world coasts and are essential actors in the constitution of ecological niches at the shoreline. <it>Ectocarpus siliculosus </it>is an emerging model for brown algal research. Its genome has been sequenced, and several tools are being developed to perform analyses at different levels of cell organization, including transcriptomic expression analyses. Several topics, including physiological responses to osmotic stress and to exposure to contaminants and solvents are being studied in order to better understand the adaptive capacity of brown algae to pollution and environmental changes. A series of genes that can be used to normalise expression analyses is required for these studies.</p> <p>Results</p> <p>We monitored the expression of 13 genes under 21 different culture conditions. These included genes encoding proteins and factors involved in protein translation (ribosomal protein 26S, EF1alpha, IF2A, IF4E) and protein degradation (ubiquitin, ubiquitin conjugating enzyme) or folding (cyclophilin), and proteins involved in both the structure of the cytoskeleton (tubulin alpha, actin, actin-related proteins) and its trafficking function (dynein), as well as a protein implicated in carbon metabolism (glucose 6-phosphate dehydrogenase). The stability of their expression level was assessed using the Ct range, and by applying both the geNorm and the Normfinder principles of calculation.</p> <p>Conclusion</p> <p>Comparisons of the data obtained with the three methods of calculation indicated that EF1alpha (EF1a) was the best reference gene for normalisation. The normalisation factor should be calculated with at least two genes, alpha tubulin, ubiquitin-conjugating enzyme or actin-related proteins being good partners of EF1a. Our results exclude actin as a good normalisation gene, and, in this, are in agreement with previous studies in other organisms.</p

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

Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis)

As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness

Monoclonal antibodies directed to fucoidan preparations from brown algae

Cell walls of the brown algae contain a diverse range of polysaccharides with useful bioactivities. The precise structures of the sulfated fucan/fucoidan group of polysaccharides and their roles in generating cell wall architectures and cell properties are not known in detail. Four rat monoclonal antibodies, BAM1 to BAM4, directed to sulfated fucan preparations, have been generated and used to dissect the heterogeneity of brown algal cell wall polysaccharides. BAM1 and BAM4, respectively, bind to a non-sulfated epitope and a sulfated epitope present in the sulfated fucan preparations. BAM2 and BAM3 identified additional distinct epitopes present in the fucoidan preparations. All four epitopes, not yet fully characterised, occur widely within the major brown algal taxonomic groups and show divergent distribution patterns in tissues. The analysis of cell wall extractions and fluorescence imaging reveal differences in the occurrence of the BAM1 to BAM4 epitopes in various tissues of Fucus vesiculosus. In Ectocarpus subulatus, a species closely related to the brown algal model Ectocarpus siliculosus, the BAM4 sulfated epitope was modulated in relation to salinity levels. This new set of monoclonal antibodies will be useful for the dissection of the highly complex and yet poorly resolved sulfated polysaccharides in the brown algae in relation to their ecological and economic significance