Alessandra De Martino

The Phaeodactylum genome reveals the evolutionary history of diatom genomes.

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (∼40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

An atypical member of the light-harvesting complex stress-related protein family modulates diatom responses to light

Diatoms are prominent phytoplanktonic organisms that contribute around 40% of carbon assimilation in the oceans. They grow and perform optimally in variable environments, being able to cope with unpredictable changes in the amount and quality of light. The molecular mechanisms regulating diatom light responses are, however, still obscure. Using knockdown Phaeodactylum tricornutum transgenic lines, we reveal the key function of a member of the light-harvesting complex stress-related (LHCSR) protein family, denoted LHCX1, in modulation of excess light energy dissipation. In contrast to green algae, this gene is already maximally expressed in nonstressful light conditions and encodes a protein required for efficient light responses and growth. LHCX1 also influences natural variability in photoresponse, as evidenced in ecotypes isolated from different latitudes that display different LHCX1 protein levels. We conclude, therefore, that this gene plays a pivotal role in managing light responses in diatoms.

Digital expression profiling of novel diatom transcripts provides insight into their biological functions

BackgroundDiatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes.ResultsWe have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity.ConclusionsThe digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.

Physiological and Molecular Evidence that Environmental Changes Elicit Morphological Interconversion in the Model Diatom Phaeodactylum tricornutum

Over the last decades Phaeodactylum tricornutum has become a model to study diatom biology at the molecular level. Cells have the peculiarity to be pleiomorphic and it is thought that this character is triggered by culture conditions, although few quantitative studies have been performed and nothing is known at the molecular level. Our aim was to quantify the effect of growth conditions on cell morphology of different P. tricornutum strains by quantitative microscopy, cellular imaging, and non-targeted transcriptomics. We show that morphotype changes can be regulated by changing culture conditions, depending on the strain, and show a common trend of increased oval cell abundance as a response to stress. Examination of expressed sequence tags (ESTs) from triradiate cells infers the importance of osmoregulation in the maintenance of this morphotype, whereas ESTs derived from oval cells grown in hyposaline and low temperature conditions show a predominance of genes encoding typical components of stress pathways, especially in signaling, cell homeostasis and lipid metabolism. This work contributes to better understand the importance of the unique capability of morphotype conversion in P. tricornutum and its relevance in acclimation to changing environmental conditions.

Mitosis in diatoms: rediscovering an old model for cell division

Diatoms are important protists that generate one fifth of the oxygen produced annually on earth. These aquatic organisms likely derived from a secondary endosymbiosis event, and they display peculiar genomic and structural features that reflect their chimeric origin. Diatoms were one of the first models of cell division and these early studies revealed a range of interesting features including a unique acentriolar microtubule‐organising centre. Unfortunately, almost nothing is known at the molecular level, in contrast to the advances in other experimental organisms. Recently the full genome sequences of two diatoms have been annotated and molecular tools have been developed. These resources offer new possibilities to re‐investigate the mechanisms of cell division in diatoms by recruiting information from more intensively studied organisms. A renaissance of the topic is further justified by the current interest in diatoms as a source of biofuels and for understanding massive diatom proliferation events in response to environmental stimuli.

Diatom cell division in an environmental context.

Studies of cell division in organisms derived from secondary endosymbiosis such as diatoms have revealed that the mechanisms are far from those found in more conventional model eukaryotes. An atypical acentriolar microtuble-organizing centre, centripetal cytokinesis combined with centrifugal cell wall neosynthesis, and the role of sex in relation to cell size restoration make diatoms an exciting system to re-investigate the evolution, differentiation and regulation of cell division. Such studies are further justified considering the ecological relevance of these microalgae in contemporary oceans and the need to understand the mechanisms controlling their growth and distribution in an environmental context. Recent work derived from genome-wide analyses on representative model diatoms reveals that the cell cycle is finely tuned to inputs derived from both endogenous and environmental signals.

CHARACTERIZATION OF TWO LIGHT-HARVESTING SUBUNITS ISOLATED FROM THE BROWN ALGA PELVETIA CANALICULATA: HETEROGENEITY OF XANTHOPHYLL DISTRIBUTION

The main light‐harvesting fraction from Pelvetia canaliculata was isolated on a sucrose density gradient from digitonin‐solubilized chloroplasts. After further solubilization by dodecyl maltoside, the bulk fraction was separated into two subunits by preparative isoelectric focusing. The more acidic brown fraction was mainly composed of 22 kDa polypeptides having an apparent pI of 4.55. Its pigment composition was very simple, containing chlorophyll (Chi) a, Chi c and fucoxanthin. The in vivo spectral properties of fucoxanthin, namely a shift in light absorption to the green and efficient energy transmission to Chi a, were conserved in this subunit. No xanthophyll associated with photoprotection was found in this band, even when obtained from photoinhibited thalli. The less acidic green band contained predominantly 22 kDa polypeptides that were resolved into numerous components by denaturing isoelectric focusing. Its pigment composition was more complex, containing, in addition, pigments of the so‐called xanthophyll cycle. In photoinhibited thalli, about half of the violaxanthin was converted into antheraxanthin and zeaxanthin. All the pigments of the xanthophyll cycle were specifically associated with this subunit, and it may thus have a central role in the thermal dissipation of the absorbed light energy as postulated for light‐harvesting complex II isolated from green plants.

Ultrastructure and Membrane Traffic During Cell Division in the Marine Pennate Diatom Phaeodactylum tricornutum

The marine pennate diatom Phaeodactylum tricornutum has become a model for diatom biology, due to its ease of culture and accessibility to reverse genetics approaches. While several features underlying the molecular mechanisms of cell division have been described, morphological analyses are less advanced than they are in other diatoms. We therefore examined cell ultrastructure changes prior to and during cytokinesis. Following chloroplast division, cleavage furrows are formed at both longitudinal ends of the cell and are accompanied by significant vesicle transport. Although neither spindle nor microtubules were observed, the nucleus appeared to be split by the furrow after duplication of the Golgi apparatus. Finally, centripetal cytokinesis was completed by fusion of the furrows. Additionally, F-actin formed a ring structure and its diameter became smaller, accompanying the ingrowing furrows. To further analyse vesicular transport during cytokinesis, we generated transgenic cells expressing yellow fluorescent protein (YFP) fusions with putative diatom orthologs of small GTPase Sec4 and t-SNARE protein SyntaxinA. Time-lapse observations revealed that SyntaxinA-YFP localization expands from both cell tips toward the center, whereas Sec4-YFP was found in the Golgi and subsequently relocalizes to the future division plane. This work provides fundamental new information about cell replication processes in P. tricornutum.