DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis

DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status

Complex patterns in phytoplankton and microeukaryote diversity along the estuarine continuum

International audienceEstuaries and coastal lagoons are included within the transitional waters category, according to the Water Framework Directive. However, criteria for their differentiation and characterisation are still under discussion and require more research. In particular, detailed observations of biodiversity in more complex transitional and coastal waters are lacking. Microscopic and molecular analyses were therefore used to investigate phytoplankton diversity and spatial community structure, in early spring, along the freshwater-to-marine continuum of the Segura River (Spain), an intensively regulated semiarid basin discharging into the Mediterranean Sea. In addition to the salinity gradient as the major factor determining taxa distribution, influence of multiple anthropogenic and climatic impacting factors (drought, confined waters, irrigation canal) leads to a significant spatial heterogeneity of the aquatic habitat types associated with variations in community composition. Several shifts within the phytoplankton distribution pattern along the continuum are revealed using multivariate analyses. An impressive bloom of the cryptophyte Plagioselmis prolonga occurred in the mixing zone, associated with a typical euryhaline community indicative of eutrophication. The 18S rDNA diversity revealed a microeukaryotic richness including several little-known groups, heterotrophic representatives, and potential parasites. By combining morphological and molecular approaches we revealed the presence of a ‘hidden’ diversity often neglected in traditional surveys

Phytoplankton Diversity and Community Composition along the Estuarine Gradient of a Temperate Macrotidal Ecosystem: Combined Morphological and Molecular Approaches

International audienc

Profiles of salinity (A), temperature (B), irradiance and phytoplankton abundance (C) along the estuarine gradient.

<p>(Stations A→F). Black dots on the profile (<b>A</b>) represent sampling points collected for the global phytoplankton analysis by microscopy, and the blue dots indicate those analyzed by both microscopy and clone library approaches. A logarithmic scale was used for the representation of phytoplankton cell abundance on the profile of irradiance(<b>C</b>).</p

Map of the Vire River estuary (Baie des Veys) with location of the sampling stations (A–F).

<p>Blue dots indicate sampling points analyzed by both microscopy and clone library approaches (referred to as VIRE River, ESTUARY and BAY). Lambert II coordinates system.</p

Taxa richness and distribution of dominant species along the estuarine gradient.

<p>(A) Total phytoplankton richness. (B) Relative abundances of dominant taxa (accounting for >10% of total phytoplankton in at least one sample) at the surface (top) and depth (down). <i>A. glacialis</i>  =  <i>Asterionellopsis glacialis</i>, <i>B.brockmanni</i>  =  <i>Brockmanniella brockmannii</i> and <i>R.imbricata</i>  =  <i>Rhizosolenia imbricata.</i> Blue dots indicate sampling points analyzed by both microscopy and clone library approaches (referred to as VIRE River, ESTUARY and BAY).</p

Phytoplankton taxonomic composition (taxa richness) in three surface samples: Molecular vs. Morphological approaches.

<p>VIRE River (station A), ESTUARY (station C) and BAY (station E). (A) Number of OTUs according to the taxonomic affiliation of the 18S rRNA gene sequences. (B) Number of taxa identified by microscopy (LM + SEM).</p

Maximum likelihood (ML) tree showing the position of the Cryptophyte OTUs (order Cryptomonadales).

<p>Tree construction was based on an alignment of 44 partial sequences (ca 650 align positions). The haptophyte <i>Haptolina hirta</i> was used as out-group. (See legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094110#pone-0094110-g004" target="_blank">Figure 4</a> for details).</p

OTUs recovered in this study (clustering at a 98% similarity threshold).

<p>A representative clone for each OTU and its phylogenetic affiliation are provided. Highest BLAST match and closest cultured organisms from GenBank are given with accession numbers and percentage similarity. The remaining columns indicate the distribution and the number of clones found in each clone library (VIRE River, ESTUARY, and BAY).</p

A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum

Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A-D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species