Papers by jean claude LOZANO
bioRxiv (Cold Spring Harbor Laboratory), Oct 18, 2023
doi: bioRxiv preprint genotyped strains from both the Banyuls bay (Mediterranean sea) and the Baf... more doi: bioRxiv preprint genotyped strains from both the Banyuls bay (Mediterranean sea) and the Baffin bay (Arctic ocean). By combining ONT long reads and Illumina short reads technologies, we produced and annotated 28 Bathycoccus sp. de novo assembled genomes of high quality, including 24 genomes of Bathycoccus prasinos strains along a latitudinal gradient between 40° and 78°N orth, one reference genome of the Bathycoccus calidus species and 3 genomes of a yet undescribed Bathycoccus species named Bathycoccus catiminus. We assessed the genetic diversity of this genus through phylogenomic analyses and highlighted the central role of this genomic resource in providing new insights into the diversity of outlier chromosomal structures. The Bathycoccus biological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean. 2. Significance statement Comparative and functional approaches for the study of eukaryotic phytoplankton and their adaptation to latitudes and seasons that rely on extensive biological and genomic resources are currently lacking. Here we report such resources and describe the natural diversity of the cosmopolitan phytoplankton Bathycoccus, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies.
Mechanisms of Development, 2001
T-box transcription factors regulate many developmental processes. Here we report the cloning and... more T-box transcription factors regulate many developmental processes. Here we report the cloning and expression analysis of ske-T, a novel sea urchin T-box gene. The distribution of the maternal ske-T transcript is uniform in the egg and early embryonic stages while zygotic expression is restricted to the skeletogenic mesenchyme lineage.
Scientific Reports, 2017
Iron is an essential micronutrient involved in many biological processes and is often limiting fo... more Iron is an essential micronutrient involved in many biological processes and is often limiting for primary production in large regions of the World Ocean. Metagenomic and physiological studies have identified clades or ecotypes of marine phytoplankton that are specialized in iron depleted ecological niches. Although less studied, eukaryotic picophytoplankton does contribute significantly to primary production and carbon transfer to higher trophic levels. In particular, metagenomic studies of the green picoalga Ostreococcus have revealed the occurrence of two main clades distributed along coast-offshore gradients, suggesting niche partitioning in different nutrient regimes. Here, we present a study of the response to iron limitation of four Ostreococcus strains isolated from contrasted environments. Whereas the strains isolated in nutrient-rich waters showed high iron requirements, the oceanic strains could cope with lower iron concentrations. The RCC802 strain, in particular, was ab...
CDC2L5, a Cdk-like kinase with RS domain, interacts with the ASF/SF2-associated protein p32 and affects splicing in vivo
Journal of Cellular Biochemistry, 2006
The human CDC2L5 gene encodes a protein of unknown physiological function. This protein is closel... more The human CDC2L5 gene encodes a protein of unknown physiological function. This protein is closely related to the cyclin‐dependent kinase (Cdks) family and contains an arginine/serine‐rich (RS) domain. The Cdks were first identified as crucial regulators of cell‐cycle progression, more recently they were found to be involved in transcription and mRNA processing. RS domains are mainly present in proteins regulating pre‐mRNA splicing, suggesting CDC2L5 having a possible role in this process. In this study, we demonstrate that CDC2L5 is located in the nucleoplasm, at a higher concentration in speckles, the storage sites for splicing factors. Furthermore, this localization is dependent on the presence of the N‐terminal sequence including the RS domain. Then, we report that CDC2L5 directly interacts with the ASF/SF2‐associated protein p32, a protein involved in splicing regulation. Overexpression of CDC2L5 constructs disturbs constitutive splicing and switches alternative splice site selection in vivo. These results argue in favor of a functional role of the CDC2L5 kinase in splicing regulation. J. Cell. Biochem. 99: 890–904, 2006. © 2006 Wiley‐Liss, Inc.
Cybip, a starfish cyclin B-binding protein, is involved in meiotic M-phase exit
Biochemical and Biophysical Research Communications, 2003
We designed a screen to identify starfish oocyte proteins able to bind monomeric cyclin B by affi... more We designed a screen to identify starfish oocyte proteins able to bind monomeric cyclin B by affinity chromatography on a cyclin B splice variant displaying low affinity for cdc2. We identified a 15kDa protein previously described as a cdk-binding protein [Biochim. Biophys. Acta Mol. Cell Res. 1589 (2002) 219-231]. Cybip is encoded by a single polymorphic gene and the native protein is matured by cleaving a signal peptide. We firmly establish the fact that it is a true cyclin B-binding protein, since the recombinant protein binds recombinant cyclin B in absence of any cdk. Finally, we show that the microinjection of GST-cybip, and of anti-cybip antibody, in maturing starfish oocytes, inhibits H1 kinase and MPF inactivation, and first polar body emission.
Frontiers in Environmental Science
Phytoplankton cells are excellent biosensors for environmental monitoring and toxicity assessment... more Phytoplankton cells are excellent biosensors for environmental monitoring and toxicity assessments in different natural systems. Green algae, in particular, appear to be more responsive to copper (Cu) disturbances. This is interesting considering that Cu pollution in coastal environments has increased over the last century, with enormous repercussions to marine ecosystems. Unfortunately, no high-throughput method exists for the environmental monitoring of Cu toxicity in seawater. To assess potential uses as biosensors of Cu pollution, high-throughput screening was performed on five luminescence reporter lines constructed in the green algae Ostreococcus tauri RCC745. The reporter line expressing the iron storage ferritin protein fused to luciferase (Fer-Luc) was the most sensitive, responding to Cu concentrations in the µM range. Fer-Luc was also the most sensitive reporter line for detecting toxicity in mining-derived polluted seawater predominantly contaminated by soluble Cu. Nevertheless, the Cyclin-Dependent-Kinase A (CDKA) reporter was most suitable for detecting the toxicity of copper-mine tailing effluents containing other metals (e.g., iron). These results highlight that Ostreococcus biosensors can serve as a reliable, inexpensive, and automated, high-throughput laboratory approach for performing seawater analyses of coastal areas subjected to metal disturbances. When challenged with Cu, O. tauri not only evidenced a rapid, transcriptional response for the tested genes, but also showed changes in a broad range of genes, especially as related to the stress response. Overall, the obtained results reinforce that a single biosensor is insufficient when dealing with complex mixtures of toxic compounds in natural environments.
Additional file 12: Figure S10. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
The Ot-Fea1 protein contains two Fea1 domains. (A) Multiple alignment of the N- and C-terminal Ot... more The Ot-Fea1 protein contains two Fea1 domains. (A) Multiple alignment of the N- and C-terminal OtFea1 domains and the C. reinhardtii Fea1 protein. R/K-E/D-X-X-E motifs are framed. (B) Domain organization of O. tauri OtFea1, P. tricornutum Isip2a and C. reinhardtii Fea1 as revealed by HMM-HMM comparison, with the Pfam database and the Phobius transmembrane topology and signal peptide predictor. (PPTX 781 kb)
Additional file 5: of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Data Sets 2. All information regarding all the genes for which expression was monitored using RNA... more Data Sets 2. All information regarding all the genes for which expression was monitored using RNAseq technology. (XLS 7032 kb)
Additional file 6: Figure S4. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Global comparison of the O. tauri and C. reinhardtii transcriptional responses to iron limitation... more Global comparison of the O. tauri and C. reinhardtii transcriptional responses to iron limitation. Gene expression data were collected from the article of Urzica et al. [72] and orthologous relationships between genes were inferred with the INPARANOID program, using default parameters. (A) Statistics regarding the number of genes for which expression had been quantified, the number of genes with LogFC values > 0.5 or
Additional file 4: of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Data Sets 1. Detailed list of the genes whose expression was significantly modified in iron depri... more Data Sets 1. Detailed list of the genes whose expression was significantly modified in iron deprivation (−Fe) compared to iron excess (+Fe) condition. (XLS 1381 kb)
Additional file 8: Figure S6. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Domain organization of ferric reductase and cytochrome b561 homologs in C. reinhardtii and O. tau... more Domain organization of ferric reductase and cytochrome b561 homologs in C. reinhardtii and O. tauri. The ferrireductase homolog (ostta09g01890) was slightly repressed, whereas the two cytochrome b561 homologs (ostta16g00370 and ostta04g02840) were significantly upregulated by iron deprivation in O. tauri cells. Domains were identified by HMM-HMM comparison, with the Pfam database. (PPTX 64 kb)
Additional file 9: Figure S7. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Effect of metals in the medium on iron uptake by O. tauri. The cells were maintained in Mf medium... more Effect of metals in the medium on iron uptake by O. tauri. The cells were maintained in Mf medium without zinc and copper (and 0.1 μM iron) for 3 months. The cells were then harvested and used to inoculate Mf medium with or without supplementation with zinc (0 or 1 μM), iron (1 or 100 nM) and copper (0 or 1 μM). After one week of growth, the cells were harvested and iron uptake kinetics were recorded with 1 μM 55Fe(III)-EDTA (1:10). Mean ± SD from 3 experiments. (PPTX 122 kb)
Additional file 1: Figure S1. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Schematic representation of the experimental design used for analysis of the short-term and long-... more Schematic representation of the experimental design used for analysis of the short-term and long-term adaptive responses of the cells to iron deprivation. In this study, 16 different samples were analyzed with RNAseq technology. They are represented here with gray circles. Transcriptome states were determined in O. tauri as a function of three different factors: i) iron deprivation, (−Fe) or control (+Fe), ii) light or dark exposure and iii) short- or long-term adaptive response (condition 1 and condition 2). Experiments comparing conditions 1 and 2 were repeated three times, with three biological replicates for each sample. (PPTX 70 kb)
Additional file 13: Figure S11. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Mass spectrometry analysis of the proteins present in the iron-containing band of the native gel ... more Mass spectrometry analysis of the proteins present in the iron-containing band of the native gel shown in Fig. 5. A: LC-MSMS-based Ostreococcus Protein identification from in-gel trypsin digestions of 55Fe-labelled proteins (from the iron band shown in Fig. 5). Right and left panels show the results of two independent experiments. Identifications were sorted by descending Mascot scores. Data presented include the Mascot score, the protein sequence coverage (as %), the number of proteins in the identified protein groups, the number of unique peptides, and of peptide search matches, together with the description of the protein in terms of number of aminoacid residues, molecular mass and calculated isoelectric point. B: MSMS-based OtFea sequence coverage. Peptides identified at a 1 % FDR are highlighted in green. C: Representative annotated fragmentation spectrum of an OtFea peptide (Charge: +2, Monoisotopic m/z: 795.88043 Da (−0.27 mmu/-0.34 ppm), MH+: 1590.75359 Da, RT: 27.91 min) an...
Additional file 2: Figure S2. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Bioinformatics protocol used to analyze raw sequencing data (FASTQ files). The quality of read se... more Bioinformatics protocol used to analyze raw sequencing data (FASTQ files). The quality of read sequences was first checked with the FASTQC program. CDS sequences from O. tauri were downloaded from the ORCAE database and used as references for read mapping with the BOWTIE program. BOWTIE was applied with default parameter values. Most of the reads were successfully aligned (>80 %), indicating a high level of sequence quality, and between 5 and 10 million mapped sequences were obtained for each RNAseq sample (data not shown). These sequences were used to estimate gene expression, counting the number of reads mapping to each CDS with the BEDTOOLS program. Expression measurements were thus obtained for more than 80 % of the CDS in O. tauri genome, yielding satisfactory sequencing coverage (data not shown). Read counts were normalized with the DESeq program and used to assess the differential expression of genes between conditions (−Fe/+Fe or LIGHT/DARK). Finally, genes were considere...
Additional file 11: Figure S9. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
A. thaliana IRT1 homolog in O. tauri contains three His-rich motifs. Pairwise alignment of A. tha... more A. thaliana IRT1 homolog in O. tauri contains three His-rich motifs. Pairwise alignment of A. thaliana Irt1 and its iron-regulated homolog from O. tauri (ostta16g02300). Transmembrane regions were predicted with TMpred software. Blue strips correspond to transmembrane helices. Histidine-rich motifs are framed. The figure was generated with Geneious version 7.1 (Biomatters). (PPTX 615 kb)
Additional file 14: Figure S12. of Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton
Comparison of ferritin iron loading in O. tauri and C. reinhardtii. Cells of the two species (inc... more Comparison of ferritin iron loading in O. tauri and C. reinhardtii. Cells of the two species (including the ferritin KO mutant of O. tauri, used as a control) were cultured as described in the methods, with different concentrations of Cu (−: no Cu added; +: 0.1 μM (O. tauri) or 1 μM (C. reinhardtii) CuSO4) and Fe (−: 1 nM (O. tauri) or 50 nM (C. reinhardtii) ferric citrate; +: 1 μM ferric citrate). After 5 days, the cells were harvested, and resuspended in iron-free Mf medium (O. tauri) or iron-free TAP medium (C. reinhardtii) supplemented with 5 μM 55Fe(III)-citrate. The cells were incubated for 3 h and then harvested by centrifugation. Whole-cell extracts were obtained and subjected to native PAGE (25 μg/lane), as described in the methods. A comparison of autoradiographs of dried gels shows that O. tauri ferritin was maximally loaded with iron when the cells had previously been grown in iron-rich conditions, whereas the main ferritin of C. reinhardtii was maximally loaded with iro...
article Evolution of Cyclin B3 Shows an Abrupt Three-Fold Size Increase, due to the Extension of a Single Exon in Placental Mammals, Allowing for New Protein–Protein Interactions
Cyclin B3 evolution has the unique peculiarity of an abrupt 3-fold increase of the protein size i... more Cyclin B3 evolution has the unique peculiarity of an abrupt 3-fold increase of the protein size in the mammalian lineage due to the extension of a single exon. We have analyzed the evolution of the gene to define the modalities of this event and the possible consequences on the function of the protein. Database searches can trace the appearance of the gene to the origin of metazoans. Most introns were already present in early metazoans, and the intron–exon structure as well as the protein size were fairly conserved in invertebrates and nonmammalian vertebrates. Although intron gains are considered as rare events, we identified two cases, one at the prochordate–chordate transition and one in murids, resulting from different mechanisms. At the emer-gence of mammals, the gene was relocated from chromosome 6 of platypus to the X chromosome in marsupials, but the exon extension occurred only in placental mammals. A repetitive structure of 18 amino acids, of uncertain origin, is detectabl...
bioRxiv, 2021
Temperature and light play a crucial role in regulating phytoplankton blooms in the Ocean. To ass... more Temperature and light play a crucial role in regulating phytoplankton blooms in the Ocean. To assess the importance of these two parameters experimentally, microcosms were conducted on seven picoplankton communities (<3 μm) sampled in December, March, June and September 2015 and 2016 in the North Western Mediterranean Sea. Each community was exposed to 4 realistic seasonal conditions (December, March, June and September). Metabarcoding was used to investigate the eukaryotic diversity in the 56 microcosms experiments in parallel to high-frequency monitoring of environmental diversity in the sea. The three major lineages identified were the Stramenopiles, Alveolata and Archaeplastida. Overall, the five-day incubations were not sufficient to reshape the initial microbial communities completely. The microcosm outcome was strongly influenced by the dynamics of phytoplankton starting communities. In pre-bloom conditions, phytoplanktonic species were the most sensitive to temperature an...
Environmental Microbiology, 2021
SummaryMarine picoplankton contribute to global carbon sequestration and nutrient recycling. Thes... more SummaryMarine picoplankton contribute to global carbon sequestration and nutrient recycling. These processes are directly related to the composition of communities, which in turn depends on microbial interactions and environmental forcing. Under regular seasonal cycles, marine communities show strong predictable patterns of annual re‐occurrences, but little is known about the effect of environmental perturbation on their organization. The aim of our study was to investigate the co‐occurrence patterns of planktonic picoeukaryote, bacteria and archaea under contrasting environmental conditions. The study was designed to have high sampling frequency that could match both the biological rhythm of marine microbes and the short time scale of extreme weather events. Our results show that microbial networks changed from year to year depending on conditions. In addition, individual taxa became less interconnected and changed neighbours, which revealed an unfaithful relationship between marin...
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Papers by jean claude LOZANO