Benoît Chénais

The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments.

Transposable elements (TEs) are present in roughly all genomes. These mobile DNA sequences are able to invade genomes and their impact on genome evolution is substantial. The mobility of TEs can induce the appearance of deleterious mutations, gene disruption and chromosome rearrangements, but transposition activity also has positive aspects and the mutational activities of TEs contribute to the genetic diversity of organisms. This short review aims to give a brief overview of the impact TEs may have on animal and plant genome structure and expression, and the relationship between TEs and the stress response of organisms, including insecticide resistance.

Metallothionein genes from hydrothermal crabs (Bythograeidae, Decapoda): Characterization, sequence analysis, gene expression and comparison with coastal crabs

Hydrothermal vent conditions can alter DNA and hydrothermal organisms may develop detoxification mechanisms and/or genetic adaptations. Hydrothermal vent animals notably synthesize a high quantity of metallothioneins (MT). Recent studies have revealed that the levels of MT within hydrothermal crustacean tissues are higher than those found in other vent animals. To improve our understanding of the environmental impacts exerted on the vent organisms, we characterized the metallothioneins (cDNA and Mt genes) of several members of the Bythograeidae (Bythograea thermydron, Cyanagraea praedator and Segonzacia mesatlantica) which is the only endemic hydrothermal crab family. In comparison, the isolation of metallothionein cDNA was also carried out in several coastal crab families. The results showed that the hydrothermal crabs possess Mt composed of three exons and two introns presenting conserved splicing signals. The cDNA sequences isolated from distinct crabs showed multiple substitutions. In spite of the unique environmental conditions, the protein sequence analysis revealed no specific amino acid residue for the MT of the three hydrothermal crabs. However, gene expression analysis performed by real-time PCR based on S. mesatlantica (hydrothermal crab) compared to Pachygrapsus marmoratus (coastal crab) confirmed the higher metallothionein induction in hydrothermal crabs suggested by others authors.

Transcription factors in microalgae: genome-wide prediction and comparative analysis

BackgroundStudying transcription factors, which are some of the key players in gene expression, is of outstanding interest for the investigation of the evolutionary history of organisms through lineage-specific features. In this study we performed the first genome-wide TF identification and comparison between haptophytes and other algal lineages.ResultsFor TF identification and classification, we created a comprehensive pipeline using a combination of BLAST, HMMER and InterProScan software. The accuracy evaluation of the pipeline shows its applicability for every alga, plant and cyanobacterium, with very good PPV and sensitivity. This pipeline allowed us to identify and classified the transcription factor complement of the three haptophytes Tisochrysis lutea, Emiliania huxleyi and Pavlova sp.; the two stramenopiles Phaeodactylum tricornutum and Nannochloropsis gaditana; the chlorophyte Chlamydomonas reinhardtii and the rhodophyte Porphyridium purpureum. By using T. lutea and Porphyridium purpureum, this work extends the variety of species included in such comparative studies, allowing the detection and detailed study of lineage-specific features, such as the presence of TF families specific to the green lineage in Porphyridium purpureum, haptophytes and stramenopiles. Our comprehensive pipeline also allowed us to identify fungal and cyanobacterial TF families in the algal nuclear genomes.ConclusionsThis study provides examples illustrating the complex evolutionary history of algae, some of which support the involvement of a green alga in haptophyte and stramenopile evolution.

Assessment of Oxidative Stress and Histopathological Biomarkers in the Parablennius Incognitus Fish as Potential Contamination Indicators of the Bay of Sousse (Tunisia)

Oxidative stress and histopathological biomarkers were investigated in the gills and liver of Parablennius incognitus fishes. Individuals sampled in the bay of Sousse were compared to fishes from a reference site, i.e. Ghdamsi Island (Tunisia). Severe biochemical and histological alterations were observed in fishes from Sousse bay and associated with urban discharges contamination. Several tissue alterations were also observed in gills, particularly lamellar epithelium detachment, disorganization of pillar cells, and hypertrophy of chloride cells. In the liver we noted particularly hypertrophy of hepatocytes, congestion and dilation of the central vein and sinusoid capillaries, pyknotic nucleus, and hepatic steatosis. The high reduction of superoxide dismutase and catalase activities in gills and of superoxide dismutase and glutathione peroxidase activities in the liver of contaminated fishes may explain the increase of lipoperoxidation in both organs of P. incognitus. The integrated biomarker response values found in individuals from the contaminated site were in good agreement with alteration of physico-chemical parameters and with the high level of Cd concentrations detected in water of the stressful place, i.e. the bay of Sousse. Oxidative stress and histopathological alterations were sensitive biomarkers to discriminate between fishes from the polluted Sousse bay site and those from the reference site, suggesting their potential utility in bio monitoring.

Electrochemically Modified Carbon and Chromium Surfaces for AFM Imaging of Double-Strand DNA Interaction with Transposase Protein

Carbon and chromium surfaces were modified by electrochemical reduction of a diazonium salt formed in situ from the sulfanilic acid. The organic layer formed was activated by phosphorus pentachloride (PCl(5)) to form a benzene sulfonil chloride (Ar-SO(2)Cl). An electrochemical study of the blocking effect and the activity of this surface was carried out on a carbon electrode. The chromium surface study was completed by X-ray photoelectron spectroscopy and atomic force microscopy to characterize the formation of a compact monolayer (0.8 nm height and roughness 0.2-0.3 nm). The compactness and the activity of this organic monolayer allowed us to affix a length dsDNA with the aim of analyzing the formation of a complex between dsDNA and a protein. The interaction of a transposase protein with its target dsDNA was investigated. The direct imaging of the nucleoproteic complex considered herein gives new insights in the comprehension of transposase-DNA interaction in agreement with biochemical data.

Functional investigations in diatoms need more than a transcriptomic approach

The particular gene complement in diatoms, inherited from various types of organisms, has contributed to the development of metabolic networks that contrast with those found in other photosynthetic organisms. To understand these networks and how they are linked, transcriptomic, proteomic and metabolomic approaches have been used over the last decade. Understanding how these networks developed and interact remains a major goal for physiologists. Metabolic compartmentalization and fluxes between compartments are still poorly known, requiring: (1) the localization of proteins and biological activities, as well as potential protein isoforms and (2) relating metabolite measurements to pathway fluxes. Moreover, when considering metabolism, the identification of transcription factors, which are largely unknown for diatoms, is necessary. Integration of the results from these different approaches will complete our understanding of cell functioning and how differences impact metabolic reorientation.

An introduction to the vast world of transposable elements – what about the diatoms?

Transposable elements (TEs) are DNA sequences that are able to move and replicate within the genomes of virtually all organisms, ranging from animals to plants, and also including protozoans, bacteria and diatoms. Initially considered to be ‘junk DNA’ with no function, TEs are now thought to play a pivotal role in the evolution of genomes and organisms. This review is intended to provide non-specialists with an introduction to the world of TEs by summarizing the information available about these elements, ranging from their impact on genome structure to their potential involvement in the evolution of species. In this review, we propose to bring together what is known about the TEs and provide an overview of recent advances concerning TEs in diatoms.

Docosahexaenoic acid inhibits the invasion of MDA‑MB‑231 breast cancer cells through upregulation of cytokeratin‑1

Docosahexaenoic acid (DHA), the main member of the omega-3 essential fatty acid family, has been shown to reduce the invasion of the triple-negative breast cancer cell line MDA-MB-231, but the mechanism involved remains unclear. In the present study, a proteomic approach was used to define changes in protein expression induced by DHA. Proteins from crude membrane preparations of MDA-MB-231 cells treated with 100 µM DHA were separated by two-dimensional electrophoresis (2-DE) and differentially expressed proteins were identified using MALDI-TOF mass spectrometry. The main changes observed were the upregulation of Keratin, type Ⅱ cytoskeletal 1 (KRT1), catalase and lamin-A/C. Immunocytochemistry analyses confirmed the increase in KRT1 induced by DHA. Furthermore, in vitro invasion assays showed that siRNA against KRT1 was able to reverse the DHA-induced inhibition of breast cancer cell invasion. In conclusion, KRT1 is involved in the anti-invasive activity of DHA in breast cancer cells.

Cadmium exposure exerts neurotoxic effects in peacock blennies Salaria pavo

Cadmium (Cd) is considered as an important factor involved in several neurological disturbances. The aim of this study was to assess the effects of Cd in the brain of peacock blennies Salaria pavo, a species used as a bioindicator of water pollution. A sublethal contamination of 2mg CdCl2 L-1 was performed over periods of 1, 4, 10 and 15 days. Total Cd accumulation was measured in brains and displayed low concentrations throughout the experiment. Partial-length cDNA of different ATP-binding cassette transporters (abcb1, abcc1, abcc2, abcg2 proteins) and acetylcholinesterase (ache) were characterized. mRNA expressions profiles displayed an up-regulation of abcc2 mRNA after 4 days of Cd exposure only while abcg2 mRNA was down-regulated after 10 days only. For AChE, the mRNA transcription and the activity of the enzyme were followed and highlighted that Cd exerted an inhibitory effect on the nervous information transmission. At the histological level, fish exhibited pathological symptoms in the optic tectum and the cerebellum and results showed that the cerebellum was the most affected organ.

Expression of the retrotransposons Surcouf and Blackbeard in the marine diatom Phaeodactylum tricornutum under thermal stress

Abstract: Transposable elements (TEs) are mobile DNA sequences thought to be involved in the genomic response to environmental stresses of organisms. The thermal stress behaviour of two retrotransposons (Surcouf and Blackbeard ) was investigated in the genome of two strains of the marine diatom Phaeodactylum tricornutum. Using quantitative reverse transcriptase polymerase chain reaction, the retrotransposon expression pattern was investigated after thermal stresses and compared with that of the small heat-shock protein (shsp). While the expression of Blackbeard was not affected by temperature changes, the retroelement Surcouf was markedly overexpressed in response to high temperature in correlation with shsp overexpression. An in silico analysis investigated the presence of regulatory heat-inducible motifs such as heat-shock elements, stress response elements and CCAAT boxes within the promoters of shsp and retrotransposons in the genome of P. tricornutum. The results of mRNA quantification are supported by the presence of heat-shock response motifs found in the promoters of shsp and the retrotransposon Surcouf.