Dataset Information

Willaertia magna c2c maky global proteome

ABSTRACT: Global proteome study of protein extracts of Willaertia magna c2c using a mass spectrometer Q Exactive HF.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Willaertia Magna

SUBMITTER: DECLOQUEMENT Philippe

LAB HEAD: Bernard La Scola

PROVIDER: PXD016724 | Pride | 2021-09-08

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	190322-SI-0148-F1-01.mgf	Mgf
	190322-SI-0148-F1-01.pride.mgf.gz	Mgf
	190322-SI-0148-F1-01.raw	Raw
	190322-SI-0148-F2-01.mgf	Mgf
	190322-SI-0148-F2-01.pride.mgf.gz	Mgf

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Publications

Insight into the Lifestyle of Amoeba Willaertia magna during Bioreactor Growth Using Transcriptomics and Proteomics.

Hasni Issam I Decloquement Philippe P Demanèche Sandrine S Mameri Rayane Mouh RM Abbe Olivier O Colson Philippe P La Scola Bernard B

Microorganisms 20200521 5

Willaertia magna C2c maky is a thermophilic free-living amoeba strain that showed ability to eliminate Legionella pneumophila, a pathogenic bacterium living in the aquatic environment. The amoeba industry has proposed the use of Willaertia magna as a natural biocide to control L. pneumophila proliferation in cooling towers. Here, transcriptomic and proteomic studies were carried out in order to expand knowledge on W. magna produced in a bioreactor. Illumina RNA ...[more]

PMID: 32455615

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Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in juvenile daphnids (daphnia magna) as aquatic vertebrate non-target model exposed to sub lethal concentrations of Fipronil. Fipronil is a widely used insecticide applied for crop protection against field pests and Ectoparasites. The Insecticide Resistance Action Committee (IRAC) classified Fipronil after its mode of action (MoA) in the target organism as a GABA-gated chloride channel blocker (Group 2). The goal is to identify toxicogenomic profiles with predictive character and identify potential molecular key events (KE) explaining upstream adverse effects. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the acute immobilisation test (OECD 202), 50 juvenile Daphnids were exposed to two sub lethal concentrations of Fipronil for 48 hours under static conditions. Each test comprised of a low exposure (LE), high exposure (HE) and a negative control (NC) group and was performed in triplicates. At 48 hours after introducing the daphnids into the test solutions, RNA and protein was extracted from living daphnids with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before messenger RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D. magna reference genome (daphmag2.4) using STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for count normalization and differential gene expression analysis with DESeq2.

Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in juvenile daphnids (daphnia magna) as aquatic vertebrate non-target model exposed to sub lethal concentrations of Imidacloprid. Imidacloprid is is a popular insecticide widely applied in agriculture and by veterinarians against ectoparasites.The Insecticide Resistance Action Committee (IRAC) classified Imidacloprid after its mode of Action (MoA) in the target organism as a nicotinic acetylcholine receptor (nAChR) competitive modulator (Group 4). The goal is to identify toxicogenomic profiles with predictive character and identify potential molecular key events (KE) explaining upstream adverse effects. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the acute immobilisation test (OECD 202), 50 juvenile Daphnids were exposed to two sub lethal concentrations of Imidacloprid for 48 hours under static conditions. Each test comprised of a low exposure (LE), high exposure (HE) and a negative control (NC) group and was performed in triplicates. At 48 hours after introducing the daphnids into the test solutions, RNA and protein was extracted from living daphnids with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before messenger RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D. magna reference genome (daphmag2.4) using STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for count normalization and differential gene expression analysis with DESeq2.

Project description:Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterising the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the waterflea, is a textbook example for predator induced phenotypic plastic defences including changes in life-history, behaviour and morphology. However, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages. We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation. D. magna is known to develop an array of morphological changes in the presence of T. cancriformis including changes of carapace morphology and cuticle hardening. To get a more comprehensive idea of this phenomenon, we studied four different genotypes originating from habitats with different predation history, reaching from predator-free to temporary habitats containing T. cancriformis. We analysed the morphologies as well as proteomes of predator-exposed and control animals. Three genotypes showed morphological changes when the predator was present. Using a high-throughput proteomics approach, we found 294 proteins which were significantly altered in their abundance after predator exposure in a general or genotype dependant manner. Proteins connected to genotype dependant responses were related to the cuticle, protein synthesis and calcium binding whereas the yolk protein vitellogenin increased in abundance in all genotypes, indicating their involvement in a more general response. Furthermore, genotype dependant responses at the proteome level correlated well with local adaptation to Triops predation. Altogether, our study provides new insights concerning genotype dependant and general molecular processes involved in predator-induced phenotypic plasticity in D. magna.

Dataset Information

Willaertia magna c2c maky global proteome

Dataset's files

Publications

Insight into the Lifestyle of Amoeba <i>Willaertia magna</i> during Bioreactor Growth Using Transcriptomics and Proteomics.

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