Biology subjects

Duponchel, S.

Publications and source records attributed to Duponchel, S..

4 recordsLinked to original sources

bioRxiv2020

Endogenous virophages populate the genomes of a marine heterotrophic flagellate

Virophages can parasitize giant DNA viruses and may provide adaptive anti-giant-virus defense in unicellular eukaryotes. Under laboratory conditions, the virophage mavirus integrates into the nuclear genome of the marine flagellate Cafeteria burkhardae and reactivates upon superinfection with the giant virus CroV. In natural systems, however, the prevalence and diversity of host-virophage associations has not been systematically explored. Here, we report dozens of integrated virophages in four globally sampled C. burkhardae strains that constitute up to 2% of their host genomes. These endogenous mavirus-like elements (EMALEs) separated into eight types based on GC-content, nucleotide similarity, and coding potential and carried diverse promoter motifs implicating interactions with different giant viruses. Between host strains, some EMALE insertion loci were conserved indicating ancient integration events, whereas the majority of insertion sites were unique to a given host strain suggesting that EMALEs are active and mobile. Furthermore, we uncovered a unique association between EMALEs and a group of tyrosine recombinase retrotransposons, revealing yet another layer of parasitism in this nested microbial system. Our findings show that virophages are widespread and dynamic in wild Cafeteria populations, supporting their potential role in antiviral defense in protists.

microbiology↗

bioRxiv2020

Demographics and Employment of Max-Planck Society's Postdocs

The recently founded Max Planck PostdocNet brings together postdoctoral researchers (or postdocs) from the Max Planck Society (MPS), provides representation for the postdoctoral community across all Max Planck Institutes (MPI) and associated institutes, and advocates for their interests on their behalf. At the 2019 founding meeting, MPS postdocs quickly raised their concerns about their employment situation and their associated social and working conditions. Subsequently, the PostdocNet conducted the first survey targeting exclusively postdoctoral researchers to gather information on their demographics, employment situations and social conditions. This report presents the results of this survey, providing a thorough characterization of the postdoc demographics as well as the working conditions experienced by the postdoctoral community of the MPS. Remarkably, the survey analysis revealed a number of disparities in the access to employment type, wage level and social benefits. These results will guide future and present MPS postdoctoral researchers and their employers at the MPS to thrive for equality and fairness. Moreover, these results should be of help to the MPS to establish, improve and maintain optimal working conditions for MPS postdocs.

scientific communication and education↗

bioRxiv2020

Visualization of giant virus particles using BONCAT labeling and STED microscopy

Giant DNA viruses of the phylum Nucleocytoviricota are being increasingly recognized as important regulators of natural protist populations. However, our knowledge of their infection cycles is still very limited due to a lack of cultured virus-host systems and molecular tools to study them. Here, we apply bioorthogonal noncanonical amino acid tagging (BONCAT) to pulse label the marine heterotrophic flagellate Cafeteria burkhardae during infection with the lytic giant virus CroV. In absence of CroV, we report efficient incorporation of the L-methionine analog L-azidohomoalanine (AHA) into newly synthesized proteins of the methionine prototrophic C. burkhardae. During CroV infection, AHA was predominantly found in viral proteins, and single CroV virions were imaged with stimulated emission depletion (STED) super-resolution microscopy. CroV particles incorporated AHA with 95-100% efficiency while retaining their infectivity, which makes BONCAT/STED a powerful tool to study viral replication cycles in this ecologically relevant marine bacterivore. SignificanceGiant DNA viruses are the dominant class of protist-infecting viruses, yet the vast majority of described giant virus-protist systems remain uncultured. One of the better studied cultured systems is composed of the stramenopile Cafeteria burkhardae (previously C. roenbergensis), the giant Cafeteria roenbergensis virus (CroV) and the virophage mavirus. C. burkhardae is a widespread marine phagotrophic protist that plays an important role in regulating bacterial populations. In addition to being grazed upon by larger zooplankton, C. burkhardae populations are controlled by the lytic giant virus CroV. In turn, CroV is parasitized by the virophage mavirus that increases host population survival in the presence of CroV and forms a mutualistic symbiosis with its host. Despite being of fundamental ecological and evolutionary interest, this tripartite host-virus-virophage system suffers from a lack of molecular tools. Here, we show that CroV particles can be fluorescently labeled and imaged by super-resolution microscopy. To achieve this we established robust procedures for analyzing protist and viral populations and implemented the use of bioorthogonal noncanonical amino acid tagging (BONCAT) in a marine unicellular flagellate.

microbiology↗

bioRxiv2019

Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis

The heterotrophic stramenopile Cafeteria roenbergensis is a globally distributed marine bacterivorous protist. This unicellular flagellate is host to the giant DNA virus CroV and the virophage mavirus. We sequenced the genomes of four cultured C. roenbergensis strains and generated 23.53 Gb of Illumina MiSeq data (99-282 x coverage per strain) and 5.09 Gb of PacBio RSII data (13-54 x coverage). Using the Canu assembler and customized curation procedures, we obtained high-quality draft genome assemblies with a total length of 34-36 Mbp per strain and contig N50 lengths of 148 kbp to 464 kbp. The C. roenbergensis genome has a GC content of ~70%, a repeat content of ~28%, and is predicted to contain approximately 7857-8483 protein-coding genes based on a combination of de novo, homology-based and transcriptome-supported annotation. These first high-quality genome assemblies of a Bicosoecid fill an important gap in sequenced Stramenopile representatives and enable a more detailed evolutionary analysis of heterotrophic protists.

genomics↗