A5057768395- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Plant and Fungal Interactions Research
- Virology and Viral Diseases
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Protein Structure and Dynamics
- Animal Virus Infections Studies
- Viral gastroenteritis research and epidemiology
- Glycosylation and Glycoproteins Research
- Cytomegalovirus and herpesvirus research
- Microbial Community Ecology and Physiology
- Viral Infections and Vectors
- Legionella and Acanthamoeba research
- Biochemical and Molecular Research
- Advanced X-ray Imaging Techniques
- Polyomavirus and related diseases
- Microbial Metabolic Engineering and Bioproduction
- Monoclonal and Polyclonal Antibodies Research
- MXene and MAX Phase Materials
- Virus-based gene therapy research
- Mechanisms of cancer metastasis
- Evolution and Genetic Dynamics
Centre National de la Recherche Scientifique
2015-2025
Aix-Marseille Université
2016-2025
Institut de Microbiologie de la Méditerranée
2016-2025
Laboratoire Information Génomique et Structurale
2015-2025
Centre National pour la Recherche Scientifique et Technique (CNRST)
2012-2025
Institut de Biosciences et Biotechnologies
2021
Colmar Inra Research Centre
2018
Inserm
2018
École Normale Supérieure de Lyon
2018
Université Claude Bernard Lyon 1
2018
We recently reported the discovery and preliminary characterization of Mimivirus, largest known virus, with a 400-nanometer particle size comparable to mycoplasma. Mimivirus is double-stranded DNA virus growing in amoebae. now present its 1,181,404–base pair genome sequence, consisting 1262 putative open reading frames, 10% which exhibit similarity proteins functions. In addition exceptional size, exhibits many features that distinguish it from other nucleocytoplasmic large viruses. The most...
Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. This organism was susceptible to most antibiotics the 1970s. It has now become major cause hospital-acquired infections worldwide due its remarkable propensity rapidly acquire resistance determinants wide range antibacterial agents. Here we use comparative genomic approach identify complete repertoire genes exhibited by multidrug-resistant A. strain AYE, which epidemic France, as...
Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba, initiated reappraisal upper limits viral world, both in terms particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions typical parasitic bacteria. The diversity these giant viruses (the Megaviridae) was assessed by sampling variety aquatic environments their associated sediments worldwide. We report isolation two viruses, one off coast central Chile, other from freshwater pond near Melbourne...
Significance Giant DNA viruses are visible under a light microscope and their genomes encode more proteins than some bacteria or intracellular parasitic eukaryotes. There two very distinct types infect unicellular protists such as Acanthamoeba . On one hand, Megaviridae possess large pseudoicosahedral capsids enclosing megabase-sized adenine–thymine-rich genome, on the other, recently discovered Pandoraviruses exhibit micron-sized amphora-shaped particles guanine–cytosine-rich of up to 2.8...
Mimivirus, a DNA virus infecting acanthamoeba, was for long time the largest known both in terms of particle size and gene content. Its genome encodes 979 proteins, including first four aminoacyl tRNA synthetases (ArgRS, CysRS, MetRS, TyrRS) ever found outside cellular organisms. The discovery that Mimivirus encoded trademark functions prompted wealth theoretical studies revisiting concept associated large viruses with emergence early eukaryotes. However, evolutionary significance these...
We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns an x-ray free-electron laser. Three-dimensional imaging requires assembly many two-dimensional into internally consistent Fourier volume. Since each is randomly oriented when exposed to pulse, relative orientations have be retrieved data alone. achieve this with modified version expand, maximize and compress algorithm validate our result using new...
Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report comparison two newly sequenced genomes A. baumannii. The human isolate AYE whereas strain SDF, which was isolated from body lice, antibiotic susceptible. As reference for this analysis, genome soil-living bacterium baylyi ADP1 used. most interesting dissimilarities...
Significance The saga of giant viruses (i.e. visible by light microscopy) started in 2003 with the discovery Mimivirus. Two additional types infecting Acanthamoeba have been discovered since: Pandoraviruses (2013) and Pithovirus sibericum (2014), latter one revived from 30,000-y-old Siberian permafrost. We now describe Mollivirus , a fourth type virus isolated same permafrost sample. These four exhibit different virion structures, sizes (0.6–1.5 µm), genome length (0.6–2.8 Mb), replication...
Large dsDNA viruses are involved in the population control of many globally distributed species eukaryotic phytoplankton and have a prominent role bloom termination. The genus Phaeocystis ( Haptophyta , Prymnesiophyceae ) includes several high-biomass-forming species, such as globosa blooms which occur mostly coastal zone North Atlantic Sea. Here, we report 459,984-bp-long genome sequence P. virus strain PgV-16T, encoding 434 proteins eight tRNAs and, thus, largest fully sequenced to date...
Mimivirus, a virus infecting Acanthamoeba , is the prototype of Mimiviridae latest addition to nucleocytoplasmic large DNA viruses. The Mimivirus genome encodes close 1000 proteins, many them never before encountered in virus, such as four amino-acyl tRNA synthetases. To explore physiology this exceptional and identify genes involved building its characteristic intracytoplasmic “virion factory,” we coupled electron microscopy observations with massively parallel pyrosequencing polyadenylated...
With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now most complex viruses since their discovery 2013. Our isolation three new strains from distant locations environments is used perform comparative genomics analysis emerging worldwide-distributed Pandoraviridae family. Thorough annotation combining transcriptomic, proteomic, bioinformatic analyses reveals many non-coding transcripts...
The organization of genomic DNA into defined nucleosomes has long been viewed as a hallmark eukaryotes. This paradigm challenged by the identification "minimalist" histones in archaea and more recently discovery genes that encode fused remote homologs four eukaryotic Marseilleviridae, subfamily giant viruses infect amoebae. We demonstrate viral doublet are essential for infectivity, localize to cytoplasmic factories after virus infection, ultimately found mature virions. Cryogenic electron...
One quarter of the Northern hemisphere is underlain by permanently frozen ground, referred to as permafrost. Due climate warming, irreversibly thawing permafrost releasing organic matter for up a million years, most which decomposes into carbon dioxide and methane, further enhancing greenhouse effect. Part this also consists revived cellular microbes (prokaryotes, unicellular eukaryotes) well viruses that have remained dormant since prehistorical times. While literature abounds on...
This paper presents 3DCoffee@igs, a web-based tool dedicated to the computation of high-quality multiple sequence alignments (MSAs). 3D-Coffee makes it possible mix protein sequences and structures in order increase accuracy alignments. Structures can be either provided as PDB identifiers or directly uploaded into server. Given set structures, pairs are aligned with SAP while sequence–structure Fugue. The resulting collection pairwise is then combined an MSA T-Coffee algorithm. server its...
The successful identification of the residues that contact ligand has important implications, especially in view increasing use antibodies various medical and industrial applications. Analysis crystallographically derived, three-dimensional structures five antibody-antigen complexes available amino acid sequence data on antibody variable regions reveals antigen are main also most variable. It is proposed a good first guess identity specificity-determining can be made from an examination...
ABSTRACT Acanthamoeba polyphaga mimivirus is the largest known virus in both particle size and genome complexity. Its 1.2-Mb encodes 911 proteins, among which only 298 have predicted functions. The composition of purified isolated virions was analyzed by using a combined electrophoresis/mass spectrometry approach allowing identification 114 proteins. Besides expected major structural components, viral packages 12 proteins unambiguously associated with transcriptional machinery, 3 DNA repair,...
Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture blank shots (no particle intercepted), and exposures one or particles. Experimental data sets also often contain unintentional contamination with different species. We present unsupervised method able to sort experimental without recourse templates, specific noise models, user-directed learning. The results show 90% agreement manual classification.