Pierre Pontarotti
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View article: <i>HLA Class Ib</i> and <i>MICA/MICB</i> Expression in Human Tissues and Cell Types: Reshuffling Immune Players
<i>HLA Class Ib</i> and <i>MICA/MICB</i> Expression in Human Tissues and Cell Types: Reshuffling Immune Players Open
Abnormal expression of HLA class Ib, MICA and MICB molecules is associated with the evolution of pathological conditions and clinical settings. Here, we use RNA‐sequencing data from two publicly‐available projects, from different human org…
View article: The phylogenomic approach suggests that butyrophilins have ligands beyond gamma-delta receptors
The phylogenomic approach suggests that butyrophilins have ligands beyond gamma-delta receptors Open
International audience
View article: Global lessons from antibiotic resistance: metformin-hydrolyzing genes in transposable elements, a new threat for type II diabetic patients?
Global lessons from antibiotic resistance: metformin-hydrolyzing genes in transposable elements, a new threat for type II diabetic patients? Open
Metformin drug, widely used to treat type II diabetic patients, is a major pharmaceutical pollutant of wastewater and rivers. This environmental exposure has driven the evolution of bacteria, such as Aminobacter and Pseudomonas , to degrad…
View article: Long-Term Intra-Host Evolution of SARS-CoV-2 in an Immunocompromised Patient: Recombination and Within-Host Mutations Driving Viral Adaptation
Long-Term Intra-Host Evolution of SARS-CoV-2 in an Immunocompromised Patient: Recombination and Within-Host Mutations Driving Viral Adaptation Open
An immuno-compromised patient with lymphoma experienced a prolonged SARS-CoV-2 infection lasting 14 months, initially infected with B.1.160, followed by B.1.1.7. This study focused on intra-host single nucleotide variants (iSNVs) and singl…
View article: Hairpin loop mutations determine the evolution of SARS-CoV-2
Hairpin loop mutations determine the evolution of SARS-CoV-2 Open
One of the bases of genetic organization is the occurrence of stem-loops or hairpins which may constitute a foundation of genetic evolution both in viruses and other organisms. Stem-loops are theoretically made up of a stable part, the dou…
View article: The disappearance of ORF8 in specialized coronaviruses: the Cheshire cat paradigm
The disappearance of ORF8 in specialized coronaviruses: the Cheshire cat paradigm Open
We studied the fate of a gene called ORF8 in different coronaviruses species during their passage to humans. We renamed this ORF ‘Mistigri’ because ORF8 in coronaviruses does not necessarily correspond to the same coding sequences. We show…
View article: APOBEC cellular enzymes as ‘Court Jesters’ in SARS-CoV-2 evolution
APOBEC cellular enzymes as ‘Court Jesters’ in SARS-CoV-2 evolution Open
Human cellular APOBEC enzymes were largely reported as involved in innate antiviral defenses. We previously highlighted that in SARS-CoV-2 genomes obtained in our center, nearly half of ‘hyperfertile’ or ‘fertile’ mutations while 23% of ne…
View article: Impact of RAG Transposon Co-option on the Evolution of the Jawed Vertebrate Immune System
Impact of RAG Transposon Co-option on the Evolution of the Jawed Vertebrate Immune System Open
This article aims to review the current knowledge in comparative immunology and present updated hypotheses regarding the evolution of the immune system. Our primary focus is the co-option of the RAG transposon and its role in the developm…
View article: Symbiosis, hybridization, and speciation in Mediterranean octocorals (Octocorallia, Eunicellidae)
Symbiosis, hybridization, and speciation in Mediterranean octocorals (Octocorallia, Eunicellidae) Open
Understanding how species can form and remain isolated in the marine environment still stimulates active research. Here we study the differentiation and the possibility of hybridization among three temperate octocorals: Eunicella cavolini,…
View article: Genomic features of carbapenem-resistant Klebsiella pneumoniae isolated in French Polynesia and description of a novel transposon Tn7722 responsible for NDM-1 dissemination
Genomic features of carbapenem-resistant Klebsiella pneumoniae isolated in French Polynesia and description of a novel transposon Tn7722 responsible for NDM-1 dissemination Open
AIM: We aimed to characterize the phenotype and genotype of 17 carbapenem-resistant Klebsiella pneumoniae (CRKP) strains isolated from 2006 to 2021 in French Polynesia and to identify potential mobile genetic elements (MGEs) associated wit…
View article: “Outlaw” mutations in quasispecies of SARS-CoV-2 inhibit replication
“Outlaw” mutations in quasispecies of SARS-CoV-2 inhibit replication Open
The evolution of SARS-CoV-2, the agent of COVID-19, has been remarkable for its high mutation potential, leading to the appearance of variants. Some mutations have never appeared in the published genomes, which represent consensus, or b…
View article: Symbiotic status does not preclude hybridisation in Mediterranean octocorals
Symbiotic status does not preclude hybridisation in Mediterranean octocorals Open
Understanding how species can form and remain isolated in the marine environment is still an active research area. Correctly delimiting species if also of interest for biodiversity conservation and for a wide range of biological studies. H…
View article: The IL-17 pathway intertwines with neurotrophin and TLR/IL-1R pathways since its domain shuffling origin
The IL-17 pathway intertwines with neurotrophin and TLR/IL-1R pathways since its domain shuffling origin Open
The IL-17 pathway displays remarkably diverse functional modes between different subphyla, classes, and even orders, yet its driving factors remains elusive. Here, we demonstrate that the IL-17 pathway originated through domain shuffling b…
View article: Mechanisms of acquisition of the vanA operon among vancomycin-resistant Staphylococcus aureus genomes: The tip of the iceberg?
Mechanisms of acquisition of the vanA operon among vancomycin-resistant Staphylococcus aureus genomes: The tip of the iceberg? Open
View article: Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic
Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic Open
View article: Intrinsically linked lineage-specificity of transposable elements and lncRNAs reshapes transcriptional regulation species- and tissue-specifically
Intrinsically linked lineage-specificity of transposable elements and lncRNAs reshapes transcriptional regulation species- and tissue-specifically Open
Lineage-specificity of transcriptional regulation by lncRNAs critically determines whether mouse models reliably mimic human diseases. To address this question, we identified human/mouse-specific lncRNAs from GENCODE-annotated human and mo…
View article: Resistance‐associated mutations to the anti‐SARS‐CoV‐2 agent nirmatrelvir: Selection not induction
Resistance‐associated mutations to the anti‐SARS‐CoV‐2 agent nirmatrelvir: Selection not induction Open
Mutations associated with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) resistance to antiprotease nirmatrelvir were reported. We aimed to detect them in SARS‐CoV‐2 genomes and quasispecies retrieved in our institute before …
View article: Is it time to switch to a formulation other than the live attenuated poliovirus vaccine to prevent poliomyelitis?
Is it time to switch to a formulation other than the live attenuated poliovirus vaccine to prevent poliomyelitis? Open
The polioviruses (PVs) are mainly transmitted by direct contact with an infected person through the fecal-oral route and respiratory secretions (or more rarely via contaminated water or food) and have a primary tropism for the gut. After t…
View article: From viral democratic genomes to viral wild bunch of quasispecies
From viral democratic genomes to viral wild bunch of quasispecies Open
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or “democratic” genomes. They represent the genomes most frequently found in the clinical samples of patients but do not accou…
View article: Cover Image, Volume 95, Number 11, November 2023
Cover Image, Volume 95, Number 11, November 2023 Open
Front Cover Caption: The cover image is based on the Review From viral democratic genomes to viral wild bunch of quasispecies by Philippe Colson et al., https://doi.org/10.1002/jmv.29209.
View article: Insights into RAG Evolution from the Identification of “Missing Link” Family A <i>RAGL</i> Transposons
Insights into RAG Evolution from the Identification of “Missing Link” Family A <i>RAGL</i> Transposons Open
A series of “molecular domestication” events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1–RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order…
View article: The return of the “Mistigri” (virus adaptative gain by gene loss) through the SARS‐CoV‐2 XBB.1.5 chimera that predominated in 2023
The return of the “Mistigri” (virus adaptative gain by gene loss) through the SARS‐CoV‐2 XBB.1.5 chimera that predominated in 2023 Open
Severe acute respiratory syndrome coronavirus 2 XBB.1.5 is the first recombinant lineage to predominate at the country and global scales. Very interestingly, like the Marseille‐4B subvariant (or B.1.160) and the pandemic variant B.1.1.7 (o…
View article: Integration of the immune memory into the pathogen‐driven <scp>MHC</scp> polymorphism hypothesis
Integration of the immune memory into the pathogen‐driven <span>MHC</span> polymorphism hypothesis Open
Major histocompatibility complex (MHC) genes (referred to as human leukocyte antigen or HLA in humans) are a key component of vertebrate immune systems, coding for proteins which present antigens to T‐cells. These genes are outstanding in …
View article: Insights into RAG evolution from the identification of “missing link” family A<i>RAGL</i>transposons
Insights into RAG evolution from the identification of “missing link” family A<i>RAGL</i>transposons Open
A series of “molecular domestication” events are thought to have converted an invertebrate RAG-like (RAGL) transposase into the RAG1-RAG2 (RAG) recombinase, a critical enzyme for adaptive immunity in jawed vertebrates. The timing and order…
View article: Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality
Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality Open
The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-la…
View article: Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms
Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms Open
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily…
View article: The return of the “Mistigri” through the SARS-CoV-2 XBB.1.5 chimera that predominated in 2023
The return of the “Mistigri” through the SARS-CoV-2 XBB.1.5 chimera that predominated in 2023 Open
The number of SARS-CoV-2 recombinants identified during the pandemic has increased since the era of Omicron variants, but XBB.1.5 (or Omicron 23A) is the first lineage comprised of hybrid genomes to predominate at the country and global sc…
View article: Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic
Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic Open
RNA viruses, including SARS-CoV-2, evolve by mutation acquisition, or by hybridization between viral genomes. The SARS-CoV-2 pandemic provided an exceptional opportunity to analyze the mutations that appeared over a three-year period. In t…
View article: ‘Cannibalism’ of exogenous DNA sequences: The ancestral form of adaptive immunity which entails recognition of danger
‘Cannibalism’ of exogenous DNA sequences: The ancestral form of adaptive immunity which entails recognition of danger Open
Adaptive immunity is a sophisticated form of immune response capable of retaining the molecular memory of a very great diversity of target antigens (epitopes) as non-self. It is capable of reactivating itself upon a second encounter with a…
View article: Parallel evolution of amphioxus and vertebrate small-scale gene duplications
Parallel evolution of amphioxus and vertebrate small-scale gene duplications Open