Philippe Lopez
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View article: Transcriptional landscape of the cell cycle in a model thermoacidophilic archaeon reveals similarities to eukaryotes
Transcriptional landscape of the cell cycle in a model thermoacidophilic archaeon reveals similarities to eukaryotes Open
Similar to many eukaryotes, the thermoacidophilic archaeon Saccharolobus islandicus follows a defined cell cycle program, with two growth phases, G1 and G2, interspersed by a chromosome replication phase (S), and followed by genome segrega…
View article: New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean
New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean Open
Background Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel v…
View article: Interspecific interactions and aging: Prediction of gerogenic bacteria and critical human protein targets of microbial infections
Interspecific interactions and aging: Prediction of gerogenic bacteria and critical human protein targets of microbial infections Open
Bacteria permeate every niche of the human body with major consequences on our health and senescence that have not been fully described. Here, we predict which bacteria and which bacterial proteins could interfere with proteins associated …
View article: Transcriptional landscape of the archaeal cell cycle is broadly conserved in eukaryotes
Transcriptional landscape of the archaeal cell cycle is broadly conserved in eukaryotes Open
The cell cycle is a series of events that occur from the moment of cell birth to cell division. In eukaryotes, cell growth, genome replication, genome segregation, and cytokinesis are strictly coordinated, defining discrete cell cycle phas…
View article: Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems
Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems Open
Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the enti…
View article: Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems
Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems Open
SUMMARY Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, that are under considerable threat from climate change. Despite their ecological and evolutionary importance, this phylogenetic …
View article: New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean
New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean Open
Background Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel v…
View article: A broadly distributed new class of quorum sensing signals mediate bacterial intercellular signaling
A broadly distributed new class of quorum sensing signals mediate bacterial intercellular signaling Open
The gram-positive bacteria use quorum sensing secreted peptides to communicate and control critical bacterial phenotypes. All the bacterial peptides are produced in a longer inactive form that is secreted and processed into shorter active …
View article: Bursts of novel composite gene families at major nodes in animal evolution
Bursts of novel composite gene families at major nodes in animal evolution Open
A molecular level perspective on how novel phenotypes evolve is contingent on our understanding of how genomes evolve through time, and of particular interest is how novel elements emerge or are lost. Mechanisms of protein evolution such a…
View article: Large-Scale Identification of Known and Novel RRNPP Quorum-Sensing Systems by RRNPP_Detector Captures Novel Features of Bacterial, Plasmidic, and Viral Coevolution
Large-Scale Identification of Known and Novel RRNPP Quorum-Sensing Systems by RRNPP_Detector Captures Novel Features of Bacterial, Plasmidic, and Viral Coevolution Open
Gram-positive Firmicutes bacteria and their mobile genetic elements (plasmids and bacteriophages) encode peptide-based quorum-sensing systems (QSSs) that orchestrate behavioral transitions as a function of population densities. In their si…
View article: Interactomics: Dozens of Viruses, Co-evolving With Humans, Including the Influenza A Virus, may Actively Distort Human Aging
Interactomics: Dozens of Viruses, Co-evolving With Humans, Including the Influenza A Virus, may Actively Distort Human Aging Open
Some viruses (e.g., human immunodeficiency virus 1 and severe acute respiratory syndrome coronavirus 2) have been experimentally proposed to accelerate features of human aging and of cellular senescence. These observations, along with evol…
View article: Proximate Drivers of Population-Level Lizard Gut Microbial Diversity: Impacts of Diet, Insularity, and Local Environment
Proximate Drivers of Population-Level Lizard Gut Microbial Diversity: Impacts of Diet, Insularity, and Local Environment Open
Diet has been suggested to be an important driver of variation in microbiota composition in mammals. However, whether this is a more general phenomenon and how fast changes in gut microbiota occur with changes in diet remains poorly unders…
View article: Data of Proximate Drivers of Population-Level Lizard Gut Microbial Diversity: Impacts of Diet, Insularity, and Local Environment
Data of Proximate Drivers of Population-Level Lizard Gut Microbial Diversity: Impacts of Diet, Insularity, and Local Environment Open
Raw data of the study
View article: Hundreds of out-of-frame remodelled gene families in the E. coli pangenome
Hundreds of out-of-frame remodelled gene families in the E. coli pangenome Open
International audience
View article: Hundreds of Out-of-Frame Remodeled Gene Families in the<i>Escherichia coli</i>Pangenome
Hundreds of Out-of-Frame Remodeled Gene Families in the<i>Escherichia coli</i>Pangenome Open
All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesiz…
View article: For consideration as an Article in the Discoveries section of MBE Aging at evolutionary crossroads: longitudinal gene co-expression network analyses of proximal and ultimate causes of aging in bats
For consideration as an Article in the Discoveries section of MBE Aging at evolutionary crossroads: longitudinal gene co-expression network analyses of proximal and ultimate causes of aging in bats Open
How, when and why do organisms, their tissues and their cells age remain challenging issues, although researchers have identified multiple mechanistic causes of aging, and three major evolutionary theories have been developed to unravel th…
View article: Aging at Evolutionary Crossroads: Longitudinal Gene Co-expression Network Analyses of Proximal and Ultimate Causes of Aging in Bats
Aging at Evolutionary Crossroads: Longitudinal Gene Co-expression Network Analyses of Proximal and Ultimate Causes of Aging in Bats Open
How, when, and why do organisms, their tissues, and their cells age remain challenging issues, although researchers have identified multiple mechanistic causes of aging, and three major evolutionary theories have been developed to unravel …
View article: RRNPP_detector: a tool to detect RRNPP quorum sensing systems in chromosomes, plasmids and phages of gram-positive bacteria
RRNPP_detector: a tool to detect RRNPP quorum sensing systems in chromosomes, plasmids and phages of gram-positive bacteria Open
Gram-positive bacteria (e.g. Firmicutes) and their mobile genetic elements (plasmids, bacteriophages) encode peptide-based quorum sensing systems (QSSs) that regulate behavioral transitions in a density-dependent manner. In their simplest …
View article: Large-scale identification of viral quorum sensing systems reveals density-dependent sporulation-hijacking mechanisms in bacteriophages
Large-scale identification of viral quorum sensing systems reveals density-dependent sporulation-hijacking mechanisms in bacteriophages Open
Communication between viruses supported by quorum sensing systems (QSSs) were found to optimize the fitness of temperate bacteriophages of Bacilli by guiding the transition from the host-destructive lytic cycle to the host-protective lysog…
View article: The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View
The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View Open
Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appe…
View article: Marine Ultrasmall Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen, and Sulfur
Marine Ultrasmall Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen, and Sulfur Open
Recently, we uncovered the genetic components from six carbon fixation autotrophic pathways in cleaned ultrasmall size fractions from marine samples (<0.22 µm) gathered worldwide by the Tara Oceans Expedition. This first finding suggest…
View article: Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication
Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication Open
The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways suc…
View article: Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms
Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms Open
The evolutionary stability of temperate bacteriophages at low abundance of susceptible bacterial hosts lies in the trade-off between the maximization of phage replication, performed by the host-destructive lytic cycle, and the protection o…