Bacteria from the same species can differ widely in their gene content. In E. coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have enabled to unravel genes required for fitness in various experimental conditions at the genome scale, most studies have focused on model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell largely remains to be investigated. Here, we developed a new CRISPR interference platform for highthroughput gene repression that is compatible with most E. coli isolates and closely-related species. We applied it to assess the importance of ~3,400 nearly ubiquitous genes in 3 growth media in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens highlighted extensive variations in gene essentiality between strains and conditions. Unlike variations in gene expression level, variations in gene essentiality do not recapitulate the strains' phylogeny. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we showed how mobile genetic elements can trigger the essentiality of core genes that are usually nonessential. This study provides new insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species in bacterial genomics..

Bacteria from the same species can differ widely in their gene content. In E. coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have enabled to unravel genes required for fitness in various experimental conditions at the genome scale, most studies have focused on model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell largely remains to be investigated. Here, we developed a new CRISPR interference platform for highthroughput gene repression that is compatible with most E. coli isolates and closely-related species. We applied it to assess the importance of ~3,400 nearly ubiquitous genes in 3 growth media in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens highlighted extensive variations in gene essentiality between strains and conditions. Unlike variations in gene expression level, variations in gene essentiality do not recapitulate the strains' phylogeny. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we showed how mobile genetic elements can trigger the essentiality of core genes that are usually nonessential. This study provides new insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species in bacterial genomics.

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Microbiote et immunité : nouveaux mécanismes, nouveaux acteurs Microbiota and immunity: new mechanisms, new actors Le dossier thématique qui suit a été rédigé par les étudiants de Master 1 de Biologie de l’École normale supérieure (ENS) de Lyon à l’issue de l’UE Microbiologie Moléculaire et Structurale (2018- 19). Le Master de Biologie de l’ENS de Lyon, cohabilité par l’université Claude Bernard Lyon 1, accueille chaque année environ 50 étudiants en M1 et en M2 et propose une formation de haut niveau à la recherche en biosciences. Chaque étudiant y construit son parcours à la carte, en choisissant ses options parmi un large panel de modules, favorisant ainsi une approche pluridisciplinaire des sciences du vivant, et ce en relation étroite avec les laboratoires de recherche du tissu local, national et international. En participant à diverses activités scientifiques connexes aux UE de leur formation, les étudiants préparent également l’obtention du diplôme de l’ENS de Lyon, qui valide leur scolarité à l’ENS. La rédaction du présent dossier, qui vise à transmettre de façon claire les principaux messages issus d’articles scientifiques publiés récemment dans le domaine de la microbiologie, constitue l’une de ces activités connexes proposées aux étudiants. Ces dernières années, des progrès immenses ont été réalisés dans la compréhension des interactions entre le microbiote bactérien, notamment intestinal, et l’immunité (→). (→) Voir le numéro thématique Le microbiote, cet inconnu qui réside en nous, m/s n° 11, novembre 2016, pages 921-1016 En parallèle, de nouvelles avancées techniques ont permis d’identifier et de caractériser les virus présents au sein du microbiote, rendant possible une meilleure appréhension de la diversité du virobiote et de ses impacts fonctionnels. Le présent dossier illustre quelques aspects de ces relations entre microbiote au sens large et immunité.