title: Finding sRNA-associated phenotypes by competition assays: An example with Staphylococcus aureus.
abstract: Bacteria optimize their fitness in response to a changing environment by tight regulation of gene expression. Regulation can be controlled at both transcriptional and post-transcriptional levels via key players such as sigma factors, regulatory proteins and regulatory RNAs. The identification of phenotypes associated with gene deletions is the established method for finding gene functions but may require testing many conditions for each studied mutant. As regulatory RNAs often contribute to fine-tuning gene expression, phenotypes associated with their inactivation are often weak and difficult to detect. Nevertheless, minor phenotypes conferring modest advantages, may allow bacteria to emerge after some generations under selective pressure. A strategy employing DNA barcodes can be used to perform competition experiments between mutants and to monitor fitness associated with mutations in different growth conditions. We combined this strategy with deep sequencing to study regulatory RNAs in Staphylococcus aureus, a major opportunistic pathogen.
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Thao Nguyen
authors.initials: TN
authors.lastname: Le Lam
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Morvan
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Wenfeng
authors.initials: W
authors.lastname: Liu
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Chantal
authors.initials: C
authors.lastname: Bohn
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Yan
authors.initials: Y
authors.lastname: Jaszczyszyn
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France. Electronic address: philippe.bouloc@u-psud.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Bouloc
mesh_terms: D001681:Biological Assay; D058893:DNA Barcoding, Taxonomic; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D056084:Genetic Fitness; D056265:Microbial Interactions / Q000235:genetics*; D009154:Mutation; D010641:Phenotype; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism; D013211:Staphylococcus aureus / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D014169:Transformation, Bacterial
chemical_list: D012329:RNA, Bacterial; D058727:RNA, Small Untranslated; D012808:Sigma Factor
keywords: Fitness; Gene disruption; IM08B; Regulatory RNA; pIMAY; pMAD