title: Global repositioning of transcription start sites in a plant-fermenting bacterium.
abstract: Bacteria respond to their environment by regulating mRNA synthesis, often by altering the genomic sites at which RNA polymerase initiates transcription. Here, we investigate genome-wide changes in transcription start site (TSS) usage by Clostridium phytofermentans, a model bacterium for fermentation of lignocellulosic biomass. We quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing, which combines capture of synthetically capped 5' mRNA fragments with template-switching reverse transcription. We find the locations and expression levels of TSS for hundreds of genes change during metabolism of different plant substrates. We show that TSS reveals riboswitches, non-coding RNA and novel transcription units. We identify sequence motifs associated with carbon source-specific TSS and use them for regulon discovery, implicating a LacI/GalR protein in control of pectin metabolism. We discuss how the high resolution and specificity of Capp-Switch enables study of condition-specific changes in transcription initiation in bacteria.
authors.affiliation: 1CEA, DRF, IG, Genoscope, Évry 91000, France.|CNRS-UMR8030, Évry 91000, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Boutard
authors.affiliation: New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA.
authors.forename: Laurence
authors.initials: L
authors.lastname: Ettwiller
authors.affiliation: 1CEA, DRF, IG, Genoscope, Évry 91000, France.|CNRS-UMR8030, Évry 91000, France.|Université Paris-Saclay, Évry 91000, France.|Université d'Évry, Évry 91000, France.
authors.forename: Tristan
authors.initials: T
authors.lastname: Cerisy
authors.affiliation: 1CEA, DRF, IG, Genoscope, Évry 91000, France.
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.affiliation: 1CEA, DRF, IG, Genoscope, Évry 91000, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Labadie
authors.affiliation: 1CEA, DRF, IG, Genoscope, Évry 91000, France.|CNRS-UMR8030, Évry 91000, France.|Université Paris-Saclay, Évry 91000, France.|Université d'Évry, Évry 91000, France.
authors.forename: Marcel
authors.initials: M
authors.lastname: Salanoubat
authors.affiliation: New England Biolabs, Inc., Ipswich, Massachusetts 01938, USA.
authors.forename: Ira
authors.initials: I
authors.lastname: Schildkraut
authors.affiliation: 1CEA, DRF, IG, Genoscope, Évry 91000, France.|CNRS-UMR8030, Évry 91000, France.|Université Paris-Saclay, Évry 91000, France.|Université d'Évry, Évry 91000, France.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Tolonen
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D003013:Clostridium / Q000235:genetics / Q000378:metabolism; D005285:Fermentation; D020869:Gene Expression Profiling; D005798:Genes, Bacterial / Q000235:genetics; D010368:Pectins / Q000378:metabolism; D010944:Plants / Q000382:microbiology*; D012333:RNA, Messenger / Q000235:genetics; D018085:Regulon / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D010368:Pectins