title: Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
abstract: Staphylococcus aureus is a major pathogen that colonizes about 20% of the human population. Intriguingly, this Gram-positive bacterium can survive and thrive under a wide range of different conditions, both inside and outside the human body. Here, we investigated the transcriptional adaptation of S. aureus HG001, a derivative of strain NCTC 8325, across experimental conditions ranging from optimal growth in vitro to intracellular growth in host cells. These data establish an extensive repertoire of transcription units and non-coding RNAs, a classification of 1412 promoters according to their dependence on the RNA polymerase sigma factors SigA or SigB, and allow identification of new potential targets for several known transcription factors. In particular, this study revealed a relatively low abundance of antisense RNAs in S. aureus, where they overlap only 6% of the coding genes, and only 19 antisense RNAs not co-transcribed with other genes were found. Promoter analysis and comparison with Bacillus subtilis links the small number of antisense RNAs to a less profound impact of alternative sigma factors in S. aureus. Furthermore, we revealed that Rho-dependent transcription termination suppresses pervasive antisense transcription, presumably originating from abundant spurious transcription initiation in this A+T-rich genome, which would otherwise affect expression of the overlapped genes. In summary, our study provides genome-wide information on transcriptional regulation and non-coding RNAs in S. aureus as well as new insights into the biological function of Rho and the implications of spurious transcription in bacteria.
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Mäder
authors.affiliation: MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Nicolas
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
authors.forename: Maren
authors.initials: M
authors.lastname: Depke
authors.affiliation: Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Pané-Farré
authors.affiliation: Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur and CNRS ERL 3526, Paris, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Debarbouille
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
authors.forename: Magdalena M
authors.initials: MM
authors.lastname: van der Kooi-Pol
authors.affiliation: MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Cyprien
authors.initials: C
authors.lastname: Guérin
authors.affiliation: MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Sandra
authors.initials: S
authors.lastname: Dérozier
authors.affiliation: Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur and CNRS ERL 3526, Paris, France.
authors.forename: Aurelia
authors.initials: A
authors.lastname: Hiron
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Hanne
authors.initials: H
authors.lastname: Jarmer
authors.affiliation: MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Leduc
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Michalik
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
authors.forename: Ewoud
authors.initials: E
authors.lastname: Reilman
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Schaffer
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Schmidt
authors.affiliation: MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Bessières
authors.affiliation: Institut Micalis, INRA and AgroParisTech, Jouy-en-Josas, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Noirot
authors.affiliation: Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
authors.affiliation: Biology of Gram-Positive Pathogens, Department of Microbiology, Institut Pasteur and CNRS ERL 3526, Paris, France.
authors.forename: Tarek
authors.initials: T
authors.lastname: Msadek
authors.affiliation: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Völker
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
authors.forename: Jan Maarten
authors.initials: JM
authors.lastname: van Dijl
mesh_terms: D001665:Binding Sites; D015152:Blotting, Northern; D015870:Gene Expression; D005798:Genes, Bacterial; D011401:Promoter Regions, Genetic; D013211:Staphylococcus aureus / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D014157:Transcription Factors