title: Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae.
abstract: Transcription by RNA polymerase may be interrupted by pauses caused by backtracking or misincorporation that can be resolved by the conserved bacterial Gre-factors. However, the consequences of such pausing in the living cell remain obscure. Here, we developed molecular biology and transcriptome sequencing tools in the human pathogen Streptococcus pneumoniae and provide evidence that transcription elongation is rate-limiting on highly expressed genes. Our results suggest that transcription elongation may be a highly regulated step of gene expression in S. pneumoniae. Regulation is accomplished via long-living elongation pauses and their resolution by elongation factor GreA. Interestingly, mathematical modeling indicates that long-living pauses cause queuing of RNA polymerases, which results in 'transcription traffic jams' on the gene and thus blocks its expression. Together, our results suggest that long-living pauses and RNA polymerase queues caused by them are a major problem on highly expressed genes and are detrimental for cell viability. The major and possibly sole function of GreA in S. pneumoniae is to prevent formation of backtracked elongation complexes.
authors.affiliation: Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
authors.forename: Yulia
authors.initials: Y
authors.lastname: Yuzenkova
authors.affiliation: Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Pamela
authors.initials: P
authors.lastname: Gamba
authors.affiliation: Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Martijn
authors.initials: M
authors.lastname: Herber
authors.affiliation: Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Laetitia
authors.initials: L
authors.lastname: Attaiech
authors.affiliation: Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Sulman
authors.initials: S
authors.lastname: Shafeeq
authors.affiliation: Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Oscar P
authors.initials: OP
authors.lastname: Kuipers
authors.affiliation: Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany klumpp@mpikg.mpg.de.
authors.forename: Stefan
authors.initials: S
authors.lastname: Klumpp
authors.affiliation: Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK n.zenkin@newcastle.ac.uk.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Zenkin
authors.affiliation: Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands j.w.veening@rug.nl.
authors.forename: Jan-Willem
authors.initials: JW
authors.lastname: Veening
mesh_terms: D001426:Bacterial Proteins / Q000502:physiology*; D015964:Gene Expression Regulation, Bacterial; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D013296:Streptococcus pneumoniae / Q000166:cytology / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D061805:Transcription Elongation, Genetic; D061785:Transcription Initiation, Genetic; D035602:Transcriptional Elongation Factors / Q000502:physiology*
chemical_list: D001426:Bacterial Proteins; D035602:Transcriptional Elongation Factors