title: A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase.
abstract: The archaeal transcription apparatus is closely related to the eukaryotic RNA polymerase (RNAP) II system, while archaeal genomes are more similar to bacteria with densely packed genes organized in operons. This makes understanding transcription in archaea vital, both in terms of molecular mechanisms and evolution. Very little is known about how archaeal cells orchestrate transcription on a systems level. We have characterized the genome-wide occupancy of the Methanocaldococcus jannaschii transcription machinery and its transcriptome. Our data reveal how the TATA and BRE promoter elements facilitate recruitment of the essential initiation factors TATA-binding protein and transcription factor B, respectively, which in turn are responsible for the loading of RNAP into the transcription units. The occupancies of RNAP and Spt4/5 strongly correlate with each other and with RNA levels. Our results show that Spt4/5 is a general elongation factor in archaea as its presence on all genes matches RNAP. Spt4/5 is recruited proximal to the transcription start site on the majority of transcription units, while on a subset of genes, including rRNA and CRISPR loci, Spt4/5 is recruited to the transcription elongation complex during early elongation within 500 base pairs of the transcription start site and akin to its bacterial homologue NusG.
authors.affiliation: University College London, Institute for Structural and Molecular Biology, Gower Street, London WC1E 6BT, UK.
authors.forename: Katherine
authors.initials: K
authors.lastname: Smollett
authors.affiliation: University College London, Institute for Structural and Molecular Biology, Gower Street, London WC1E 6BT, UK.
authors.forename: Fabian
authors.initials: F
authors.lastname: Blombach
authors.affiliation: Institute of Microbiology and Archaea Center, Universität Regensburg, 93053 Regensburg, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Reichelt
authors.affiliation: Institute of Microbiology and Archaea Center, Universität Regensburg, 93053 Regensburg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Thomm
authors.affiliation: University College London, Institute for Structural and Molecular Biology, Gower Street, London WC1E 6BT, UK.
authors.forename: Finn
authors.initials: F
authors.lastname: Werner
mesh_terms: D019843:Archaeal Proteins / Q000378:metabolism; D020869:Gene Expression Profiling; D063747:Methanocaldococcus / Q000235:genetics*; D011485:Protein Binding; D012319:RNA Polymerase II / Q000378:metabolism*; D019642:RNA, Archaeal; D035181:TATA-Box Binding Protein / Q000378:metabolism; D035581:Transcription Factor TFIIB / Q000378:metabolism; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D019642:RNA, Archaeal; D035181:TATA-Box Binding Protein; D035581:Transcription Factor TFIIB; D035602:Transcriptional Elongation Factors; C106466:transcription factor B, Archaea; D012319:RNA Polymerase II