title: Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage.
abstract: RNA polymerase (Pol) I contains a 10-subunit catalytic core that is related to the core of Pol II and includes subunit A12.2. In addition, Pol I contains the heterodimeric subcomplexes A14/43 and A49/34.5, which are related to the Pol II subcomplex Rpb4/7 and the Pol II initiation factor TFIIF, respectively. Here we used lysine-lysine crosslinking, mass spectrometry (MS) and modeling based on five crystal structures, to extend the previous homology model of the Pol I core, to confirm the location of A14/43 and to position A12.2 and A49/34.5 on the core. In the resulting model of Pol I, the C-terminal ribbon (C-ribbon) domain of A12.2 reaches the active site via the polymerase pore, like the C-ribbon of the Pol II cleavage factor TFIIS, explaining why the intrinsic RNA cleavage activity of Pol I is strong, in contrast to the weak cleavage activity of Pol II. The A49/34.5 dimerization module resides on the polymerase lobe, like TFIIF, whereas the A49 tWH domain resides above the cleft, resembling parts of TFIIE. This indicates that Pol I and also Pol III are distantly related to a Pol II-TFIIS-TFIIF-TFIIE complex.
authors.affiliation: Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Jennebach
authors.forename: Franz
authors.initials: F
authors.lastname: Herzog
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
mesh_terms: D003432:Cross-Linking Reagents; D008239:Lysine / Q000737:chemistry; D013058:Mass Spectrometry; D008958:Models, Molecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D059367:RNA Cleavage; D012318:RNA Polymerase I / Q000737:chemistry* / Q000378:metabolism; D012335:RNA, Ribosomal / Q000378:metabolism; D035602:Transcriptional Elongation Factors / Q000378:metabolism
chemical_list: D003432:Cross-Linking Reagents; D021122:Protein Subunits; D012335:RNA, Ribosomal; D035602:Transcriptional Elongation Factors; C018648:transcription factor S-II; D012318:RNA Polymerase I; D008239:Lysine