Genetic analyses led to the discovery of a super-active mutant of the RNA polymerase I

PLoS Genet. 2019 May 28;15(5):e1008157. doi: 10.1371/journal.pgen.1008157. eCollection 2019 May.

Abstract

Most transcriptional activity of exponentially growing cells is carried out by the RNA Polymerase I (Pol I), which produces a ribosomal RNA (rRNA) precursor. In budding yeast, Pol I is a multimeric enzyme with 14 subunits. Among them, Rpa49 forms with Rpa34 a Pol I-specific heterodimer (homologous to PAF53/CAST heterodimer in human Pol I), which might be responsible for the specific functions of the Pol I. Previous studies provided insight in the involvement of Rpa49 in initiation, elongation, docking and releasing of Rrn3, an essential Pol I transcription factor. Here, we took advantage of the spontaneous occurrence of extragenic suppressors of the growth defect of the rpa49 null mutant to better understand the activity of Pol I. Combining genetic approaches, biochemical analysis of rRNA synthesis and investigation of the transcription rate at the individual gene scale, we characterized mutated residues of the Pol I as novel extragenic suppressors of the growth defect caused by the absence of Rpa49. When mapped on the Pol I structure, most of these mutations cluster within the jaw-lobe module, at an interface formed by the lobe in Rpa135 and the jaw made up of regions of Rpa190 and Rpa12. In vivo, the suppressor allele RPA135-F301S restores normal rRNA synthesis and increases Pol I density on rDNA genes when Rpa49 is absent. Growth of the Rpa135-F301S mutant is impaired when combined with exosome mutation rrp6Δ and it massively accumulates pre-rRNA. Moreover, Pol I bearing Rpa135-F301S is a hyper-active RNA polymerase in an in vitro tailed-template assay. We conclude that RNA polymerase I can be engineered to produce more rRNA in vivo and in vitro. We propose that the mutated area undergoes a conformational change that supports the DNA insertion into the cleft of the enzyme resulting in a super-active form of Pol I.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Ribosomal / genetics
  • Pol1 Transcription Initiation Complex Proteins / genetics*
  • Pol1 Transcription Initiation Complex Proteins / metabolism
  • RNA Polymerase I / genetics*
  • RNA Precursors / genetics
  • RNA, Ribosomal
  • Ribosomes / metabolism
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins / genetics
  • Transcription Factors / genetics
  • Transcription, Genetic

Substances

  • DNA, Ribosomal
  • Pol1 Transcription Initiation Complex Proteins
  • RNA Precursors
  • RNA, Ribosomal
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • RNA Polymerase I

Grants and funding

OG work was supported by the Agence Nationale de la Recherche (ANDY - www.agence-nationale-recherche.fr/) and the IDEX of Toulouse University (Clemgene and Nudgene; www.univ-toulouse.fr/universite). CFT was supported by grants BFU2013-48374-P and BFU2017-87397-P of the Spanish Ministry of Economy and Competitiveness (www.mineco.es), and by the Ramón Areces Foundation (http://www.fundacionareces.es). OC was supported by grants BFU2017-84694-P from the Spanish Ministry of Economy and Competitiveness (MINECO) and CLU-2017-03 from Junta de Castilla y León (JCyL). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.