The C-terminal tail of the yeast mitochondrial transcription factor Mtf1 coordinates template strand alignment, DNA scrunching and timely transition into elongation

Nucleic Acids Res. 2020 Mar 18;48(5):2604-2620. doi: 10.1093/nar/gkaa040.


Mitochondrial RNA polymerases depend on initiation factors, such as TFB2M in humans and Mtf1 in yeast Saccharomyces cerevisiae, for promoter-specific transcription. These factors drive the melting of promoter DNA, but how they support RNA priming and growth was not understood. We show that the flexible C-terminal tails of Mtf1 and TFB2M play a crucial role in RNA priming by aiding template strand alignment in the active site for high-affinity binding of the initiating nucleotides. Using single-molecule fluorescence approaches, we show that the Mtf1 C-tail promotes RNA growth during initiation by stabilizing the scrunched DNA conformation. Additionally, due to its location in the path of the nascent RNA, the C-tail of Mtf1 serves as a sensor of the RNA-DNA hybrid length. Initially, steric clashes of the Mtf1 C-tail with short RNA-DNA hybrids cause abortive synthesis but clashes with longer RNA-DNA trigger conformational changes for the timely release of the promoter DNA to commence the transition into elongation. The remarkable similarities in the functions of the C-tail and σ3.2 finger of the bacterial factor suggest mechanistic convergence of a flexible element in the transcription initiation factor that engages the DNA template for RNA priming and growth and disengages when needed to generate the elongation complex.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Biocatalysis
  • DNA, Fungal / chemistry
  • DNA, Fungal / genetics*
  • Markov Chains
  • Methyltransferases / chemistry
  • Methyltransferases / metabolism
  • Mitochondrial Proteins / chemistry*
  • Mitochondrial Proteins / metabolism*
  • Nucleic Acid Conformation
  • Nucleotides / metabolism
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Conformation
  • RNA, Fungal / biosynthesis
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Sequence Deletion
  • Structure-Activity Relationship
  • Templates, Genetic*
  • Transcription Elongation, Genetic*
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism*
  • Transcription Initiation, Genetic


  • DNA, Fungal
  • MTF1 protein, S cerevisiae
  • Mitochondrial Proteins
  • Nucleotides
  • RNA, Fungal
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • Methyltransferases
  • TFB2M protein, human