Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1.
Within a complex with Rai1, the 5'-3' exoribonuclease Rat1 promotes termination of RNA polymerase II (RNAPII) on protein-coding genes, but its underlying molecular mechanism is still poorly understood. Using in vitro transcription termination assays, we have found that RNAPII is prone to more effective termination by Rat1/Rai1 when its catalytic site is disrupted due to NTP misincorporation, implying that paused RNAPII, which is often found in vivo near termination sites, could adopt a similar configuration to Rat1/Rai1 and trigger termination. Intriguingly, yeast Rat1/Rai1 does not terminate Escherichia coli RNAP, implying that a specific interaction between Rat1/Rai1 and RNAPII may be required for termination. Furthermore, the efficiency of termination increases as the RNA transcript undergoing degradation by Rat1 gets longer, which suggests that Rat1 may generate a driving force for dissociating RNAPII from the template while degrading the nascent transcripts to catch up to the polymerase. These results indicate that multiple mechanistic features contribute to Rat1-mediated termination of RNAPII.
Center for RNA Research, Institute for Basic Science and Department of Biophysics and Chemical Biology, Seoul National University, 1 Gwanak-Ro, Gwanakgu, Seoul, 151-742, South Korea.
Jieun
J
Park
Center for RNA Research, Institute for Basic Science and Department of Biophysics and Chemical Biology, Seoul National University, 1 Gwanak-Ro, Gwanakgu, Seoul, 151-742, South Korea.
Myungjin
M
Kang
Center for RNA Research, Institute for Basic Science and Department of Biophysics and Chemical Biology, Seoul National University, 1 Gwanak-Ro, Gwanakgu, Seoul, 151-742, South Korea MinKyu.Kim@ucsf.edu.
Minkyu
M
Kim
D000255:Adenosine Triphosphate / Q000378:metabolism; D001483:Base Sequence; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism*; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D061806:Transcription Termination, Genetic
D009687:Nuclear Proteins; D012331:RNA, Fungal; D016601:RNA-Binding Proteins; C473024:Rai1 protein, S cerevisiae; C553428:Rtt103 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; C075577:RAT1 protein, S cerevisiae; D000255:Adenosine Triphosphate; D012319:RNA Polymerase II; D005095:Exoribonucleases