Global kinetic mechanism describing single nucleotide incorporation for RNA polymerase I reveals fast UMP incorporation

• Published in: Biophysical chemistry 2024-09, Vol.312, p.107281, Article 107281
• Main Authors: Fuller, Kaila B., Jacobs, Ruth Q., Carter, Zachariah I., Cuny, Zachary G., Schneider, David A., Lucius, Aaron L.
• Format: Article
• Language: English
• Subjects: Enzyme kinetics; Kinetics; Nucleotides - chemistry; Nucleotides - metabolism; Ribosomal RNA; RNA polymerase I; RNA Polymerase I - chemistry; RNA Polymerase I - metabolism; Transcription; Transient-state kinetics
• ISSN: 0301-4622; 1873-4200; 1873-4200
• DOI: 10.1016/j.bpc.2024.107281

RNA polymerase I (Pol I) is responsible for synthesizing ribosomal RNA, which is the rate limiting step in ribosome biogenesis. We have reported wide variability in the magnitude of the rate constants defining the rate limiting step in sequential nucleotide additions catalyzed by Pol I. in this study we sought to determine if base identity impacts the rate limiting step of nucleotide addition catalyzed by Pol I. To this end, we report a transient state kinetic interrogation of AMP, CMP, GMP, and UMP incorporations catalyzed by Pol I. We found that Pol I uses one kinetic mechanism to incorporate all nucleotides. However, we found that UMP incorporation is faster than AMP, CMP, and GMP additions. Further, we found that endonucleolytic removal of a dimer from the 3′ end was fastest when the 3′ terminal base is a UMP. It has been previously shown that both downstream and upstream template sequence identity impacts the kinetics of nucleotide addition. The results reported here show that the incoming base identity also impacts the magnitude of the observed rate limiting step. [Display omitted] •Pol I employs one universal kinetic mechanism independent of base identity.•UMP is incorporated substantially faster than GMP, CMP, and AMP.•Fast incorporation of UMP may be important for termination.