Pre-tRNA turnover catalyzed by the yeast nuclear RNase P holoenzyme is limited by product release

RNA. 2009 Feb;15(2):224-34. doi: 10.1261/rna.1309409. Epub 2008 Dec 17.

Abstract

Ribonuclease P (RNase P) is a ribonucleoprotein that catalyzes the 5' maturation of precursor transfer RNA in the presence of magnesium ions. The bacterial RNase P holoenzyme consists of one catalytically active RNA component and a single essential but catalytically inactive protein. In contrast, yeast nuclear RNase P is more complex with one RNA subunit and nine protein subunits. We have devised an affinity purification protocol to gently and rapidly purify intact yeast nuclear RNase P holoenzyme for transient kinetic studies. In pre-steady-state kinetic studies under saturating substrate concentrations, we observed an initial burst of tRNA formation followed by a slower, linear, steady-state turnover, with the burst amplitude equal to the concentration of the holoenzyme used in the reaction. These data indicate that the rate-limiting step in turnover occurs after pre-tRNA cleavage, such as mature tRNA release. Additionally, the steady-state rate constants demonstrate a large dependence on temperature that results in nonlinear Arrhenius plots, suggesting that a kinetically important conformational change occurs during catalysis. Finally, deletion of the 3' trailer in pre-tRNA has little or no effect on the steady-state kinetic rate constants. These data suggest that, despite marked differences in subunit composition, the minimal kinetic mechanism for cleavage of pre-tRNA catalyzed by yeast nuclear RNase P holoenzyme is similar to that of the bacterial RNase P holoenzyme.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Catalysis
  • Holoenzymes / chemistry
  • Holoenzymes / metabolism
  • Kinetics
  • Nucleic Acid Conformation
  • RNA Precursors / chemistry
  • RNA Precursors / metabolism*
  • Ribonuclease P / chemistry
  • Ribonuclease P / metabolism*
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Substrate Specificity

Substances

  • Holoenzymes
  • RNA Precursors
  • Saccharomyces cerevisiae Proteins
  • Ribonuclease P