Analysis of the RNA Binding Specificity Landscape of C5 Protein Reveals Structure and Sequence Preferences that Direct RNase P Specificity.
RNA binding proteins (RBPs) are typically involved in non-equilibrium cellular processes, and specificity can arise from differences in ground state, transition state, or product states of the binding reactions for alternative RNAs. Here, we use high-throughput methods to measure and analyze the RNA association kinetics and equilibrium binding affinity for all possible sequence combinations in the precursor tRNA binding site of C5, the essential protein subunit of Escherichia coli RNase P. The results show that the RNA sequence specificity of C5 arises due to favorable RNA-protein interactions that stabilize the transition state for association and bound enzyme-substrate complex. Specificity is further impacted by unfavorable RNA structure involving the C5 binding site in the ground state. The results illustrate a comprehensive quantitative approach for analysis of RNA binding specificity, and show how both RNA structure and sequence preferences of an essential protein subunit direct the specificity of a ribonucleoprotein enzyme.
Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
Hsuan-Chun
HC
Lin
Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
Jing
J
Zhao
Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
Courtney N
CN
Niland
Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
Brandon
B
Tran
Department of Biochemistry, Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
Eckhard
E
Jankowsky
Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA. Electronic address: meh2@cwru.edu.
Michael E
ME
Harris
D001483:Base Sequence; D001665:Binding Sites; D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D011487:Protein Conformation; D012322:RNA Precursors / Q000737:chemistry / Q000378:metabolism*; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D043262:Ribonuclease P / Q000737:chemistry / Q000378:metabolism*
D029968:Escherichia coli Proteins; D012322:RNA Precursors; D012329:RNA, Bacterial; D043262:Ribonuclease P; C470865:ribonuclease P, E coli
RNA binding protein; RNA specificity; enzyme kinetics; ribonuclease, tRNA
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