RNA is important for the in-cell solubility of its interacting protein : Implications in RNA-mediated protein folding

Abstract

It is one of the fundamental questions how proteins efficiently reach their proper 3D structures in the presence of off-pathways such as misfolding and aggregation, in the highly crowded environment. Traditionally, protein folding has been studied in the boundary of molecular chaperones. Despite extensive studies on various types of molecular chaperones, the effect of a binding partner (or a ligand) on the in-cell solubility of its cognate protein, including protein folding, misfolding, aggregation, and homeostasis, still remains largely undefined. RNAs are abundant in the cytoplasm, where they directly or indirectly interact with proteins over the course of their life cycle. All proteins are synthesized by ribosomal machinery, and as such, are linked to or in close contact with ribosomal RNAs (rRNAs) from the beginning of their synthesis. In addition, a great number of proteins interacts with their RNA ligands and forms RNA-protein complexes (RNP complexes). Thus, it is worth examining the effect of RNA on the folding and proteostasis of its interacting proteins, but the current concept of protein folding neither ask nor answer the effect of ligands on the in-cell solubility of their interacting proteins. Here I used RNase P as a model system and tested a possibility that M1 RNA modulates the in-cell solubility of its cognate C5 protein in the formation of RNase P. Coexpression of M1 RNA greatly increased the solubility of C5 protein in Escherichia coli. Moreover, M1 RNA substantially stimulated the refolding of C5 protein in vitro. Mutations that have the impaired binding ability between C5 protein and M1 RNA failed to increase the solubility of C5 protein. Furthermore, M1 RNA provides quality insurance of its cognate C5 protein, either by enhancing the degradation of C5 protein mutants in normal cellular condition, or by stimulating protein aggregation if the proteolytic machinery is non-functional. These results strongly suggest the chaperoning role of RNA ligands as a mediator in the folding and proteostasis of their interacting proteins and would give new insights into novel RNA functions for in-cell solubility of their interacting proteins.