A high-throughput search for intracellular factors that affect RNA folding identifies E. coli proteins PepA and YagL as RNA chaperones that promote RNA remodeling

Abstract

General RNA chaperones are RNA-binding proteins (RBPs) that interact transiently and non-specifically with RNA substrates and assist in their folding into native state. In bacteria, these chaperones impact both coding and non-coding RNAs and are particularly important for large, structured RNAs which are prone to becoming kinetically trapped in misfolded states. Currently, due to the limited number of well-characterized examples and the lack of a consensus structural or sequence motif, it is difficult to identify general RNA chaperones in bacteria. Here, we adapted a previously published in vivo RNA regional accessibility probing assay to screen genome wide for intracellular factors in E. coli affecting RNA folding, among which we aimed to uncover novel RNA chaperones. Through this method, we identified and validated eight proteins whose deletion gives changes in regional accessibility within the exogenously expressed Tetrahymena group I intron ribozyme. Further, we purified and measured in vitro properties of two of these proteins, YagL and PepA, which were especially attractive as general chaperone candidates. We showed that both proteins bind RNA and that YagL accelerates native refolding of the ribozyme from a long-lived misfolded state. Further dissection of YagL showed that a putative helix-turn-helix (HTH) domain is responsible for most of its RNA binding activity but only the full protein shows chaperone activity. Altogether, this work expands the current repertoire of known general RNA chaperones in bacteria.