Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses

Abstract

During packaging in positive-sense single-stranded RNA (+ssRNA) viruses, coat proteins (CPs) interact directly with multiple regions in genomic RNA (gRNA), but the underlying physicochemical principles remain unclear. Here we analyze the high-resolution cryo-EM structure of bacteriophage MS2 and show that the gRNA/CP binding sites, including the known packaging signal, overlap significantly with regions where gRNA nucleobase-density profiles match the corresponding CP nucleobase-affinity profiles. Moreover, we show that the MS2 packaging signal corresponds to the global minimum in gRNA/CP interaction energy in the unstructured state as derived using a linearly additive model and knowledge-based nucleobase/amino-acid affinities. Motivated by this, we predict gRNA/CP interaction sites for a comprehensive set of 1082 +ssRNA viruses. We validate our predictions by comparing them with site-resolved information on gRNA/CP interactions derived in SELEX and CLIP experiments for 10 different viruses. Finally, we show that in experimentally studied systems CPs frequently interact with autologous coding regions in gRNA, in agreement with both predicted interaction energies and a recent proposal that proteins in general tend to interact with own mRNAs, if unstructured. Our results define a self-consistent framework for understanding packaging in +ssRNA viruses and implicate interactions between unstructured gRNA and CPs in the process.

Coding From Binding? Molecular Interactions at the Heart of Translation

“…While there exists a rich literature on the so-called packaging signals (15,33,53,120), short regions inside viral genomes that interact with capsid or coat proteins (CPs) and initiate packaging, the complementarity hypothesis provides a simple answer: Viral CPs bind to the genomic RNA (gRNA) that encodes them because the rules of recognition are already built into the structure of the genetic code. We have recently analyzed the available information on the binding sites between viral gRNA and CPs coming from cryo-electron microscopy (cryo-EM), SELEX, and crosslinking-and-immunoprecipitation with sequencing (CLIP-seq) experiments (1). Notably, experimental data indicate widespread interactions between CPs and their coding regions in viral RNA: Out of 10 viruses for which data are available, only one did not show evidence of direct interactions of the CP with its own coding sequence (1).…”

“…We have recently analyzed the available information on the binding sites between viral gRNA and CPs coming from cryo-electron microscopy (cryo-EM), SELEX, and crosslinking-and-immunoprecipitation with sequencing (CLIP-seq) experiments (1). Notably, experimental data indicate widespread interactions between CPs and their coding regions in viral RNA: Out of 10 viruses for which data are available, only one did not show evidence of direct interactions of the CP with its own coding sequence (1). Moreover, the generalized complementarity hypothesis posits that proteins interact not only with their own mRNA CDS, but also with other RNA regions that are compositionally similar to it.…”