Initiation of translation in bacteria by a structured eukaryotic IRES RNA

Abstract

The central dogma of gene expression (DNA→RNA→protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive1,2. However, the core structures and conformational dynamics of ribosomes that are responsible for the steps of translation following initiation are ancient and conserved across the domains of life3,4. We asked whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here, we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 Å resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by tRNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence as an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.

Non-canonical Translation in Plant RNA Viruses

“…How the TLS interacts with the 5 ′ end to stimulate translation in the scanning-dependent manner is suggested by the crystal structure of the TYMV TLS. The TLS has a tRNA-like shape, but it uses a very different set of intramolecular interactions (Colussi et al, 2015). These interactions allow the TLS to switch conformations and to interact with the ribosome, docking within it to regulate the folding and unfolding state to permit dual functionality in viral translation and replication.…”

Viral internal ribosomal entry sites: four classes for one goal

“…To promote efficient translation initiation, IGR only require the small and large ribosomal subunits. Therefore, the CrPV IGR is active on ribosomes from various organisms such as yeast, rabbit, human, and even on prokaryotic 70S ribosomes although the translation mechanism used in the latter case is rather different . CrPV IGR contains three domains (or regions) named 1–3, each domain harboring an essential pseudoknot structure (PKI, PKII, and PKIII) (Figure ).…”

Signals across domains of life

“…The finding that a signal from an arthropod virus can function in bacteria questions this idea. Colussi et al 2 report the surprising finding that the dicistrovirus IRES can initiate protein synthesis in the bacterium Escherichia coli (a prokaryote). a, The authors constructed a messenger RNA that incorporates the IRES and introduced this to E. coli cells, where the IRES recruits the bacterial ribosome (the protein-synthesizing apparatus) to the mRNA.…”

“…Although the general steps of protein synthesis are evolutionarily conserved, the way in which ribosomes are recruited to an mRNA molecule differs depending on the specific phylogenetic domain 1 . In a paper published on Nature's website today, Colussi et al 2 reveal the surprising finding that a eukaryotic ribosomerecruiting signal is functional in prokaryotic bacteria, thereby challenging the prevailing dogma that prokaryotic and eukaryotic ribosome recruitment are mutually exclusive.…”