Structural Diversity and Phylogenetic Distribution of Valyl tRNA-like Structures in Viruses

Abstract

Viruses commonly use specifically folded RNA elements that interact with both host and viral proteins to perform functions important for diverse viral processes. Examples are found at the 3′ termini of certain positive-sense ssRNA virus genomes where they partially mimic tRNAs, including being aminoacylated by host cell enzymes. Valine-accepting tRNA-like structures (TLS Val ) are an example that share some clear homology to canonical tRNAs but have several important structural differences. Although many examples of TLS Val have been identified, we lacked a full understanding of their structural diversity and phylogenetic distribution. To address this, we undertook an in-depth bioinformatic and biochemical investigation of these RNAs, guided by recent high-resolution structures of a TLS Val . We cataloged many new examples in plant-infecting viruses but also in unrelated insect-specific viruses. Using biochemical and structural approaches, we verified the secondary structure of representative TLS Val substrates and tested their ability to be valylated, finding structural heterogeneity within this class. In a few cases, large stem-loop structures are inserted within distinct variable regions located in an area of the TLS distal to known host cell factor binding sites. In addition, we identified one virus whose TLS has switched its anticodon away from valine; the implications of this remain unclear. These results refine our understanding of the structural and functional mechanistic details of tRNA mimicry and how this may be used in viral infection.Sherlock et al.

An Expanded Class of Histidine-Accepting Viral tRNA-like Structures

“…Specifically, the sequence conservation is high in the region that contains the acceptor stem analog PK1 and the T-arm analog (3′ region). The combined length of the T-arm combined with PK1 is always 11 base pairs, one base pair shorter than in the TLS Val class (Sherlock et al 2020).…”

“…Identifying new TLS His examples promised to reveal conserved regions required for achieving the proper structure, likely locations of protein interactions required for function, and variations such as the insertions found in the divergent members of the TLS Val and TLS Tyr (Sherlock et al 2020;Bonilla et al 2020). To identify additional putative TLS His RNAs that conform to the previously proposed secondary structure model, we performed homology-based searches using the program Infernal (Nawrocki and Eddy 2013).…”

“…The single TLS identified from Furovirus had a high E value of 0.019, making it an unlikely TLS His candidate; rather, it demonstrates features of the TLS Val class and was excluded from further analyses. Interestingly, the tymoviruses mostly contain TLS Val and most examples of TLS Val are within Tymoviridae with a few in Virgaviridae (Sherlock et al 2020). While we cannot propose a specific evolutionary history of these viral lineages, this distribution suggests exchange of TLS elements between viruses can occur, likely during coinfections by two distinct viruses.…”

“…Although structural modeling of the RNA provided insight into the possible three-dimensional fold of the TMV TLS (Rietveld et al 1984;Felden et al 1996), this model remains untested. Furthermore, only five TLS His sequences have been identified, which makes analysis of this class challenging compared to the TLS Val and TLS Tyr classes (Dreher 2010;Sherlock et al 2020;Bonilla et al 2020). Hence, although the TLS His class represents a novel form of tRNA mimicry that can provide insight into diverse ways this form of mimicry can be achieved and used, it is largely mysterious.…”

Cryo-EM of a viral RNA and RNA-protein complex reveals how structural dynamics and novel tRNA mimicry combine to hijack host machinery

“…Important examples of multifunctional viral RNA elements are the tRNA-like structures (TLSs) at the 3¢ ends of certain positive-strand RNA viral genomes (16,17). These elements were thought to be present only in plant-infecting viruses, but recent evidence confirms that they exist in animal-infecting viruses and that other examples likely remain to be discovered (18). TLSs were originally identified by their ability to drive aminoacylation of viral genomic 3¢ ends by host aminoacyl-tRNA synthetases (aaRSs) and were later found to interact with other tRNA-specific enzymes including CCA-nucleotidyltransferase (CCA-NTase) and translation elongation factor 1A (eEF1A) (16,19).…”