Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain

Abstract

Mayaro virus (MAYV) is a member of Togaviridae family, which also includes Chikungunya virus as a notorious member. MAYV recently emerged in urban areas of the Americas, and this emergence emphasized the current paucity of knowledge about its replication cycle. The macro domain (MD) of MAYV belongs to the N-terminal region of its non-structural protein 3, part of the replication complex. Here, we report the first structural and dynamical characterization of a previously unexplored Alphavirus MD investigated through high-resolution NMR spectroscopy, along with data on its ligand selectivity and binding properties. The structural analysis of MAYV MD reveals a typical "macro" (ββαββαβαβα) fold for this polypeptide, while NMR-driven interaction studies provide in-depth insights into MAYV MD-ligand adducts. NMR data in concert with thermodynamics and biochemical studies provide convincing experimental evidence for preferential binding of adenosine diphosphate ribose (ADP-r) and adenine-rich RNAs to MAYV MD, thus shedding light on the structure-function relationship of a previously unexplored viral MD. The emerging differences with any other related MD are expected to enlighten distinct functions.

Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites

“…7 A, B ). Recently, the macro domain of Mayaro virus also was found to bind with these adenosine-like nucleotides but not NAD by ITC and NMR approaches at 293 K 47 .…”

“…However, how the MERS-CoV macro domain interacts with NAD metabolites and ADPR moieties buried inside PAR is still unclear. In addition, some viral macro domains possess RNA-binding ability 25,47 . The existence of NAD-capping RNA has been discovered in prokaryotes, yeast, and eukaryotes [48][49][50][51] .…”

NMR study of macro domains (MDs) from betacoronavirus: backbone resonance assignments of SARS–CoV and MERS–CoV MDs in the free and the ADPr-bound state

“…These proteins have a high degree of similarity of secondary structure identity in comparison with SARS–CoV 2 MD and other viral MDs (i.e., MAYV and VEEV) (Tsika et al 2019 ; Makrynitsa et al 2019 ). The dihedral angles predicted by TALOS + for free SARS–CoV MD and MERS–CoV and their respective ADP-ribose bound forms are in excellent agreement with the dihedral angles found in the free (2ACF for SARS–CoV MD and 5HIH for MERS–CoV MD) and ADPr bound (2FAV for SARS–CoV MD and 5HOL for MERS–CoV MD) crystal structures (Cho et al 2016 ), implying that ligand binding does not alter the overall the secondary structure within the MDs.…”

A quantitative western blot technique using TMB: Comparison with the conventional technique

“…A detailed protocol of μayaro virus macro domain (MAYV MD) expression is described elsewhere [28, 29]. Briefly, 0.5 L of M9 media were inoculated using an LB preculture.…”