A research team led by Professor Zhu Bin from the School of Life Science and Technology at Huazhong University of Science and Technology (HUST), in collaboration with Professor Wang Longfei’s team at Wuhan University, has identified a long-missing regulatory mechanism controlling coronavirus nonstructural protein 15 (nsp15). The study, titled “Metal ions govern coronavirus endoribonuclease activity”, was published in Nucleic Acids Research on Jan 15.

Coronaviruses rely on 16 nonstructural proteins to replicate their RNA genomes. Among them, nsp15 is a uracil-specific endoribonuclease (EndoU) that plays a critical role in suppressing host interferon (IFN) responses by restricting the accumulation of viral double-stranded RNA (dsRNA) in the cytosol.

While nsp15 does not directly determine viral replication efficiency, it is essential for immune evasion. However, how its RNA cleavage activity is precisely regulated during different stages of the viral life cycle has remained unresolved for decades.

Building on their earlier discovery that nsp15 functions as a dsRNA-specific nicking endoribonuclease, the team addressed a key paradox: nsp15 activity must be fully suppressed during viral RNA replication to avoid genome degradation, yet rapidly activated after replication to eliminate residual dsRNA intermediates.

Through biochemical assays, structural analysis, and cryo-electron microscopy of SARS-CoV-2 nsp15/dsRNA complexes, the researchers discovered that cobalt (Co²⁺) and nickel (Ni²⁺) ions can enhance nsp15 RNA cleavage activity by up to two orders of magnitude – an exceptionally rare phenomenon among nucleases.

In contrast, zinc ions (Zn²⁺) were found to completely inhibit nsp15 activity and competitively block Co²⁺- and Ni²⁺-mediated activation. Structural and mutational analyses showed that metal ions bind near the nsp15 active site, where they modulate the enzyme’s allosteric regulation and dsRNA-binding affinity. These regulatory effects were observed across nsp15 proteins from multiple coronaviruses and were particularly pronounced in highly pathogenic strains, including SARS-CoV-2, without affecting related host nucleases.

The study proposes a metal ion-dependent regulatory model in which Zn²⁺ suppresses nsp15 during viral genome replication, ensuring replication fidelity, while subsequent replacement by Co²⁺ or Ni²⁺ activates nsp15 to efficiently degrade dsRNA intermediates and evade host immune surveillance. Disruption of this balance – through excessive activation or inhibition – would severely impair the coronavirus life cycle.

The findings identify nsp15 activity regulation as a critical balance point in coronavirus replication and immune evasion and reveal new therapeutic opportunities. Metal ions, their derivatives, metal ion metabolic pathways, regulatory factors, and the metal-binding sites of nsp15 may all serve as promising targets for the development of novel antiviral drugs.

Doctoral student Wang Xionglue from HUST and Doctor Li Jing from Wuhan University are co-first authors of the paper. HUST is the first author affiliation, with Wang Xionglue, Wang Longfei, and Zhu serving as corresponding authors.

Source: School of Life Science and Technology of HUST