SARS-CoV2 Nsp1 is a metal-dependent DNA and RNA endonuclease

Structure-function mapping and mechanistic insights on the SARS CoV2 Nsp1

Non-structural protein 1 (Nsp1) is a key component of the infectious process caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), responsible for the COVID-19 pandemic. Our previous data demonstrated that Nsp1 can degrade both RNA and DNA in the absence of the ribosome, a process dependent on the metal ions Mn2+, Ca2+, or Mg2+ (Salgueiro et al., SARS-CoV2 Nsp1 is a metal-dependent DNA and RNA endonuclease. Biometals. 2024;37:1127-1146). The protein is composed of two structural domains: the N-terminal domain (NTD) and C-terminal domain (CTD), connected by a loop. To elucidate the function of each structural domain, we generated four truncated versions of Nsp1 containing either the NTD or the CTD. Our results indicate that the Nsp1SARS-CoV2 domains play distinct functional roles. Specifically, the NTD is involved in nucleotide binding and regulation, while the CTD acts as the catalytic domain. Moreover, a tyrosyl radical was detected during the nuclease activity, and an in-depth analysis of the different constructs suggested that Y136 could be involved in this process. Indeed, our results show that Y136F Nsp1 variant lacks DNA nuclease activity but retains its RNA nuclease activity. Furthermore, we observed that the CTD has a propensity to associate with hydrophobic environments, suggesting that it might associate with cell membranes. However, the cellular function of this association requires further investigation. This study sheds light on the functions of the individual domains of Nsp1, providing valuable insights into its mechanism of action in Coronaviruses.

The Unusual Role of Ribonuclease L in Innate Immunity

Ribonuclease L is an endonuclease that is activated as part of the dsRNA-driven innate immune response. Active RNase L cleaves pathogenic RNAs as a way to eliminate infections. However, there are additional and unexpected ways that RNase L causes changes in the host that promote an immune response and contribute to its role in host defense. Central to these unconventional mechanisms is the observation that RNase L also degrades the mRNA of the host. In turn, mRNA fragments that RNase L generates can be translated. This causes activation of a ribosome collision sensor that leads to downstream signaling and cell death. Additionally, the liberation of RNA binding proteins after RNA decay appears to affect gene expression. In this review, we discuss these and other recent advances that focus on novel and unusual ways RNase L contributes to innate immunity.

The emerging role of SARS-CoV-2 nonstructural protein 1 (nsp1) in epigenetic regulation of host gene expression

Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes widespread changes in epigenetic modifications and chromatin architecture in the host cell. Recent evidence suggests that SARS-CoV-2 nonstructural protein 1 (nsp1) plays an important role in driving these changes. Previously thought to be primarily involved in host translation shutoff and cellular mRNA degradation, nsp1 has now been shown to be a truly multifunctional protein that affects host gene expression at multiple levels. The functions of nsp1 are surprisingly diverse and include not only the downregulation of cellular mRNA translation and stability, but also the inhibition of mRNA export from the nucleus, the suppression of host immune signaling, and, most recently, the epigenetic regulation of host gene expression. In this review, we first summarize the current knowledge on SARS-CoV-2-induced changes in epigenetic modifications and chromatin structure. We then focus on the role of nsp1 in epigenetic reprogramming, with a particular emphasis on the silencing of immune-related genes. Finally, we discuss potential molecular mechanisms underlying the epigenetic functions of nsp1 based on evidence from SARS-CoV-2 interactome studies.