Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification

Abstract

SAMHD1 impedes infection of myeloid cells and resting T lymphocytes by retroviruses, and the enzymatic activity of the protein—dephosphorylation of deoxynucleotide triphosphates (dNTPs)—implicates enzymatic dNTP depletion in innate antiviral immunity. Here we show that the allosteric binding sites of the enzyme are plastic and can accommodate oligonucleotides in place of the allosteric activators, GTP and dNTP. SAMHD1 displays a preference for oligonucleotides containing phosphorothioate bonds in the Rp configuration located 3’ to G nucleotides (GpsN), the modification pattern that occurs in a mechanism of antiviral defense in prokaryotes. In the presence of GTP and dNTPs, binding of GpsN-containing oligonucleotides promotes formation of a distinct tetramer with mixed occupancy of the allosteric sites. Mutations that impair formation of the mixed-occupancy complex abolish the antiretroviral activity of SAMHD1, but not its ability to deplete dNTPs. The findings link nucleic acid binding to the antiretroviral activity of SAMHD1, shed light on the immunomodulatory effects of synthetic phosphorothioated oligonucleotides and raise questions about the role of nucleic acid phosphorothioation in human innate immunity.

cGAS/STING-DEPENDENT SENSING OF ENDOGENOUS RNA

“…In addition to these established functions of SAMHD1, one group reported an exoribonuclease activity of the protein (Choi et al, 2015; Ryoo et al, 2014, 2016). However, RNAse activity of SAMHD1 was not reproduced by other studies (Seamon et al, 2015; Antonucci et al, 2016; Bloch et al, 2017; Yu et al, 2021), including our own (Wittmann et al, 2015). Therefore, if and how SAMHD1 regulates RNA metabolism in cells, remains to be fully elucidated.…”

Structural and functional characterization explains loss of dNTPase activity of the cancer-specific R366C/H mutant SAMHD1 proteins

“…R366C/H mutants showed reduced nucleic acid binding activity: SAMHD1 has been shown to bind nucleic acids, which seems to play a role in HIV-1 restriction (27,28). We investigated whether the R366C/H mutations induced changes in nucleic acid binding using a fluorescent polarization assay.…”

“…R366C and R366H showed J o u r n a l P r e -p r o o f reduced nucleic acid binding affinity in this assay (Figure 6E). It is possible that this is a consequence of overlap between the dNTPase catalytic site and the nucleic acid binding domain (28). However, it is unclear at present that this altered nucleic acid binding activity has a connection to cancer cell phenotypes.…”

“…SAMHD1 also blocks long terminal repeat (LTR)–mediated HIV-1 transcription ( 25 ), a process known to require NF-κB ( 26 ). Finally, SAMHD1 binds single-stranded nucleic acids, primarily when in the monomeric form ( 27 , 28 ).…”

Pathology and Anticatalysis treatment of exacerbated COVID-19

“…The binding sites are plastic, and the allosteric binding sites can adjust oligonucleotides in place of the allosteric activators GTP and dNTP. The binding of G-nucleotide-containing oligonucleotides in the presence of GTP and dNTPs promotes the formation of a specific tetramer with mixed occupancy of the allosteric sites responsible for the antiretroviral activity of SAMHD1 (59). This shows the immunomodulatory effects of synthetic phosphorothioate oligonucleotides on ACE2 and NRP1's interactions with SARS-CoV-2.…”