The SAMHD1 Virolog in Mimiviridae as a Defense against Virophages

Sterile α motif and HD domain-containing protein (SAMHD1) is the only deoxyribonucleoside

triphosphohydrolase in humans to break down dNTPs into the deoxy-bases and triphosphates to

regulate dNTP molecular levels in a nucleotide- and metal-dependent mechanism. SAMHD1 plays

critical roles in antiviral defense, cancer biology, and cell cycle progression. Therefore, SAMHD1

is a crucial therapeutic target for viral restriction and cancer treatment. Human SAMHD1 employs

a strict allosteric regulation to oligomerize into active tetramers upon nucleotide binding. We

carried out bioinformatic analyses that demonstrated the unexpected occurrence of SAMHD1 in

giant viruses (Mimiviridae family), which are comparable to bacteria in size and genome

complexity but also become infected by phages. Previous studies identified a defense system in

Mimivirus to help protect against virophages. Based on this, we hypothesize that viral SAMHD1s

play an alternative antiviral strategy, similar to mammals, to deplete dNTP levels and prevent

virophage replication. We aim to investigate the diversity and evolutions of SAMHD1 in giant

viruses utilizing bioinformatic tools and uncover details of the metallocofactor and allosteric

activation of Kv SAMHD1. We found that Mimiviridae SAMHD1 sequences cluster based on

genus, and in the phylogenetic tree, sequences are segregated into two major branches mostly

based on the environmental niches of their hosts. We selected SAMHD1 from Klosneuvirus KNV1

(Kv SAMHD1) and Acanthamoeba polyphaga mimivirus (Ap SAMHD1) orthologs for further

study. Like Hs SAMHD1, Kv SAMHD1 harbors a dinuclear metal center at the active site. The

mutation of a conserved histidine residue at the active site disrupts the coordination of the second

metal ion and abolishes the enzymatic activity. We also discovered that allosteric site 1 is essential

for the allosteric activation of Kv SAMHD1, while allosteric site 2 is not critical for activity but

regulates the allosteric inhibition by guanosine-based nucleotides. In summary, Kv SAMHD1

shares core mechanistic features with Hs SAMHD1, albeit with less strict allosteric regulation.

Our work sheds light on elucidating the activity and allosteric regulation of viral SAMHD1s and

proposing that SAMHD1 acts as an auxiliary virophage defense system in this family of viruses.