viruses Review SAMHD1 . and Viral Ways around It Janina Deutschmann and Thomas Gramberg * Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany; [email protected] * Correspondence: [email protected] Abstract: The SAM and HD domain-containing protein 1 (SAMHD1) is a dNTP triphosphohydrolase that plays a crucial role for a variety of different cellular functions. Besides balancing intracellular dNTP concentrations, facilitating DNA damage repair, and dampening excessive immune responses, SAMHD1 has been shown to act as a major restriction factor against various virus species. In addition to its well-described activity against retroviruses such as HIV-1, SAMHD1 has been identified to reduce the infectivity of different DNA viruses such as the herpesviruses CMV and EBV, the poxvirus VACV, or the hepadnavirus HBV. While some viruses are efficiently restricted by SAMHD1, others have developed evasion mechanisms that antagonize the antiviral activity of SAMHD1. Within this review, we summarize the different cellular functions of SAMHD1 and highlight the countermeasures viruses have evolved to neutralize the restriction factor SAMHD1. Keywords: SAMHD1; restriction factor; viral antagonism; HIV; herpesviruses; viral kinases; Vpx; dNTP hydrolase; viral interference 1. The dNTPase SAMHD1 The SAM and HD domain-containing protein 1 (SAMHD1) is a ubiquitously expressed Citation: Deutschmann, J.; deoxynucleotide triphosphohydrolase (dNTPase) of 626 amino acids (Figure1). In general, Gramberg, T. SAMHD1 . and Viral sterile alpha motif (SAM) domains have been shown to mediate protein–protein interaction Ways around It. Viruses 2021, 13, 395. or nucleic acid binding; however, its function in SAMHD1 is still unclear. The enzymatically https://doi.org/10.3390/v13030395 active HD domain, defined by two pairs of histidine and aspartate residues in its active center, on the other hand is essential for retroviral restriction and tetramerization of the Academic Editor: Sébastien Nisole protein [1–3]. Although nuclear localization of SAMHD1 is mediated through an N- terminal nuclear localization signal (NLS), neither the antiviral activity nor the dNTPase Received: 12 February 2021 function of SAMHD1 seem to be influenced by its localization [4–6]. Oligomerization Accepted: 25 February 2021 of SAMHD1 is required for its catalytic dNTPase activity and is induced upon cofactor Published: 2 March 2021 binding at two allosteric sites within the protein [7–12]. At allosteric site 1, dGTP or GTP binding leads to SAMHD1 dimerization, while the subsequent binding of any dNTP to Publisher’s Note: MDPI stays neutral allosteric site 2 induces tetramer formation [1,13,14]. with regard to jurisdictional claims in SAMHD1 converts dNTPs into deoxynucleosides (dN) and inorganic triphosphates published maps and institutional affil- (PPPi) and thereby counteracts the de novo dNTP synthesis, primarily conducted by iations. ribonucleotide reductase (RNR) and cellular deoxynucleoside kinases, which are mainly active during the S phase of the cell cycle [15–18]. RNR catalyzes the formation of dNTPs from ribonucleotides, while deoxynucleoside kinases, such as thymidine kinases (TK), add phosphates to nucleosides to form deoxynucleoside triphosphates [19,20]. This ensures Copyright: © 2021 by the authors. a highly balanced dNTP pool during the progression of the cell cycle, with a sufficient Licensee MDPI, Basel, Switzerland. supply of dNTPs for efficient genome replication in dividing cells and limited levels of This article is an open access article dNTPs in nondividing and resting cells [1,14,21]. The cyclin-dependent kinases (CDK) 1 distributed under the terms and and 2, together with cyclin A, phosphorylate SAMHD1 at the threonine residue 592 (T592) conditions of the Creative Commons Attribution (CC BY) license (https:// during the S and G2 phase of the cell cycle [22,23]. SAMHD1 is dephosphorylated during α creativecommons.org/licenses/by/ the M/G1 phase transition by the PP2A-B55 phosphatase and is dephosphorylated in the 4.0/). G0 and G1 phases [24]. Thus, SAMHD1 is phosphorylated during the progression of the Viruses 2021, 13, 395. https://doi.org/10.3390/v13030395 https://www.mdpi.com/journal/viruses Viruses 2021, 13, x FOR PEER REVIEW 2 of 16 Viruses 2021, 13, 395 2 of 16 dephosphorylated during the M/G1 phase transition by the PP2A-B55α phosphatase and is dephosphorylated in the G0 and G1 phases [24]. Thus, SAMHD1 is phosphorylated cellduring cycle, the which progression correlates of the with cell the cycle, demand which of cellularcorrelates dNTPs. with However,the demand at thisof cellular pointit isdNTPs. unclear However, whether at the this phosphorylation point it is unclear at T592whether indeed the regulatesphosphorylation the dNTPase at T592 activity indeed of SAMHD1regulates the [25 –dNTPase28]. activity of SAMHD1 [25–28]. FigureFigure 1. 1.Cellular Cellular functionsfunctions ofof SAMHD1.SAMHD1. The dNTP triphosphohydrolase SAMHD1 SAMHD1 is is an an important important regulator regulator of of dNTP dNTP levels. A correct balance of the cellular dNTP pool has been shown to be important for cell-cycle control and genome levels. A correct balance of the cellular dNTP pool has been shown to be important for cell-cycle control and genome integrity. SAMHD1 is a mediator of double-strand break (DSB) repair and ensures the progression of DNA replication. integrity. SAMHD1 is a mediator of double-strand break (DSB) repair and ensures the progression of DNA replication. Mutations in the SAMHD1 gene have been identified in various types of cancer. Furthermore, SAMHD1 potently restricts Mutationsviral infectivity in the SAMHD1of retrovirusesgene haveand DNA been identifiedviruses, and in variousblocks the types activity of cancer. of endogenous Furthermore, retroelements. SAMHD1 potently Mutations restricts in viralSAMHD1 infectivity are correlated of retroviruses with autoimmune and DNA viruses,diseases andsuch blocksas Aicardi–Goutières the activity of syndrome, endogenous resulting retroelements. in elevated Mutations type I IFN in SAMHD1levels. SAMHD1are correlated also impairs with autoimmune the innate immune diseases sensing such asof Aicardi–Goutiviral infectionsè resby interfering syndrome, with resulting cGAS/STING in elevated nucleic type acid I IFN levels.recognition SAMHD1 and NF alsoκB/IRF impairs signaling the innate pathways. immune sensing of viral infections by interfering with cGAS/STING nucleic acid recognition and NFκB/IRF signaling pathways. 2. DNA Replication and DNA Damage Repair 2. DNA Replication and DNA Damage Repair By degrading cellular dNTPs, SAMHD1 is a major regulator of nucleotide homeostasis.By degrading A highly cellular balanced dNTPs, dNTP SAMHD1 pool is aessential major regulator for genomic of nucleotide integrity, homeostasis. including Aproper highly DNA balanced replication dNTP and pool efficient is essential repair for of genomicDNA breaks. integrity, An imbalance including can proper lead DNAto a replicationderegulated and cell-cycle efficient progression repair of DNAand therefore breaks. Aninduce imbalance replication can leadstress, to awhich deregulated might cell-cycleeventually progression result in the andaccumulation therefore induceof genomic replication mutations stress, [29,30]. which During might host eventually genome resultreplication, in the SAMHD1 accumulation was offound genomic to be mutations recruited [ 29to, 30replication]. During foci host to genome regulate replica- the tion,progression SAMHD1 of the was replication found to fork. be recruited Here, SAMHD1 to replication activates foci the to 3′ regulate-5′-exonuclease the progression MRE11, 0 0 ofthereby the replication promoting fork. the Here, MRE11-mediated SAMHD1 activates degradation the 3 -5 of-exonuclease nascent DNA MRE11, at stalled thereby promotingreplication theforks, MRE11-mediated which has been degradationsuggested to ofprevent nascent the DNA induction at stalled of type replication I interferons forks, which(IFN) through has been the suggested aberrant toaccumulation prevent the of induction single-stranded of type DNA I interferons (ssDNA). (IFN) In addition, through thestimulation aberrant of accumulation MRE11 by SAMHD1 of single-stranded leads to DNAactivation (ssDNA). of the In ATR-CHK1 addition, stimulation checkpoint, of MRE11resulting by in SAMHD1 restart and leads progression to activation of stalled of the replication ATR-CHK1 forks checkpoint, [31]. resulting in restart and progressionSAMHD1 has of stalledalso been replication described forks to [31be]. important for DNA damage repair by promotingSAMHD1 homologous has also beenrecombination described (HR) to be [32]. important SAMHD1 for was DNA identified damage to repair localize by pro-to motingDNA double-strand homologous recombinationbreaks (DSBs) (HR)and [to32 ].recruit SAMHD1 members was identifiedof the DSB to localizerepair (DSBR) to DNA double-strandmachinery [32,33]. breaks It directly (DSBs) binds and to to recruit the C-terminal members binding of the DSBprotein repair interacting (DSBR) protein machin- ery(CtIP), [32 ,leading33]. It directly to its recruitment binds to the to C-terminalDSBs and consequently binding protein to the interacting activation protein of MRE11 (CtIP), as leadingpart of tothe its MRE11-Rad50-NBS1 recruitment to DSBs (MRN) and consequently DSBR complex, to the which activation is responsible of MRE11 asfor part the of theresection MRE11-Rad50-NBS1