Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase

Zhu, Chunfeng; Gao, Wenying; Zhao, Ke; Qin, Xinghu; Zhang, Yinjie; Peng, Xin; Zhang, Lei; Dong, Yuhui; Zhang, Wenyan; Li, Peng; Wei, Wei; Gong, Yong; Yu, Xiao Fang

doi:10.1038/ncomms3722

Cited by 105 publications

(188 citation statements)

References 48 publications

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“…30 Zhu et al also found that dGTP-triggered tetramer formation of SAMHD1 is important for dNTP depletion and SAMHD1-mediated inhibition of LINE-1 transposition. 35 Results from our group confirmed the restriction of LINE-1 by SAMHD1 and also suggested an alternative mechanism of action. 29 The first key observation of our study is that SAMHD1 expression enhances the localization of LINE-1 RNP into cytoplasmic stress granules.…”

supporting

confidence: 74%

Stress out the LINEs

Liang

Guo

2015

Mobile Genetic Elements

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Occupying 17% of human genome, the mobile long interspersed element 1 (LINE-1 or L1) continues to modulate the landscape of our genome by inserting into new loci and, as a result, causing sporadic diseases. It is not surprising that human cells have evolved a battery of mechanisms to control and limit the activity of LINE-1. Our recent study unravels such a mechanism that is imposed by the stress granule pathway. This mechanism functions by sequestering the LINE-1 RNA-protein complex within the cytoplasmic stress granules and thus inhibiting the nuclear import of LINE-1 RNA and its subsequent reverse transcription and integration into cellular DNA. Conditions that promote stress granule formation, such as expression of the SAMHD1 protein, further reduce LINE-1 retrotransposition.KEYWORDS host restriction; LINE-1; SAMHD1; stress granule; retrotransposition Approximately 45% of human genome has been derived from transposable elements. 1 These include DNA transposons, long terminal repeat (LTR) retrotransposons (also called endogenous retroviruses), and non-LTR retrotransposons. Long interspersed element 1 (LINE-1) belongs to non-LTR retrotransposons and comprises »17% of human genome. 1 Compared to the other transposons that have mostly become inactive, approximately 100 copies of LINE-1 are still active. 2 Retrotransposition of these LINE-1s is associated with nearly 100 human diseases. 3 LINE-1 encodes two proteins called ORF1 and ORF2. ORF1 is an RNA-binding protein and associates with LINE-1 RNA. [4][5][6][7] ORF2 is an enzyme that has endonuclease and reverse transcriptase activities. 8,9 ORF1, ORF2 and LINE-1 RNA together form an RNP complex that needs to enter the nucleus where LINE-1 RNA is reverse transcribed and integrated into cellular DNA. [10][11][12] Humans have survived LINE-1 invasion and amplification over millions of years thanks to the evolution of a battery of mechanisms that control LINE-1 activity. Some of these mechanisms begin to be unraveled as a result of intensive research in the past couple of decades. One such mechanism is suppression of LINE-1 transcription by methylating LINE-1 DNA. [13][14][15] In support of this mechanism, knockdown or knockout genes that are involved in DNA methylation leads to increase in the activities of LINE-1 and other transposons. 13 In the course of embryonic development there are a couple of waves of DNA demythlyation. DNA demethylation inevitably activates LINE-1 RNA expression. 16 To control retrotransposition of LINE-1 and other transposable elements, primordial germ cells (PGCs) are equipped with the piRNA machinery to inactivate LINE-1 so as to protect the integrity of genome DNA in germ cells. 17,18 Recent studies have revealed that cells have a rich layer of mechanisms that check LINE-1 activity at the post-transcription stage. Many of these mechanisms involve cellular factors that have been shown to restrict viral infections. One example is the APOBEC family of proteins that are cytidine deaminase and inactivate viral or LINE-1 DNA by intro...

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supporting

confidence: 74%

Stress out the LINEs

Liang

Guo

2015

Mobile Genetic Elements

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“…The majority of the mutations were predicted to be deleterious by using in silico analysis: 87% were predicted to be damaging by at least one of four computational tools (Grantham, SIFT, PolyPhen2, and CADD), 72% by two or more tools, and 50% by three tools (Table S1) (37)(38)(39)(40). Four of the mutations (R145, D207, R366, and R451) are located at amino acid residues that have been reported to have functional significance in in vitro studies (27,41,42).…”

Section: Samhd1mentioning

confidence: 99%

Heterozygous colon cancer-associated mutations of SAMHD1 have functional significance

Rentoft

Lindell

Tran

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

102

155

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Even small variations in dNTP concentrations decrease DNA replication fidelity, and this observation prompted us to analyze genomic cancer data for mutations in enzymes involved in dNTP metabolism. We found that sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), a deoxyribonucleoside triphosphate triphosphohydrolase that decreases dNTP pools, is frequently mutated in colon cancers, that these mutations negatively affect SAMHD1 activity, and that several SAMHD1 mutations are found in tumors with defective mismatch repair. We show that minor changes in dNTP pools in combination with inactivated mismatch repair dramatically increase mutation rates. Determination of dNTP pools in mouse embryos revealed that inactivation of one SAMHD1 allele is sufficient to elevate dNTP pools. These observations suggest that heterozygous cancer-associated SAMHD1 mutations increase mutation rates in cancer cells.

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“…Unlike GTP, dGTP can activate its own hydrolysis and is known to serve as a transactivator for hydrolysis of other substrate dNTPs at low concentrations (17). However, it should also act as an inhibitor of dNTP hydrolysis at higher concentrations (20,22). To explore these properties of dGTP, we determined the concentration dependence of the initial rates of dGTP hydrolysis at an SAMHD1 concentration of 0.2 μM and variable concentrations of dGTP in the range of 5 μM to 5 mM ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The structural basis for the increased dimer affinity apparently results from docking of the guanine base of GTP into the highly specific guanine binding site on one monomer and the formation of electrostatic interactions between its triphosphate group and the second monomer of the dimer (Fig. S9 A and B) (22). Hence, GTP serves as a nucleotide tether to bring together monomers.…”

Section: Discussionmentioning

confidence: 99%

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GTP activator and dNTP substrates of HIV-1 restriction factor SAMHD1 generate a long-lived activated state

Hansen

Seamon

Cravens

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

187

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The HIV-1 restriction factor sterile α-motif/histidine-aspartate domain-containing protein 1 (SAMHD1) is a tetrameric protein that catalyzes the hydrolysis of all dNTPs to the deoxynucleoside and tripolyphosphate, which effectively depletes the dNTP substrates of HIV reverse transcriptase. Here, we establish that SAMHD1 is activated by GTP binding to guanine-specific activator sites (A1) as well as coactivation by substrate dNTP binding to a distinct set of nonspecific activator sites (A2). Combined activation by GTP and dNTPs results in a long-lived tetrameric form of SAMHD1 that persists for hours, even after activating nucleotides are withdrawn from the solution. These results reveal an ordered model for assembly of SAMHD1 tetramer from its inactive monomer and dimer forms, where GTP binding to the A1 sites generates dimer and dNTP binding to the A2 and catalytic sites generates active tetramer. Thus, cellular regulation of active SAMHD1 is not determined by GTP alone but instead, the levels of all dNTPs and the generation of a persistent tetramer that is not in equilibrium with free activators. The significance of the long-lived activated state is that SAMHD1 can remain active long after dNTP pools have been reduced to a level that would lead to inactivation. This property would be important in resting CD4 + T cells, where dNTP pools are reduced to nanomolar levels to restrict infection by HIV-1. dNTP induced oligomerization | enzyme catalysis | innate immunity T he steady-state composition and concentration of deoxynucleotide triphosphate pools in mammalian cells are highly regulated because of the mutagenic consequences of dNTP imbalances in dividing cells (1, 2) as well as the important antiviral effects of dNTP pool depletion in quiescent cells (3,4). In all cell types, the ultimate pool balance is determined by dNTP-dependent regulatory pathways that affect the activities of enzymes involved in both synthesis and degradation of dNTPs (5-7). The most important highly up-regulated synthetic enzyme during S phase of dividing cells is the R1/R2 isoform of ribonucleotide triphosphate reductase, which ensures that dNTP precursors are plentiful for DNA synthesis (8). However, in quiescent cells of the immune system (resting CD4 + T cells, macrophages, and dendritic cells), where dNTP pools are ∼10-fold lower than dividing cells, the ultimate pool levels are likely determined by a balance between the activities of the R1/p53R2 isoform of ribonucleotide triphosphate reductase and the degradative dNTP triphosphohydrolase sterile α-motif/histidineaspartate domain-containing protein 1 (SAMHD1) (9). The highly dynamic nature of dNTP pools demands finely tuned mechanisms for feedback regulation of these enzymes by dNTPs as well as coarse regulatory mechanisms (posttranslational modifications, transcriptional regulation, and proteasomal targeting) that serve to turn these activities on and off at appropriate stages of the cell cycle and in specific cell types (10, 11). dNTP triphosphohydrolase enzymes, such as SAMHD1,...

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Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase

Cited by 105 publications

References 48 publications

Stress out the LINEs

Stress out the LINEs

Heterozygous colon cancer-associated mutations of SAMHD1 have functional significance

GTP activator and dNTP substrates of HIV-1 restriction factor SAMHD1 generate a long-lived activated state

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