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. 2014 Dec;88(24):14222-31.
doi: 10.1128/JVI.01763-14. Epub 2014 Oct 1.

The 2'-5'-oligoadenylate synthetase 3 enzyme potently synthesizes the 2'-5'-oligoadenylates required for RNase L activation

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The 2'-5'-oligoadenylate synthetase 3 enzyme potently synthesizes the 2'-5'-oligoadenylates required for RNase L activation

Mikkel Søes Ibsen et al. J Virol. 2014 Dec.

Abstract

The members of the oligoadenylate synthetase (OAS) family of proteins are antiviral restriction factors that target a wide range of RNA and DNA viruses. They function as intracellular double-stranded RNA (dsRNA) sensors that, upon binding to dsRNA, undergo a conformational change and are activated to synthesize 2'-5'-linked oligoadenylates (2-5As). 2-5As of sufficient length act as second messengers to activate RNase L and thereby restrict viral replication. We expressed human OAS3 using the baculovirus system and purified it to homogeneity. We show that recombinant OAS3 is activated at a substantially lower concentration of dsRNA than OAS1, making it a potent in vivo sensor of dsRNA. Moreover, we find that OAS3 synthesizes considerably longer 2-5As than previously reported, and that OAS3 can activate RNase L intracellularly. The combined high affinity for dsRNA and the capability to produce 2-5As of sufficient length to activate RNase L suggests that OAS3 is a potent activator of RNase L. In addition, we provide experimental evidence to support one active site of OAS3 located in the C-terminal OAS domain and generate a low-resolution structure of OAS3 using SAXS.

Importance: We are the first to purify the OAS3 enzyme to homogeneity, which allowed us to characterize the mechanism utilized by OAS3 and identify the active site. We provide compelling evidence that OAS3 can produce 2'-5'-oligoadenylates of sufficient length to activate RNase L. This is contrary to what is described in the current literature but agrees with recent in vivo data showing that OAS3 harbors an antiviral activity requiring RNase L. Thus, our work redefines our understanding of the biological role of OAS3. Furthermore, we used a combination of mutagenesis and small-angle X-ray scattering to describe the active site and low-resolution structure of OAS3.

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Figures

FIG 1
FIG 1
Alignment of pOAS1, hOAS1, and OAS domains 1, 2, and 3 of OAS3 and purification of recombinant OAS3. (A) An alignment displaying residues conserved between hOAS1, pOAS1, and the three OAS domains of OAS3, denoted D1, D2, and D3, respectively. The numbers of amino acids spanned by each OAS domain in the full-length OAS3 are given in parentheses. Asterisks denote the three aspartic acid residues constituting the active sites of pOAS1 and hOAS1. Daggers denote residues crucial for dsRNA binding. A plus sign denotes the conserved lysine at position 212 in pOAS1. (B) A total of 1.5 mg OAS3 was loaded on a HiLoad 16/60 Superdex 200 column. OAS3 eluted in a single peak from the HiLoad 16/60 Superdex 200 column, and fractions D15 to E9 were collected. The chromatograms of the molecular mass markers used to estimate the mass of OAS3 is shown. (C) Coomassie-stained 8% SDS-PAGE. Load, sample loaded onto the HiLoad 16/60 Superdex 200 column; D15 to E9, fractions D15 to E9; Pool, pooled peak fractions; Concentrated, concentrated pool of the peak fractions; Marker, a low-molecular-mass marker (in kDa); pOAS1, the purified pOAS1.
FIG 2
FIG 2
Determination of the linear enzymatic rate and sensitivity toward dsRNA for pOAS1 and OAS3. (A) Enzymatic activities were investigated for pOAS1 and OAS3 and plotted against the protein concentration. The enzymatic rate is displayed as the synthesis of 2-5A in nmol per min. The cutouts show an enlarged section of the linear interval of enzymatic rates with the best linear regression. (B) Sensitivity toward dsRNA was investigated using fixed concentrations of 2 nM OAS3 (circles) and 6 nM pOAS1 (squares) plotted against increasing amounts of poly(I·C). The experimental data were analyzed by nonlinear regression using the model indicated in Materials and Methods.
FIG 3
FIG 3
Lengths of 2-5As synthesized by OAS3 and pOAS1 and their capability in activating RNase L. (A) Radiogram of a 20% PAGE showing the lengths of 2-5As synthesized by OAS3 and pOAS1 at various levels of enzymatic activity. Enzymatic activity levels are displayed as synthesized 2-5A in nmol per min for each lane. ATP and 2-5As of various lengths are depicted. The concentration of pOAS1 in the outermost left lane is 48 nM. The concentration of pOAS1, from left to right, is 2.4 nM, 3.6 nM, 4.8 nM, and 6 nM. The concentration of OAS3, from left to right, is 0.8 nM, 1.2 nM, 1.6 nM, and 2 nM. The OAS proteins were activated with 100 μg/ml poly(I·C) for 1 h. (B) Quantification of the 2-5A species synthesized at similar enzymatic activity for OAS3 (0.013 nmol/min) and pOAS1 (0.015 nmol/min). (C) RNase L activity was determined by assaying the integrity of 28S and 18S rRNA. Flp-In T-REx 293 cells stably transfected with hOAS1-FLAG or OAS3-FLAG were either mock transfected or transfected with poly(I·C), and cellular RNA extracts were separated using the Experion HighSens RNA analysis kit. Comparable expression levels of hOAS1-FLAG and OAS3-FLAG were confirmed by Western blot analysis on cell lysates using antibodies against FLAG and GAPDH.
FIG 4
FIG 4
Mapping crucial amino acids for enzymatic activity in OAS3. (A) TLC showing the activity of 2 nM OAS3 WT, 2 nM OAS3 WT without (w/o) poly(I·C), ∼20 nM D816A/D818A, and ∼5 nM R844X. The OAS3 WT was purified to homogeneity, while D816A/D818A and R844X were purified by one-step cation chromatography. ATP and 2-5A species are indicated. The activity is indicated under each lane by a plus sign for active or a minus sign for inactive (less than 1% activity compared to the wild type). (B) A Western blot confirming the presence of OAS3 WT, D816A/D818A, and R844X assessed for activity as described for panel A. (C) TLC showing the activity of homogenous OAS3 and several immunoprecipitated mutants. ATP and 2-5A species are indicated. The activity is indicated under each lane by a plus sign for active or a minus sign for inactive (less than 1% activity compared to the wild type). (D) A Western blot confirming the presence of the immunoprecipitated OAS3 mutants.
FIG 5
FIG 5
Overview, analysis, and modeling of SAXS data of OAS3. (A) Experimental scattering from OAS3 (circles) and theoretical scattering curves of ab initio modeling by DAMMIF (continuous orange line) and rigid-body modeling by SASREF (continuous red line) and Bunch (continuous blue line). The inset shows the Guinier region. (B) P(r) function for OAS3 computed from scattering patterns using GNOM. (C) Radius of gyration distribution of initial ensemble pool (purple line) and selected structures (black line) using EOM. (D) Docking of the rigid-body model obtained from Bunch to the representative DAMMIF-derived ab initio model shape envelope. (E) Docking of the rigid-body model obtained by SASREF to the representative DAMMI-derived ab initio model envelope.

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