Biochemical and Phylogenetic Characterization of the dUTPase from the Archaeal Virus SIRV

The derived amino acid sequence from a 474-base pair open reading frame in the genome of the Sulfolobus islandicus rod-shaped virus SIRV shows striking similarity to bacterial dCTP deaminases and to dUTPases from eukaryotes, bacteria, Poxviridae, and Retroviridae. The putative gene was expressed in Escherichia coli, and dUTPase activity of the recombinant enzyme was demonstrated by hydrolysis of dUTP to dUMP. Deamination of dCTP by the enzyme was not detected. Phylogenetic analysis based on amino acid sequences of the characterized enzyme and its homologues showed that the dUTPase-encoding dut genes and the dCTP deaminase-encoding dcd genes constitute a paralogous gene family. This report is the first identification and functional characterization of an archaeal dUTPase and the first phylogeny derived for the dcd-dut gene family. The derived amino acid sequence from a 474-base pair open reading frame in the genome of the Sulfolobus islandicus rod-shaped virus SIRV shows striking similarity to bacterial dCTP deaminases and to dUTPases from eukaryotes, bacteria, Poxviridae, and Retroviridae. The putative gene was expressed in Escherichia coli, and dUTPase activity of the recombinant enzyme was demonstrated by hydrolysis of dUTP to dUMP. Deamination of dCTP by the enzyme was not detected. Phylogenetic analysis based on amino acid sequences of the characterized enzyme and its homologues showed that the dUTPase-encoding dut genes and the dCTP deaminase-encoding dcd genes constitute a paralogous gene family. This report is the first identification and functional characterization of an archaeal dUTPase and the first phylogeny derived for the dcd-dut gene family. Little is known about the biosynthesis of nucleic acid precursors in archaea. It has been demonstrated that the extremely thermophilic archaeon Sulfolobus acidocaldarius is unable to utilize exogenous thymidine for biosynthesis of nucleic acids, presumably due to a lack of thymidine kinase (1Muskhelishvili G. Karseladze M. Prangishvili D. Biochemistry (Engl. Transl. Biokhimiya). 1990; 55: 517-524Google Scholar). Thus, the de novo pathway must be the only supplier of thymidine nucleotides in Sulfolobus. Generally, the immediate thymidine nucleotide precursor in the endogenous de novo synthesis is dUMP. Three pathways for dUMP synthesis are known: (i) deamination of dCTP to dUTP by dCTP deaminase (2′-deoxycytidine-5′-triphosphate aminohydrolase, EC3.5.4.13) and successive hydrolysis of dUTP to dUMP by dUTPase (2′-deoxyuridine 5′-triphosphatase, EC 3.6.1.23); (ii) deamination of dCMP to dUMP by dCMP deaminase (2′-deoxycytidine-monophosphate aminohydrolase, EC 3.5.4.12); and (iii) reduction of UDP or UTP to dUDP or dUTP, respectively, by ribonucleotide reductases followed by hydrolysis of dUTP to dUMP by dUTPase. The conversion of dUDP to dUMP is most probably done via phosphorylation to dUTP. In bacteria, the latter pathway contributes much less to dUMP synthesis than the pathways through deamination of deoxycytidine nucleotides (2O'Donovan G.A. Molineux M. Kohyiama M. DNA Synthesis. Plenum Press, New York1978: 209-232Google Scholar). In higher organisms and in certain bacteria as well as in T-even phage-infected Escherichia coli cells, the deamination occurs at the monophosphate level, whereas in most enterobacteria, it occurs at the triphosphate level (3Beck C.F. Eisenhardt A.R. Neuhard J. J. Biol. Chem. 1975; 250: 609-616Abstract Full Text PDF PubMed Google Scholar). Only one enzyme involved in the de novo pathway of thymidylate biosynthesis has recently been detected in Sulfolobus cells, thymidylate synthetase (4Nyce G.W. White R.H. J. Bacteriol. 1996; 178: 914-916Crossref PubMed Google Scholar), the ubiquitous enzyme that catalyzes the conversion of dUMP to dTMP. In the course of sequencing the genome of the Sulfolobus islandicus rod-shaped virus SIRV (5Zillig W. Kletzin A. Schleper C. Holz I. Janekovic D. Hain H. Lanzendörfer M. Kristjansson J.K. Syst. Appl. Microbiol. 1994; 16: 609-628Crossref Scopus (204) Google Scholar), we found an open reading frame (ORF) 1The abbreviations used are: ORF, open reading frame; PCR, polymerase chain reaction. that encodes a putative protein with considerable similarity to both bacterial dCTP deaminases and dUTPases from eukaryotes, bacteria, Poxviridae, and Retroviridae. In the latter case, the homologous region is part of the gag-pol polyproteins (6Sonigo P. Barker C. Hunter E. Wain-Hobson S. Cell. 1986; 45: 375-385Abstract Full Text PDF PubMed Scopus (243) Google Scholar, 7Moore R. Dixon M. Smith R. Peters G. Dickson C. J. Virol. 1987; 61: 480-490Crossref PubMed Google Scholar, 8Querat G. Audoly G. Sonigo P. Vigne R. Virology. 1990; 175: 434-447Crossref PubMed Scopus (110) Google Scholar, 9York D.F. Vigne R. Verwoerd D.W. Querat G. J. Virol. 1992; 66: 4930-4939Crossref PubMed Google Scholar, 10Andresson O.S. Elser J.E. Tobin G.J. Greenwood J.D. Gonda M.A. Georgsson G. Andresdottir V. Benediktsdottir E. Carlsdottir H.M. Maentylae E.O. Rafnar B. Palsson P.A. Casey J.W. Petursson G. Virology. 1993; 193: 89-105Crossref PubMed Scopus (80) Google Scholar). This dual similarity led us to functionally characterize the novel SIRV gene, which was accomplished by expression of the encoded protein in E. coli, with subsequent enzymatic tests. It also inspired a phylogenetic analysis of the dcd-dut gene family. Furthermore, the recent discovery of two members of this gene family in the whole genome sequence of Methanococcus jannaschii (11Bult C.J. White O. Olsen G.J. Zhou L. Fleischmann R.D. Sutton G.G. Blake J.A. FitzGerald L.M. Clayton R.A. Gocayne J.D. Kerlavage A.R. Dougherty B.A. Tomb J.-F. Adams M.D. Reich C.I. Overbeek R. Kirkness E.F. Weinstock K.G. Merrick J.M. Glodek A. Scott J.L. Geoghagen N.S.M. Weidman J.F. Fuhrmann J.L. Nguyen D. Utterback T.R. Kelley J.M. Peterson J.D. Sadow P.W. Hanna M.C. Cotton M.D. Roberts K.M. Hurst M.A. Kaine B.P. Borodovsky M. Klenk H.-P. Fraser C.M. Smith H.O. Woese C.R. Venter J.C. Science. 1996; 273: 1058-1073Crossref PubMed Scopus (2285) Google Scholar) made it obvious that a biochemical characterization of at least one archaeal member of this gene family is crucial for functional discrimination of these genes. SIRV was grown in cells of S. islandicus isolate REN2H1 (5Zillig W. Kletzin A. Schleper C. Holz I. Janekovic D. Hain H. Lanzendörfer M. Kristjansson J.K. Syst. Appl. Microbiol. 1994; 16: 609-628Crossref Scopus (204) Google Scholar) and purified by polyethyleneimine precipitation followed by cesium chloride gradient centrifugation. The pGEX-2T expression vector, containing the Schistosoma japonicum glutathione S-transferase gene under the control of the tac promoter (12Smith D.B. Johnson K.S. Gene (Amst.). 1988; 67: 31-40Crossref PubMed Scopus (5046) Google Scholar), was purchased from Pharmacia Biotech Inc. Virus DNA was prepared as described earlier (5Zillig W. Kletzin A. Schleper C. Holz I. Janekovic D. Hain H. Lanzendörfer M. Kristjansson J.K. Syst. Appl. Microbiol. 1994; 16: 609-628Crossref Scopus (204) Google Scholar). Plasmids were prepared with a plasmid kit from QIAGEN Inc. Oligonucleotides were synthesized on an Applied Biosystems Model 380B DNA synthesizer according to the manufacturer's instructions. Double-stranded DNA was sequenced using the U. S. Biochemical Corp. Sequenase 2.0 kit following the manufacturer's instructions. Oligonucleotide primers were complementary either to adjacent vector sequences or to portions of previously sequenced parts of the cloned DNA. To ensure accuracy, both DNA strands were sequenced. The putativedut gene was amplified from SIRV DNA by the polymerase chain reaction (PCR) using Vent polymerase (New England Biolabs Inc.). Primer P1 (5′-TTATTGAATTCATCTTCTTTTGCTAATGTGAC-3′) corresponded to the 5′-end of the putative gene, and primer P1r (5′-ATCGAGGATCCATGATTCTTTCAGATAG-3′) corresponded to the 3′-end of the coding region. To facilitate the subsequent cloning steps, aBamHI restriction site was introduced in the former primer, and an EcoRI site was introduced in the latter primer. PCR was performed in a GTC-2 genetic thermal cycler (Precision Scientific) under the following conditions: 3 min of initial denaturation at 94 °C followed by 33 cycles of 1 min at 94 °C, 1 min at 50 °C, and 1 min at 72 °C each. The amplified DNA fragments were purified using QIAquick Spin PCR columns (QIAGEN Inc.) and subsequently cleaved with BamHI and EcoRI restriction endonucleases. The digested BamHI-EcoRI fragments were ligated into BamHI-EcoRI-cut pGEX-2T plasmid. The ligation mixture was incubated for 45 min at 16 °C using the Pharmacia Ready-To-Go™ T4 ligase kit. E. coli JM83 competent cells were transformed with the recombinant vector as described by Smith and Johnson (12Smith D.B. Johnson K.S. Gene (Amst.). 1988; 67: 31-40Crossref PubMed Scopus (5046) Google Scholar). The presence of the cloned insert in transformants was checked by plasmid preparation and subsequent digestion with appropriate restriction enzymes. To ensure that no mutations had been introduced by the PCR amplification, the entire insert was sequenced with Pharmacia primers complementary to pGEX-2T sequences adjacent to the cloning sites. An E. coliJM83 recombinant clone containing pGEX-2T with the correct insert was grown at 37 °C in 500 ml of Luria-Bertani medium containing 100 μg of ampicillin/ml until the A 600 reached 0.8. Cells were collected 3.5 h after induction with 0.5 mmisopropyl-β-d-thiogalactopyranoside and subsequently resuspended in 10 ml of phosphate-buffered saline (137 mmNaCl, 2.7 mm KCl, 4.3 mmNa2HPO4·7H2O, and 1.4 mm KH2PO4). The resuspended cells were lysed with 1 mg/ml lysozyme; DNA was removed by digestion with 100 μg/ml DNase I, and cell debris was removed by a 20-min centrifugation at 20,000 × g. The supernatant was mixed with 1 ml of a 50% suspension of glutathione-agarose beads (Sigma) in phosphate-buffered saline. The agarose beads with the bound enzyme were collected by centrifugation, washed five times with 3 ml of phosphate-buffered saline, and resuspended in 1 ml of phosphate-buffered saline. Five NIH units/ml thrombin (purchased from Sigma) was added to the suspension to release the expressed enzyme from the agarose beads. After gently mixing for 1 h at room temperature, the beads were collected by centrifugation. The expressed enzyme in the supernatant was concentrated in Centricon-10 Quick-Start tubes (Amicon, Inc.). Electrophoresis was performed on 0.7-mm gels as described by Schagger and Von Jagow (13Schägger H. Von Jagow G. Anal. Biochem. 1987; 166: 368-379Crossref PubMed Scopus (10477) Google Scholar) with 4.5% polyacrylamide in the stacking gel and 16% in the separating gel. Gels were stained with Coomassie Blue R-250. The standard assay was carried out by 1 h of incubation at 56 °C in a 75-μl volume containing 20 mm potassium phosphate buffer, pH 6.8, 1.35 mmdithiothreitol, 7 mm MgCl2, 0.15 mm[3H]dUTP (specific activity of 1.65 μCi/μmol), and the appropriate amount of the recombinant enzyme. Five-μl samples of the reaction mixtures were applied to polyethyleneimine-cellulose plates (Merck). Prior to the application of the samples, 30 nmol each of dUTP, dUDP, and dUMP were applied to the start line of the chromatogram. The plates were developed in one dimension with 1m formic acid and 0.5 m LiCl and, after drying, examined under UV light. The marker spots corresponding to dUTP, dUDP, and dUMP were cut out; nucleotides were eluted by washing excised sections with 2 m LiCl; and radiolabel was quantified by scintillation counting. dCTP deaminase activity was determined by a spectrophotometric method based on the difference between the molecular extinction coefficients of deoxycytidine and deoxyuridine (3Beck C.F. Eisenhardt A.R. Neuhard J. J. Biol. Chem. 1975; 250: 609-616Abstract Full Text PDF PubMed Google Scholar). The assay was carried out at 56 °C in time intervals between 10 and 120 min. The reaction volume was 400 μl and contained 20 mm potassium phosphate buffer, pH 6.8, 1.35 mmdithiothreitol, a range of MgCl2 concentrations (0–25 mm), 1 mm dCTP, and different amounts of the recombinant enzyme (2.5–50 μg). Amino acid sequences were retrieved from public data bases. Multiple alignment of the sequences was performed with the help of the computer program CLUSTAL (14Higgins D.G. Sharp P.M. Comput. Appl. Biosci. 1989; 5: 151-154PubMed Google Scholar). Final adjustments considering obvious similarities not indicated by the alignment program were done manually after visual inspection. Phylogenies were inferred and analyzed for statistical confidence using distance, parsimony, and bootstrapping programs from the PHYLIP package (Version 3.572PC) (15Felsenstein J. Cladistics. 1989; 5: 164-166Google Scholar) and PAUP (Version 3.1.1) (16Swofford D.L. PAUP: Phylogenetic Analysis Using Parsimony, Users Manual, Version 3.1.1. Smithonian Institution, Washington, D. C.1993Google Scholar). The ORF analyzed in this report was found in a 2101-base pair-longEcoRI-ClaI restriction fragment of SIRV DNA. The nucleotide sequence of the ORF and its flanking regions is presented in Fig. 1. The GC content of the coding region is 27%, close to the average GC content of SIRV DNA (25%). 2D. Prangishvili, H.-P. Klenk, G. Jakobs, A. Schmiechen, C. Hanselmann, I. Holz, and W. Zillig, unpublished data. The putative translation start codon (ATG) is 1482 base pairs from the EcoRI cloning site, and the TTA stop codon is 145 base pairs from the ClaI cloning site. A typical archaeal “box A” promoter motif, TTAAA (17Hain J. Reiter W.-D. Hüdepohl U. Zillig W. Nucleic Acids Res. 1992; 20: 5423-5428Crossref PubMed Scopus (117) Google Scholar), is found 61–66 nucleotides upstream of the translation start codon. A typical Sulfolobus terminator motif, TTTTTYT (18Reiter W.-D. Palm P. Zillig W. Nucleic Acids Res. 1988; 16: 2445-2459Crossref PubMed Scopus (108) Google Scholar), is located 11–17 nucleotides downstream of the translation termination codon (Fig. 1). A polypeptide presumably encoded by this ORF has 158 amino acid residues and an inferred molecular mass of 16.2 kDa. When the PIR protein sequence data base (19George D.G. Barker W.C. Hunt L.T. Nucleic Acids Res. 1986; 14: 11-15Crossref PubMed Scopus (209) Google Scholar) was searched with this amino acid sequence, the highest sequence similarities were found with hypothetical protein-3 from Desulfurolobus ambivalens (88%) (20Kletzin A. Nucleic Acids Res. 1992; 20: 5389-5396Crossref PubMed Scopus (87) Google Scholar); with dCTP deaminase from E. coli (at that time, the only known dCTP deaminase; 58%); and with dUTPases from retroviruses, lentiviruses, and poxviruses (49–59%). Statistical tests for the significance of the similarities to these sequences resulted in scores significantly higher than the mean scores between random sequences. To find out the enzymatic properties of the protein presumably encoded by the ORF, this region of the viral genome was amplified by PCR and inserted into pGEX-2T, an E. coli expression vector containing the glutathione S-transferase gene regulated by the tac promoter and followed immediately by a cloning site containing, at the 5′-end, a sequence encoding a thrombin cleavage site. The sequence of the cloned DNA fragment was shown to be identical to the original SIRV sequence. The recombinant protein expressed in E. coli was induced and had an apparent molecular mass of ∼42 kDa (Fig. 2), close to that predicted by the fusion of the 26-kDa glutathioneS-transferase and the ∼16.2-kDa SIRV protein. The fusion protein was bound to immobilized glutathione, and after removal of the nonspecifically bound material, the expressed SIRV protein was released by thrombin cleavage. It had an apparent molecular mass of ∼15 kDa, slightly smaller than the predicted mass. Analysis on a 16% SDS-polyacrylamide gel showed it to be 94% pure (Fig. 2). The synthesized protein was tested for putative dUTPase activity by incubation with 3H-labeled dUTP and subsequent chromatography of the reaction products on polyethyleneimine In spots corresponding to dUTP, dUDP, and was quantified by scintillation the are shown in I. The was found in two one the of the dUTP and the the of dUMP. with Thus, the expressed protein was of dUTP to dUMP and was a as by the to the sequence the expressed enzyme was also tested for dCTP deaminase in the dCTP was as a of incubation of dCTP with the expressed as described under and not dCTP deaminase activity be out for the recombinant of recombinant in assay in spots corresponding in a are the for molecular phylogenetic Fig. 3 shows the amino acid sequence of the novel SIRV dUTPase with known and homologues and most viral homologues found in the public sequence data by W. W. J. Biol. 1990; PubMed Scopus Google Scholar). are for the dCTP and are for the putative archaeal D. ambivalens and M. jannaschii amino are sequences acid acid and (Fig. to the previously described sequence of dUTPases J. Nucleic Acids Res. 1990; PubMed Scopus Google acid to to and acid and to The latter two amino in dUTPase to residues in the to be for the of dUTP J.M. J.A. 1996; Full Text Full Text PDF PubMed Scopus Google Scholar); acid is to be for discrimination between dUTP and UTP G. Biol. 1996; PubMed Scopus Google Scholar). described by J. Nucleic Acids Res. 1990; PubMed Scopus Google Scholar) is less in the putative archaeal dUTPases and in dCTP less in archaeal dUTPases is J. Nucleic Acids Res. 1990; PubMed Scopus Google Scholar), to be for the activity of dUTPases G. K.S. 1992; Scopus Google Scholar, B. PubMed Scopus Google Scholar); in the enzyme from M. the region is found in dUTPases is on the alignment phylogenetic determined by PAUP using the similarity the novel sequence to be most to the D. ambivalens hypothetical at a of The dCTP deaminases are at an average of dUTPases at bacterial dUTPases at and viral homologues at SIRV dUTPase is also the to the protein encoded by M. with a phylogenetic of with for dCTP deaminases and for bacterial and Fig. shows a phylogenetic of the deaminase family. The shown in this was derived with a method the in and tested by to the of the and the phylogenetic of the samples, a of the phylogeny not be region in the of the the between dCTP deaminases and as well as the of the archaeal the of bacterial and the between and was also by based on a method the PHYLIP program The highest in an initial data base with the SIRV gene described was to putative protein-3 from D. ambivalens (20Kletzin A. Nucleic Acids Res. 1992; 20: 5389-5396Crossref PubMed Scopus (87) Google Scholar). The respectively, were to two functionally different of the thymidine nucleotide biosynthesis dCTP deaminase and dUTPase. the indicated a to dCTP deaminase from E. coli than to functional indicated that the protein encoded by the gene has dUTPase no dCTP deaminase This the in about for genes and products by sequence for gene with characterized from the products of two E. coli dcd L. B. J. Bacteriol. 1992; PubMed Google Scholar) and dut H.O. J. PubMed Scopus Google Scholar), and viral dut genes Virology. PubMed Scopus Google Scholar, Virology. Scopus Google Scholar, B. L. S. J. Virol. 1994; PubMed Google Scholar, Virology. 1993; PubMed Scopus Google Scholar, O. J. Virology. 1994; PubMed Scopus Google Scholar), no of or viral member of the dcd-dut gene family has been hypothetical protein-3 from D. ambivalens was as a dCTP C. C. Nucleic Acids Res. PubMed Scopus Google Scholar). the D. ambivalens is the to the SIRV gene analyzed this enzyme be as a dUTPase based on the functional and phylogenetic described members of the dcd-dut gene family been in the whole genome sequence of M. and (11Bult C.J. White O. Olsen G.J. Zhou L. Fleischmann R.D. Sutton G.G. Blake J.A. FitzGerald L.M. Clayton R.A. Gocayne J.D. Kerlavage A.R. Dougherty B.A. Tomb J.-F. Adams M.D. Reich C.I. Overbeek R. Kirkness E.F. Weinstock K.G. Merrick J.M. Glodek A. Scott J.L. Geoghagen N.S.M. Weidman J.F. Fuhrmann J.L. Nguyen D. Utterback T.R. Kelley J.M. Peterson J.D. Sadow P.W. Hanna M.C. Cotton M.D. Roberts K.M. Hurst M.A. Kaine B.P. Borodovsky M. Klenk H.-P. Fraser C.M. Smith H.O. Woese C.R. Venter J.C. Science. 1996; 273: 1058-1073Crossref PubMed Scopus (2285) Google Scholar). on sequence both genes were as dCTP the biochemical and phylogenetic shown it is that M. jannaschii probably not two homologous dCTP one dUTPase and one dCTP deaminase paralogous members of the dcd-dut gene family. The identification of both genes in the genome also us to that the de novo biosynthesis pathway for thymidine nucleotides in M. jannaschii deamination of dCTP to dUTP by dCTP deaminase and successive hydrolysis of dUTP to dUMP and by dUTPase in the of this pathway in this It that SIRV encodes its of in cells be not to of a virus with a GC content of only GC content of the DNA of Sulfolobus a close of the SIRV is It is also that dUTPase from SIRV is involved in the dUTP at a level that of into DNA is and the DNA are not J. A. J. Biol. Chem. Full Text PDF PubMed Google Scholar). for reading of the