A New Subfamily of the Nudix Hydrolase Superfamily Active on 5-Methyl-UTP (Ribo-TTP) and UTP

A new subfamily of the Nudix hydrolases, identified by conserved amino acids upstream and downstream of the Nudix box, has been characterized. The cloned, expressed, and purified orthologous enzymes have major activities on the non-canonical nucleoside triphosphate 5-methyl-UTP (ribo-TTP) and the canonical nucleotide UTP. In addition to their homologous signature sequences and their similar substrate specificities, the members of the subfamily are inhabitants of or are related to the bacterial rhizosphere. We propose the acronym and mnemonic, utp, for the gene designating this unique UTPase. A new subfamily of the Nudix hydrolases, identified by conserved amino acids upstream and downstream of the Nudix box, has been characterized. The cloned, expressed, and purified orthologous enzymes have major activities on the non-canonical nucleoside triphosphate 5-methyl-UTP (ribo-TTP) and the canonical nucleotide UTP. In addition to their homologous signature sequences and their similar substrate specificities, the members of the subfamily are inhabitants of or are related to the bacterial rhizosphere. We propose the acronym and mnemonic, utp, for the gene designating this unique UTPase. The Nudix hydrolases, so named because they catalyze the hydrolysis of Nucleoside diphosphates linked to some other moiety x (1Bessman M.J. Frick D.N. O'Handley S.F. J. Biol. Chem. 1996; 271: 25059-25062Abstract Full Text Full Text PDF PubMed Scopus (583) Google Scholar), constitute a superfamily of enzymes with representatives in all three kingdoms. The members of this superfamily can be identified by a highly conserved amino acid signature sequence called the Nudix box, viz. in which X represents any amino acid and U is a bulky hydrophobic amino acid, usually Ile, Leu, or Val. A current BLAST (2Altschul S.F. Madden T.L. Schaffer A.A. Zhang J. Zhang Z. Miller W. Lipman D.J. Nucleic Acids Res. 1997; 25: 3389-3402Crossref PubMed Scopus (59382) Google Scholar) search of the data banks for polypeptides and expressed sequence tags containing the above sequence, reveals over 1100 open reading frames from more than 250 species ranging from viruses to humans. We have been systematically cloning, expressing, and characterizing members of the superfamily, and without exception, all of the enzymes identified so far hydrolyze nucleoside diphosphate derivatives including nucleotide sugars, dinucleoside polyphosphates, coenzymes, (deoxy)nucleoside triphosphates, and ADP-ribose. Since the same amino acid signature sequence, the Nudix box, represents the nucleotide binding and catalytic site for all these proteins (3Bullions, L. C. (1993) Studies on the mutT Enzyme from Escherichia coli and Streptococcus pneumoniae. Ph.D. thesis, The Johns Hopkins UniversityGoogle Scholar, 4Lin J. Abeygunarwardana C. Frick D.N. Bessman M.J. Mildvan A.S. Biochemistry. 1997; 36: 1199-1211Crossref PubMed Scopus (80) Google Scholar, 5Gabelli S.B. Bianchet M.A. Bessman M.J. Amzel L.M. Nat. Struct. Biol. 2001; 8: 467-472Crossref PubMed Scopus (112) Google Scholar), the different specificities toward the respective substrates must lie in a region or in regions peripheral to this area. By aligning amino acid sequences of those enzymes hydrolyzing a similar spectrum of substrates, we have identified certain landmark amino acids outside of the Nudix box, enabling us to classify some of the members of the superfamily into distinct subfamilies (6Dunn C.A. O'Handley S.F. Frick D.N. Bessman M.J. J. Biol. Chem. 1999; 274: 32318-32324Abstract Full Text Full Text PDF PubMed Scopus (134) Google Scholar). This has been of singular value, because it has allowed us to predict the enzymatic activity of unidentified open reading frames involved in physiological processes, merely by observing specific telltale amino acid patterns peculiar to each subfamily. In this paper, we describe the cloning, expression, purification, and identification of members of a new subfamily of the Nudix hydrolases, highly active on 5-methyl-UTP (ribo-TTP) and UTP, and recognizable by characteristic amino acid sequences outside of the Nudix box. The expression plasmid pET-24a(+) (Kmr) and Escherichia coli HMS174 (DE3) were from Novagen (Madison WI); Agrobacterium tumefaciens strain GV3101 was a gift from Judith Bender, The Johns Hopkins School of Public Health; Pseudomonas aeruginosa, strain BB3/216/ATCC27853, was a gift from Thomas Cebula of the Food and Drug Administration; and Caulobacter crescentus strain CB15 was a gift of Lucy Shapiro, Stanford University, and Bert Ely, the University of South Carolina. The plasmid, pTrc99A (Ampr), and Sephadex G-100 were from Amersham Biosciences, and the restriction enzymes, PCR kits, calf intestinal alkaline phosphatase, and yeast inorganic pyrophosphatase were from Stratagene (La Jolla, CA). The canonical nucleotide substrates and common chemicals were from Sigma or Invitrogen, and 5-methyl-UTP was from TriLink Biotechnologies (San Diego, CA). The PCR primers were synthesized by Integrated DNA Technologies, Inc. (Coralville, IA). Protein assay reagent was from Bio-Rad. Cloning of A. tumefaciens orf147 and Its Orthologs—Standard cloning technology was used. Briefly, orf147 was amplified directly from one colony of A. tumefaciens strain GV3101 using the DNA PCR. NdeI and BamHI restriction sites were incorporated at the start and end of the gene, respectively, and the amplified DNA was purified, digested with NdeI and BamHI, and ligated into pET24a(+) to place the gene under transcriptional control of the T7 lac promoter. The resultant plasmid, pETORF147 was transformed into E. coli DH5a for storage and into HMS174 (DE3) for protein expression. The orthologous genes from P. aeruginosa and C. crescentus were cloned using similar procedures. For complementation studies, the gene was cut out of pETORF147 with XbaI and HindIII and ligated into the corresponding sites of pTrc99A putting orf147 under control of the trc promoter. The resulting plasmid, pTrcORF147, was transformed into DH5α. Growth and Expression of HMS174:pETorf147, ORF147, and Its Orthologs—One colony of the expression strain was inoculated into 40 ml of LB medium containing 30 μg/ml kanamycin, incubated at 37 °C on a rotary shaker overnight, transferred to 2 liters of the same medium, and grown to an A 600 of 0.8. The culture was derepressed by the addition of isopropyl-β-d-thiogalactopyranoside to a concentration of 0.5 mm and grown for an additional 3 h, after which the cells were harvested by centrifugation and washed in buffered isotonic saline solution. Purification of the Enzymes—The washed cells were frozen at –80 °C overnight and resuspended in 2.5 volumes of buffer A (50 mm Tris-Cl, pH 7.5, 1 mm EDTA, 0.1 mm dithiothreitol). The supernatant (fraction I) containing the expressed protein was collected by centrifugation, and 10% streptomycin sulfate in buffer A was added to a final concentration of 1.5% to precipitate nucleic acids. These were removed by centrifugation, and the supernatant (fraction II) was brought to 60% saturation with ammonium sulfate. The precipitate was collected and dissolved in a minimal volume of buffer A (fraction III), and chromatographed on a Sephadex G-100 gel filtration column equilibrated and eluted with buffer A plus 200 mm sodium chloride. The fractions were located by A 280 absorbance and identified by their migration on an SDS-PAGE gel. Those containing the purified protein were pooled, assayed, and stored at –80 °C (fraction IV). All of the orthologs of ORF147, including those from A. tumefaciens, P. aeruginosa, and C. crescentus were purified by similar procedures. Enzyme Assays—The standard reaction contained in 50 μl: 50 mm Tris-Cl, pH 9.0, 5 mm Mg2+, 2 mm substrate, 0.5 unit of yeast inorganic pyrophosphatase for substrates such as (deoxy)nucleoside triphosphates and their derivatives, or 4 units of alkaline phosphatase for all other substrates and 0.1–2 milliunits of purified enzyme. The solution was incubated at 37 °C for 15 min, stopped by the addition of 250 μl of 4 mm EDTA, and the liberated inorganic orthophosphate was assayed by the colorimetric procedure of Fiske and SubbaRow (7Fiske C.H. SubbaRow Y. J. Biol. Chem. 1925; 66: 375-400Abstract Full Text PDF Google Scholar) as modified by Ames and Dubin (8Ames B.N. Dubin D.T. J. Biol. Chem. 1960; 235: 769-775Abstract Full Text PDF PubMed Google Scholar). A unit of enzyme hydrolyzes 1 μmol of substrate per min. Complementation Test for the mutT Mutator Phenotype—Gene orf147 was cloned into pTrc99A and transformed into E. coli strain SB3 lacking a functional mutT gene. The mutation frequencies were calculated from the number of colonies resistant to nalidixic acid or streptomycin as described in O'Handley et al. (9O'Handley S.F. Frick D.N. Bullions L.F. Mildvan A.S. Bessman M.J. J. Biol. Chem. 1996; 271: 24649-24654Abstract Full Text Full Text PDF PubMed Scopus (59) Google Scholar). Recognition of the Putative Subfamily—Our customary procedure for identifying the activity of a new open reading frame containing the Nudix box involves BLAST searches (10Altschul S.F. Gish W. Meyers E.W. Lipman D.J. J. Mol. Biol. 1990; 203: 403-410Crossref Scopus (69597) Google Scholar) and Clustal alignments (11Higgins D.G. Thompson J.D. Gibson T.J. Methods Enzymol. 1996; 266: 383-402Crossref PubMed Scopus (1288) Google Scholar) of the amino acid sequence of the unknown polypeptide. When this was done for an open reading frame from A. tumefaciens, we identified a group of polypeptides with conserved sequences upstream and downstream of the Nudix box (Fig. 1). Since these regions were different from any landmark amino acids described previously (6Dunn C.A. O'Handley S.F. Frick D.N. Bessman M.J. J. Biol. Chem. 1999; 274: 32318-32324Abstract Full Text Full Text PDF PubMed Scopus (134) Google Scholar, 12Cartwright J.L. Gasmi L. Spiller D.G. McLennan A.G. J. Biol. Chem. 2000; 275: 32925-32930Abstract Full Text Full Text PDF PubMed Scopus (57) Google Scholar), we hypothesized that the associated polypeptides represented a new subfamily of Nudix hydrolases. Accordingly, we investigated this possibility by isolating the expressed proteins and identifying the enzymatic activities of some of the members of the group. Gene Cloning, Expression, and Protein Purification—Cloning of the genes from single colonies of the individual organisms proceeded pro forma; the inserts were sequenced and were as described in the data banks. All three of the orthologous genes from A. tumefaciens, P. aeruginosa, and C. crescentus expressed proteins in soluble form when introduced into E. coli but with different levels of expression. As with some of the other Nudix hydrolases (6Dunn C.A. O'Handley S.F. Frick D.N. Bessman M.J. J. Biol. Chem. 1999; 274: 32318-32324Abstract Full Text Full Text PDF PubMed Scopus (134) Google Scholar, 9O'Handley S.F. Frick D.N. Bullions L.F. Mildvan A.S. Bessman M.J. J. Biol. Chem. 1996; 271: 24649-24654Abstract Full Text Full Text PDF PubMed Scopus (59) Google Scholar, 13Frick D.N. Bessman M.J. J. Biol. Chem. 1995; 270: 1529-1534Abstract Full Text Full Text PDF PubMed Scopus (85) Google Scholar, 14Conyers G.B. Bessman M.J. J. Biol. Chem. 1999; 274: 1203-1206Abstract Full Text Full Text PDF PubMed Scopus (61) Google Scholar, 15O'Handley S.F. Dunn C.A. Bessman M.J. J. Biol. Chem. 2001; 276: 5421-5426Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar), the expressed proteins were extractable into buffer merely by freezing and thawing the cells. This left the bulk of the cellular proteins behind, thereby considerably simplifying the purification. The procedure described under “Methods” led to essentially homogeneous proteins (Fig. 2). Identification of Enzyme Activity and Substrate Specificity— A unifying property of the Nudix hydrolases is their activity on nucleoside diphosphate derivatives, although these substrates may vary widely for different members of the superfamily. Starting with the purified enzyme expressed from the A. tumefaciens gene, we examined a large number of nucleoside diphosphate derivatives as potential substrates, and we found that UTP was hydrolyzed at the highest rate of all those naturally occurring metabolites tested (Table I). However, we noted an apparent inconsistency in our substrate survey when we observed that dTTP was hydrolyzed at a measurable rate, ∼18% of UTP, whereas dUTP was not a significant substrate. This seemed surprising since it appeared to us that UTP resembled dUTP more closely than it did dTTP, and so it called our attention to the methyl group as a potentially important feature involved in substrate recognition. Accordingly, we tested 5-methyl-UTP and found it is hydrolyzed at three times the rate of UTP. This is shown in Table I along with a comparison to the purified orthologous proteins from P. aeruginosa and C. crescentus. The enzymes from P. aeruginosa and A. tumefaciens have similar specificities, but the active site of the C. crescentus enzyme is more accommodating and has approximately equal activities on UTP and the other pyrimidine ribonucleoside triphosphate, CTP.Table IEnzyme SpecificitySubstrateA. tumefaciensP. aeruginosaC. crescentusSpecific activityRelative activitySpecific activityRelative activitySpecific activityRelative activityunits/mg%units/mg%units/mg%5-Methyl-UTP261(100)227(100)82(100)UTP903483376173dTTP16611568CTP1<0.51<0.55969ATP, dATP, GTP, dGTP, dCTP, dUTP, UDP, dTDP, FAD, NADH, Ap5A,aAp5A is adenosine (5′)-pentaphospho-(5′)-adenosine UDP-glucose, ADP-ribose<0.5<0.2<0.5<0.3<0.5<0.7a Ap5A is adenosine (5′)-pentaphospho-(5′)-adenosine Open table in a new tab A comparison of some of the kinetic properties of the three enzymes is shown in Table II. The combined higher k cat and lower Km for 5-methyl-UTP leads to a 10-fold higher catalytic constant, k cat/Km , over that for UTP for the A. tumefaciens and P. aeruginosa enzymes. These inequalities are not nearly as marked for C. crescentus resulting in less than a 2-fold difference in the values of the catalytic constants for the two substrates, supporting the notion that its catalytic site is more accommodating than those of the other two enzymes. In this respect, it is interesting to note that all known eukaryotic UMP kinases, enzymes involved in the phosphorylation of UMP to UDP, are equally active on UMP and CMP (16Yan H. Tsai M.-D. Adv. Enzymol. Relat. Areas Mol. Biol. 1999; 73: 103-134Crossref PubMed Google Scholar), suggesting that there may be similarities in the active sites of these kinases and the C. crescentus enzyme. Work in progress on the x-ray crystal structure of members of the family should be informative in ascertaining the basis of these observations. 1S. B. Gabelli, work in progress.Table IIKinetic analysis of the enzymesOrganismSubstrateVmaxKmkcatk cat/Kmunits/mgmms-1m-1s-1A. tumefaciens5-CH3UTP2610.12 ± 0.04726.0 × 105UTP900.48 ± 0.08265.1 × 104P. aeruginosa5-CH3UTP2280.18 ± 0.05633.5 × 105UTP530.49 ± 0.08143.0 × 104C. crescentus5-CH3UTP820.21 ± 0.05199.1 × 104UTP620.11 ± 0.04141.3 × 105 Open table in a new tab Products of the Reaction—With one possible exception (17Frick D.N. Townsend B.D. Bessman M.J. J. Biol. Chem. 1995; 270: 24086-24091Abstract Full Text Full Text PDF PubMed Scopus (64) Google Scholar), virtually all of the Nudix hydrolases studied so far catalyze a nucleophilic attack by water on a pyrophosphate linkage. An analysis of the products of UTP hydrolysis with purified A. tumefaciens UTPase indicates that this enzyme also catalyzes an attack on the pyrophosphate linkage. Fig. 3A shows that after a 30-min incubation, the UTP peak decreased, a UMP peak appeared, and there was no apparent formation of UDP. This indicates that there was either a direct conversion of UTP to UMP with the release of inorganic pyrophosphate or that UTP was hydrolyzed to UDP as the rate-limiting step, and the UDP was then rapidly converted to UMP. The second pathway is ruled out for two reasons. First, as shown in Fig. 3B, no inorganic orthophosphate is formed during the course of the reaction, as would be required for conversion of UTP to UDP, unless inorganic pyrophosphatase is present. Second, UDP itself is not a substrate of the enzyme as shown in Table I. Therefore, Reaction 1 describes the stoichiometry, UTP+H2O→UMP+PPiReaction1(Eq. 1) Five other Nudix hydrolase nucleoside triphosphatases are known with major activities on dGTP (18Bhatnagar S.K. Bessman M.J. J. Biol. Chem. 1988; 263: 8953-8957Abstract Full Text PDF PubMed Google Scholar), dATP (19O'Handley S.F. Frick D.N. Bullions L.C. Mildvan A.S. Bessman M.J. FASEB J. 1995; 9 (abstr.): 1299Google Scholar), dCTP (15O'Handley S.F. Dunn C.A. Bessman M.J. J. Biol. Chem. 2001; 276: 5421-5426Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar), 3′-amino-3′-dATP (20Espinosa J.C. Tercero J.A. Rubio M.A. Jimenez A. J. Bacteriol. 1999; 181: 4914-4918Crossref PubMed Google Scholar), and dTTP 2C. A. Dunn, D. Smith, and M. J. Bessman, all the respective and inorganic in the with the the UTPase described is UTP and it is the of these enzymes to to our this gene and enzyme has not been described we propose the acronym and mnemonic, as its of the A. tumefaciens UTPase for of the other Nudix hydrolases, this be by or In to the A. tumefaciens of the other members of the superfamily, alkaline and is active at pH The protein from a gel filtration column as for an protein and as a in solution. Complementation Nudix is also a nucleoside although it has a different from the UTPase described (1Bessman M.J. Frick D.N. O'Handley S.F. J. Biol. Chem. 1996; 271: 25059-25062Abstract Full Text Full Text PDF PubMed Scopus (583) Google Scholar, S.K. Bessman M.J. J. Biol. Chem. 1988; 263: 8953-8957Abstract Full Text PDF PubMed Google Scholar, S.K. Bullions L.C. Bessman M.J. J. Biol. Chem. 266: Full Text PDF PubMed Google Scholar). we tested a plasmid containing the UTPase gene for its to a mutT strain of E. the mutT strain to ± colonies per the strain transformed with a mutT gene the same number as a mutT However, the mutT strain when transformed with the UTPase gene ± were when nalidixic acid was for streptomycin as the not These the UTPase as an of this subfamily of Nudix hydrolases 1) is the the members of the or is the of the properties they is the of their for In to the this group of open reading frames (Fig. 1) was from over 1100 Nudix hydrolases identified by BLAST (10Altschul S.F. Gish W. Meyers E.W. Lipman D.J. J. Mol. Biol. 1990; 203: 403-410Crossref Scopus (69597) Google Scholar) searches of the data banks. Clustal (11Higgins D.G. Thompson J.D. Gibson T.J. Methods Enzymol. 1996; 266: 383-402Crossref PubMed Scopus (1288) Google Scholar) alignments the upstream and the downstream of the Nudix box, and these two amino acid the signature sequence of the family and it as a distinct subfamily of The conserved the Nudix box, is not since it is in other Nudix hydrolases with A unifying feature of these bacterial is their to either directly as in the or P. aeruginosa, Pseudomonas tumefaciens, Pseudomonas or as by For in the and are related to involved in or in and the plasmid containing the Nudix gene in the is related to the plasmid in the The C. although not found in the same as the other members of the of its from including and and has gene for their usually associated with was from An of the of the enzyme for is more We are not of any of in the nucleotide of any to of the organisms the although we are also not of for this nucleoside the other is the common in and from it has been that which catalyzes the of to can also UMP as the with the formation of J. Biol. Chem. Full Text PDF PubMed Google Scholar). The formation of the corresponding triphosphate would activities of a nucleotide and nucleoside not tested on the of purified UMP A. Y. PubMed Scopus Google Scholar) that be to and the step, the phosphorylation to would because of the of nucleoside be incorporated into since it has been that and eukaryotic can for UTP during P. Biochemistry. Scopus Google Scholar, C. M. Nucleic Acids 8: Scholar). would have on the physiological of is has been shown that E. coli lacking in their no in rate, protein and However, there is a distinct of cells over those lacking in J. Bacteriol. PubMed Google Scholar). An interesting the described and Nudix hydrolase from E. coli (15O'Handley S.F. Dunn C.A. Bessman M.J. J. Biol. Chem. 2001; 276: 5421-5426Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar). The enzyme also the non-canonical of the substrate, As out (1Bessman M.J. Frick D.N. O'Handley S.F. J. Biol. Chem. 1996; 271: 25059-25062Abstract Full Text Full Text PDF PubMed Scopus (583) Google Scholar), the Nudix hydrolases may be of as enzymes, hydrolyzing potentially or during or the of during the of the The enzymes of this subfamily to this is an to these related then they have a to with the other the of the enzymes may be to the of the nucleoside triphosphate, UTP, and be related to the S.K. Bullions L.C. Bessman M.J. J. Biol. Chem. 266: Full Text PDF PubMed Google Scholar), (19O'Handley S.F. Frick D.N. Bullions L.C. Mildvan A.S. Bessman M.J. FASEB J. 1995; 9 (abstr.): 1299Google Scholar), (15O'Handley S.F. Dunn C.A. Bessman M.J. J. Biol. Chem. 2001; 276: 5421-5426Abstract Full Text Full Text PDF PubMed Scopus (43) Google Scholar), and Nudix hydrolases the of the nucleotide