JOURNAL OF BACTERIOLOGY, Nov. 1977, p. 641-649 Copyright c 1977 American Society for Microbiology
Vol. 132, No. 2 Printed in U.S.A.
Purification and Partial Characterization of the Principal Deoxyribonucleic Acid Polymerase from Mycoplasmatales L. BRUCE MILLS,' ERIC J. STANBRIDGE,2 W. DAVID SEDWICK,' AND DAVID KORN'* Laboratory of Experimental Oncology, Department of Pathology, Stanford University School of Medicine, Stanford, California 94305,1 and Department of Medical Microbiology, University of California, Irvine, College of Medicine, Irvine, California 926642 Received for publication 16 May 1977
In this report we present the first description of the isolation and partial characterization of the deoxyribonucleic acid (DNA) polymerase activity from two species of Mycoplasmatales, Mycoplasma orale type 1 and M. hyorhinis. We have identified only a single DNA polymerase species in the mycoplasma crude extracts, and the enzymes from the two organisms are very similar in their structural and enzymatic properties. The purified polymerase from each source has a specific activity of >50,000 U/mg of protein, a sedimentation coefficient of 5.6s, and an estimated molecular weight by gel filtration of 130,000. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the most highly purified M. orale fraction contains a single major protein band of 130,000 daltons, which we believe may represent the polymerase protein. The enzymes are most reactive with gapped (activated) DNA and show a marked preference for this primer template over oligodeoxyribonucleotide-initiated homoribo- or homodeoxyribopolymers. The most purified preparations are devoid of contaminating endonuclease activity and also appear to lack associated 5' -* 3'- or 3' - 5'-exonuclease activities, as determined by highly sensitive assays. The absence of the 3' -* 5'exonuclease is particularly remarkable in that this activity is essentially ubiquitous among the DNA polymerases that have thus far been characterized from procaryotes.
The Mycoplasmatales comprise a group of microorganisms that are the smallest known free-living procaryotes. They are characterized by their minute size (0.25 to 1.0 ,um in diameter), the absence of a cell wall, and a relatively small genome (5 x 101 to 10 x 101 daltons) of presumably limited complexity that has been shown to be a single, circular, double-stranded deoxyribonucleic acid (DNA) molecule (14, 19, 24). Limited studies to date have indicated that mycoplasma DNA replication appears to be semiconservative and to proceed unidirectionally from one or a few growing-point regions (21) that may be in a membrane-associated complex (22). The capacity of at least one Acholeplasma species to carry out light and dark repair of ultraviolet-irradiated DNA has also been described (23). Apart from these few published reports, however, almost nothing is yet known about the biochemical basis of DNA replication in these organisms. Aside from their intrinsic interest, mycoplasmas have increasingly been recognized as common and troublesome contaminants of cell cultures, difficult to detect and difficult to eradicate (19, 24). Moreover, there is now abundant
evidence that such contamination, often unrecognized, can have profound effects on cultured cell properties, including alterations of metabolic properties, induction of chromosomal aberrations, and modifications of cellular morphology that can be mistaken for virus-provoked cytopathic effects (19, 24). In view of the intensive effort that is currently being expended in many laboratories on the identification and characterization of DNA polymerase activities from a variety of cultured eucaryotic cells, we felt it was important to document the properties of the DNA polymerases of representative Mycoplasmatales. In this paper, we present the purification and partial characterization of the principal DNA polymerase activity that we have isolated from crude extracts of two Mycoplasma species that are well-recognized cell culture contaminants, Mycoplasma orale type 1 and M. hyorhinis. In corroboration of the potential value of this undertaking, we note that at least one reported species of eucaryotic DNA polymerase, mitochondrial D-DNA polymerase from HeLa cells (7, 28), has recently been suggested to be a possible mycoplasma activity resulting from
641
642
MILLS ET AL.
J. BACTERIOL.
fuged at 10,000 rpm for 20 min at 4°C. The pellet, which contained organisms and particulate constituents from the growth medium, was washed twice with phosphate-buffered saline (PBS) and then stored frozen at - 70°C as an unpurified mycoplasma pellet. Initial efforts to isolate the DNA polymerase MATERIALS ANI) METHOI)S activity from such pellets revealed unpredictable Materials. Unlabeled deoxyribonucleotides were variations in column chromatographic behavior, purchased from P-L Biochemicals; 3Hldeoxythymi- which we attributed to the presence of undefined dine 5'-triphosphate (dTTP) was from New England medium components in the crude extract. We thereNuclear Corp.; calf thymus DNA was from Calbi- fore introduced an additional procedure to purify ochem; Triton X-100 was from Beckman Instru- the mycoplasma organisms. The crude pellets were ments, Inc.; Sephadex G-25 and G-200 were from suspended in 20 ml of PBS, and 5-ml portions were Pharmacia Fine Chemicals, Inc.; diethylaminoethyl overlayered on 30-ml discontinuous 30 to 60% (wt/ (DEAE)-cellulose (DE-52) and phosphocellulose (P- wt) sucrose gradients in PBS and centrifuged in an 11) resins were from Whatman; acrylamide, bisme- SW25.1 rotor at 10,000 rpm for 60 min. The visible thylene acrylamide, and N,N, N,' N'-tetramethyl- bands of mycoplasma were collected, pooled, susenediamine were from Bio-Rad Laboratories; BDH pended in PBS, and pelleted. The washing and sodium dodecyl sulfate (SDS) was from Gallard- centrifugation steps were repeated, and the final Schlesinger; bovine serum albumin and 7S immu- pellet was stored at -70'C as a purified mycoplasma noglobulin were from Sigma Chemical Co.; ovalbu- preparation. Just before the last centrifugation, the min was from Pharmacia; and ,3-galactosidase was PBS suspension was assayed for mycoplasma CFU. from Worthington Biochemical Corp. Coomassie The majority of harvests yielded a total of 1 x 101' brilliant blue was from Schwarz/Mann, and amido to 5 x 1012 CFU. Standard I)NA polvmerase assay. The standard black lOB was from Baker. LKB ampholytes were used for isoelectric focusing. Polydeoxyadenylate assay was run for 10 min at 37TC and contained the lpoly(dA)d was from Collaborative Research, and following in a total volume of 0.25 ml: tris(hydroxypolyadenylate [poly(A)] and poly(deoxyadenylate- methyl )aminomethane Tris )-hydrochloride (pH deoxythymidylate) Lpoly(dA-dT) were from Miles 8.5), 10 mM; ,6-mercaptoethanol, 2.0 mM; bovine Laboratories, Inc. Heat-denatured calf thymus serum albumin, 50 ug; MgCl2, 20 mM; KCl, 100 DNA-cellulose (Cellex-N-1; Bio-Rad) was prepared mM; activated calf thymus DNA (20), 200 gtg/ml; (1) by D. C. Eichler, Stanford University. Oligo(dT)rm deoxyadenosine 5'-triphosphate, deoxyguanosine 5'and oligo(dT)7-[3H]deoxycytidylate (dC)7) (specific triphosphate, deoxycytidine 5'-triphosphate, and activity, 14,000 cpm/pmol) were prepared (26) by T. dTTP, 100 ,kM each; liH]dTTP, 40 mCi/mmol; and S-F. Wang, Stanford University, using d(pT)4 (Col- enzyme. In addition, 0.1% Triton X-l00 was incorlaborative Research) as initiator. Terminal deoxy- porated into the reaction with the most highly nucleotidyl-transferase (13,000 U/mg), purified from purified enzyme fractions, since it appeared to calf thymus, was a gift from R. L. Ratliff, Los enhance the reproducibility of the assays. The reacAlamos Scientific Laboratory; bacteriophage T4 tions were terminated and processed as previously DNA polymerase, phosphocellulose fraction (15) described (20). One unit of DNA polymerase activity (-15,000 U/mg), was from N. G. Nossal, National is defined as the amount catalyzing the incorporaInstitutes of Health; ColEl form I [1'C]DNA (4,000 tion of 1 nmol of labeled deoxythymidine 5'-monocpm/,tg) and PM2 form I 1IHIDNA (1,600 cpm/,ug) phosphate into acid-insoluble product in 60 min at were the gift of D. A. Clayton, Stanford University; 37'C under standard reaction conditions. Specific and specifically incised, ultraviolet-irradiated E. activity is expressed as units per milligram of procoli V:'H]DNA (1.7 x 105 cpm//Ig) was provided by tein. All enzymatic properties were determined under conditions of linearity with respect to time K. H. Cook, Stanford University. Growth and harvest of mycoplasmas. M. hvor- and protein. hinis and M. orale type I were grown in a modified Glycerol gradient centrifugation. Linear 20 to Hayflick medium (9) consisting of 85 volumes of 40% (vol/vol) glycerol gradients were prepared in 50 beef heart infusion broth (Difco). 10 volumes of mM potassium phosphate (pH 7.5) and 1 mM each unheated horse serum (Irvine Scientific), 5 volumes ethylenediaminetetraacetic acid (EDTA) and /3of a 25% stock solution of freshly prepared yeast mercaptoethanol. with or without KCl at 0.5 M. extract (Standard Brands, Inc.), and glucose and Enzyme sample (0.25 ml) was layered onto the top arginine at a final concentration of 1%J. ()wt/vol) of the gradient and overlayered with mineral oil. each. Penicillin G at a final concentration of 100 U/ Sedimentation was carried out at 50,000 rpm for 24 ml was added to prevent bacterial contamination. h at 5C in an SW50.1 rotor. Fractions of 0.25 ml Flasks containing 500 ml of prewarmed growth were collected dropwise from the bottom of the tube, medium were inoculated with 5 ml of an actively and portions were tested in the standard polymerase growing culture at a density of 10'; to 10 organisms assay. Polyacrylamide gel electrophoresis. SDS-poly-. per ml and incubated 3 to 4 days at 37°C. Growth of organisms was monitored by assay of colony-form- acrylamide gels, 3 mm in diameter and containing ing units (CFU) on agar (19). Two hours before 7% acrylamide, were prepared and run according to harvest, 50 to 100 ml of prewarmed growth medium Laemmli (11), without stacking gel. Samples were was added to each culture. The cultures were centri- prepared for electrophoresis by alternate concentra-
culture contamination (la). The properties of that enzyme are very similar to those of the highly purified mycoplasma polymerases that we describe in this report.
VOL. 132, 1977
DNA POLYMERASE FROM MYCOPLASMATALES
tion against dry Sephadex G-200 beads and dialysis versus 0.05 M Tris-hydrochloride (pH 7.2), 1% SDS, 1% f3-mercaptoethanol, and 20% (vol/vol) glycerol, until the sample volume had been reduced to
Vol. 132, No. 2 Printed in U.S.A.
Purification and Partial Characterization of the Principal Deoxyribonucleic Acid Polymerase from Mycoplasmatales L. BRUCE MILLS,' ERIC J. STANBRIDGE,2 W. DAVID SEDWICK,' AND DAVID KORN'* Laboratory of Experimental Oncology, Department of Pathology, Stanford University School of Medicine, Stanford, California 94305,1 and Department of Medical Microbiology, University of California, Irvine, College of Medicine, Irvine, California 926642 Received for publication 16 May 1977
In this report we present the first description of the isolation and partial characterization of the deoxyribonucleic acid (DNA) polymerase activity from two species of Mycoplasmatales, Mycoplasma orale type 1 and M. hyorhinis. We have identified only a single DNA polymerase species in the mycoplasma crude extracts, and the enzymes from the two organisms are very similar in their structural and enzymatic properties. The purified polymerase from each source has a specific activity of >50,000 U/mg of protein, a sedimentation coefficient of 5.6s, and an estimated molecular weight by gel filtration of 130,000. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the most highly purified M. orale fraction contains a single major protein band of 130,000 daltons, which we believe may represent the polymerase protein. The enzymes are most reactive with gapped (activated) DNA and show a marked preference for this primer template over oligodeoxyribonucleotide-initiated homoribo- or homodeoxyribopolymers. The most purified preparations are devoid of contaminating endonuclease activity and also appear to lack associated 5' -* 3'- or 3' - 5'-exonuclease activities, as determined by highly sensitive assays. The absence of the 3' -* 5'exonuclease is particularly remarkable in that this activity is essentially ubiquitous among the DNA polymerases that have thus far been characterized from procaryotes.
The Mycoplasmatales comprise a group of microorganisms that are the smallest known free-living procaryotes. They are characterized by their minute size (0.25 to 1.0 ,um in diameter), the absence of a cell wall, and a relatively small genome (5 x 101 to 10 x 101 daltons) of presumably limited complexity that has been shown to be a single, circular, double-stranded deoxyribonucleic acid (DNA) molecule (14, 19, 24). Limited studies to date have indicated that mycoplasma DNA replication appears to be semiconservative and to proceed unidirectionally from one or a few growing-point regions (21) that may be in a membrane-associated complex (22). The capacity of at least one Acholeplasma species to carry out light and dark repair of ultraviolet-irradiated DNA has also been described (23). Apart from these few published reports, however, almost nothing is yet known about the biochemical basis of DNA replication in these organisms. Aside from their intrinsic interest, mycoplasmas have increasingly been recognized as common and troublesome contaminants of cell cultures, difficult to detect and difficult to eradicate (19, 24). Moreover, there is now abundant
evidence that such contamination, often unrecognized, can have profound effects on cultured cell properties, including alterations of metabolic properties, induction of chromosomal aberrations, and modifications of cellular morphology that can be mistaken for virus-provoked cytopathic effects (19, 24). In view of the intensive effort that is currently being expended in many laboratories on the identification and characterization of DNA polymerase activities from a variety of cultured eucaryotic cells, we felt it was important to document the properties of the DNA polymerases of representative Mycoplasmatales. In this paper, we present the purification and partial characterization of the principal DNA polymerase activity that we have isolated from crude extracts of two Mycoplasma species that are well-recognized cell culture contaminants, Mycoplasma orale type 1 and M. hyorhinis. In corroboration of the potential value of this undertaking, we note that at least one reported species of eucaryotic DNA polymerase, mitochondrial D-DNA polymerase from HeLa cells (7, 28), has recently been suggested to be a possible mycoplasma activity resulting from
641
642
MILLS ET AL.
J. BACTERIOL.
fuged at 10,000 rpm for 20 min at 4°C. The pellet, which contained organisms and particulate constituents from the growth medium, was washed twice with phosphate-buffered saline (PBS) and then stored frozen at - 70°C as an unpurified mycoplasma pellet. Initial efforts to isolate the DNA polymerase MATERIALS ANI) METHOI)S activity from such pellets revealed unpredictable Materials. Unlabeled deoxyribonucleotides were variations in column chromatographic behavior, purchased from P-L Biochemicals; 3Hldeoxythymi- which we attributed to the presence of undefined dine 5'-triphosphate (dTTP) was from New England medium components in the crude extract. We thereNuclear Corp.; calf thymus DNA was from Calbi- fore introduced an additional procedure to purify ochem; Triton X-100 was from Beckman Instru- the mycoplasma organisms. The crude pellets were ments, Inc.; Sephadex G-25 and G-200 were from suspended in 20 ml of PBS, and 5-ml portions were Pharmacia Fine Chemicals, Inc.; diethylaminoethyl overlayered on 30-ml discontinuous 30 to 60% (wt/ (DEAE)-cellulose (DE-52) and phosphocellulose (P- wt) sucrose gradients in PBS and centrifuged in an 11) resins were from Whatman; acrylamide, bisme- SW25.1 rotor at 10,000 rpm for 60 min. The visible thylene acrylamide, and N,N, N,' N'-tetramethyl- bands of mycoplasma were collected, pooled, susenediamine were from Bio-Rad Laboratories; BDH pended in PBS, and pelleted. The washing and sodium dodecyl sulfate (SDS) was from Gallard- centrifugation steps were repeated, and the final Schlesinger; bovine serum albumin and 7S immu- pellet was stored at -70'C as a purified mycoplasma noglobulin were from Sigma Chemical Co.; ovalbu- preparation. Just before the last centrifugation, the min was from Pharmacia; and ,3-galactosidase was PBS suspension was assayed for mycoplasma CFU. from Worthington Biochemical Corp. Coomassie The majority of harvests yielded a total of 1 x 101' brilliant blue was from Schwarz/Mann, and amido to 5 x 1012 CFU. Standard I)NA polvmerase assay. The standard black lOB was from Baker. LKB ampholytes were used for isoelectric focusing. Polydeoxyadenylate assay was run for 10 min at 37TC and contained the lpoly(dA)d was from Collaborative Research, and following in a total volume of 0.25 ml: tris(hydroxypolyadenylate [poly(A)] and poly(deoxyadenylate- methyl )aminomethane Tris )-hydrochloride (pH deoxythymidylate) Lpoly(dA-dT) were from Miles 8.5), 10 mM; ,6-mercaptoethanol, 2.0 mM; bovine Laboratories, Inc. Heat-denatured calf thymus serum albumin, 50 ug; MgCl2, 20 mM; KCl, 100 DNA-cellulose (Cellex-N-1; Bio-Rad) was prepared mM; activated calf thymus DNA (20), 200 gtg/ml; (1) by D. C. Eichler, Stanford University. Oligo(dT)rm deoxyadenosine 5'-triphosphate, deoxyguanosine 5'and oligo(dT)7-[3H]deoxycytidylate (dC)7) (specific triphosphate, deoxycytidine 5'-triphosphate, and activity, 14,000 cpm/pmol) were prepared (26) by T. dTTP, 100 ,kM each; liH]dTTP, 40 mCi/mmol; and S-F. Wang, Stanford University, using d(pT)4 (Col- enzyme. In addition, 0.1% Triton X-l00 was incorlaborative Research) as initiator. Terminal deoxy- porated into the reaction with the most highly nucleotidyl-transferase (13,000 U/mg), purified from purified enzyme fractions, since it appeared to calf thymus, was a gift from R. L. Ratliff, Los enhance the reproducibility of the assays. The reacAlamos Scientific Laboratory; bacteriophage T4 tions were terminated and processed as previously DNA polymerase, phosphocellulose fraction (15) described (20). One unit of DNA polymerase activity (-15,000 U/mg), was from N. G. Nossal, National is defined as the amount catalyzing the incorporaInstitutes of Health; ColEl form I [1'C]DNA (4,000 tion of 1 nmol of labeled deoxythymidine 5'-monocpm/,tg) and PM2 form I 1IHIDNA (1,600 cpm/,ug) phosphate into acid-insoluble product in 60 min at were the gift of D. A. Clayton, Stanford University; 37'C under standard reaction conditions. Specific and specifically incised, ultraviolet-irradiated E. activity is expressed as units per milligram of procoli V:'H]DNA (1.7 x 105 cpm//Ig) was provided by tein. All enzymatic properties were determined under conditions of linearity with respect to time K. H. Cook, Stanford University. Growth and harvest of mycoplasmas. M. hvor- and protein. hinis and M. orale type I were grown in a modified Glycerol gradient centrifugation. Linear 20 to Hayflick medium (9) consisting of 85 volumes of 40% (vol/vol) glycerol gradients were prepared in 50 beef heart infusion broth (Difco). 10 volumes of mM potassium phosphate (pH 7.5) and 1 mM each unheated horse serum (Irvine Scientific), 5 volumes ethylenediaminetetraacetic acid (EDTA) and /3of a 25% stock solution of freshly prepared yeast mercaptoethanol. with or without KCl at 0.5 M. extract (Standard Brands, Inc.), and glucose and Enzyme sample (0.25 ml) was layered onto the top arginine at a final concentration of 1%J. ()wt/vol) of the gradient and overlayered with mineral oil. each. Penicillin G at a final concentration of 100 U/ Sedimentation was carried out at 50,000 rpm for 24 ml was added to prevent bacterial contamination. h at 5C in an SW50.1 rotor. Fractions of 0.25 ml Flasks containing 500 ml of prewarmed growth were collected dropwise from the bottom of the tube, medium were inoculated with 5 ml of an actively and portions were tested in the standard polymerase growing culture at a density of 10'; to 10 organisms assay. Polyacrylamide gel electrophoresis. SDS-poly-. per ml and incubated 3 to 4 days at 37°C. Growth of organisms was monitored by assay of colony-form- acrylamide gels, 3 mm in diameter and containing ing units (CFU) on agar (19). Two hours before 7% acrylamide, were prepared and run according to harvest, 50 to 100 ml of prewarmed growth medium Laemmli (11), without stacking gel. Samples were was added to each culture. The cultures were centri- prepared for electrophoresis by alternate concentra-
culture contamination (la). The properties of that enzyme are very similar to those of the highly purified mycoplasma polymerases that we describe in this report.
VOL. 132, 1977
DNA POLYMERASE FROM MYCOPLASMATALES
tion against dry Sephadex G-200 beads and dialysis versus 0.05 M Tris-hydrochloride (pH 7.2), 1% SDS, 1% f3-mercaptoethanol, and 20% (vol/vol) glycerol, until the sample volume had been reduced to
