US20020192788A1 - Deoxynucleoside kinase from insect cells for the synthesis of nucleoside monophosphates - Google Patents

Deoxynucleoside kinase from insect cells for the synthesis of nucleoside monophosphates Download PDF

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Publication number
US20020192788A1
US20020192788A1 US09/416,579 US41657999A US2002192788A1 US 20020192788 A1 US20020192788 A1 US 20020192788A1 US 41657999 A US41657999 A US 41657999A US 2002192788 A1 US2002192788 A1 US 2002192788A1
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kinase
recombinant kinase
synthesis
recombinant
nucleoside
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Abandoned
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US09/416,579
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English (en)
Inventor
Hans-Georg Ihlenfeldt
Brigitte Munch-Petersen
Jure Piskur
Leif Sondergaard
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Roche Diagnostics GmbH
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Roche Diagnostics GmbH
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Priority claimed from DE1998146838 external-priority patent/DE19846838A1/de
Priority claimed from DE1999114644 external-priority patent/DE19914644A1/de
Application filed by Roche Diagnostics GmbH filed Critical Roche Diagnostics GmbH
Assigned to ROCHE DIAGNOSTICS GMBH reassignment ROCHE DIAGNOSTICS GMBH ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: PISKUR, JURE, SONDERGAARD, LEIF, MUNCH-PETERSEN, BRIGITTE, IHLENFELDT, HANS-GEORG
Publication of US20020192788A1 publication Critical patent/US20020192788A1/en
Priority to US10/680,635 priority Critical patent/US7625735B2/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1205—Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases

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  • the subject of the present invention is a recombinant kinase from insect cells such as e.g. Drosophila Melanogaster, remaining stable during the synthesis of nucleoside monophosphates without the addition of stabilizing SH reagents, without stabilizing proteins and detergents and accepting all four natural deoxynucleosides.
  • a further subject matter of the present invention is a DNA sequence encoding the kinase according to the invention as well as a procedure for preparation of the kinase according to the invention and its use during the synthesis of nucleoside monophosphates.
  • (Deoxy)-nucleoside kinases catalyze the phosphorylation of nucleosides or deoxynucleosides, respectively, to the corresponding nucleotide monophosphates and have therefore an important role in the “salvage pathway” of the nucleotide metabolism.
  • deoxynucleoside monophosphates are starting products for the deoxynucleoside tri-phosphates which are used to a very increasing extent as reagents for the PCR reaction.
  • deoxynucleoside monophosphates are at present accessible by three ways:
  • stable means that the yield rate for the catalyzed reaction does practically not decrease within 5 hours, preferably 10 hours, particularly preferably within 12 hours at 37° C. It is surprising that the enzyme remains stable for such a long time without addition of stabilizers containing thiol. This stability has not been observed in other kinases until now (1-9). By leaving out these stabilizers when using the kinase according to the invention in the synthesis the synthesis gets cheaper and, above all, the product purification can be simplified to a great extent.
  • kinases have a considerably higher substrate specificity; as a consequence, for the synthesis of the individual nucleosides it is no more necessary to have the corresponding specific kinase.
  • Particularly advantageous is the low specificity for the synthesis of modified nucleoside analogues, such as dideoxynucleosides or base- or sugar-modified nucleosides.
  • Base-modified nucleosides are for example 7-deaza-nucleosides, C-nucleosides and nucleotides labelled with reporter groups (dye, digoxigenin, biotin) at the base.
  • Sugar-modified nucleosides are for example azathymidine, arabinosyl-thymidine.
  • the kinetic constants of the Drosophila kinase compared to known analogous enzymes are listed in table 1.
  • the specific activity kc of the kinase according to the invention is several times higher than that of the kinases known before.
  • the activity of the enzyme was measured as described in the reference: Munch-Peterson et al. (1991) J.Biol.Chem. 266, 9032-9038. By this, a considerably lower amount of enzyme is necessary to synthesize the dNMPs. (factor 3.5—14000, cf. Kc values in table 1).
  • the specificity constant (k c /K M ) of the kinase according to the invention exceeds that of the hitherto known kinases by several powers and is in the region of the diffusion constant. This leads to the complete yield when the kinase is added to the d-NMP synthesis. They are higher by factor 2-6500 than the hitherto known kinases, s. FIG. 1.
  • the enzyme according to the invention is still stable at 60° C. what is advantageous for the reaction procedure.
  • a further subject matter of the invention are kinases from other non-vertebrate organisms, in particular from other animal species of the Hexapoda class showing comparable properties to those of the Drosophila kinase.
  • kinases essentially having the above described stability and the above described substrate specificity.
  • Peferred kinases are those isolated from the subclass of Pterygota and particularly preferable are those from the Diptera class, particularly preferable from the Drosophilidae family.
  • a further subject matter of the invention is a DNA sequence as well as functional fragments thereof coding for the kinase according to the invention.
  • the DNA sequence according to the invention is characterized in that the primers listed in the following hybridize onto the DNA sequence of the kinase according to the invention: GGGAAGTGGCAGGAGTAGCTCCCG SEQ ID No.: 2 CTCCCGTTGTAG CCG TCGCCCTTCTGG SEQ ID No.: 3 GAC GACTGGCTCGGG CAG CTCTTCACCGCG TTG SEQ ID No.: 4 TTCGATTTTTATTACCTCGCGAGGTAA SEQ ID No.: 5 AGGTAA AAA TCGCGAGCGATA ACG AAGCAC SEQ ID No.: 6 CACCGCATGCTTGCGTAGGCCGTCGCCCGAGCAAGACTCCTC SEQ ID No.: 7 GACTACATGTTTCTAGGGTTCTTCACC SEQ ID No.: 8
  • a further subject matter of the invention are also such kinases and DNA sequences onto the DNA sequence of which hybridize oligonucleotides with the SEQ ID No.: 2, 3, 5, 7 and 8 or with the SEQ ID No.: 2, 4, 5, 7 and 8 or with the SEQ ID No.: 2. 5, 6, 7 and 8.
  • Hybridization 0.75 M NaCl, 0.15 Tris, 10 mM EDTA, 0.1% sodium pyrophosphate, 0.1% SLS, 0.03% BSA, 0.03% Ficoll 400, 0.03% PVP and 100 ⁇ d/ml boiled calf thymus DNA at 50° C. for approx. 12 hours.
  • DNA sequence according to the invention is obtainable from Drosophila Melanogaster by the procedure described in the following:
  • a pBluescript SK +/ ⁇ phagmide containing a 1.1 kbp cDNA insert which contains among others the presumed gene coding for the deoxynucleoside kinase was obtained from the Berkeley Drosophila genome sequencing project (clone LD15983).
  • the first 600 base pairs of the 5′ end of the 1.1 kbp cDNA cloned via EcoRI and XhoI in the multiple cloning site (MCS) of the phagmide were already sequenced by Harvey et al., University of California, Berkeley.
  • Dm-TK1 and Dm-TK2/SEQ ID NO.9 5′TCCCAATCTCACGTGCAGATC-3′ and SEQ ID NO 10: 5′-TTCATCGAAGAGTCCATTCAC-3′ which enabled complete sequencing of the insert.
  • Dm-TK1 is a 21 bp sense primer binding upstream from the presumed translation start region.
  • Dm-TK2 was designed as 21 bp sense primer according to the 3′ region of the cDNA part already sequenced.
  • the structure gene coding for the Dm-dNK could be isolated from the 1.1 kbp cDNA insert of the pBluescript SK +/ ⁇ phagmide by the “polymerase chain reaction” technique (PCR) (Mullis, K. B. and Faloona, F. A., Methods in Enzymol. 155 (1987) 335-350).
  • PCR polymerase chain reaction
  • the PCR preparation was applied to an agarose gel and the 750 Bp structure gene was isolated from the agarose gel.
  • the PCR fragment was cut with the EcoRI and HindIII restriction endonucleases for 1 hour at 37° C.
  • the pUC18 plasmid was cut with the EcoRI and HindIII restriction endonucleases for 1 hour at 37° C., the preparation was then separated by agarose gel electrophoresis and the 2635 Bp vector fragment isolated. Subsequently, the PCR fragment and the vector fragment were ligated by T4-DNA-ligase.
  • the structure gene was cloned in appropriate expression vectors in such a way that the structure gene is inserted in the right orientation under the control of an appropriate promoter, preferably an inducible promoter, particularly preferably the lac-, lacUV5-, tac- or T5 promoter.
  • an appropriate promoter preferably an inducible promoter, particularly preferably the lac-, lacUV5-, tac- or T5 promoter.
  • Preferred expression vectors are pUC plasmids with lac- or lacUV5 promoters or pKK plasmids.
  • the structure gene was cut out of the plasmid pUC 18 for the Dm-dNK by means of EcoRI and HindIII, the restriction preparation was separated by agarose gel electrophoresis and the approx. 750 Bp fragment was isolated from the agarose gel. Simultaneously, the expression vectors were cut with EcoRI and HindIII, the restriction preparation was separated by agarose gel electrophoresis and the resulting vector fragment was isolated from the agarose gel. The resulting fragments were ligated as described. The appropriate insertion of the gene was verified by restriction analysis and sequencing.
  • Preferred expression vectors are also pUC18, pKK177-3, pKKT5.
  • pKKT5 is obtained from pKK177-3 (Kopetzki et al. 1989, Mol. Gen. Genet. 216:149-155) by exchanging the tac- promotors with the T5-promoter derived from the plasmid pDS (Bujard et al. 1987, Methods Enzymol. 155:416-433).
  • the EcoRI-endonuclease restriction site was removed from the sequence of the T5-promotor by point mutation.
  • Competent cells of different E. coli strains were prepared according to the Hanahan method (J. Mol. Biol. 166 (1983) pp. 557). 200 ⁇ l of the resulting cells were mixed with 20 ng of isolated plasmid DNA (expression vectors). After 30 min. incubation on ice a thermal shock (90 sec. at 42° C.) was carried out. Subsequently, the cells were transferred in 1 ml LB-medium and incubated for phenotypical expression for 1 hour at 37° C. Aliquots of this transformation preparation were plated on LB plates with ampicillin as a selection marker and then incubated for 15 hours at 37° C.
  • Appropriate host cells are E. coli K12 JM83, JM101, JM105, NM522, UT5600, TG1, RR1 ⁇ M15, E.coli HB101, E.coli B.
  • Dm-dNK clones containing plasmid were inoculated in 3 ml Lb amp medium and incubated in the shaker at 37° C. At an optical density of 0.5 at 550 nm the cells were induced with 1 mM IPTG and incubated in the shaker for 4 hours at 37° C. Subsequently, the optical density of the individual expression clones was determined an aliquot with an OD 550 of 3/ml was taken and the cells were centrifuged (10 min. at 6000 rpm, 4° C.).
  • the cells were resuspended in 400 ⁇ l TE buffer (50 mM TRIS/50 mM EDTA, pH 8.0), released by ultrasound and then the soluble protein fraction was separated from the insoluble protein fraction by centrifugation (10 min., 14000 rpm, 4° C.). A buffer containing SDS and ⁇ -mercaptoethanol was added to all fractions and the proteins were denatured by boiling (5 min. at 100° C.). Subsequently, each quantity of 10 ⁇ l was analyzed by means of a 15% analytical SDS gel (Laemmli U. K. (1970) Nature 227: pp. 555-557).
  • a further subject matter of the invention is a method for production of the nucleoside monophosphates which is characterized in more detail by the following steps:
  • nucleotide triphosphate as a phosphate group donor in catalytic amounts
  • nucleoside monophosphate As a nucleoside monophosphate according to the invention the original nucleoside monophosphates, deoxynucleoside monophosphates, dideoxynucleoside monophosphates as well as other sugar- and base-modified nucleoside monophosphates are applicable.
  • a further subject matter of the present invention is the use of the kinase according to the invention in the synthesis of the nucleoside monophosphate.
  • FIG. 1
  • FIG. 2 [0057]FIG. 2:
  • FIG. 2 shows the formation of d-CMP from cytidine under the conditions mentioned in example 2.
  • FIG. 3 [0059]FIG. 3:
  • FIG. 3 shows the formation of d-AMP from adenosine and d-GMP from guanosine under the conditions mentioned in example 4.
  • FIG. 4 is a diagrammatic representation of FIG. 4
  • FIG. 4 shows the formation of d-CMP from cytidine under the conditions mentioned in example 3.
  • FIG. 5 [0063]FIG. 5:
  • FIG. 5 shows the DNA sequence of the clone.
  • FIG. 6 is a diagrammatic representation of FIG. 6
  • FIG. 6 shows the temperature optimum of the nucleoside kinase from D. Melanogaster.
  • FIG. 7 [0067]
  • FIG. 7 shows the stability of the recombinant Dm-nucleoside kinase compared to isolated Dm-nucleoside kinase.
  • FIG. 7A was determined without addition of BSA
  • FIG. 7B with addition of BSA.
  • TK1 thymidine kinase
  • An E. coli strain BL21 was transformed with a pGEX-2T vector (Amersham Pharmacia Biotec), in which the structure gene of the Dm kinase was cloned, by means of the CaCl 2 method (Sam-brook, Molecular cloning, 2 nd ed. Cold Spring Harbor Laboratory press).
  • a transformed colony was suspended in 100 ml LB medium (10 mg tryptone, 5 mg yeast extract, 8 mg NaCl per 1), containing 50 ⁇ g/ml ampicilline, over night at 37° C. The next day, the culture was adjusted to an OD of 0.6 in 1 l of LB medium and the expression was induced by 100 ⁇ l IPTG. The culture temperature of 25° C.
  • the cells were resuspended in 100 ml of buffer A (20 mM of potassium phosphate (pH 7.5), 5 mM MgCl 2 , 1 mM DTT, 10% glycerin, 1% Triton X100 and 0.1 mM phenylsulfonylfluorides). The mixture was broken up by the French press. The homogenized substance was centrifuged (20000 rpm/15 min.) and filtered with a 1 ⁇ m Whatman glass micro filter and a 0.45 ⁇ m cellulose acetate filter.
  • buffer A (20 mM of potassium phosphate (pH 7.5), 5 mM MgCl 2 , 1 mM DTT, 10% glycerin, 1% Triton X100 and 0.1 mM phenylsulfonylfluorides). The mixture was broken up by the French press. The homogenized substance was centrifuged (20000 rpm/15 min.) and filtered with a 1 ⁇
  • the homogenized substance was applied to a GSH column (15 ⁇ 45 mm), equilibrated with 10 column volumes of buffer B (140 mM NaCl, 2.7 mM KCL, 10 mM Na 2 HPO 4 , 1.8 mM KH 2 PO 4 , 1 mM DTT, 10% glycerol, 1% Triton X100, 0.1, mM phenylsulfonylfluoride, 5 mM benzamidine, 50 mM aminocaproic acid).
  • buffer B 140 mM NaCl, 2.7 mM KCL, 10 mM Na 2 HPO 4 , 1.8 mM KH 2 PO 4 , 1 mM DTT, 10% glycerol, 1% Triton X100, 0.1, mM phenylsulfonylfluoride, 5 mM benzamidine, 50 mM aminocaproic acid).
  • the column was washed with 50 bed volumes of buffer B and 10 volumes of buffer C (140 mM NaCl, 2.7 mM KCl, 10 mM NaH 2 PO 4 , 1.8 mM KH 2 PO 4 ) and afterwards the fusion protein was split by recirculation of 1 column volume of buffer C with 400 U thrombin for 2 hours.
  • the Dm-nucleoside kinase was then eluted with 3 column volumes of buffer C.
  • the yield is determined by the integration of the peak areas using HPLC.
  • the half-life in Tris buffer in the presence of MgCl 2 is 50 h, without MgCl 2 31 h and in pure water 28 h.
  • the native Dm-kinase has a half-life of ⁇ 12 min. under the same conditions.

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US09/416,579 1998-10-12 1999-10-12 Deoxynucleoside kinase from insect cells for the synthesis of nucleoside monophosphates Abandoned US20020192788A1 (en)

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DE1998146838 DE19846838A1 (de) 1998-10-12 1998-10-12 Deoxynukleosidkinase aus Insektenzellen zur Nukleosidmonophosphatsynthese
DE19846838.5 1998-10-12
DE19914644.6 1999-03-31
DE1999114644 DE19914644A1 (de) 1999-03-31 1999-03-31 Deoxynukleosidkinase aus Insektenzellen zur Nukleosidmonophosphatsynthese

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021188840A1 (en) * 2020-03-19 2021-09-23 Rewrite Therapeutics, Inc. Methods and compositions for directed genome editing
US11649442B2 (en) 2017-09-08 2023-05-16 The Regents Of The University Of California RNA-guided endonuclease fusion polypeptides and methods of use thereof

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* Cited by examiner, † Cited by third party
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CN1429268A (zh) * 2000-05-12 2003-07-09 沃尔夫冈·肯特 新型脱氧核苷激酶多底物变体
CN105647995B (zh) * 2016-02-29 2019-03-08 山东大学 一种提取2′，3′-环形核苷单磷酸的方法
JP6701450B2 (ja) * 2017-07-05 2020-05-27 オリシロジェノミクス株式会社 Ｄｎａの産生方法及びｄｎａ断片連結用キット

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11649442B2 (en) 2017-09-08 2023-05-16 The Regents Of The University Of California RNA-guided endonuclease fusion polypeptides and methods of use thereof
US11649443B2 (en) 2017-09-08 2023-05-16 The Regents Of The University Of California RNA-guided endonuclease fusion polypeptides and methods of use thereof
WO2021188840A1 (en) * 2020-03-19 2021-09-23 Rewrite Therapeutics, Inc. Methods and compositions for directed genome editing
US11193123B2 (en) 2020-03-19 2021-12-07 Rewrite Therapeutics, Inc. Methods and compositions for directed genome editing
US11352623B2 (en) 2020-03-19 2022-06-07 Rewrite Therapeutics, Inc. Methods and compositions for directed genome editing

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EP0999275A3 (de) 2002-09-25
CA2284101A1 (en) 2000-04-12
EP0999275B1 (de) 2005-01-19
US7625735B2 (en) 2009-12-01
CA2284101C (en) 2009-01-27
US20060252131A1 (en) 2006-11-09
ATE287452T1 (de) 2005-02-15
DE69923274T2 (de) 2006-03-30
DE69923274D1 (de) 2005-02-24
EP0999275A2 (de) 2000-05-10
JP2000139481A (ja) 2000-05-23
DK0999275T3 (da) 2005-05-30
JP4350235B2 (ja) 2009-10-21

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