HEPARINASE GENE FROM FLAVOBACTERIUM HEPARINUM

Abstract: The cloning of the heparinase gene from Flavobacterium Heparinum using the polymerase chain reaction is described. The Open Reading Frame (ORF) corresponded to 1152 base pairs encoding a precursor protein of MW 43,800 daltons. The amino acid sequence reveals a 20-residue leader peptide. The gene was expressed in two expression systems in E. Coli.

Description: HEPARINASE GENE FROM FLAVOBACTERIUM HEPARINUM Background of the Invention This invention is generally in the area of heparinases and is specifically directed to the gene encoding heparinase I, expressed in Flavobacterium heparinum. The United States government has rights in this invention by virtue of grant number 25810 from the National Institutes of Health. Heparin is an anticoagulant that activates serine protease inhibitors (serpins) , which play a key role in the blood clotting cascade, as described by Da us et al.. Nature 246:355-357 (1973). According to Lindahl et al.. Trends Biochem . Sci . 11:221-225 (1986) , heparin is the most acidic natural polymer known to date. It consists of a major 1,4-linked disaccharide repeating unit of D-uronic acid 1,4-β-D-glucosamine, and has an average of four negative charges (three sulfate groups and one carboxylate group) per monosaccharide unit. Heparin is both polydisperse, having an average molecular weight between 3,000 and 45,000 daltons, and heterogenous due to partial epimerization of D-glucuronic acid to L-iduronic acid and incomplete N- and 0- sulfation, as reported by Kusche et al., Proc. Natl . Acad. Sci . , 77:6551-6555 (1980) and Comper, Polymer Monograph 7, 1981. In addition, proteoglycans like heparin have a wide range of biological influences, including in blood chemistry, growth factor interaction and wound healing, interaction with basic structural proteins in the extracellular matrix and in cellular mediated immune responses. The basic nature of protein/peptide heparin/complex carbohydrate interaction is important. Although heparin seems fairly heterogenous, it is now quite clear that different heparin fractions exhibit distinct and unique properties indicating some compositional and possibly structural specificity for its biological role, as reviewed by Cardin, A. D. and H. J. R. Weintraub, Arteriosclerosis 9, 21-32 (1989). Heparinase, also referred to as heparin lyase, is the only known enzyme capable of degrading heparin that has been extensively characterized. It has been designated EC 4.2.2.7 by the Enzyme Commission. According to Galliher, et al., Eur. J. Appl . Microbiol . 15:252 (1982), the enzyme is a polysaccharide lyase found in the periplasmic space of Flavobacterium heparinum, a Gram-negative soil isolate. F. heparinum utilizes heparin as its sole source of carbon and nitrogen, as described by Hoving and Linker, «7. Biol . Chem. 245:6170 (1970). Heparinase is the initial enzyme of heparin catabolism. Although constitutively expressed in low amounts, Galliher, et al., App. Environ. Microbiol . 41:360 (1981), have discovered that enzyme expression is induced by heparin and reversibly repressed by sulfate in the medium. Lindhardt, et al., Appl . Bioche . Biotechnol . 9:41 (1984), have shown that heparinase is inhibited by other polyanionic polysaccharides. Heparinase has been purified by standard chromatographic techniques and its enzymatic properties characterized extensively, as described by scientists including Yang, et al., J. Biol . Chem . 260:1849 (1985). The enzyme is a 44,000 dalton monomeric protein with a pi of approximately 9. Heparinase acts as an eliminase, leaving behind an unsaturated double bond at the non-reducing end group. This double bond is exploited in an assay for heparinase activity by the absorbance of the unsaturated product at 232 nm. The enzyme is marginally tolerant to salts and is very specific for heparin, having a k d of 30 nM. Heparinase has an activation energy of 4.5 kcal/mol, a km of 8 x 10-6 and a V ax of 4 x 10-7 M/min. Heparin is often used in surgery to prevent blood clotting and to increase the compatibility of extracorporeal devices such 30 as heart-lung and kidney dialysis machines. The enzymatic degradation of heparin by heparinase is sufficient to eliminate the anticoagulation properties of heparin in surgery. As described by Langer, et al. in Biomaterials : Inter-facial Phenomenon and Applications , Adv. in Chem . Symposium Series , Chap. 13, pp. 493-509 (1982), this property has led to the use of heparinase as an immobilized bioreactor in conjunction with heart-lung or kidney dialysis machines to deheparinize blood. Commercial application of the heparinase bioreactor is pending clinical trials. A principal problem in the use of the heparinase bioreactor is the availability of sufficient amounts of pure heparinase to be immobilized onto a surface. This is primarily because the amount of heparinase constitutively expressed in F. heparinum is very low. Inducing expression of heparinase in F. heparinum with heparin is very expensive due to the amounts of heparin needed and the size of the fermentation to produce reasonable amounts of heparinase for any practical applications. Cloning and expression of the heparinase gene is important in several ways. First, the only enzyme cloned and characterized to date which acts to depolymerise proteoglycans is heparinase. Second, heparin is the only anticoagulant commonly used in surgery so deheparinizing blood is an important medical problem. Moreover, heparinase catalyzed degradation of heparin into lower molecular weight heparin molecules can be used to yield products with specific anticoagulant activity, as discussed by Rosenf ld and Danishefsky, Biochem . J. 237:639-646 (1986) . Designing recombinant heparinases with altered activitie(s) would be interesting academically, as well as commercially. For example, heparinase can be used to deheparinize blood because the enzyme cleaves right at the AT-III binding oligomer. On the other hand, by further understanding the mechanism of the enzyme binding and depolymerizing heparin, recombinant heparinases with altered specificity could be designed, i.e. an AT-III binding heparin fragment not cleaved by the recombinant enzyme. This would be a very useful way of generating an AT-III binding heparin oligosaccharide, which currently is not available in large amounts, for use as an anticoagulant. Producing heparinases which could help and or improve in the enzyme purification or immobilization would also be quite valuable. For example, a tag (a particular peptide sequence) could be added at a region which does not alter the activity of the enzyme but makes the immobilization chemistry very efficient. This would help in improving enzyme loading onto the immobilization matrix. It is therefore an object of the present invention to provide the gene encoding heparinase and a system for expression to facilitate the production of large amounts of heparinase. It is another object of the present invention to provide methods and means for modifying the gene to produce recombinant heparinases having altered specificity and other desirable properties. It is another object of the present invention to provide pure heparinase for use in the area of cytokine-proteoglycan interactions, as a tool or diagnostic as exemplified by fibroblast growth factor - heparin interactions. Summary of the Invention The cloning of the heparinase gene from Flavobacterium Heparinum using the polymerase chain reaction is described. Two degenerate oligonucleotides, based on amino acid sequence derived from tryptic peptides of purified heparinase were used in the PCR with Flavobacterium genomic DNA as the template to generate a 600 base pairs probe. This probe was used to screen a pUC 18 Flavobacterium genomic library. The Open Reading Frame (ORF) corresponded to 1152 base pairs encoding a precursor protein of MW 43,800 daltons. Eleven different tryptic peptides (approximately 48% of the total amino acids) mapped into the ORF. The amino acid sequence reveals a 20-residue leader peptide. Heparinase can be expressed from the gene. Additionally, the gene can be modified to produce heparinase with altered enzymatic activity, specificity, or binding properties. The sequence can also be used as a probe in the isolation of genes encoding other related enzymes. Brief Description of the Drawings Figure 1 is a schematic representation of the PCR products Y1:C and D:C which are 600 and 160 basepairs, respectively. The 600 basepair PCR product was used as a template with D and C as primers to generate the 160 basepair D:C product. Figure 2 is the restriction map of the genomic DNA pUC 18 plasmid, pRS.HEP51, having an insert containing the heparinase gene. The plasmid is 5631 bases long and has approximately 2300 bases of insert. The heparinase gene is in the Kpn I-Kpnl fragment. Figure 3 is a Kpnl-Kpnl fragment map showing the heparinase gene structure with the different tryptic peptides mapping into the open reading frame. Six different peptides mapped into the heparinase gene translation region. Detailed Description of the Invention The gene encoding heparinase in F. heparinum has been cloned. The nucleotide and amino acid sequences are shown below: The following sequence (Sequence No. 1, base pairs 1 to 172, inclusive) encodes a leader peptide: CCTTT TGGGA GCAAA GGCAG AACCA TCTCC GAACA AAGGC AGAAC CAGCC TGTAA ACAGA CAGCA ATTCA TCCGC TTTCA ACCAA AGTGA AAGCA TTTAA TACAA TACCA GAATG TCGCA TTTCC CTTTC AGCGT ACTTT TTGGG TAAAT AACCA ATAAA AACTA AAGAC GG The following sequence (Sequence No. 1, base pairs 173 to 1379, inclusive) encodes the heparinase: ATG AAA AAA CAA ATT CTA TAT CTG ATT GTA CTT CAG CAA CTG TTC CTC TGT TCG GCT TAC GCC CAG CAA AAA AAA TCC GGT AAC ATC CCT TAC CGG GTA AAT GTG CAG GCC GAC AGT GCT AAG CAG AAG GCG ATT ATT GAC AAC AAA TGG GTG GCA GTA GGC ATC AAT AAA CCT TAT GCA TTA CAA TAT GAC GAT AAA CTG CGC TTT AAT GGA AAA CCA TCC TAT CGC TTT GAG CTT AAA GCC GAA GAC AAT TCG CTT GAA GGT TAT GCT GCA GGA GAA ACA AAG GGC CGT ACA GAA TTG TCG TAC AGC TAT GCA ACC ACC AAT GAT TTT AAG AAA TTT CCC CCA AGC GTA TAC CAA AAT GCG CAA AAG CTA AAA ACC GTT TAT CAT TAC GGC AAA GGG ATT TGT GAA CAG GGG AGC TCC CGC AGC TAT ACC TTT TCA GTG TAC ATA CCC TCC TCC TTC CCC GAC AAT GCG ACT ACT ATT TTT GCC CAA TGG CAT GGT GCA CCC AGC AGA ACG CTT GTA GCT ACA CCA GAG GGA GAA ATT AAA ACA CTG AGC ATA GAA GAG TTT TTG GCC TTA TAC GAC CGC ATG ATC TTC AAA AAA AAT ATC GCC CAT GAT AAA GTT GAA AAA AAA GAT AAG GAC GGA AAA ATT ACT TAT GTA GCC GGA AAG CCA AAT GGC TGG AAG GTA GAA CAA GGT GGT TAT CCC ACG CTG GCC TTT GGT TTT TCT AAA GGG TAT TTT TAC ATC AAG GCA AAC TCC GAC CGG CAG TGG CTT ACC GAC AAA GCC GAC CGT AAC AAT GCC AAT CCC GAG AAT AGT GAA GTA ATG AAG CCC TAT TCC TCG GAA TAC AAA ACT TCA ACC ATT GCC TAT AAA ATG CCC TTT GCC CAG TTC CCT AAA GAT TGC TGG ATT ACT TTT GAT GTC GCC ATA GAC TGG ACG AAA TAT GGA AAA GAG GCC AAT ACA ATT TTG AAA CCC GGT AAG CTG GAT GTG ATG ATG ACT TAT ACC AAG AAT AAG AAA CCA CAA AAA GCG CAT ATC GTA AAC CAG CAG GAA ATC CTG ATC GGA CGT AAC GAT GAC GAT GGC TAT TAC TTC AAA TTT GGA ATT TAC AGG GTC GGT AAC AGC ACG GTC CCG GTT ACT TAT AAC CTG AGC GGG TAC AGC GAA ACT GCC AGA TAG (stop codon) The following is the amino acid sequence (Sequence No. 2) of heparinase: Met Lys Lys Gin lie Leu Tyr Leu lie Val Leu Gin Gin Leu Phe Leu Cys Ser Ala Tyr Ala Gin Gin Lys Lys Ser Gly Asn lie Pro Tyr Arg Val Asn Val Gin Ala Asp Ser Ala Lys Gin Lys Ala lie lie Asp Asn Lys Trp Val Ala Val Gly lie Asn Lys Pro Tyr Ala Leu Gin Tyr Asp Asp Lys Leu Arg Phe Asn Gly Lys Pro Ser Tyr Arg Phe Glu Leu Lys Ala Glu Asp Asn Ser Leu Glu Gly Tyr Ala Ala Gly Glu Thr Lys Gly Arg Thr Glu Leu Ser Tyr Ser Tyr Ala Thr Thr Asn Asp Phe Lys Lys Phe Pro Pro Ser Val Tyr Gin Asn Ala Gin Lys Leu Lys Thr Val Tyr His Tyr Gly Lys Gly lie Cys Glu Gin Gly Ser Ser Arg Ser Tyr Thr Phe Ser Val Tyr lie Pro Ser Ser Phe Pro Asp Asn Ala Thr Thr lie Phe Ala Gin Trp His Gly Ala Pro Ser Arg Thr Leu Val Ala Thr Pro Glu Gly Glu lie Lys Thr Leu Ser lie Glu Glu Phe Leu Ala Leu Tyr Asp Arg Met lie Phe Lys Lys Asn lie Ala His Asp Lys Val Glu Lys Lys Asp Lys Asp Gly Lys lie Thr Tyr Val Ala Gly Lys Pro Asn Gly Trp Lys Val Glu Gin Gly Gly Tyr Pro Thr Leu Ala Phe Gly Phe Ser Lys Gly Tyr Phe Tyr lie Lys Ala Asn Ser Asp Arg Gin Trp Leu Thr Asp Lys Ala Asp Arg Asn Asn Ala Asn Pro Glu Asn Ser Glu Val Met Lys Pro Tyr Ser Ser Glu Tyr Lys Thr Ser Thr lie Ala Tyr Lys Met Pro Phe Ala Gin Phe Pro Lys Asp Cys Trp lie Thr Phe Asp Val Ala lie Asp Trp Thr Lys Tyr Gly Lys Glu Ala Asn Thr lie Leu Lys Pro Gly Lys Leu Asp Val Met Met Thr Tyr Thr Lys Asn Lys Lys Pro Gin Lys Ala His He Val Asn Gin Gin Glu He Leu He Gly Arg Asn Asp Asp Asp Gly Tyr Tyr Phe Lys Phe Gly He Tyr Arg Val Gly Asn Ser Thr Val Pro Val Thr Tyr Asn Leu Ser Gly Tyr Ser Glu Thr Ala Arg. Example 1: Isolation and analysis of CDNA encoding heparinase in F. heparinum. Because preliminary cloning attempts by others utilizing 1) antibody screening, 2) screening for functionally active heparinase in E. cόli and 3) screening for the heparinase gene using probes derived from protein sequences regenerated by cyanogen bromine (CNBr) chemical digest were unsuccessful, the polymerase chain reaction was used to clone the heparinase gene. The reverse phase purified heparinase was reduced, alkylated and digested with trypsin to obtain approximately 60 peptide peaks which were separated and collected by reverse phase HPLC monitored at 210 nm and at 277 nn (for tyrosine and tryptophan) , as described below. Tryptic Digest and Protein Sequence Analyses Heparinase was purified as described by Dietrich, et al. , J. Biol . Chem . 248:6408 (1973), Otatani et al. , Carbohyd. Res. 88:291 (1981), and Yang et al. , J. Biol . Chem. 260:1849 (1985), which are incorporated by reference herein. A final purification step was carried out by High Performance Liquid Chromatography (HPLC) using a reverse phase column that exploits the hydrophobic residues of the protein. A nano ole (approximately 45 μg) of the purified enzyme was denatured in 50 μl of an 8 M urea, 0.4 M ammonium carbonate solution, reduced with 5 mM dithiothreitol (DTT) at 50°C, cooled to room temperature, and alkylated with 10 mM iodoacetamide for 15 minutes in the dark. The total reaction volume was 200 μl. To this reaction mixture, 1/25th w/w of trypsin was added and digestion carried out at 37°C for 24 hour. The reaction was terminated by heating the sample at 65°C for 2 minutes. The digest was separated by reverse phase HPLC using a gradient of 0 to 80% acetonitrile. The tryptic peptides were monitored at 210 and 277 nm. The tryptic peaks were collected in Eppendorff tubes. Based on the homogeneity of the peptide peak, eight different peaks were sequenced using an Applied Biosystems sequencer, model 477, with an on-line model 120 PTH amino acid analyzer located in the Biopolymers lab. Center for Cancer Research, MIT. The sequences are set forth in Table I below. The designation (K,R) is used in Table I to indicate that trypsin cuts at either lysine or arginine residues. The asterisks in Table I represent amino acids that could not be determined. The peptide designated td Lx is the longest peptide sequenced having 38 residues. Native heparinase was also sequenced to determine the N-terminus amino acids. Table I: Sequences of Tryptic Peptides of Heparinase Pe tide Amino Acid Sequence (K, R) G I C E Q G S S R (K, R) T V Y H Y G K (K, R) T S T I A Y K (K, R) F G I Y R (K, R) A D I V N Q Q E I L I G R D D * G Y Y F K td 39 (K, R) I T Y V A G K P N G N K V E Q G G Y P T L A F * td 43 (K, R) M P F A Q F P K D C W I T F D V A I D * T K td 40 (K, R) N L S G Y S E T A R tdm4 K N I A H D K V E K K td 72 K T L S I E E F L A L Y D R td Lx R S Y T F S V Y I P S S F P D N A T T I F A W H G A P S R T L V T P E I K Three sets of primers were designed and synthesized, as shown in Table II. Primers were synthesized with an Applied Biosystems sequencer, model 477, with an on-line model 120 PTH amino acid analyzer located in the Biopolymers lab, Center for Cancer Research, MIT. These primer sets were used in the PCR amplification system for cloning the heparinase gene. The symbol "I" represents the nucleotide inosine. The amino acids of each peptide, depicted in boldface type, represent the residues chosen for the primer design. Two different sets of primers were constructed for tryptic peptide 33 to reduce the degree of inosine substitution at the 3' end of the primer. Table II: Heparinase Primer Design Peptide: td 04 Amino Acid Sequence: K G I C E Q G S S R primers: yl 5 - AAA GGI AT(T/C/A) TG(T/C) GA(A/G) CA(A/G) GG -3' y2 5'- CC (C/T)TG (C/T)TC (G/A)CA (T/G/A)AT ICC TTT -3' Peptide: td 43 Amino Acid Sequence: (K, R) M P P A Q F P K D E W I T F C V A I D * T K primers: D 5'- ATG CCI TT(T/C) GCI CA(A/G) TT(T/C) CCI AA(A/G) GA(T/C) GA -3' E 3'- TAC GGI AA(A/G) CGI GT(T/C) AA(A/G) GGI TT(T/C) CT(A/G) CT -5' Peptide: td 33 Amino Acid Sequence: (K, R) A D I V N Q Q E I L I G R D D * G Y Y F K A primers : A 5'- ATI AA(T/C) CA(A/G) GA(A/G)ATI (C/T)TI AT(T/C/A) GG -3' B 5'- CCIATIA(G/A) IAT (T/C)TC (T/C)TG (T/C)TG (A/G)TT ICA (A/C)AT C 5'- CCIATIA(G/A) IAT (T/C)TC (T/CTG (T/C)TG (A/G)TT ICA (T/G)AT -31 Of the six RHPLC peaks initially sequenced (Table I) , three were chosen for primer design. Three sets of primers were designed (Table II) . The PCR product of the combination the primers td43 and td33 was about 150 base pairs in length. The combination of td4 and td33 primers were about 600 base pairs. Primer td43 was 5' to primer td33 and primer td4 was 5' to td43 primer. Using the PCR product of td4 and td33 as a template and td43 and td4 as primers the predicted 150 base pair product was obtained confirming that td43 was between td4 and td33. The 600 basepair product shown in Figure 1 represents about 51% of the approximated total 1170 base pairs for the heparinase gene, assuming 43,000 dalton for heparinase and a 110 dalton average amino acid with a molecular weight corresponding to about 390 amino acids times three which is 1170 bases. The 600 base pair probe was chosen for screening a pUC 18 library by high stringency colony hybridization. Two positive clones were identified which were carried through for three rounds of colony purification. Genomic DNA. RNA. and Plasmid Library The F. heparinum genomic DNA was isolated by the A.S.A.P.™ kit (Boehringer Mannheim, Indianapolis, IN) with the following modifications. The DNA was desalted over a Sephadex™ G-50 column (Nick column, Pharmacia, Piscataway, NJ) and concentrated using a Centricon™ P-30 (Amicon Division, Beverly, MA) to a final volume of 100 1. From 1 x 10 9 cells, 105-115 g of DNA typically were obtained. Total cellular mRNA was isolated using the guanidine thiocyanate procedure set forth in the Promega technical information publication TB 087 12/89, Promega Corp., Madison, WI 53711. A pUC 18 plasmid was obtained from Dr. A.J. Sinskey, of the Department of Biology at the Massachusetts Institute of Technology. The library was constructed using the F. heparinum genomic DNA. The genomic DNA was sonicated and modified by adding EcoRI linkers and then ligated to the pUC 18 vector. DH5a was transformed with the pUC 18 genomic library. Amplification of the PCR Product Amplification of the heparinase tryptic digest primers was carried out in a 25 1 reaction volume containing 50 mM KCl, 10 mM Tris HC1 (pH 8.3), 1.5 mM MgCl 2 and 0.01% gelatin plus the four deoxyribose nucleotide triphosphates (dNTPs) at 200 M, using 0.5 M primer and 3 1 of the genomic DNA as the template, 2.5 units of the Taq polymerase (Cetus Corp., Emeryville, CA) and 25 1 of mineral oil. The samples were placed on an automated heating block (DNA thermal cycler, Perkin Elmer Corp., Norwalk, CT) programmed for step cycles of temperatures 92°C (2 minutes) , 50°C (1 minute) and 72°C (3 minutes) . This cycle was repeated 35 times. The final cycle had a 72°C 10 minute extension. The PCR products were analyzed on a 0.8% agarose gel containing 0.6 μg/ml ethidium bromide. The control reaction was provided by the Cetus kit. Screening of the Flavobacterium heparinum pUC 18 σenomic library The pUC 18 library was titered to give approximately 1500 colonies to be tested by the probe generated by PCR. Each plate had approximately 100 colonies which were grown directly on nitrocellulose, to an appropriate small size, and then duplicated to be grown further overnight. The PCR probe was labelled using the Random Hexanucleotide™ kit (RHN) (IBI Biochemicals Ltd.) which is described briefly as follows. One icrogram DNA from the PCR product run was isolated from a low melt agarose gel, denatured by boiling at 95°C for 10 minutes, -and then chilled on ice. To the denatured DNA were added 10 mM dNTPs (dATP, dGTP, dCTP, dTTP) , random hexanucleotides in the reaction buffer, and 50 μCi of 32 PdCTP(3000 Ci/mmole) . The reaction was carried with Klenow for 30 minutes at 37°C and terminated using 0.2 M EDTA. Following the labelling reaction, the labelled probe was purified from the free nucleotide by using a Sephadex G-50 column (Nick Column, Pharmacia, Piscataway, NJ) . The colonies were screened with the labelled probe using standard colony hybridization procedures as described by Maniatis et al.. Molecular Cloning: A Laboratory Manual , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, incorporated herein by reference. Two positive clones were isolated and the plasmids tested for their ability to generate the 600 basepair PCR product. Both of the clones tested positive and were further characterized by restriction mapping. Clone pRS Hep 51 is a 2.3 kb insert in pUC 18 (shown in Figure 2) with a Kpn-Kpn fragment of about 1.6 kb. This fragment was a positive template for generating a 600 basepair PCR product. The Kpnl-Kpnl fragment of pRS 51 was subcloned into M13 and sequenced. DNA Sequencing DNA sequencing was performed using phage M13 and employing the dideoxyadenosine 5'-alpha- 35 S-triphosphate and Sequenase (US Biochemical Corp, Cleveland, OH) as described by the manufacturer. The sequence data was obtained using successive nested deletions in M13 using T4 DNA polymerase as per Cyclone I Biosystems (International Biotechnologies Inc. , New Haven, CT) or sequenced using synthetic oligonucleotide primers. The sequence reveals a single, continuous open reading frame (ORF) of 1152 basepairs corresponding to 384 amino acids and a leader sequence of about 21 amino acids*. The PCR product spans from 566 to 1216 bases from the start site and corresponds to about 57% of the total gene. Initially six different tryptic peptides mapped into the ORF. Subsequently, five other peptides were sequenced for structural studies and all of them mapped into the ORF, for a total of about 48% of the total 367 amino acids. There are three cysteines in all, one associated with the signal peptide. The signal peptide is typical of prokaryotic sequences, having a charged N-terminal region, a core hydrophobic region and a cleavage region with a standard Ala.xxx.Ala site for cleavage. Example 2: Expression of the heparinase gene in E. coli. Two different expression systems were selected for the expression of heparinase in E. coli : the Omp A expression system and the pKK hyper-expression system. The plasmid designs for both expression systems are shown in Table III. 30 Omp A expression system The Omp A expression system secretes the protein of interest into the periplasmic space, as directed by the Omp A signal sequence, described by Ghrayeb, et al., EMBO J. 3:2437 (1984), incorporated herein by reference. This system was chosen since heparinase is naturally expressed into the periplasmic space of F. heparinum. The plasmid is under the control of the lac repressor and is induced by the addition of IPTG (isopropyl-β-D thiogalactoside) to the medium. The plasmid was inserted in the pIN-III Omp A-3 vector. The heparinase insert was generated by PCR utilizing the N terminal and the C terminal sequences of heparinase with two appropriate restriction sites suitable for cloning into the EcoRI-BamEI sites. Two primers were constructed as shown in Table II. The insert was amplified by 5 cycles of PCR and ligated to the Omp A pIN vector with the E. coli periplasmic leader sequence. DH5α was transformed and expression was induced with 1 mM IPTG for 3-5 hours. As shown in Table III, the construct of the Omp A expression system results in two extra amino acids at the amino terminal of the heparinase gene, Gly and He. The heparinase sequence begins with a Gin. The pKK expression system The pKK expression system is used for over-expression of proteins in accordance with the methods of Brosius and Holy, Proc. Natl . Acad. Sci . , 81: 6929 (1984) and Jaffe et al. , Biochem . 27:1869 (1988) , incorporated by reference herein. This system contains a strong tac promotor which, in appropriate hosts, is regulated by the lac repressor and induced by the addition of IPTG, as in the Omp A system. The plasmid pKK223-3 has a pUC 8 multiple cloning site and a strong rrnB ribosomal terminator immediately following the tac promotor. The ribosomal binding site of the plasmid was utilized by cloning the heparinase gene into a Smal site, which is about 12 bases from the start codon ATG. Like the Omp A construction, the heparinase insert is obtained by PCR with Smal and Jfindlll restriction sites at the N and the C terminals of the protein. As shown in Table III, the native heparinase leader sequence was used for over-production into the periplasm. Periplasmic proteins of E. coli were isolated by osmotic shock. Briefly, 1.5 ml of cells were centrifuged after induction and washed with 10 mM Tris pH 7.5. The cells were then suspended in 20% sucrose in 10 mM Tris pH 7.5 and 5 μl of 0.5 M EDTA. After a five minute incubation on ice, the cells were centrifuged and osmotically shocked by adding approximately 150 μl water. The periplasmic extract was used to determine enzyme activity. Heparinase activity was determined by monitoring the wavelength at 232 nm and by the Azure A methods of Bernstein et al. , Methods of Immunology 137:515 (1988), incorporated herein by reference. The periplasmic extracts were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) using the method of Laemmli, Nature 227:690 (1974) and stained using Coumassie blue. In addition, a Western blot assay was performed to confirm the presence of heparinase using a heparinase monoclonal antibody. Heparinase was electrophoretically transferred from the SDS-PAGE gel onto nitrocellulose using the method of Gershoni and Palade, Analytical Biochem. 131:1 (1983), and then incubated with the monoclonal antibody. This antibody was stained using a secondary antibody conjugated to horseradish peroxidase. Table III: Design of OmpΑ and pKK plasmids for expression of Recombinant Heparinase in E.coli Omp A secretion Expression system N Gly He Gin Lys Thr Ala Arg End C XXX GGA ATT CAG AAA ACT GCC AGA TAG GGATCCXXX XXX CCT TAA GTC TTT TGA CTT ACT ATC CCTAGGXXX FcoRI Bam HI pKK over-Expression system N Met Lys Lys Ala Arg End XXX Taa CCC GGG ATG AAA AAA GCC AGA TAG AAG CTT CCG XXX XXX ATT GGC CCC TAC TTT TTT CGG TCT ATC TTC GAA GGC XXX Sma I Hind III RNA Dot Blot Assay The total cellular PNA was immobilized onto a Zeta probe™ membrane (Biorad, Richmond, CA) by alkaline RNA denaturation and fixation, and probed using the 600 base PCR product, used in screening for the heparinase gene. The hybridization was carried out with dot blot apparatus in accordance with the method of Thomas, Proc. Natl . Acad Sci. 77:5201 (1980). The RNA signal under different growth conditions has been investigated by Galliher, et al. , JEϊur. J. Appl . Microbiol . (1982). It was established by those studies that heparinase at the protein level is optimally expressed under low sulphur conditions, which removes the requirement of heparin for induction. Heparinase mRNA signal under low sulphur growth conditions was therefore studied with and without heparin induction. Both the OmpA and the pKK systems expressed heparinase. The OmpA system did not efficiently transport heparinase to the periplasm. For reasons not known, a large fraction of recombinant heparinase was retained in the cytoplasmic region along with the Omp A signal sequence. At lower temperatures (25°-30°C) of growth, there was some secretion into the periplasmic space. The pKK overproduction system produced heparinase only in the periplasmic space. The pKK system used the native F .heparinum heparinase leader sequence in which there was no problem with the transport of the recombinant protein with a foreign leader sequence. The pKK system expressed heparinase without any aberrant processing, although the expression was again optimal at lower temperatures. The presence of heparinase in the periplasm was confirmed by western blotting and by comparing in situ tryptic digest of the recombinant heparinase with that of the native heparinase, in terms of the peak profiles and some peaks which were isolated and sequenced. A positive signal was obtained for the isolated F. heparinum mRNA using the 600 basepair probe derived from the PCR which has been used for isolating the heparinase gene, confirming that the gene isolated was a F. heparinum gene cloned in E. coli . The expressed heparinase appeared to have at least some heparinase activity. The sequence can be modified to alter specific enzymatic activity or binding specificity or affinity by substitution of one or more amino acids, using site directed mutagenesis or substitution of oligomers into the sequence encoding the heparinase. Methods and materials to accomplish this are known to those skilled in the art. The modified gene is then expressed and the product routinely screened for the altered activity. Although described with reference to two specific expression systems, other expression systems are well known and commercially available. The heparinase gene can be expressed in these systems, using similar vectors and signal peptides or leader sequences. Modifications and variations of the present invention will be obvious to those skilled in the art. Such modifications and variations are intended to come within the scope of the following claims. SEQUENCE LISTING (1) GENERAL INFORMATION: (i) APPLICANT: Massachusetts Institute, of Technology (ii) TITLE OF INVENTION: The Heparinase Gene from Flavobac (iii) NUMBER OF SEQUENCES: 2 (iv) CORRESPONDENCE ADDRESS: (A) ADDRESSEE: Kilpatrick St Cody (B) STREET: 1100 Peachtree Street, Suite 2800 (C) CITY: Atlanta (D) STATE: Georgia (E) COUNTRY: US (F) ZIP: 30309-4530 (v) COMPUTER READABLE FORM: (A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS (D) SOFTWARE: Patentin Release #1.0, Version #1.25 (vi) CURRENT APPLICATION DATA: (A) APPLICATION NUMBER: (B) FILING DATE: (C) CLASSIFICATION: (viii) ATTORNEY/AGENT INFORMATION: (A) NAME: Pabst, Patrea L. (B) REGISTRATION NUMBER: 31,284 (C) REFERENCE/DOCKET NUMBER: MIT5546 (ix) TELECOMMUNICATION INFORMATION: (A) TELEPHONE : 404-815-6508 (B) TELEFAX: 404-815-6555 (2) INFORMATION FOR SEQ ID NO:l: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1379 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA (ϋi) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE: (A) ORGANISM: Flavobacterium heparinum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:l: CCTTTTGGGA GCAAAGGCAG AACCATCTCC GAACAAAGGC AGAACCAGCC TGTAAACAGA 60 CAGCAATTCA TCCGCTTTCA ACCAAAGTGA AAGCATTTAA TACAATACCA GAATGTCGCA 120 TTTCCCTTTC AGCGTACTTT TTGGGTAAAT AACCAATAAA AACTAAAGAC GGATGAAAAA 180 ACAAATTCTA TATCTGATTG TACTTCAGCA ACTGTTCCTC TGTTCGGCTT ACGCCCAGCA 240 AAAAAAATCC GGTAACATCC CTTACCGGGT AAATGTGCAG GCCGACAGTG CTAAGCAGAA 300 GGCGATTATT GACAACAAAT GGGTGGCAGT AGGCATCAAT AAACCTTATG CATTACAATA 360 TGACGATAAA CTGCGCTTTA ATGGAAAACC ATCCTATCGC TTTGAGCTTA AAGCCGAAGA 420 CAATTCGCTT GAAGGTTATG CTGCAGGAGA AACAAAGGGC CGTACAGAAT TGTCGTACAG 480 CTATGCAACC ACCAATGATT TTAAGAAATT TCCCCCAAGC GTATACCAAA ATGCGCAAAA 540 GCTAAAAACC GTTTATCATT ACGGCAAAGG GATTTGTGAA CAGGGGAGCT CCCGCAGCTA 600 TACCTTTTCA GTGTACATAC CCTCCTCCTT CCCCGACAAT GCGACTACTA TTTTTGCCCA 660 ATGGCATGGT GCACCCAGCA GAACGCTTGT AGCTACACCA GAGGGAGAAA TTAAAACACT 720 GAGCATAGAA GAGTTTTTGG CCTTATACGA CCGCATGATC TTCAAAAAAA ATATCGCCCA 780 TGATAAAGTT GAAAAAAAAG ATAAGGACGG AAAAATTACT TATGTAGCCG GAAAGCCAAA 840 TGGCTGGAAG GTAGAACAAG GTGGTTATCC CACGCTGGCC TTTGGTTTTT CTAAAGGGTA 900 TTTTTACATC AAGGCAAACT CCGACCGGCA GTGGCTTACC GACAAAGCCG ACCGTAACAA 960 TGCCAATCCC GAGAATAGTG AAGTAATGAA GCCCTATTCC TCGGAATACA AAACTTCAAC 1020 CATTGCCTAT AAAATGCCCT TTGCCCAGTT CCCTAAAGAT TGCTGGATTA CTTTTGATGT 1080 CGCCATAGAC TGGACGAAAT ATGGAAAAGA GGCCAATACA ATTTTGAAAC CCGGTAAGCT 1140 GGATGTGATG ATGACTTATA CCAAGAATAA GAAACCACAA AAAGCGCATA TCGTAAACCA 1200 GCAGGAAATC CTGATCGGAC GTAACGATGA CGATGGCTAT TACTTCAAAT TTGGAATTTA 1260 CAGGGTCGGT AACAGCACGG TCCCGGTTAC TTATAACCTG AGCGGGTACA GCGAAACTGC 1320 CAGATAGCAA AAGCCCTAAG CGCATCCGAT AGGGCTTTTC TTATATTTAC AATAAAATT 1379 (2) INFORMATION FOR SEQ ID NO:2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 384 amino acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: peptide (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (v) FRAGMENT TYPE: N-terminal (vi) ORIGINAL SOURCE: (A) ORGANISM: Flavobacterium heparinum (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: Met Lys Lys Gin He Leu Tyr Leu He Val Leu Gin Gin Leu Phe Leu 1 5 10 15 Cys Ser Ala Tyr Ala Gin Gin Lys Lys Ser Gly Asn He Pro Tyr Arg 20 25 30 Val Asn Val Gin Ala Asp Ser Ala Lys Gin Lys Ala He He Asp Asn 35 40 45 Lys Trp Val Ala Val Gly He Asn Lys Pro Tyr Ala Leu Gin Tyr Asp 50 55 60 Asp Lys Leu Arg Phe Asn Gly Lys Pro Ser Tyr Arg Phe Glu Leu Lys 65 70 75 80 Ala Glu Asp Asn Ser Leu Glu Gly Tyr Ala Ala Gly Glu Thr Lys Gly 85 90 95 Arg Thr Glu Phe Pro Pro Ser Val Tyr Gin Asn Ala Gin Lys Leu Lys Thr Val Tyr 115 120 125 His Tyr Gly Lys Gly He Cys Glu Gin Gly Ser Ser Arg Ser Tyr Thr 130 135 140 Phe Ser Val Tyr He Pro Ser Ser Phe Pro Asp Asn Ala Thr Thr He 145 150 155 160 Phe Ala Gin Trp His Gly Ala Pro Ser Arg Thr Leu Val Ala Thr Pro 165 170 175 Glu Gly Glu He Lys Thr Leu Ser He Glu Glu Phe Leu Ala Leu Tyr 180 185 190 Asp Arg Met He Phe Lys Lys Asn He Ala His Asp Lys Val Glu Lys 195 200 205 Lys Asp Lys Asp Gly Lys He Thr Tyr Val Ala Gly Lys Pro Asn Gly 210 215 220 Trp Lys Val Glu Gin Gly Gly Tyr Pro Thr Leu Ala Phe Gly Phe Ser 225 230 235 240 Lys Gly Tyr Phe Tyr He Lys Ala Asn Ser Asp Arg Gin Trp Leu Thr 245 250 255 Asp Lys Ala Asp Arg Asn Asn Ala Asn Pro Glu Asn Ser Glu Val Met Lys Pro Tyr Ser Ser Glu Tyr Lys Thr Ser Thr He Ala Tyr Lys Met 275 280 285 Pro He Asp Trp Thr Lys Tyr Gly Lys Glu Ala Asn Thr He Leu Lys Pro 305 310 315 320 Gly Lys Leu Asp Val Met Met Thr Tyr Thr Lys Asn Lys Lys Pro Gin 325 330 335 Lys Ala His He Val Asn Gin Gin Glu He Leu He Gly Arg Asn Asp 340 345 350 Asp Asp Gly Tyr Tyr Phe Lys Phe Gly He Tyr Arg Val Gly Asn Ser 355 360 365 Thr Val Pro Val Thr Tyr Asn Leu Ser Gly Tyr Ser Glu Thr Ala Arg 370 375 380

Claims: We claim: 1. An isolated nucleic acid molecule isolated from Flavobacterium heparinum encoding heparinase I. 2. The nucleic acid molecule of claim 1 having the nucleotide sequence (Sequence No. 1, base pairs 173 to 1324, inclusive) consisting essentially of: ATGAAAAA 180 ACAAATTCTA TATCTGATTG TACTTCAGCA ACTGTTCCTC TGTTCGGCTT 230 ACGCCCAGCA AAAAAAATCC GGTAACATCC CTTACCGGGT AAATGTGCAG 280 GCCGACAGTG CTAAGCAGAA GGCGATTATT GACAACAAAT GGGTGGCAGT 330 AGGCATCAAT AAACCTTATG CATTACAATA TGACGATAAA CTGCGCTTTA 380 ATGGAAAACC ATCCTATCGC TTTGAGCTTA AAGCCGAAGA CAATTCGCTT 430 GAAGGTTATG CTGCAGGAGA AACAAAGGGC CGTACAGAAT TGTCGTACAG 480 CTATGCAACC ACCAATGATT TTAAGAAATT TCCCCCAAGC GTATACCAAA 530 ATGCGCAAAA GCTAAAAACC GTTTATCATT ACGGCAAAGG GATTTGTGAA 580 CAGGGGAGCT CCCGCAGCTA TACCTTTTCA GTGTACATAC CCTCCTCCTT 630 CCCCGACAAT GCGACTACTA TTTTTGCCCA ATGGCATGGT GCACCCAGCA 680 GAACGCTTGT AGCTACACCA GAGGGAGAAA TTAAAACACT GAGCATAGAA 730 GAGTTTTTGG CCTTATACGA CCGCATGATC TTCAAAAAAA ATATCGCCCA 780 TGATAAAGTT GAAAAAAAAG ATAAGGACGG AAAAATTACT TATGTAGCCG 830 GAAAGCCAAA TGGCTGGAAG GTAGAACAAG GTGGTTATCC CACGCTGGCC 880 TTTGGTTTTT CTAAAGGGTA TTTTTACATC AAGGCAAACT CCGACCGGCA 930 GTGGCTTACC GACAAAGCCG ACCGTAACAA TGCCAATCCC GAGAATAGTG 980 AAGTAATGAA GCCCTATTCC TCGGAATACA AAACTTCAAC CATTGCCTAT 1030 AAAATGCCCT TTGCCCAGTT CCCTAAAGAT TGCTGGATTA CTTTTGATGT 1080 CGCCATAGAC TGGACGAAAT ATGGAAAAGA GGCCAATACA ATTTTGAAAC 1130 CCGGTAAGCT GGATGTGATG ATGACTTATA CCAAGAATAA GAAACCACAA 1180 AAAGCGCATA TCGTAAACCA GCAGGAAATC CTGATCGGAC GTAACGATGA 1230 CGATGGCTAT TACTTCAAAT TTGGAATTTA CAGGGTCGGT AACACCACGG 1280 TCCCGGTTAC TTATAACCTG AGCGGGTACA GCGAAACTGC CAGA. 1320 3. The nucleic acid molecule of claim 1 encoding the amino acid sequence (Sequence No. 2) consisting essentially of: Met Lys Lys Gin He Leu Tyr Leu He Val Leu Gin Gin Leu Phe 1 5 10 15 Leu Cys Ser Ala Tyr Ala Gin Gin Lys Lys Ser Gly Asn He Pro 20 25 30 Tyr Arg Val Asn Val Gin Ala Asp Ser Ala Lys Gin Lys Ala He 35 40 45 He Asp Asn Lys Trp Val Ala Val Gly He Asn Lys Pro Tyr Ala 50 55 60 Leu Gin Tyr Asp Asp Lys Leu Arq Phe Asn Gly Lys Pro Ser Tyr 65 70 75 Arg Phe Glu Leu Lys Ala Glu Asp Asn Ser Leu Glu Gly Tyr Ala 80 85 90 Ala Gly Glu Thr Lys Gly Arg Thr Glu Leu Ser Tyr Ser Tyr Ala 95 100 105 Thr Thr Asn Asp Phe Lys Lys Phe Pro Pro Ser Val Tyr Gin Asn 110 115 120 Ala Gin Lys Leu Lys Thr Val Tyr His Tyr Gly Lys Gly He Cys 125 130 135 Glu Gin Gly Ser Ser Arg Ser Tyr Thr Phe Ser Val Tyr He Pro 140 145 150 Ser Ser Phe Pro Asp Asn Ala Thr Thr He Phe Ala Gin Trp His 155 160 165 Gly Ala Pro Ser Arg Thr Leu Val Ala Thr Pro Glu Gly Glu He 170 175 180 Lys Thr Leu Ser He Glu Glu Phe Leu Ala Leu Tyr Asp Arg Met 185 190 195 He Phe Lys Lys Asn He Ala His Asp Lys Val Glu Lys Lys Asp 200 205 210 Lys Asp Gly Lys He Thr Tyr Val Ala Gly Lys Pro Asn Gly Trp 215 220 225 Lys Val Glu Gin Gly Gly Tyr Pro Thr Leu Ala Phe Gly Phe Ser 230 235 240 Lys Gly Tyr Phe Tyr He Lys Ala Asn Ser Asp Arg Gin Trp Leu 245 250 255 Thr Asp Lys Ala Asp Arg Asn Asn Ala Asn Pro Glu Asn Ser Glu 260 265 270 Val Met Lys Pro Tyr Ser Ser Glu Tyr Lys Thr Ser Thr He Ala 275 280 285 Tyr Lys Met Pro Phe Ala Gin Phe Pro Lys Asp Cys Trp He Thr 290 295 300 Phe Asp Val Ala He Asp Trp Thr Lys Tyr Gly Lys Glu Ala Asn 305 310 315 Thr He Leu Lys Pro Gly Lys Leu Asp Val Met Met Thr Tyr Thr 320 325 330 Lys Asn Lys Lys Pro Gin Lys Ala His He Val Asn Gin Gin Glu 335 340 345 He Leu He Gly Arg Asn Asp Asp Asp Gly Tyr Tyr Phe Lys Phe 350 355 360 Gly He Tyr Arg Val Gly Asn Ser Thr Val Pro Val Thr Tyr Asn 365 370 375 Leu Ser Gly Tyr Ser Glu Thr Ala Arg. 380 4. The nucleic acid molecule of claim 1 further comprising an expression vector. 5. The nucleic acid molecule of claim 1 further comprising a nucleic acid fragment encoding a signal peptide. 6. The nucleic acid molecule of claim 6 wherein the signal peptide is encoded by the nucleic acid (Sequence No. 1, base pairs l to 172, inclusive) consisting essentially of: CCTTTTGGGA GCAAAGGCAG AACCATCTCC GAACAAAGGC AGAACCAGCC 50 TGTAAACAGA CAGCAATTCA TCCGCTTTCA ACCAAAGTGA AAGCATTTAA 100 TACAATACCA GAATGTCGCA TTTCCCTTTC AGCGTACTTT TTGGGTAAAT 150 AACCAATAAA AACTAAAGAC GA. 180 7. The nucleic acid molecule of claim 6 wherein the signal peptide directs the transport of the protein from the cytoplasm to the periplasm. 8. The nucleic acid molecule of claim 1 wherein the nucleic acid molecule encodes a heparinase having binding heparin with a different affinity than the heparinase encoded by Sequence No. 1. 9. The nucleic acid molecule of claim 1 wherein the nucleic acid molecule encodes a heparinase having a specific activity different from the specific activity of the heparinase encoded by Sequence No. 1. 10. The nucleic acid molecule of claim 1 in a procaryotic cell other than F. heparinum which is capable of expressing the molecule. 11. The nucleic acid molecule of claim 11 in a procaryotic cell cultured under low sulfate conditions which is capable of expressing the molecule.

Inventors: COONEY CHARLES L, LANGER ROBERT S, MOREMEN KELLEY, SASISEKHARAN RAMNATH, ZIMMERMANN JOSEPH J, COONEY, CHARLES, L., LANGER, ROBERT, S., MOREMEN, KELLEY, SASISEKHARAN, RAMNATH, ZIMMERMANN, JOSEPH, J.
Applicants: MASSACHUSETTS INST TECHNOLOGY, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
Application year: 1992
Main classification: C12N15
IPC codes: C12N1, C12N9, C12N15, C12R1