# Patent

## Title
Heparin/heparosan synthase from P. multocida and methods of making and using same

## Abstract

The presently claimed and disclosed invention relates, in general, to dual action heparin synthases and, more particularly, to dual action heparin synthases obtained from Pasteurella multocida. The presently claimed and disclosed invention also relates to heparosan, heparin and heparin-like molecules provided by recombinant techniques and methods of using such molecules and also the identification or prediction of heparin synthases or component single action enzymes. The presently claimed and disclosed invention also relates to methods, and molecules produced according to such methods, for using the presently claimed and disclosed heparosan and/or heparin synthase for polymer grafting and the production of non-naturally occurring chimeric polymers incorporating stretches of one or more acidic GAG molecules, such as heparin, chondroitin, hyaluronan, and/or heparosan.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a divisional of U.S. Ser. No. 10/142,143, filed May 8, 2002, now U.S. Pat. No. 7,307,159, issued Dec. 11, 2007; which claims priority under 35 U.S.C. §119(e) of provisional applications U.S. Ser. No. 60/289,554, filed May 8, 2001; U.S. Ser. No. 60/296,386, filed Jun. 6, 2001; U.S. Ser. No. 60/303,691, filed Jul. 6, 2001; and U.S. Ser. No. 60/313,258, filed Aug. 17, 2001. The entire contents of each of the above-referenced patent applications are hereby expressly incorporated herein by reference.


STATEMENT REGARDING FEDERALLY FUNDED RESEARCH
The government owns certain rights in and to this application pursuant to a grant from the National Science Foundation (NSF), Grant No. MCB-9876193.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The presently claimed and disclosed invention relates, in general, to dual action heparin synthases and, more particularly, to dual action heparin synthases obtained from Pasteurella multocida. The presently claimed and disclosed invention also relates to heparosan, heparin and heparin-like molecules produced according to recombinant techniques and methods of using such molecules. The presently claimed and disclosed invention also relates to methods, and molecules produced according to such methods, for using the presently claimed and disclosed heparosan and/or heparin synthases for polymer grafting and the production of non-naturally occurring chimeric polymers incorporating stretches of one or more acidic GAG molecules, such as heparin, chondroitin, hyaluronan, and/or heparosan.
2. Background Information Relating to this Application
Glycosaminoglycans [GAGs] are long linear polysaccharides consisting of disaccharide repeats that contain an amino sugar and are found in most animals. Chondroitin [β(1,4)GlcUA-β(1,3)GalNAc]n, heparin/heparosan (β1,4)GlcUA-[α(1, 4)GlcNAc]n, and hyaluronan [β(1,4)GlcUA-β(1,3)GlcNAc]n are the three most prevalent GAGs found in humans and are also the only known acidic GAGs. Chondroitin and heparin typically have n=20 to 100, while hyaluronan typically has n=103. Chondroitin and heparin are synthesized as glycoproteins and are sulfated at various positions in vertebrates. Hyaluronan is not sulfated in vertebrates. A substantial fraction of the GlcUA residues of heparin and chondroitin are epimerized to form iduronic acid. A simplified nomenclature has been developed for these GAGs. For example, heparin/heparosan's structure is noted as β4-GlcUA-α4-GlcNAc.
The capsular polysaccharide produced by the Type D strain of Pasteurella multocida is N-acetyl heparosan (heparosan is unmodified heparin—i.e., sulfation or epimerization have not occurred). In vertebrates, one or more modifications including O-sulfation of certain hydroxyls, deacetylation and subsequent N-sulfation, or epimerization of glucuronic acid to iduronic acid modifies the precursor N-acetyl heparosan to heparin/heparan. Hereinafter, for convenience and/or ease of discussion, heparin and/or heparosan are defined as polymers having the β4GlcUA-α4GlcNAc backbone.
Many lower animals possess these same GAGs or very similar molecules. GAGs play both structural and recognition roles on the cell surface and in the extracellular matrix. By virtue of their physical characteristics, namely a high negative charge density and a multitude of polar hydroxyl groups, GAGs help hydrate and expand tissues. Numerous proteins bind selectively to one or more of the GAGs. Thus the proteins found on cell surfaces or the associated extracellular matrices (e.g., CD44, collagen, fibronectin) of different cell types may adhere or interact via a GAG intermediate. Also GAGs may sequester or bind certain proteins (e.g., growth or coagulation factors) to cell surfaces.
Certain pathogenic bacteria produce an extracellular polysaccharide coating, called a capsule, which serves as a virulence factor. In a few cases, the capsule is composed of GAG or GAG-like polymers. As the microbial polysaccharide is identical or very similar to the host GAG, the antibody response is either very limited or non-existent. The capsule is thought to assist in the evasion of host defenses such as phagocytosis and complement. Examples of this clever strategy of molecular camouflage are the production of an authentic HA polysaccharide by Gram-negative Type A Pasteurella multocida and Gram-positive Group A and C Streptococcus. The HA capsule of these microbes increases virulence by 102 to 103-fold as measured by LD50 values, the number of colony forming units that will kill 50% of the test animals after bacterial challenge.
The invasiveness and pathogenicity of certain E. coli strains has also been attributed to their polysaccharide capsules. Two Escherichia coli capsular types, K4 and K5, make polymers composed of GAG-like polymers. The E. coli K4 polymer is an unsulfated chondroitin backbone decorated with fructose side-branches on the C3 position of the GlcUA residues. The K5 capsular material is a polysaccharide, called heparosan, identical to mammalian heparin except that the bacterial polymer is unsulfated and there is no epimerization of GlcUA to iduronic acid.
The studies of GAG biosynthesis have been instrumental in understanding polysaccharide production in general. The HA synthases were the first GAG glycosyltransferases to be identified at the molecular level. These enzymes utilize UDP-sugar nucleotide substrates to produce large polymers containing thousands of disaccharide repeats. The genes encoding bacterial, vertebrate, and viral HAS enzymes have been cloned. In all these cases, expression studies have demonstrated that transformation with DNA encoding a single HAS polypeptide conferred the ability of foreign hosts to synthesize HA. Except for the most recent HAS to be identified, P. multocida pmHAS, these proteins have similar amino acid sequences, repeating conserved amino acid motifs, and predicted topology in the membrane. Likewise, as presently disclosed and claimed herein, heparosan and/or heparin synthases have been identified that confer upon a foreign host the ability to produce heparin.
With respect to related microbial GAG synthases other than the HASs, the E. coli K5 heparin glycosyltransferases, KfiA (SEQ ID NO:7) and KfiC (SEQ ID NO:8), have been identified by genetic and biochemical means. These K5 glycosyltransferases synthesize heparosan (unsulfated and unepimerased heparin) in vivo. The KfiA and KfiC require KfiB (SEQ ID NO:9), an accessory protein, with unknown function in order to synthesize heparosan, however. In vitro, the reactions are limited to adding one or two sugars; as such, it appears that some co-factor or reaction condition is missing—thus, extended polymerization does not occur in vitro when KfiA, KfiB, and KfiC are used. As such, the presently claimed and disclosed heparosan/heparin synthases provide a novel heretofore unavailable means for recombinatly producing heparin (the sulfated and epimerized molecule). In contrast to the HASs, the pmCS chondroitin synthase(s), and the presently disclosed and claimed heparin synthases, it appears that K5 requires two proteins, KfiA and KfiC, to transfer the sugars of the disaccharide repeat to the growing polymer chain. The presently claimed and disclosed heparin synthases (designated “pmHS and PgIA”) are dual action enzymes capable of transferring both sugars of the growing heparin polymer chain. These enzymes polymerize heparosan in vivo and in vitro.
Many P. multocida isolates produce GAG or GAG-like molecules as assessed by enzymatic degradation and removal of the capsule of living bacterial cells. Type A P. multocida, the major fowl cholera pathogen, makes a capsule that is sensitive to hyaluronidase. Subsequent NMR structural studies of capsular extracts confirmed that HA was the major polysaccharide present. A specific HA-binding protein, aggrecan, also interacts with HA from Type A P. multocida. Two other distinct P. multocida types, a swine pathogen, Type D, and a minor fowl cholera pathogen, Type F, produce polymers that are chondroitin or chondroitin-like based on the observation that their capsules are degraded by Flavobacterium chondroitin AC lyase. After enzymatic removal of the capsule, both types were more readily phagocytosed by neutrophils in vitro. The capsule of Type D cells, but not Type F cells, also appear to be degraded by heparinase III, indicating that a heparin-type molecule is present as well.
Heparin acts as an anticoagulant and is used to avoid coagulation problems during extra corporal circulation and surgery as well as for treatment after thrombosis has been diagnosed. Heparin is used in the prevention and/or treatment of deep venous thrombosis, pulmonary embolism, mural thrombus after myocardial infarction, post thrombolytic coronary rethrombosis, unstable angina, and acute myocardial infarction. In addition to use as a treatment for various medical conditions, heparin is also used to coat medical instruments and implants, such as stents, to prevent blood clotting. Using heparin to coat various medical items eliminates the need to prescribe anti-clotting medication in some cases.
Where heparin is used to treat medical conditions as those described above, two different methods and two different types of heparin are used. The two methods are intravenous infusion of standard heparin and injection of low molecular mass heparin. Patients undergoing intravenous infusion are hospitalized and the activated partial thromoplastin time (aPTT) is monitored. This type of treatment requires that the patient remain hospitalized until warfarin is administered to achieve an International Normalized Ratio (INR) between 2.0 and 3.0 often resulting in a three to seven day hospital stay. The alternative treatment involves twice daily injections of low-molecular-weight heparin. The injection treatment allows the patient to self-administer or have a visiting nurse or family member administer the injections.
Low molecular weight heparin has a molecular weight of 1,000 to 10,000 Daltons as compared to the molecular weight of standard heparin of 5,000 to 30,000 Daltons. Low molecular weight heparin binds less strongly to protein than standard heparin, has enhanced bioavailability, interacts less with platelets and yields more predictable blood levels. The predictability of blood levels eliminates the need to monitor the aPPT. In addition, low molecular weight heparin offers a lower likelihood of bleeding and no reports of thrombocytopenia or osteoporosis have been issued with respect to low molecular weight heparin.
In the presently claimed and disclosed invention, the monosaccharide composition of the P. multocida Type D polysaccharide has been identified and analyzed. The DNA sequence information of the Type A HA biosynthesis locus and the Type F biosynthesis locus allowed for the prediction of the general properties of the Type D locus. From this information on potential precursor genes required by a heparin synthase, pmHS was identified (P. multocida Heparin Synthase), the first dual action microbial heparin synthase to be identified and molecularly cloned from any source. With respect to the pmHS, a single polypeptide is responsible for the copolymerization of the GlcUA and GlcNAc sugars—i.e., it is a dual action enzyme as opposed to the single action nature of the at least three enzymes of E. coli K5 heparosan biosynthesis locus that are required for heparin production. The identification of pmHS also allowed for the identification of the existence of another heparin synthase found in Type A, D and F P. multocida. A gene with unknown function, called PgIA, was found in a genome sequencing project of Type A P. multocida; no enzymatic function (or any function) has been previously described with respect to this PgIA gene. Hereinafter, and is contemplated and included within the presently disclosed and claimed invention, is disclosed that the PgIA enzyme, which is 70% identical to pmHS, is also a heparin synthase. This unexpected cryptic gene is functional in vitro in recombinant systems. The Type D capsular polymer has been identified as a heparin polymer. Organisms with the heparin synthase gene (Type D P. multocida) as new sources of heparin polymer have also been identified, purified, and characterized.
SUMMARY OF THE INVENTION
The presently claimed and disclosed invention relates, in general, to dual action heparin synthases and, more particularly, to dual action heparin synthases obtained from Pasteurella multocida. The presently claimed and disclosed invention also relates to heparosan, heparin and heparin-like molecules produced according to recombinant techniques and methods of using such molecules. The presently claimed and disclosed invention also relates to methods, and molecules produced according to such methods, for using the presently claimed and disclosed heparosan and/or heparin synthases for polymer grafting and the production of non-naturally occurring chimeric polymers incorporating stretches of one or more acidic GAG molecules, such as heparin, chondroitin, hyaluronan, and/or heparosan.



BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
FIG. 1 graphically depicts Sequence Similarity of pmHS with KfiA and KfiC. Elements of the Pasteurella heparosan synthase, HS1 (containing residues 91-240SEQ ID NO: 23) and HS2 (containing residues 441-540; SEQ ID NO:26) are very similar to portions of two proteins from the E. coli K5 capsular locus (A, residues 75-172 of KfiA, SEQ ID NO:27 ; C, residues 262-410 of KfiC, SEQ ID NO:24) as shown by this modified Multalin alignment (ref. 21; numbering scheme corresponds to the pmHS sequence). The HS1 and HS2 elements may be important for hexosamine transferase or for glucuronic acid transferase activities, respectively. (con, consensus symbols: asterisks, [K or R] and [S or T]; %, any one of F,Y,W; $, any one of L,M; !, any one of I,V; #, any one of E,D,Q,N). The consensus sequence of the alignment of HS1 and KfiC has been assigned SEQ ID NO:25, while the consensus sequence of the alignment of HS2 and KfiA is assigned SEQ ID NO:28.
FIG. 2 depicts pmHS Activity Dependence on Acceptor and Enzyme Concentration. Various amounts of crude membranes containing the full-length enzyme, pmHS1-617, were incubated in 50 μl of buffer containing 50 mM Tris, pH 7.2, 10 mM MgCl2, 10 mM MnCl2, 500 μM UDP-[14C]GlcUA (0.15 μCi), and 500 μM UDP-GlcNAc. Three parallel sets of reactions were performed with either no acceptor (circles) or two concentrations of heparosan polymer acceptor (uronic acid: 0.6 μg, squares; 1.7 μg, triangles). After 40 min, the reaction was terminated and analyzed by paper chromatography. The background incorporation due to vector membranes alone (630 μg total protein; not plotted) with the high concentration of acceptor was 75 dpm [14C]GlcUA. The activity of pmHS is greatly stimulated by exogenous acceptor.
FIG. 3 Gel Filtration Analysis of Radiolabeled Polymer Synthesized in vitro. The crude membranes containing pmHS (0.7 mg total protein) were incubated with UDP-[14C]GlcUA and UDP-[3H]GlcNAc (each 500 μM, 0.4 μCi) in a 200 μl reaction volume either in the presence (top panel) or absence (bottom panel) of acceptor polymer (1 μg uronic acid). After various reaction times (denoted on curves: 20, 60, or 270 min), portions of the samples (75%) were analyzed on the PolySep column (calibration elution times in minutes: void volume, 9.8; 580 kDa dextran, 12.3; 145 kDa dextran, 12.75, totally included volume, 16.7). The starting acceptor polymer eluted at 12.8 min. Large polymers composed of both radiolabeled sugars (14C, C; 3H, H) in an equimolar ratio were synthesized by pmHS.
FIG. 4(A-D) graphically depicts the alignment of the pmHS (two clones: A2, B10) with PgIA, KfiA, KfiC, and DcbF. pmHS is shown in various forms: HSA1 and HSA2 are the two putative domains of pmHS; pORF=partial open reading frame which was obtained before complete sequence determined; recon=reconstructed open reading frame with sequence from multiple sources. FIG. 4A: KfiC, SEQ ID NO:29; HSA1, SEQ ID NO:30; KfiA, SEQ ID NO:7; HSA2, SEQ ID NO:31; Consensus, SEQ ID NO:32. FIG. 4B: pmHS, SEQ ID NO:2; pgIA, SEQ ID NO:6; DcbF, SEQ ID NO:17; Consensus, SEQ ID NO:33. FIG. 4C: A2, SEQ ID NO:2; B10, SEQ ID NO:4; pgIA, SEQ ID NO:6; DcbF, SEQ ID NO:17; Consensus, SEQ ID NO:34. FIG. 4D: pmHS, SEQ ID NO:2; pgIA, SEQ ID NO:6; DcbF, SEQ ID NO:17; and Consensus, SEQ ID NO:35.



DETAILED DESCRIPTION OF THE INVENTION
Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not limited in its application to the details of construction and the arrangement of the components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments or of being practiced or carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein is for purpose of description and should not be regarded as limiting.
As used herein, the term “nucleic acid segment” and “DNA segment” are used interchangeably and refer to a DNA molecule which has been isolated free of total genomic DNA of a particular species. Therefore, a “purified” DNA or nucleic acid segment as used herein, refers to a DNA segment which contains a Heparin Synthase (“HS”) coding sequence yet is isolated away from, or purified free from, unrelated genomic DNA, for example, total Pasteurella multocida or, for example, mammalian host genomic DNA. Included within the term “DNA segment”, are DNA segments and smaller fragments of such segments, and also recombinant vectors, including, for example, plasmids, cosmids, phage, viruses, and the like.
Similarly, a DNA segment comprising an isolated or purified pmHS (Pasteurella multocida Heparin Synthase) gene or a PgIA gene refers to a DNA segment including HS coding sequences isolated substantially away from other naturally occurring genes or protein encoding sequences. In this respect, the term “gene” is used for simplicity to refer to a functional protein, polypeptide or peptide encoding unit. As will be understood by those in the art, this functional term includes genomic sequences, cDNA sequences or combinations thereof. “Isolated substantially away from other coding sequences” means that the gene of interest, in this case pmHS or PgIA, forms the significant part of the coding region of the DNA segment, and that the DNA segment does not contain large portions of naturally-occurring coding DNA, such as large chromosomal fragments or other functional genes or DNA coding regions. Of course, this refers to the DNA segment as originally isolated, and does not exclude genes or coding regions later added to, or intentionally left in the segment by the hand of man.
Due to certain advantages associated with the use of prokaryotic sources, one will likely realize the most advantages upon isolation of the HS genes from Pasteurella multocida. One such advantage is that, typically, eukaryotic enzymes may require significant post-translational modifications that can only be achieved in an eukaryotic host. This will tend to limit the applicability of any eukaryotic HS genes that are obtained. Additionally, such eukaryotic HS genes are dainty, fragile, and difficult, if not impossible, to transfer into prokaryotic hosts for large scale polymer production. Moreover, those of ordinary skill in the art will likely realize additional advantages in terms of time and ease of genetic manipulation where a prokaryotic enzyme gene is sought to be employed. These additional advantages include (a) the ease of isolation of a prokaryotic gene because of the relatively small size of the genome and, therefore, the reduced amount of screening of the corresponding genomic library; and (b) the ease of manipulation because the overall size of the coding region of a prokaryotic gene is significantly smaller due to the absence of introns. Furthermore, if the product of the HS genes (i.e., the enzyme) requires posttranslational modifications or cofactors, these would best be achieved in a similar prokaryotic cellular environment (host) from which the gene was derived.
Preferably, DNA sequences in accordance with the present invention will further include genetic control regions which allow the expression of the sequence in a selected recombinant host. Of course, the nature of the control region employed will generally vary depending on the particular use (e.g., cloning host) envisioned.
In particular embodiments, the invention concerns isolated DNA segments and recombinant vectors incorporating DNA sequences which encode a HS gene such as pmHS or PgIA. In the case of pmHS, the isolated DNA segments and recombinant vectors incorporating DNA sequences which include within their amino acid sequences an amino acid sequence in accordance with SEQ ID NO:2 or SEQ ID NO:4; for PgIA, an amino acid sequence in accordance with SEQ ID NO: 6. Moreover, in other particular embodiments, the invention concerns isolated DNA segments and recombinant vectors incorporating DNA sequences which encode a gene that includes within its amino acid sequence the amino acid sequence of an HS gene or DNA, and in particular to a HS gene or cDNA, corresponding to Pasteurella multocida Heparin Synthases—pmHS and PgIA. For example, where the DNA segment or vector encodes a full length HS protein, or is intended for use in expressing the HS protein, preferred sequences are those which are essentially as set forth in SEQ ID NO:2 or SEQ ID NO:4 or SEQ ID NO:6. Additionally, sequences which have at least one or more amino acid motifs (discussed in detail hereinafter) and encode a functionally active heparosan/heparin synthase are contemplated for use.
The presently claimed and disclosed pmHS includes SEQ ID NOS:1 and 3 (nucleotide sequence) and SEQ ID NOS:2 and 4 (amino acid sequences) that have been assigned GenBank Accession Nos. AAL84702 and AAL84705, respectively. The presently claimed and disclosed PgIA includes SEQ ID NO:5 (nucleotide sequence) and SEQ ID NO:6 (amino acid sequence) that have been assigned GenBank Accession No. NP—245351. Amino acid motifs for enzymatically active heparosan/heparin synthases are disclosed in detail hereinafter.
Nucleic acid segments having heparin synthase activity may be isolated by the methods described herein. The term “a sequence essentially as set forth in SEQ ID NO:2 or 4 or 6” means that the sequence substantially corresponds to a portion of SEQ ID NO:2 or 4 or 6 and has relatively few amino acids which are not identical to, or a biologically functional equivalent of, the amino acids of SEQ ID NO:2 or 4 or 6. The term “biologically functional equivalent” is well understood in the art and is further defined in detail herein, as a gene having a sequence essentially as set forth in SEQ ID NO:2 or 4 or 6, and that is associated with the ability of prokaryotes to produce heparin/heparosan or a “heparin like” polymer or a heparin synthase polypeptide. For example, PgIA is approximately 70% identical to pmHS and PgIA is shown, hereinafter, to be an enzymatically active heparin/heparosan synthase.
One of ordinary skill in the art would appreciate that a nucleic acid segment encoding enzymatically active heparin synthase may contain conserved or semi-conserved substitutions to the sequences set forth in SEQ ID NOS: 1, 2, 3, 4, 5 or 6 and yet still be within the scope of the invention.
In particular, the art is replete with examples of practitioner's ability to make structural changes to a nucleic acid segment (i.e., encoding conserved or semi-conserved amino acid substitutions) and still preserve its enzymatic or functional activity. See for example: (1) Risler et al. “Amino Acid Substitutions in Structurally Related Proteins. A Pattern Recognition Approach.” J. Mol. Biol. 204:1019-1029 (1988) [“ . . . according to the observed exchangeability of amino acid side chains, only four groups could be delineated; (i) Ile and Val; (ii) Leu and Met, (iii) Lys, Arg, and Gln, and (iv) Tyr and Phe.”]; (2) Niefind et al. “Amino Acid Similarity Coefficients for Protein Modeling and Sequence Alignment Derived from Main-Chain Folding Anoles.” J. Mol. Biol. 219:481-497 (1991) [similarity parameters allow amino acid substitutions to be designed]; and (3) Overington et al. “Environment-Specific Amino Acid Substitution Tables: Tertiary Templates and Prediction of Protein Folds,” Protein Science 1:216-226 (1992) [“Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns . . . ” Compatible changes can be made]. Each of these articles, to the extent that they provide additional details to one of ordinary skill in the art in the methods of making such conserved or semi-conserved amino acid substitutions, are hereby expressly incorporated herein in their entirety as though set forth herein.
These references and countless others available to one of ordinary skill in the art, indicate that given a nucleic acid sequence, one of ordinary skill in the art could make substitutions and changes to the nucleic acid sequence without changing its functionality. Also, a substituted nucleic acid segment may be highly identical and retain its enzymatic activity with regard to its unadulterated parent, and yet still fail to hybridize thereto (i.e., spHAS and seHAS, 70% identical yet do not hybridize under standard hybridization conditions as defined hereinafter). Therefore, the ability of two sequences to hybridize to one another can be a starting point for comparison but should not be the only ending point—rather, one of ordinary skill in the art must look to the conserved and semi-conserved amino acid stretches between the sequences between the sequences and also must assess functionality. Thus, given that two sequences may have conserved and/or semi-conserved amino acid stretches, functionality must be assessed.
One of ordinary skill in the art would also appreciate that substitutions can be made to the pmHS nucleic acid segment listed in SEQ ID NO: 1 or 3 tha do not affect the amino acid sequences they encode or result in conservative or semi-conservative substitutions in the amino acid sequences they encode without deviating outside the scope and claims of the present invention. Standardized and accepted functionally equivalent amino acid substitutions are presented in Table I.








TABLE I






Conservative and Semi-


Amino Acid Group
Conservative Substitutions







NonPolar R Groups
Alanine, Valine, Leucine, Isoleucine,



Proline, Methionine, Phenylalanine,



Tryptophan


Polar, but uncharged, R Groups
Serine, Threonine,



Cysteine, Asparagine, Glutamine


Negatively Charged R Groups
Aspartic Acid, Glutamic Acid


Positively Charged R Groups
Lysine, Arginine, Histidine









A particular example would be SEQ ID NO NOS: 2 and 4, both of which encode a functionally active HS and yet have a single substitution at position 455 (Threonine for Isoleucine), and yet both enzymes are still capable of producing heparosan. Such a conservative or semi-conservative scheme is even more evident when comparing pmHS with PgIA—they are only  ̃70% identical and yet still both produce functionally active HS enzymes.
Another preferred embodiment of the present invention is a purified nucleic acid segment that encodes a protein in accordance with SEQ ID NO:2 or 4 or 6 further defined as a recombinant vector. As used herein, the term “recombinant vector” refers to a vector that has been modified to contain a nucleic acid segment that encodes a HS protein, or fragment thereof. The recombinant vector may be further defined as an expression vector comprising a promoter operatively linked to said HS encoding nucleic acid segment.
A further preferred embodiment of the present invention is a host cell, made recombinant with a recombinant vector comprising a HS gene. The preferred recombinant host cell may be a prokaryotic cell. In another embodiment, the recombinant host cell is an eukaryotic cell. As used herein, the term “engineered” or “recombinant” cell is intended to refer to a cell into which a recombinant gene, such as a gene encoding HS, has been introduced. Therefore, engineered cells are distinguishable from naturally occurring cells which do not contain a recombinantly introduced gene. Engineered cells are thus cells having a gene or genes introduced through the hand of man. Recombinantly introduced genes will either be in the form of a cDNA gene, one or more copies of a genomic gene, or will include genes positioned adjacent to a promoter not naturally associated with the particular introduced gene.
Where one desires to use a host other than Pasteurella, as may be used to produce recombinant heparin/heparosan synthase, it may be advantageous to employ a prokaryotic system such as E. coli, B. subtilis, Lactococcus sp., (see, for example, U.S. patent application Ser. No. 09/469,200, which discloses the production of HA through the introduction of a HAS gene into Bacillus host—the contents of which are expressly incorporated herein in their entirety), or even eukaryotic systems such as yeast or Chinese hamster ovary, African green monkey kidney cells, VERO cells, or the like. Of course, where this is undertaken it will generally be desirable to bring the heparin/heparosan synthase gene under the control of sequences which are functional in the selected alternative host. The appropriate DNA control sequences, as well as their construction and use, are generally well known in the art as discussed in more detail hereinbelow.
In preferred embodiments, the heparin/heparosan synthase-encoding DNA segments further include DNA sequences, known in the art functionally as origins of replication or “replicons”, which allow replication of contiguous sequences by the particular host. Such origins allow the preparation of extrachromosomally localized and replicating chimeric segments or plasmids, to which HS DNA sequences are ligated. In more preferred instances, the employed origin is one capable of replication in bacterial hosts suitable for biotechnology applications. However, for more versatility of cloned DNA segments, it may be desirable to alternatively or even additionally employ origins recognized by other host systems whose use is contemplated (such as in a shuttle vector).
The isolation and use of other replication origins such as the SV40, polyoma or bovine papilloma virus origins, which may be employed for cloning or expression in a number of higher organisms, are well known to those of ordinary skill in the art. In certain embodiments, the invention may thus be defined in terms of a recombinant transformation vector which includes the HS coding gene sequence together with an appropriate replication origin and under the control of selected control regions.
Thus, it will be appreciated by those of ordinary skill in the art that other means may be used to obtain the HS gene or cDNA, in light of the present disclosure. For example, polymerase chain reaction or RT-PCR produced DNA fragments may be obtained which contain full complements of genes or cDNAs from a number of sources, including other strains of Pasteurella or from eukaryotic sources, such as cDNA libraries. Virtually any molecular cloning approach may be employed for the generation of DNA fragments in accordance with the present invention. Thus, the only limitation generally on the particular method employed for DNA isolation is that the isolated nucleic acids should encode a biologically functional equivalent HS, and in a more preferred embodiment, the isolated nucleic acids should encode an amino acid sequence that contains at least one of the HS amino acid motifs described in detail hereinafter.
Once the DNA has been isolated it is ligated together with a selected vector. Virtually any cloning vector can be employed to realize advantages in accordance with the invention. Typical useful vectors include plasmids and phages for use in prokaryotic organisms and even viral vectors for use in eukaryotic organisms. Examples include pKK223-3, pSA3, recombinant lambda, SV40, polyoma, adenovirus, bovine papilloma virus and retroviruses. However, it is believed that particular advantages will ultimately be realized where vectors capable of replication in both Lactococcus or Bacillus strains and E. coli or P. multocida are employed.
Vectors such as these, exemplified by the pSA3 vector of Dao and Ferretti or the pAT19 vector of Trieu-Cuot, et al., allow one to perform clonal colony selection in an easily manipulated host such as E. coli, followed by subsequent transfer back into a food grade Lactococcus or Bacillus strain for production of heparin/heparosan. These are benign and well studied organisms used in the production of certain foods and biotechnology products—otherwise known in the art as GRAS (Generally Regarded As Safe). GRAS organisms are advantageous in that one can augment the Lactococcus or Bacillus strain's ability to synthesize heparin/heparosan through gene dosaging (i.e., providing extra copies of the HA synthase gene by amplification) and/or the inclusion of additional genes to increase the availability of the heparin/heparosan precursors UDP-GlcUA and UDP-GlcNAc and/or the inclusion of genes that include enzymes that will make modifications (such as sulfation and epimerization) to the heparosan polymer in order to convert it to heparin. Sugar precursors are made by the enzymes with UDP-glucose dehydrogenase and UDP-N-acetylglucosamine pyrophosphorylase activity, respectively. The inherent ability of a bacterium to synthesize heparin/heparosan is also augmented through the formation of extra copies, or amplification, of the plasmid that carries the heparin/heparosan synthase gene. This amplification can account for up to a 10-fold increase in plasmid copy number and, therefore, the HS gene copy number.
Another procedure that would further augment HS gene copy number is the insertion of multiple copies of the gene into the plasmid. Another technique would include integrating the HS gene into chromosomal DNA. This extra amplification would be especially feasible, since the HS gene size is small. In some scenarios, the chromosomal DNA-ligated vector is employed to transfect the host that is selected for clonal screening purposes such as E. coli or Bacillus, through the use of a vector that is capable of expressing the inserted DNA in the chosen host. In certain instances, especially to confer stability, genes such as the HS gene, may be integrated into the chromosome in various positions in an operative fashion. Unlike plasmids, integrated genes do not need selection pressure for maintenance of the recombinant gene.
Where an eukaryotic source such as dermal or synovial fibroblasts or rooster comb cells is employed, one will desire to proceed initially by preparing a cDNA library. This is carried out first by isolation of mRNA from the above cells, followed by preparation of double stranded cDNA and ligation of the cDNA with the selected vector. Numerous possibilities are available and known in the art for the preparation of the double stranded cDNA, and all such techniques are believed to be applicable. A preferred technique involves reverse transcription utilizing an enzyme having reverse transcriptase activity. Once a population of double stranded cDNAs is obtained, a cDNA library is prepared in the selected host by accepted techniques, such as by ligation into the appropriate vector and amplification in the appropriate host. Due to the high number of clones that are obtained, and the relative ease of screening large numbers of clones by the techniques set forth herein, one may desire to employ phage expression vectors, such as λgt11, λgt12, λGem11, and/or λZAP for the cloning and expression screening of cDNA clones.
In certain other embodiments, the invention concerns isolated DNA segments and recombinant vectors that include within their sequence a nucleic acid sequence essentially as set forth in SEQ ID NO:1 or 3 or 5. The term “essentially as set forth in SEQ ID NO:1 or 3 or 5” is used in the same sense as described above with respect to the amino acid sequences and means that the nucleic acid sequence substantially corresponds to a portion of SEQ ID NO:1 or 3 or 5, and has relatively few codons that are not identical, or functionally equivalent, to the codons of SEQ ID NO:1 or 3 or 5 and encodes a enzymatically active HS. The term “functionally equivalent codon” is used herein to refer to codons that encode the same amino acid, such as the six codons for arginine or serine, and also refers to codons that encode biologically equivalent amino acids. “Biologically Equivalent Amino Acids” of Table I refers to residues that have similar chemical or physical properties that may be easily interchanged for one another.
It will also be understood that amino acid and nucleic acid sequences may include additional residues, such as additional N- or C-terminal amino acids or 5′ or 3′ nucleic acid sequences, and yet still be essentially as set forth in one of the sequences disclosed herein, so long as the sequence meets the criteria set forth above, including the maintenance of biological protein activity where protein expression and enzymatic activity is concerned. The addition of terminal sequences particularly applies to nucleic acid sequences which may, for example, include various non-coding sequences flanking either of the 5′ or 3′ portions of the coding region or may include various internal sequences, which are known to occur within genes.
Likewise, deletion of certain portions of the polypeptide can be desirable. For example, functional truncated versions of pmHAS, the Pasteurella hyaluronan synthase, missing the carboxyl terminus enhances the utility for in vitro use. The truncated pmHAS enzyme is a soluble protein that is easy to purify in contrast to the full-length protein (972 residues). Also, expression level of the enzyme increases greatly as the membrane is not overloaded. It is also contemplated that a truncated version of pmHS would also be useful and is contemplated as falling within the scope of the presently claimed and disclosed invention. Such a truncated version would also be highly soluble and increase expression of the enzyme; the native membrane proteins are found in low levels and are not soluble without special treatment with detergents.
Allowing for the degeneracy of the genetic code as well as conserved and semi-conserved substitutions, sequences which have between about 40% and about 80%; or more preferably, between about 80% and about 90%; or even more preferably, between about 90% and about 99% of nucleotides which are identical to the nucleotides of SEQ ID NO:1 or 3 or 5 will be sequences which are “essentially as set forth in SEQ ID NO:1 or 3 or 5”. In a preferred embodiment, the sequences would be 70% identical. Sequences which are essentially the same as those set forth in SEQ ID NO:1 or 3 or 5 may also be functionally defined as sequences which are capable of hybridizing to a nucleic acid segment containing the complement of SEQ ID NO:1 or 3 or 5 under standard or less stringent hybridizing conditions. Suitable standard hybridization conditions will be well known to those of skill in the art and are clearly set forth hereinbelow. As certain domains and active sites are formed from a relatively small portion of the total polypeptide, these regions of sequence identity or similarity may be present only in portions of the gene. Additionally, sequences which are “essentially as set forth in SEQ ID NO:1 or 3 or 5” will include those amino acid sequences that have at least one of the amino acid motifs (described hereinafter in detail) and that also retain the functionality of an enzymatically active HS.
As is well known to those of ordinary skill in the art, most of the amino acids in a protein are present to form the “scaffolding” or general environment of the protein. The actual working parts responsible for the specific desired catalysis are usually a series of small domains or motifs. Thus, a pair of enzymes that possess the same or similar motifs would be expected to possess the same or similar catalytic activity, thus they are functionally equivalent. Utility for this hypothetical pair of enzymes may be considered interchangeable unless one member of the pair has a subset of distinct, useful properties. In a similar vein, certain non-critical motifs or domains may be dissected from the original, naturally occurring protein and function will not be affected; removal of non-critical residues does not perturb the important action of the remaining critical motifs or domains. By analogy, with sufficient planning and knowledge, it is possible to translocate motifs or domains from one enzyme to another polypeptide to confer the new enzyme with desirable characteristics intrinsic to the domain or motif. Such motifs for HS are disclosed in particularly hereinafter.
The term “standard hybridization conditions” as used herein, is used to describe those conditions under which substantially complementary nucleic acid segments will form standard Watson-Crick base-pairing. A number of factors are known that determine the specificity of binding or hybridization, such as pH, temperature, salt concentration, the presence of agents such as formamide and dimethyl sulfoxide, the length of the segments that are hybridizing, and the like. When it is contemplated that shorter nucleic acid segments will be used for hybridization, for example fragments between about 14 and about 100 nucleotides, salt and temperature preferred conditions for overnight standard hybridization will include 1.2-1.8×HPB (High Phosphate Buffer) at 40-50° C. or 5×SSC (Standard Saline Citrate) at 50° C. Washes in low salt (10 mM salt or 0.1×SSC) are used for stringent hybridizations with room temperature incubations of 10-60 minutes. Washes with 0.5× to 1×SSC, 1% Sodium dodecyl sulfate at room temperature are used in lower stringency washes for 15-30 minutes. For all hybridizations: (where 1×HPB=0.5 m NaCl, 0.1 m Na2HPO4, 5 mM EDTA, pH 7.0) and (where 20×SSC=3 m NaCl, 0.3 m Sodium Citrate with pH 7.0).
Naturally, the present invention also encompasses DNA segments which are complementary, or essentially complementary, to the sequence set forth in SEQ ID NOS:1, 2, 3, 4, 5, or 6. Nucleic acid sequences which are “complementary” are those which are capable of base-pairing according to the standard Watson-Crick complementarity rules. As used herein, the term “complementary sequences” means nucleic acid sequences which are substantially complementary, as may be assessed by the same nucleotide comparison set forth above, or as defined as being capable of hybridizing to the nucleic acid segment of SEQ ID NO:1, 2, 3, 4, 5, or 6 under the above-defined standard hybridization conditions.
The nucleic acid segments of the present invention, regardless of the length of the coding sequence itself, may be combined with other DNA sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, epitope tags, poly histidine regions, other coding segments, and the like, such that their overall length may vary considerably. For example, functional spHAS-(Histidine)6 and x1 HAS1-(Green Fluorescent Protein) fusion proteins have been reported. It is therefore contemplated that a nucleic acid fragment of almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol.
Naturally, it will also be understood that this invention is not limited to the particular nucleic acid and amino acid sequences of SEQ ID NOS:1, 2, 3, 4, 5, or 6. Recombinant vectors and isolated DNA segments may therefore variously include the HS coding regions themselves, coding regions bearing selected alterations or modifications in the basic coding region, or they may encode larger polypeptides which nevertheless include HS coding regions or may encode biologically functional equivalent proteins or peptides which have variant amino acid sequences.
The DNA segments of the present invention encompass biologically functional equivalent HS proteins and peptides. Such sequences may arise as a consequence of codon redundancy and functional equivalency which are known to occur naturally within nucleic acid sequences and the proteins thus encoded. Alternatively, functionally equivalent proteins or peptides may be created via the application of recombinant DNA technology, in which changes in the protein structure may be engineered, based on considerations of the properties of the amino acids being exchanged. Changes designed by man may be introduced through the application of site-directed mutagenesis techniques, e.g., to introduce improvements to the enzyme activity or to antigenicity of the HS protein or to test HS mutants in order to examine HS activity at the molecular level.
Also, specific changes to the HS coding sequence will result in the production of heparin/heparosan having a modified size distribution or structural configuration. One of ordinary skill in the art would appreciate that the HS coding sequence can be manipulated in a manner to produce an altered HS which in turn is capable of producing heparin/heparosan having differing polymer sizes and/or functional capabilities. The utility of such a modified polymer is easily appreciated from the above “Background of the Invention.” For example, the HS coding sequence may be altered in such a manner that the HS has an altered sugar substrate specificity so that the HS creates a new heparin/heparosan-like chimeric polymer incorporating a different structure via the inclusion of a previously unincorporated sugar or sugar derivative. This newly incorporated sugar results in a modified heparin/heparosan having different and unique functional properties. As will be appreciated by one of ordinary skill in the art given the HS coding sequences, changes and/or substitutions can be made to the HS coding sequence such that these desired properties and/or size modifications can be accomplished.
Basic knowledge on the substrate binding sites (e.g., the UDP-GlcUA site or UDP-GlcNAc site or oligosaccharide acceptor site) of pmHS or pgIA allows the targeting of residues for mutation to change the catalytic properties of the site. The identity of important catalytic residues of pmHAS, another GAG synthase, have recently been elucidated (Jing & DeAngelis, 2000, Glycobiology vol 10; pp. 883-889 the contents of which are expressly incorporated herein in their entirety). Appropriate changes at or near these residues alters UDP-sugar binding. Changes of residues in close proximity should allow other precursors to bind instead of the authentic heparin/heparosan sugar precursors; thus a new, modified polymer is synthesized. Polymer size changes are caused by differences in the synthase's catalytic efficiency or changes in the acceptor site affinity. Polymer size changes have been made in seHAS and spHAS (U.S. patent application Ser. Nos. 09/559,793 and 09/469,200, the contents of which are expressly incorporated herein by reference) as well as the vertebrate HAS, xIHAS1 (DG42) (Pummill & DeAngelis, in press and which is also incorporated herein in its entirety) by mutating various residues. As pmHS is a more malleable, robust enzyme than these other enzymes, similar or superior versions of mutant pmHS or pgIA which synthesize modified polymers are easily produced.
The term “modified structure” as used herein denotes a heparin/heparosan polymer containing a sugar or derivative not normally found in the naturally occurring heparin/heparosan polypeptide. The term “modified size distribution” refers to the synthesis of heparin/heparosan molecules of a size distribution not normally found with the native enzyme; the engineered size could be much smaller or larger than normal.
One of ordinary skill in the art given this disclosure would appreciate that there are several ways in which the size distribution of the heparin/heparosan polymer made by the HS could be regulated to give different sizes. First, the kinetic control of product size can be altered by environmental factors such as decreasing temperature, decreasing time of enzyme action and/or by decreasing the concentration of one or both sugar nucleotide substrates. Decreasing any or all of these variables will give lower amounts and smaller sizes of heparin/heparosan product. The disadvantages of these extrinsic approaches are that the yield of product is also decreased and it is difficult to achieve reproducibility from day to day or batch to batch. Secondly, the alteration of the intrinsic ability of the enzyme to synthesize a large or small heparin/heparosan product. Changes to the protein are engineered by recombinant DNA technology, including substitution, deletion and addition of specific amino acids (or even the introduction of prosthetic groups through metabolic processing). Such changes that result in an intrinsically slower enzyme then allow for more reproducible control of heparin/heparosan size by kinetic means. The final heparin/heparosan size distribution is determined by certain characteristics of the enzyme that rely on particular amino acids in the sequence. Among the residues absolutely conserved between the now known HS enzymes, there is a set of amino acids at unique positions that control or greatly influence the size of the polymer that the enzyme can make.
Finally, using post-synthesis processing larger molecular weight heparin can be degraded with specific glycasidases or ultrasonication, acids or a combination thereof to make lower molecular weight heparin/heparosan. This practice, however, is very difficult to achieve reproducibility and one must meticulously repurify the heparin/heparosan to remove the cleavage reagent and unwanted digestion products.
Structurally modified heparin/heparosan is no different conceptually than altering the size distribution of the heparin/heparosan product by changing particular amino acids in the desired HS and/or more particularly, but not limiting thereto, pmHS or PgIA. Derivatives of UDP-GlcNAc, in which the acetyl group is missing from the amide (UDP-GlcN) or replaced with another chemically useful group (for example, phenyl to produce UDP-GlcNPhe), are expected to be particularly useful. The free amino group would be available for chemical reactions to derivatize heparin/heparosan in the former case with GlcN incorporation. In the latter case, GlcNPhe, would make the polymer more hydrophobic or prone to making emulsions. The strong substrate specificity may rely on a particular subset of amino acids among the residues that are conserved. Specific changes to one or more of these residues creates a functional HS that interacts less specifically with one or more of the substrates than the native enzyme. This altered enzyme then utilizes alternate natural or special sugar nucleotides to incorporate sugar derivatives designed to allow different chemistries to be employed for the following purposes: (i) covalently coupling specific drugs, proteins, or toxins to the structurally modified heparin/heparosan for general or targeted drug delivery, radiological procedures, etc. (ii) covalently cross linking the heparin/heparosan itself or to other supports to achieve a gel, or other three dimensional biomaterial with stronger physical properties, and (iii) covalently linking heparin/heparosan to a surface to create a biocompatible film or monolayer.
EXPERIMENTAL
As stated hereinabove, Pasteurella multocida Type D, a causative agent of atrophic rhinitis in swine and pasteurellosis in other domestic animals, produces an extracellular polysaccharide capsule that is a putative virulence factor. It has been reported that the capsule of Type D was removed by treating microbes with heparin lyase III. A 617-residue enzyme, pmHS, and a 651-residue enzyme, PgIA, which are both authentic heparosan (unsulfated, unepimerized heparin) synthase enzymes have been molecularely cloned and are presently claimed and disclosed herein. Recombinant Escherichia coli-derived pmHS or PgIA catalyzes the polymerization of the monosaccharides from UDP-GlcNAc and UDP-GlcUA. Other structurally related sugar nucleotides do not substitute. Synthase activity was stimulated about 7- to 25-fold by the addition of an exogenous polymer acceptor. Molecules composed of  ̃500 to 3,000 sugar residues were produced in vitro. The polysaccharide was sensitive to the action of heparin lyase III but resistant to hyaluronan lyase. The sequence of pmHS enzyme is not very similar to the vertebrate heparin/heparan sulfate glycosyltransferases, EXT1/2, or to other Pasteurella glycosaminoglycan synthases that produce hyaluronan or chondroitin. Certain motifs do exist however, between the pmHS, pgIA, and KfiA and KfiC thereby leading to deduced amino acid motifs that are conserved throughout this class of GAG synthases for the production of heparin/heparosan The pmHS enzyme is the first microbial dual-action glycosyltransferase to be described that forms a polysaccharide composed of β4GlcUA-α4GlcNAc disaccharide repeats. In contrast, heparosan biosynthesis in E. coli K5 requires at least two separate polypeptides, KfiA and KfiC, to catalyze the same polymerization reaction.
Glycosaminoglycans [GAGs] are long linear polysaccharides consisting of disaccharide repeats that contain an amino sugar (1-2). Heparin/heparan [β4GlcUA-α4GlcNAc]n, chondroitin [β4GlcUA-β3GalNAc]n, and hyaluronan [β4GlcUA-β3GlcNAc]n are three prevalent GAGs and the only known acidic GAGs. In the former two polymers, usually n=20 to 100 while in the case of HA, typically n=103-4. In vertebrates, one or more modifications including O-sulfation of certain hydroxyls, deacetylation and subsequent N-sulfation, or epimerization of glucuronic acid to iduronic acid are found in most GAGs except HA(3). A few clever microbes also produce GAG chains, however, sulfation or epimerization have not been described. The GAGs in pathogenic bacteria are found as extracellular polysaccharide coatings, called capsules, which serve as virulence factors(4). The capsule is thought to assist in the evasion of host defenses such as phagocytosis and complement. As the microbial polysaccharide is identical or very similar to the host GAG, the antibody response is either very limited or non-existent.
The invasiveness and pathogenicity of certain Escherichia coli strains has been attributed to their polysaccharide capsule(4). Two E. coli capsular types, K5 and K4, make polymers composed of GAG-like polymers. The K5 capsular material is a polysaccharide called heparosan, N-acetylheparosan, or desulfoheparin, which are identical to mammalian heparin/heparin sulfate except that the bacterial polymer is unsulfated and there is no epimerization of GlcUA to iduronic acid(5). The E. coli K4 polymer is an unsulfated chondroitin backbone decorated with fructose side-branches on the C3 position of the GlcUA residues(6).
The E. coli K5 capsule biosynthesis locus contains the open reading frames KfiA-D (also called Kfa in some reports; GenBank Accession Number X77617). At first, KfiC was stated to be a dual-action glycosyltransferase responsible for the alternating addition of both GlcUA and GlcNAc to the heparosan chain(7). However, a later report by the same group reported that another protein, KfiA, was actually the αGlcNAc-transferase required for Heparosan polymerization(8). Therefore, at least these two enzymes, KfiA and KfiC, the βGlcUA-transferase, work in concert to form the disaccharide repeat and the first report, that KfiC was a dual-action enzyme, was in error. Another deduced protein in the operon, KfiB, was suggested to stabilize the enzymatic complex during elongation in vivo, but perhaps not participate directly in catalysis(8). The identity and the sequence of the E. coli K4 capsular glycosyltransferase(s) has recently been reported. This enzyme, KfoC, is approximately 60% identical to the Pasteurella chondroitin synthase (pmCS) and is also a dual-action enzyme.
Many P. multocida isolates produce GAG or GAG-like molecules as assessed by enzymatic degradation and removal of the capsule of living bacterial cells(9,10). Carter Type A P. multocida, the major causative agent of fowl cholera and pasteurellosis, makes an HA capsule(11). A single polypeptide, the HA synthase, pmHAS, polymerizes the HA chain by transferring both GlcUA and GlcNAc(12). Type F P. multocida, the minor fowl cholera pathogen, produces a capsule composed of an unsulfated chondroitin sensitive to Flavobacterium chondroitin AC lyase(9,13,14). Again, a dual-action chondroitin synthase, pmCS, polymerizes the chondroitin chain(14). The capsule of another distinct P. multocida, Type D, was reported to be sensitive to heparin lyase III(9) which thereby led to the presently claimed and disclosed invention—the identification and characterization of pmHS (P. multocida heparin/heparosan synthase) and PgIA, the first and only known bacterial dual-action heparosan synthases.
Prior to recombinantly obtaining the pmHS gene and heterologously expressing it in a recombinant system, activity assays of P. multocida Type D enzymes were completed. Native membranes were prepared from a wild-type encapsulated Type D strain (P-3881; DeAngelis et al., 1996, the entirety of which is expressly incorporated herein in its entirety). The membranes were tested for in vitro sugar incorporation monitored by paper chromatography analysis. Characterization of the ability to co-polymerize the two sugars and utilize metal ions was performed. First, detection of co-polymerization activity of the Type D P. multocida strain was determined in vitro. The membranes+UDP-[14C]GlcUA (300 μM; 1.5×105 dpm)+various combinations of the 2nd sugar (UDP-GlcNAc, 900 μM) and/or EDTA chelator (45 mM) were mixed in 50 mM Tris, pH 7.2 with 20 mM MnCl2 and 20 mM MgCl2 reaction buffer. All reactions were performed at 30 degrees Celsius for 2.5 hours. The incorporation was measured by paper chromatography as disclosed in DeAngelis et al., 1996. The results of this co-polymerization activity are summarized in Table II.









TABLE II





UDP-GlcNAc Added?
EDTA Added?
Incorporation (dpm)

















No
No
520


Yes
No
9150


No
Yes
35


Yes
Yes
160









Thus, it is apparent that the Type D P. multocida strain P-3881 has a metal-dependent enzyme that copolymerized both heparin precursors into a polymer.
Second, the metal requirement of the Type D P. multocida HS activity was tested in vitro. Membranes+UDP-[14C]GlcUA+UDP-GlcNAc and buffer without the metals were mixed in a similar fashion as the preceding experiment except that various metals or EDTA (20 mM) were added as noted in Table III. The results of this metal specificity are summarized in Table III.










TABLE III







Metal
dpm



















None
13



Mg
2960



Mn
3070



Mn + Mg
3000



Co
120










Thus, it is apparent that the Type D P. multocida HS requires either manganese or magnesium ion for enzymatic activity.
Further, the sugar specificity of the Type D P. multocida strain was determined in vitro in similar experiments. The ability to co-polymerize the sugars that compose the authentic backbone was tested by performing two parallel reactions:
A. UDP-[14C]GlcUA+various combinations of 2nd UDP-sugars.
B. UDP-[3H]GlcNAc+various combinations of 2nd UDP-sugars
The results of these experiments are summarized in Table IV. Significant 14C-GlcUA incorporation required UDP-GlcNAc and, conversely, significant 3H-GlcNAc incorporation required UDP-GlcUA; the enzyme copolymerizes the polysaccharide chain with both authentic heparin UDP-sugar precursors.










TABLE IV









A. Hexosamine-transfer




2nd Sugar Added
14C dpm incorporation







None
330



UDP-GlcNAc
2290



UDP-GalNAc
2790



UDP-Glc
450







B. Uronic Acid Transfer




2nd Sugar Added
3H dpm incorporation







None
170



UDP-GlcUA
1000



UDP-GalUA
290



UDP-Glc
185










It should be added that the above-described results show that the native Type D P. multocida membrane enzymes have relaxed hexosamine transfer specificity in vitro. Such relaxed hexosamine transfer specificity is an advantage for syntheses where the UDP-sugar supplied can be manipulated. In such a manner, novel and non-naturally occurring polymers can be created. These novel, non-naturally occurring polymers have significant utility and novel biological properties.
Experimental Procedures for Isolating HS Genes and Testing Function
Materials and Pasteurella Strains—Unless otherwise noted, all chemicals were from Sigma or Fisher, and all molecular biology reagents were from Promega. The wild-type encapsulated Type D P. multocida isolates, P-934 (swine), P-3881 (bovine), P-4058 (rabbit), and P-5695 (swine), were obtained from the USDA collection (Ames, Iowa). The strains were grown in brain heart infusion (Difco) at 37° C.
Analysis of Genomic DNA and Isolation of Capsule Biosynthesis Locus DNA—Preliminary data from Southern blot analysis using pmHAS-based hybridization probes(12) suggested that the Type A synthase and the putative Type D synthase were not very similar at the DNA level. However, PCR suggested that the UDP-glucose dehydrogenase genes, which encode an enzyme that produces the UDP-GlcUA precursor required for both HA and heparin biosynthesis, were very homologous. In most encapsulated bacteria, the precursor-forming enzymes and the transferases are located in the same operon. To make a hybridization probe predicted to detect the capsule locus, Type D chromosomal DNA served as a template in PCR reactions utilizing degenerate oligonucleotide primers (sense: GARTTYBTIMRIGARGGIAARGCIYTITAYGAY (SEQ ID NO:12); antisense: RCARTAICCICCRTAICCRAAISWXGGRTTRTTRTARTG (SEQ ID NO:13), where I=inosine; R=A or G; S=C or G; W=A or T; Y=C or T) corresponding to a conserved central region in many known UDP-glucose dehydrogenase genes. The  ̃0.3-kb amplicon was generated using Taq DNA polymerase (Fisher), gel-purified, and labeled with digoxigenin (High Prime system, Boehringer Mannheim).
A lambda library of Sau3A partially digested P-3881 DNA ( ̃4-9 kb average length insert) was made using the BamHI-cleaved λZap ExpressTM vector system (Stratagene). The plaque lifts were screened by hybridization (5×SSC, 50° C.; 16 hrs) with the digoxigenin-labeled probe using the manufacturer guidelines for colorimetric development. E. coli XLI-Blue MRF′ was co-infected with the purified, individual positive lambda clones and ExAssist helper phage to yield phagemids. The resulting phagemids were transfected into E. coli XLOLR cells to recover the plasmids. Sequence analysis of the plasmids using a variety of custom primers as well as the GPS-1 Genome Priming System (New England Biolabs) revealed a novel open reading frame, which we called pmHS (DNA sequence facilities at Oklahoma State University and University of Oklahoma HSC). We amplified and sequenced the ORF from several highly encapsulated isolates (see hereinbelow); very similar sequences were obtained.
Expression of Recombinant P. multocida Heparosan Synthase—The pmHS ORF (617 amino acids) was amplified from the various Type D genomic DNA template by 18 cycles of PCR (16) with Taq polymerase. For constructing the full-length enzyme, the sense primer (ATGAGCTTATTTAAACGTGCTACTGAGC (SEQ ID NO: 14)) corresponded to the sequence at the deduced amino terminus of the ORF and the antisense primer (TTTACTCGTTATAAAAAGATAAACACGGAATAAG (SEQ ID NO:15)) encoded the carboxyl terminus including the stop codon. In addition, a truncated version of pmHS was produced by PCR with the same sense primer but a different antisense primer (TATATTTACAGCAGTATCATTTTCTAAAGG (SEQ ID NO:16)) to yield a predicted 501-residue protein, DcbF (SEQ ID NO:17) (GenBank Accession Number AAK17905)15; this variant corresponds to residues 1-497 of pmHS followed by the residues TFRK.
The amplicons were cloned using the pETBlue-1 Acceptor system (Novagen) according to the manufacturer's instructions. The Taq-generated single A overhang is used to facilitate the cloning of the open reading frame downstream of the T7 promoter and the ribosome binding site of the vector. The ligated products were transformed into E. coli NovaBlue and plated on LB carbenicillin (50 μg/ml) and tetracycline (13 μg/ml) under conditions for blue/white screening. White colonies were analyzed by PCR-based screening and by restriction digestion. Plasmids with the desired ORF were transformed into E. coli Tuner, the T7 RNA polymerase-containing expression host, and maintained on LB media with carbenicillin and chloramphenicol (34 μg/ml) at 30° C. Mid-log phase cultures were induced with β-isopropylthiogalactoside (0.2 mM final) for 5 hrs. The cells were harvested by centrifugation, frozen, and membranes were prepared according to a cold lysozyme/sonication method 16 except 0.1 mM mercaptoethanol was included during the sonication steps. Membrane pellets were suspended in 50 mM Tris, pH 7.2, 0.1 mM EDTA and protease inhibitors.
Assays for Heparosan Synthase Activity—Incorporation of radiolabeled monosaccharides from UDP-[14C]GlcUA and/or UDP-[3H]GlcNAc precursors (NEN) was used to monitor heparosan synthase activity. Samples were assayed in a buffer containing 50 mM Tris, pH 7.2, 10 mM MgCl2, 10 mM MnCl2, 0-0.6 mM UDP-GlcUA, and 0-0.6 mM UDP-GlcNAc at 30° C. Depending on the experiment, a Type D acceptor polymer processed by extended ultrasonication of a capsular polysaccharide preparation (isolated by cetylpyridinium chloride precipitation of the spent Type D culture media)14 was also added to the reaction mixture. The reaction products were separated from substrates by descending paper (Whatman 3M) chromatography with ethanol/1 M ammonium acetate, pH 5.5, development solvent (65:35). The origin of the paper strip was cut out, eluted with water, and the incorporation of radioactive sugars into polymer was detected by liquid scintillation counting with BioSafe II cocktail (RPI).
The metal preference of pmHS was assessed by comparing the signal from a “no metal” control reaction (0.5 mM EDTA) to reactions containing 10 to 20 mM manganese, magnesium, or cobalt chloride. To test the transfer specificity of pmHS, various UDP-sugars (UDP-GalNAc, UDPGalUA, or UDP-Glc) were substituted for the authentic heparosan precursors. The data from the recombinant construct containing pmHS gene from the P4058 strain is presented, but the results were similar to constructs derived from the P-934 or P-5695 strains.
Size Analysis and Enzymatic Degradation of Labeled Polymers—Gel filtration chromatography was used to analyze the size distribution of the labeled polymers. Separations were performed with a Polysep-GFC-P 4000 column (300×7.8 mm; Phenomenex) eluted with 0.2 M sodium nitrate at 0.6 ml/min. Radioactivity was monitored with an in-line Radioflow LB508 detector (EG & G Berthold; 500 μl flow cell) using Unisafe I cocktail (1.8 ml/min; Zinsser). The column was standardized with fluorescein-labeled dextrans of various sizes. To further characterize the radiolabeled polymers, depolymerization tests with specific glycosidases was performed. The high molecular weight product was purified by paper chromatography. The origin of the strips was washed with 80% ethanol, air-dried, then extracted with water. The water extract was lyophilized, resuspended in a small volume of water and split into three aliquots. Two aliquots were treated with glycolytic enzymes for 2 days at 37° C. (Flavobacterium heparin lyase III, 6.7 mU/il, 50 mM sodium phosphate, pH 7.6, or Streptomyces HA lyase, 333 milliunits/il, 50 mM sodium acetate, pH 5.8). The last aliquot was mock-treated without enzyme in acetate buffer. The aliquots were quenched with SDS, subjected to paper chromatography, and the radiolabel at the origin was measured by liquid scintillation counting.
Results
Molecular Cloning of the Type D P. multocida Heparosan Synthase—A PCR product which contained a portion of the Type D UDP-glucose dehydrogenase gene was used as a hybridization probe to obtain the rest of the Type D P. multocida capsular locus from a lambda library. We found a functional heparosan synthase, which we named pmHS, in several distinct Type D strains from different host organisms isolated around the world. In every case, an open reading frame of 617 residues with very similar amino acid sequence (98-99% identical) was obtained. In the latter stages of our experiments, another group deposited a sequence from the capsular locus of a Type D organism in GenBank15. In their annotation, the carboxyl terminus of the pmHS homolog is truncated and mutated to form a 501-residue protein that was called DcbF (GenBank Accession Number AAK17905) (SEQ ID NO:17). No functional role for the protein except “glycosyltransferase” was described and no activity experiments were performed. As described herein, membranes or cell lysates prepared from E. coli with the recombinant dcbF gene do not possess heparosan synthase activity. The gene annotated as DcbF (SEQ ID NO:18) is truncated at the carboxyl terminus in comparison to the presently claimed and described P. multocida HS clones. The truncated (T) or the full-length (FL) open reading frames of DcbF were cloned into the expression system pETBlue-1 vector, as described hereinabove. Membranes isolated from the same host strain, E. coli Tuner with the various recombinant plasmids were tested in HS assays with both radiolabeled UDP-sugars. The results of these experiments are summarized in Table V.










TABLE V









Clone











[14C]GlcUA Incorp.
[3H]GlcNAc Incorp.



(dpm)
(dpm)















Negative Control
160 
 40



B1(FL)
  710(*)
  1040(*)



012(T)
40
 265



013(T)
70
1610



019(T)
55
1105



N2(T)
70
1910



N4(T)
70
 880



N5(T)
80
 650










Five-fold less FL enzyme than T enzymes were tested in these parallel assays. At most, only a single GlcNAc sugar is added to the exogenously supplied acceptor in the truncated enzymes (T). Full-length HS from Type D P. multocida, however, adds both sugars (*) to the nascent chain. Thus, the previously annotated and deposited DcbF gene is not a functional heparosan synthase.
Another deduced gene was recently uncovered by the University of Minnesota in their Type A P. multocida genome project 17, called PgIA (GenBank Accession Number AAK02498), encoding 651 amino acids that are similar to pmHS (73% identical in the major overlapping region). However, the PgIA gene is not located in the putative capsule locus. This group made no annotation of the function of PgIA. Our studies show that this PgIA protein also polymerizes GlcUA and GlcNAc residues to form heparosan. We also found that a Type D strain and a Type F strain also appear to contain a homologous PgIA gene as shown by PCR and activity analysis.
As mentioned before, during the pmHS cloning project in the present inventor(s)' laboratory, investigators at the Univ. of Minnesota published the complete genome of a Pasteurella multocida isolate. The fragments of the presently claimed and disclosed pmHS gene were utilized as the query in a BLAST search. A gene annotated as pgIA, but with no ascribed, predicted or demonstrated function was found to be very similar to the pmHS gene. The pgIA gene is not in the main capsule locus found by either the DeAngelis or the Adler groups. The pgIA open reading frame was obtained from two different encapsulated strains: Type A (P-1059 from a turkey—this strain is not the same as the Univ. of Minnesota strain—clones denoted as “A”) and Type D (P-3881 from a cow—clones denoted as “D”). The pgIA gene was amplified from chromosomal templates prepared by method of Pitcher et al (Letters in Applied Microbiology, 1989). PCR with Taq polymerase (18 cycles) using custom flanking oligonucleotide primers that correspond to the region of the start codon and the stop codon of pgIA. An appropriate size amplicon corresponding to the pgIA gene was found in both Type A and D strains; this result was rather unexpected if one considers that the capsular compositions are HA and N-acetylheparosan polysaccharides, for Type A and Type D strains, respectively. The resulting  ̃1.9 kilobase PCR amplicons were ligated into an expression vector, pETBlue-1 (Novagen), transformed into the cloning host, E. coli Novablue (Novagen), and selected on LB carbenicillin and tetracycline plates at 30° C. The colonies were screened for the presence of insert in the proper orientation by PCR with a combination of vector and insert primers. Clones were streak isolated, small cultures were grown, and preparations of the plasmid DNA were made. The plasmids were transformed into the expression host, E. coli Tuner (Novagen), and selected on LB with carbenicillin and chloramphenicol.
After streak isolation, small cultures were grown at 30° C. as the starting inoculum (1:100) for larger cultures (50 ml) for protein expression and activity assay. These cultures were grown in the same LB supplemented with 1% casein amino acids and trace element solution with vigorous shaking (250 rpm) at 30° C. The cells were grown to mid-logarithmic phase (2.5 hours), induced with 0.5 mm IPTG, and grown for 4.5 hours. Cells were collected by centrifugation and frozen at −80° C. overnight. The membrane preparations were isolated by cold lysozyme/ultrasonication method of DeAngelis et al (J. Biol. Chem., 1998; pmHAS isolation the contents of which are expressly incorporated herein in their entirety) except that 0.1 mM mercaptoethanol was used as the reducing agent. The membranes were assayed for radioactive sugar incorporation and descending paper chromatography (according to the methodology of DeAngelis and Padget-McCue, J. Biol. Chem., 2000, the contents of which are expressly incorporated herein in their entirety).
In general, a mixture with membranes, 50 mM Tris, pH 7.2, 1 mM MgCl2, 10 mM MnCl2, 0.4 mM UDP-[3H]GlcNAc, 0.2 mM UDP-[14C]GlcUA, and heparin oligosaccharide acceptor (2 μg uronic acid) were incubated at 30° C. for 2.5 hours before analysis by paper chromatography. As expected for a polysaccharide synthase, both sugars were incorporated into polymer (Table VI). Negative controls using membranes from a plasmid with an irrelevant control insert, do not show incorporation (data not shown). Therefore, PgIA is a dual-action synthase capable of sugar biosynthesis as shown by functional expression of activity of one recombinant gene in a foreign host that normally does not make GlcUA/GlcNAc polymers. The relaxed specificity of UDP-sugar incorporation of PgIA should be of use for the design and production of new polymers with altered characteristics.







TABLE VI







In vitro incorporation of sugar


by membranes containing recombinant pgIA.











CLONE
[3H]GlcNAc (dpm)
[14C]GlcUA (dpm)







PgIA-A2
50,400
54,900



PgIA-A4
39,100
41,000



PgIA-D4
32,500
34,200



PgIA-D7
44,800
46,600










The typical background for negative controls is less the 200 dpm incorporation. Type A and Type D isolates have the PgIA, a synthase that incorporates both GlcUA and GlcNAc sugars. (A=Type A; D=Type D; #=independent clone number).
Table VII shows PgIA Sugar Specificity test results. The experiments summarized in Table VII are similar to the experiments summarized in Table VI (with less enzyme) except that other UDP-sugars that are not normally found in heparin or heparosan were also tested (note—60 minute incubation times, 50 μl reactions). The Type A and the Type D enzymes behave in a similar fashion with relaxed sugar specificity in this test. The PgIA system can add a glucose instead of a GlcNAc sugar. The ability to co-polymerize the sugars that compose the authentic heparin backbone were tested by performing two parallel reactions:

    
    
        UDP-[14C]GlcUA+various combinations of 2nd UDP-sugars.
        UDP-[3H]GlcNAc+various combinations of 2nd UDP-sugars.
    
    









TABLE VII







Panel I. Type A PgIA-A2













2nd Sugar
[3H]GlcNAc Incorporated into Polymer (dpm)







none
450



UDP-GlcUA
12,900



UDP-GalUA
400



UDP-Glc
430







2nd Sugar
[14C]GlcUA Incorporated into Polymer (dpm)







none
60



UDP-GlcNAc
7,700



UDP-GalNAc
60



UDP-Glc
985











Panel II. Type D PgIA-D7













2nd Sugar
[3H]GlcNAc Incorporated into Polymer (dpm)







none
570



UDP-GlcUA
13,500



UDP-GalUA
530



UDP-Glc
500







2nd Sugar
[14C]GlcUA Incorporated into Polymer (dpm)







none
60



UDP-GlcNAc
6,500



UDP-GalNAc
40



UDP-Glc
660










Table VIII. Acceptor Usage of PgIA from Types A and D
The Type A and the Type D clones were tested for stimulation by addition of the Type D polysaccharide acceptor (described hereinbefore with respect to pmHS). Weaker stimulation of activity by acceptor on pgIA was observed in comparison to pmHS (comparison is not shown here).










[14C-GlcUA] incorporation











Clone
Acceptor
NO Acceptor







A2
1560
1210



D7
1240
1080










P. multocida Type F-derived recombinant pgIA is thus also a heparosan synthase. As shown in the following Table IX, the Type F PgIA can incorporate the authentic heparin sugars.







TABLE IX







Activity of pgIA from Type F














3H-GlcNAc
14C-GlcUA



Membranes
Acceptor
(dpm)
(dpm)
















Blank
0
8
8



PgIA F 3
+
7100
3100



PgIA F 4
0
6100
3800



PgIA F 4
+
11000
6400



PgIA F 18
0
20000
10000



PgIA F 18
+
23000
12000



PgIA D 7
0
36000
17000










The pgIA homolog of P. multocida Type F strain P-4218 was amplified with flanking primers as described for the Type A and D strains. The ORF was subcloned into the pETBlue-1 system in E. coli Tuner cells for use as a source of membrane preparations as described. Three independent clones (F 3,4,18) were assayed under standard HS assay measuring radiolabeled sugar incorporation with paper chromatography. A negative control, membranes from “Blank” vector and a positive control, the Type D pgIA clone D7, were tested in parallel. Reactions plus/minus the Type D polymer acceptor were assayed.
The next best heterologous matches for the pmHS enzyme in the Genbank database are KfiA and KfiC proteins from E. coli K5; these two proteins work together to make the heparosan polymer.(7,8) There is a good overall alignment of the enzyme sequences if smaller portions of pmHS ORF are aligned separately with KfiA (pmHS2, SEQ ID NO:11) and KfiC (pmHS1, SEQ ID NO:10) (FIG. 1). The MULTALIN alignment program (Corpet, 1988) identified regions that were very similar. Some of the most notable sequence similarities occur in the regions containing variants of the DXD amino acid sequence motif. Indeed, the first 1-360 residues of pmHS1 (denoted also as HSA1: SEQ ID NO:10) align with an approximate 38% identity to the E. coli KfiC, a single action GlcUA-transferase, while the 361-617 residues of pmHS2 (denoted also HSA2: SEQ ID NO:11) align with an approximate 31% identity to the E. coli KfiA, a GlcNAc-transferase. Thus, the pmHS is a naturally occurring fusion of two different glycosyltransferase domains. The pmHS is a dual action enzyme that alone makes heparin/heparosan polymers because both sugar transferase sites exist in one polypeptide enzyme.
Heterologous Expression of a Functional P. multocida Heparosan Synthase—
Membrane extracts derived from E. coli Tuner cells containing the plasmid encoding pmHS, but not samples from cells with the vector alone, synthesized polymer in vitro when supplied with both UDP-GlcUA and UDP-GlcNAc simultaneously. The identity of the polymer as heparosan was verified by its sensitivity to Flavobacterium heparin lyase III ( ̃97% destroyed after treatment) and its resistance to the action of Streptomyces HA lyase. No substantial incorporation of radiolabeled [14C]GlcUA into polymer was observed if UDP-GlcNAc was omitted, or if UDP-GalNAc was substituted for UDP-GlcNAc. Conversely, in experiments using UDP-[3H]GlcNAc, substantial incorporation of radiolabel into polymer was only noted when UDP-GlcUA was also present. UDP-GalUA or UDP-Glc did not substitute for UDP-GlcUA. No polymerization or transferase activity was detected if the divalent metal ions were chelated with EDTA. Maximal activity was observed in reactions that contained Mn ion, but Mg also supported substantial incorporation (65%-85% maximal). Cobalt was a poorer cofactor ( ̃30% maximal). The addition of the heparosan polymer acceptor increased sugar incorporation catalyzed by pmHS at least 7- to 25-fold in comparison to parallel reactions without acceptor (FIG. 2) in analogy to observations of pmHAS18 and pmCS14. The acceptor stimulation of activity is due to the lower efficiency or slower rate of initiation of a new polymer chain in comparison to the elongation stage in vitro. The exogenous acceptor sugar associates with the recombinant enzyme's binding site for the nascent chain and then is elongated rapidly.
Analysis by gel filtration chromatography indicated that recombinant pmHS produced long polymer chains ( ̃1-3×103 monosaccharides or  ̃200-600 kDa) in vitro without acceptor (FIG. 3). If acceptor polymer was supplied to parallel reaction mixtures, then higher levels of shorter chains ( ̃0.1-2×103 monosaccharides or  ̃20-400 kDa added to acceptor) were more rapidly produced. Radioactivity from both labeled GlcUA and GlcNAc sugars co-migrated as a single peak in all chromatography profiles. Some chains also appear to be initiated de novo in reactions with acceptor as evidenced by the small peak of higher molecular weight material near the void volume. Apparently, once pmHS either starts a new chain or binds an existing chain, then rapid elongation is performed.
We found in parallel tests that membranes or lysates prepared from recombinant cells containing the predicted dbcF gene15 (SEQ ID NO:17), a truncated version of pmHS, in the same expression vector, do not exhibit heparosan synthase activity. Even with large amounts of total protein, repeated polymerization was not observed and no significant radiolabel incorporation above background levels was noted.
Discussion
We have molecularly cloned a dual-action glycosyltransferase responsible for polymerizing the heparosan backbone component of the Type D P. multocida capsular polysaccharide. As discussed earlier, the first 497 residues of the pmHS protein are virtually identical to the hypothetical DcbF sequence. We have sequenced the DNA from the equivalent P-934 isolate obtained from the same USDA collection as reported15, as well as several other Type D strains, but our results do not agree with the dcbF open reading frame. The Adler group appears to have made a sequencing error that resulted in a frame-shift mutation; a conceptual premature termination led to the creation of the erroneously truncated dcbF annotation. Recently, we have determined that the Pasteurella hyaluronan synthase, pmHAS, contains two active sites in a single polypeptide by generating mutants that transfer only GlcUA or only GlcNAc19. Interestingly, mixing the two different mutant pmHAS proteins reconstituted the HA synthase activity. We hypothesized that one domain, called A1, is responsible for GlcNAc transfer and the other domain, called A2, is responsible for GlcUA transfer19. The chondroitin synthase, pmCS, transfers a different hexosamine, GalNAc, and also appears to contain a similar two-domain structure14. The amino acid sequence of the heparosan synthase, pmHS, however, is very different from other Pasteurella GAG synthases, pmHAS and pmCS. The pmHAS and pmHS enzymes both perform the task of polymerizing the identical monosaccharides; HA and heparin only differ with respect to their linkages. The creation of different anomeric linkages probably requires very distinct active sites due to the disparity between a retaining (to form α-linkages) and an inverting (to form β-linkages) transfer mechanism. The putative dual-action vertebrate heparin synthases, EXT1 (SEQ ID NO:19) and EXT 2 (SEQ ID NO:20), also appears to have two transferase domains, but the amino acid sequences are not similar to pmHS20. Thus, by aligning pgIA, pmHS (B10 and A2 clones), KfiA, or KfiC, deduced amino acid sequence motifs have been identified. Such motifs are listed below and the alignment is shown in FIG. 4 A-G.
Two distinct regions of pmHS (pmHS1 and pmHS2) are similar to the E. coli K5 KfiA or KfiC proteins suggesting the limits of the sugar transfer domains (FIG. 1). On the basis of sequence similarity, if the Kfi studies are correct, then GlcUA transfer and GlcNAc transfer occur at the amino and carboxyl portions of pmHS, respectively. The pmHS protein may be the result of the fusion of two ancestral single-action enzymes. The efficiency and convenience of combining the two required enzyme activities into a single polypeptide seems clear, but as a counterexample, the E. coli KfiA and KfiC proteins remain separate entities. Interestingly, pgIA, a gene with no reported function from a Type A17 isolate is ( ̃70%) similar to the pmHS gene of a Type D strain. In parallel expression experiments, PgIA from Type A or D or F strains also appear to be heparosan synthases, as shown hereinabove. It is quite puzzling that the Type A strain would have a heparosan synthase as well as the known HA synthase. The major Type A capsular polymer was shown to be HA, but in retrospect, a small amount of heparosan would be difficult or impossible to detect in these characterization studies11. A possible scenario for the presence of a heparosan synthase in the Type A bacteria is that the pgIA gene is repressed or silent and not expressed in this host under laboratory conditions. The pgIA gene could also be a cryptic remnant from an ancestral organism (i.e., before Types A and D and F diverged) that has been maintained and the gene product is still functional. Another interesting possibility is that in Type A organisms either the pmHAS or the pgIA gene is utilized at different times depending on conditions or stage of infection; using different capsular polymers could serve as a phase-shift mechanism.
Comparisons of the two known sets of heparin/heparosan biosynthesis enzymes from the E. coli K5 Kfi locus, the PgIA enzyme, and the pmHS from Type D capsular locus, allows for the initial assessment and bioinformatic prediction of new enzymes based on the amino acid sequence data. The closer the match (% identity) in a single polypeptide for the two sequence motifs described hereinafter (corresponding to the critical elements of the GlcUA-transferase and the GlcNAc-transferase), the higher the probability that the query enzyme is a new heparin/heparosan synthase (a single dual-action enzyme). The closer the match (% identity) in two polypeptides (especially if encoded in the same operon or transcriptional unit) for the two sequence motifs, the higher the probability that the query enzymes are a pair of single-action glycosyltransferases. Thus, one of ordinary skill in the art would appreciate that given the following motifs, one would be able to ascertain and ascribe a probable heparin synthase function to a newly discovered enzyme and then test this ascribed function in a manner to confirm the enzymatic activity. Thus, single dual-action enzymes possessing enzymatic activity to produce heparin/heparosan and having at least one of the two disclosed motifs are contemplated as being encompassed by the presently claimed and disclosed invention.








Motif I:









(SEQ ID NO:21)









QTYXN(L/I)EX4DDX(S/T)(S/T)D(K/N)(T/S)X6IAX(S/T)



 


(S/T)(S/T)(K/R)V(K/R)X6NXGXYX16FQDXDDX(C/S)H(H/P)


 


ERIXR


 


Motif II:








(SEQ ID NO:22)









(K/R)DXGKFIX12-17DDDI(R/I)YPXDYX3MX40-50VNXLGTGTV







Motif I corresponds to the GlcUA transferase portion of the enzyme, while Motif II corresponds to the GlcNAc transferase portion of the enzyme. With respect to the motifs:

    
    
        X=any residue parentheses enclose a subset of potential residues [separated by a slash]

that may be at a particular position (e.g., —(K/R) indicates that either K or R may be found at the position—i.e., there are semiconserved residues at that position.

    
    


The consensus X spacing is shown with the number of residues in subscript (e.g., X12-17), but there are weaker constraints on these particular residues, thus spacing may be longer or shorter. Conserved residues may be slightly different in a few places especially if a chemically similar amino acid is substituted (e.g., K for a R, or E for a D). Overall, at the 90% match level, the confidence in this predictive method is very high, but even a 70-50% match level without excessive gap introduction (e.g., altered spacing between conserved residues) or rearrangements (miss-positioning with respect to order of appearance in the amino to carboxyl direction) would also be considered to be within the scope of these motifs. One of ordinary skill in the art, given the present specification, general knowledge of the art, as well as the extensive literature of sequence similarity and sequence statistics (e.g., the BLAST information website at www.ncbi.nlm.mih.gov), would appreciate the ability of a practitioner to identify potential new heparin/heparosan synthases based upon sequence similarity or adherence to the motifs presented herein and thereafter test for functionality by means of heterozologous expression, to name but one example.
Bacteria-derived heparosan may be converted by epimerization and sulfation into a polymer that resembles the mammalian heparin and heparan sulfate because all the modifying enzymes have been identified 3. In general, sulfation with chemical reagents (SO3, chlorosulfonic acid) or sulfo-transferases (i.e., 2-0-GlcUA-sulfotransferase, etc.) And PAPs precursor is possible. N-sulfation can be done by using either chemical means (hydrazinolysis and subsequent N-sulfation) or enzymatic means with dual function deacetylase/N-sulfotransferase. For creation of iduronic acid, epimerization can be performed enzymatically with heparin epimerase or chemically with super-critical carbon dioxide. The art is replete with articles, methods, and procedures for sulfating and epimerizing heparosan to form heparin. Example, include Leali, et al., Fibroblast Growth Factor-2 AntagonistActivity and Angiostatic Capacity of Sulfated E. coli KS Polysaccharide Derivatives, J. Biol. Chem., Vol. 276, No. 41, Oct. 12, 2001, pp. 37900-902; Esko, et al., Molecular Diversity of Heparin Sulfate, J. Clin. Invest. 108: 169-173 (2001); and Crawford, et al., Cloning, Golgi Localization, and Enzyme Activity of the Full-Length Heparin/Heparosan Sulfate—Glucuronic Acid C5-Epimerase, J. Biol. Chem., Vol. 276, No. 24, Jun. 15, 2001, pp. 21530-543, the contents of each being hereby expressly incorporated by reference in their entirety. Thus, given the present specification which discloses and teaches methods for the recombinant production of Heparosan, one of ordinary skill in the art would be capable of producing Heparin therefrom. As such, Heparin obtained through the process of sulfating and epimerizing Heparosan is contemplated as falling within the scope of the presently disclosed and claimed invention.
pmHS or PgIA (or an improved recombinant version) may be a more economical and useful sources of heparosan than E. coli K5 for several reasons. pmHS and PgIA have a higher intrinsic biosynthetic capacity for capsule production. The Pasteurella capsule radius often exceeds the cell diameter when observed by light microscopy of India Ink-prepared cells. On the other hand, visualization of the meager E. coli K5 capsule often requires electron microscopy. From a safety standpoint, E. coli K5 is a human pathogen, while Type D Pasteurella has only been reported to cause disease in animals. Furthermore, with respect to recombinant gene manipulation to create better production hosts, the benefits of handling only a single gene encoding pmHS or PgIA, dual action synthases, in comparison to utilizing KfiA and C (and probably KfiB) are obvious. The in vitro properties of pmHS and pgIA are also superior; these enzymes can make large chains in vitro either with or without an exogenous acceptor sugar, but KfiA and KfiC do not.
The discovery of pmHS and PgIA expands the known GAG biosynthesis repertoire of P. multocida. Depending on the Carter capsular type, this widespread species produces HA, heparosan, or chondroitin.
Thus, it should be apparent that there has been provided in accordance with the present invention purified nucleic acid segments having coding regions encoding enzymatically active heparosan synthase, methods of producing heparosan from the pmHS or pgIA gene, and the use of heparosan produced from a heparosan synthase encoded by the pmHS or pgIA gene, that fully satisfies the objectives and advantages set forth above. Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications, and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications, and variations that fall within the spirit and broad scope of the appended claims.
REFERENCES
The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

    1. Roden, L. (1980) in The Biochemistry of Glycoproteins and Proteoglycans (Lennarz, W. J., ed) pp. 267-371, Plenum Publishing Corp., New York
    2. Lidholt, K. (1997) Biochem. Soc. Trans. 25, 866-870
    3. Esko, J. D. and Lindahl U. (2001) J. Clin. Invest., 108:169-173
    4. Roberts, I. S. (1996) Annu. Rev. Microbiol. 50, 285-315
    5. Vann, W. F., Schmidt, M. A., Jann, B., and Jann, K. (1981) Eur. J. Biochem. 116, 359-364
    6. Rodriguez, M. L., Jann, B., and Jann, K. (1988) Eur. J. Biochem. 177, 117-124
    7. Griffiths, G., Cook, N. J., Gottfridson, E., Lind, T., Lidholt, K., and Roberts, I. S. (1998) J. Biol. Chem., 273, 11752-11757
    8. Hodson, N., Griffiths, G., Cook, N., Pourhossein, M., Gottfridson, E., Lind, T., Lidholt, K. and Roberts, I. S. (2000) J. Biol. Chem., 275:27311-27315.
    9. Rimler, R. B. (1994) Vet. Rec. 134, 191-192
    10. Rimler, R. B., Register, K. B., Magyar, T., and Ackermann, M. R. (1995) Vet. Microbiol. 47, 287-294
    11. Rosner, H., Grimmecke, H. D., Knirel, Y. A., and Shashkov, A. S. (1992) Carb. Res. 223, 329-333
    12. DeAngelis, P. L., Jing, W., Drake, R. R. and Achyuthan, A. M. (1998) J. Biol. Chem. 273, 8454-8458
    13. Rimler, R. B. and Rhoades, K. R. (1987) J. Clinic. Microbiol. 25, 615-618
    14. DeAngelis, P. L. and Padgett-McCue, A. J. (2000) J. Biol. Chem., 275: 24124-24129
    15. Townsend, K. M., Boyce, J. D., Chung, J. Y., Frost, A. J., and Adler, B. (2001) J. Clin. Microbiol. 39:924-929
    16. DeAngelis, P. L., and Weigel, P. H. (1994) Biochem. 33, 9033-9039
    17. May, B. J., Zhang, Q., Li, L. L., Paustian, M. L., Whittam, T. S., and Kapur, V. (2001) Proc. Natl. Acad. Sci. U.S.A. 98:3460-3465
    18. DeAngelis, P. L. (1999) J. Biol. Chem. 274, 26557-26562
    19. Jing, W. and DeAngelis, P. L. (2000) Glycobiology 10: 883-889
    20. Duncan, G., McCormick, C., and Tufaro, F. (2001) J. Clin. Invest. 108: 511-516
    21. Corpet, F. (1988) Nucleic Acids Res. 16:10881-10890 18

## Claims

1. A purified nucleic acid segment comprising a coding region encoding enzymatically active heparin synthase, wherein the heparin synthase is a single protein that is a dual-action catalyst that utilizes UDP-GlcUA and UDP-GlcNAc to synthesize heparin, and wherein the purified nucleic acid segment is at least one of:
(a) a purified nucleic acid segment encoding the Pasteurella multocida heparin synthase of SEQ ID NO:6;
(b) the purified nucleic acid segment of SEQ ID NO:5;
(c) a purified nucleic acid segment that is at least 90% identical to SEQ ID NO:5; and
(d) a purified nucleic acid segment that hybridizes to a sequence, which is fully complementary to SEQ ID NO:6 under hybridization conditions of 5× Standard Saline Citrate (SSC) at 50° C. overnight, followed by washing in 0.1×SSC at room temperature for 10-60 minutes.

2. A recombinant vector selected from the group consisting of a plasmid, cosmid, phage, integrated cassette and virus vector, wherein the recombinant vector comprises:
a purified nucleic acid segment having a coding region encoding enzymatically active heparin synthase, wherein the heparin synthase is a single protein that is a dual-action catalyst that utilizes UDP-GlcUA and UDP-GlcNAc to synthesize heparin, and wherein the purified nucleic acid segment is at least one of:
(a) a purified nucleic acid segment encoding the Pasteurella multocida heparin synthase of SEQ ID NO:6;
(b) the purified nucleic acid segment of SEQ ID NO:5;
(c) a purified nucleic acid segment that is at least 90% identical to SEQ ID NO:5; and
(d) a purified nucleic acid segment that hybridizes to a sequence, which is fully complementary to SEQ ID NO:6 under hybridization conditions of 5×SSC at 50° C. overnight, followed by washing in 0.1×SSC at room temperature for 10-60 minutes.

3. The recombinant vector of claim 2, wherein the plasmid further comprises an expression vector.

4. The recombinant vector of claim 3, wherein the expression vector comprises a promoter operatively linked to the enzymatically active heparin synthase coding region.

5. A recombinant host cell, wherein the recombinant host cell is electroporated, transformed, transfected, or transduced to introduce a recombinant vector into the host cell, wherein the recombinant vector comprises:
a purified nucleic acid segment having a coding region encoding enzymatically active heparin synthase, wherein the heparin synthase is a single protein that is a dual-action catalyst that utilizes UDP-GlcUA and UDP-GlcNAc to synthesize heparin, and wherein the purified nucleic acid segment is at least one of:
(a) a purified nucleic acid segment encoding the Pasteurella multocida heparin synthase of SEQ ID NO:6;
(b) the purified nucleic acid segment of SEQ ID NO:5;
(c) a purified nucleic acid segment that is at least 90% identical to SEQ ID NO:5; and
(d) a purified nucleic acid segment that hybridizes to a sequence, which is fully complementary to SEQ ID NO:6 under hybridization conditions of 5×SSC at 50° C. overnight, followed by washing in 0.1×SSC at room temperature for 10-60 minutes.

6. The recombinant host cell of claim 5, wherein the host cell produces heparin.

7. The recombinant host cell of claim 6, wherein the heparin is unsulfated.

8. The recombinant host cell of claim 6, wherein the heparin is sulfated.

9. The recombinant host cell of claim 6, wherein the heparin is epimerized.

10. The recombinant host cell of claim 6, wherein the heparin is sulfated and epimerized.

11. The recombinant host cell of claim 5, wherein the recombinant host cell is a prokaryotic cell.

12. The recombinant host cell of claim 5, wherein the recombinant host cell is a eukaryotic cell.