US20040073018A1

US20040073018A1 - Human methionine synthase: cloning, and methods for evaluating risk of neural tube defects, cardiovascular disease, and cancer

Info

Publication number: US20040073018A1
Application number: US10/607,712
Authority: US
Inventors: Roy Gravel; Rima Rozen; Daniel Leclerc; Philippe Goyette; Eric Campeau
Original assignee: Individual
Current assignee: Individual
Priority date: 1996-11-27
Filing date: 2003-06-27
Publication date: 2004-04-15
Also published as: US6703197B1

Abstract

The invention features a method for detecting an increased likelihood of hyperhomocysteinemia and, in turn, an increased or decreased likelihood of neural tube defects or cardiovascular disease. The invention also features therapeutic methods for reducing the risk of neural tube defects, colon cancers and related cancers. Also provided are the sequences of the human methionine synthase gene and protein and compounds and kits for performing the methods of the invention.

Description

CROSS REFERENCE TO RELATED APPLICATIONS

This invention claims priority from U.S. Provisional Applications Serial Nos. 60/031,964 and 60/050,310, filed Nov. 27, 1996 and Jun. 20, 1997, respectively.[0001]

FIELD OF THE INVENTION

The invention relates to the diagnosis and treatment of patients at risk for methionine synthase deficiency and associated altered risk for diseases such as neural tube defects, cardiovascular disease, and cancer.

BACKGROUND OF THE INVENTION

Methionine synthase (EC 2.1.1.13, 5-methyltetrahydrofolate-homocysteine methyltransferase) catalyses the remethylation of homocysteine to methionine in a reaction in which methylcobalamin serves as an intermediate methyl carrier. This occurs by transfer of the methyl group of 5-methyltetrahydrofolate to the enzyme-bound cob(I)alamin to form methylcobalamin with subsequent transfer of the methyl group to homocysteine to form methionine. Over time, cob(I)alamin may become oxidized to cob(II)alamin rendering the enzyme inactive. Regeneration of the functional enzyme occurs through the methionine synthase-mediated methylation of the cob(II)alamin in which S-adenosylmethionine is utilized as methyl donor. In E. coli, two flavodoxins have been implicated in the reductive activation of methionine synthase (Fujii, K. and Huennekens, F. M. (1974) J. Biol. Chem., 249, 6745-6753). A methionine synthase-linked reducing system has yet to be identified in mammalian cells.

Deficiency of methionine synthase activity results in hyperhomocysteinemia, homocystinuria, and megaloblastic anemia without methylmalonic aciduria (Rosenblatt, D. S. (1995) The Metabolic and Molecular Bases of Inherited Disease. McGraw-Hill, New York, pp. 3111-3128; Fenton, W. A. and Rosenberg, L. E. (1995) The Metabolic and Molecular Bases of Inherited Disease. McGraw-Hill, New York, pp. 3129-3149). Two classes of methionine synthase-associated genetic diseases have been proposed based on complementation experiments between patient fibroblast cell lines (Watkins, D. and Rosenblatti D. S. (1988) J. Clin. Invest., 81, 1690-1694). One complementation group, cblE, has been postulated to be due to deficiency of the reducing system required for methionine synthesis (Rosenblatt, D. S., Cooper, B. A., Pottier, A., Lue-Shing, H., Matiaszuk, N. and Grauer, K. (1984) J. Clin. Invest., 74, 2149-2156). Cells from patients in the cblE group fail to incorporate ¹⁴C-methyltetrahydrofolate into methionine in whole cells but have significant methionine synthase activity in cell extracts in the presence of a potent reducing agent. The second complementation group, cblG group, is thought to result from defects of the methionine synthase apoenzyme. Mutant cells from this group show deficient methionine synthase activity in both whole cells and cell extracts (Watkins, D. and Rosenblatt, D. S. (1988) J. Clin. Invest., 81, 1690-1694; Watkins, D. and Rosenblatt, D. S. (1989) Am. J Med. Genet., 34, 427-434). Moreover, some cblG patients show defective binding of cobalamin to methionine synthase in cells incubated with radiolabelled cyanocobalamin (Sillaots, S. L., Hall, C. A., Hurteloup, V., and Rosenblatt, D. S. (1992) Biochem. Med. Metab. Biol., 47, 242-249).

The cobalamin-dependent methionine synthase of E. coli has been crystallized and the structure of its active site determined (Luschinsky, C. L., Drummond, J. T., Matthews, R. G., and Ludwig, M. L. (1992) J. Molec. Biol., 225, 557-560; Drennan, C. L., Huang, S., Drummond, J. T., Matthews, R. G., and Ludwig, M. L. (1994) Science, 266, 1669-1674.). The gene encoding methionine synthase has not been cloned from mammals.

SUMMARY OF THE INVENTION

We have cloned a gene for mammalian methionine synthase from humans and discovered that mutations in this gene are associated with hyperhomocysteinemia. Hyperhomocysteinemia is a condition that has been implicated in cardiovascular disease and neural tube defects. The presence of such mutations in methionine synthase gene are, thus, associated with increased risk for cardiovascular disease, altered risk for neural tube defects, and decreased risk of colon cancer. The invention features methods for risk detection and treatment of patients with hyperhomocysteinemia, cardiovascular disease, neural tube defects, and cancer. The invention also features compounds and kits which may be used to practice the methods of the invention, methods and compounds for treating or preventing these conditions and methods of identifying therapeutics for the treatment and prevention of these conditions.

In the first aspect, the invention provides purified wild-type mammalian methionine synthase gene, and mutated and polymorphic versions of the mammalian methionine synthase gene, fragments of the wild-type, mutated, and polymorphic gene, and sense and antisense sequences which may be used in the methods of the invention. Preferably, the gene is human. The proteins encoded therefrom are also an aspect of the invention as is a methionine synthase polypeptide having conservative substitutions. Preferably, the protein is a recombinant or purified protein having a mutation conferring hypeihomocysteinemia when present in a mammal. In addition, nucleic acids, including genomic DNA, mRNA, and cDNA, and the nucleic acid set forth in SEQ ID NO: 1, or degenerate variants thereof, are provided. The shorter nucleic acid sequences are appropriate for use in cloning, characterizing mutations, the construction of mutations, and creating deletions. In one embodiment, the nucleic acid set forth in SEQ ID NO: 1 is a probe that hybridizes at high stringency to sequences found within the nucleic acid of SEQ ID NO: 1. In further embodiments, the probe has a sequence complementary to at least 50% of at least 60 nucleotides, or the sequence is complementary to at least 90% of at least 18 nucleotides. Protein fragments also are provided. The shorter peptides may be used, for example, in the generation of antibodies to the methionine synthase protein. In some embodiments of this aspect of the invention nucleic acid fragments useful for detection of mutations in the region of the methionine synthase gene which encodes the cobalamin binding domain, and for detecting those mutations which indicate an increased likelihood of hyperhomocysteinemia, are preferred. Most preferred fragments are those useful for detecting the 2756 A→G, Δbp 2640-2642, and 2758 C→G mutations/polymorphisms. Given Applicants' discovery, one skilled in the art may readily determine which nucleic acids, detection methods, and mutations are most useful. Mutant proteins encoded by these mutations, including, but not limited to, H920D, ΔIle 881, and D919G are also provided by the invention. Such mutant and polymorphic polypeptides may have decreased or increased biological activity, relative to wild-type methionine synthase.

In a related aspect, the invention provides antibodies that specifically bind mammalian methionine synthase, and a method for generating such an antibody. The antibody may specifically bind a wild-type methionine synthase, or a mutant or polymorphic methionine synthase. A method for detecting a wild-type, mutant, or polymorphic methionine synthase using the antibody is also provided by the invention.

In a second aspect, the invention provides a method for detecting an increased or decreased risk for hyperhomocysteinemia in a fetus or individual patient. Such a fetus or patient is at increased or decreased risk for neural tube defects and/or cardiovascular disease and at a decreased risk of developing colon cancer. The method includes detection of mutations in the methionine synthase gene present in the fetus, the individual patient, and/or the blood relatives of the fetus and patient. The presence of mutations, particularly in the cobalamin binding domain, indicate an altered (e.g., increased or decreased) risk of hyperhomocysteinemia, neural tube defects, cancer, and cardiovascular disease.

In a related aspect, the invention provides kits for the detection of mutations in the human methionine synthase gene. Such kits may include, for example, nucleic acid sequences, including probes, useful for PCR, SSCP, or RFLP detection of such mutations. Antibodies specific for proteins having mutations, correlated with an increased likelihood of hyperhomocysteinemia, may also be included in the kits of the invention.

In a fourth aspect, the invention features a method for screening for compounds which alter methionine synthase expression or ameliorate or exacerbate conditions of hyperhomocysteinemia. In various embodiments, the invention includes monitoring mutant or wild-type mammalian methionine synthase biological activity by monitoring methionine synthase enzymatic activity, or monitoring methionine synthase gene expression levels, by monitoring methionine synthase gene transcription, RNA stability, RNA translation and/or protein stability. In preferred embodiments the methionine synthase gene or protein being monitored is a gene or protein having a mutation associated with hyperhomocysteinemia, and samples are selected from purifed or partially purified methionine synthase, cell lysate, a cell, or an animal. Standard assay techniques known to those skilled in the art may be employed in the various embodiments. Compounds detected using this screen can be used to prevent or treat cardiovascular disease and neural tube defects or, in the alternative, to prevent or treat colon cancer. Kits for performing the above screens are also a part of the invention.

In a related aspect, the invention provides nucleic acids encoding wild-type, polymorphic, and mutated methionine synthase, in which the nucleic acid is operably linked to regulatory sequences, comprising a promoter, for the expression of the encoded polypeptides. In one embodiment, the promoter is inducible. The invention also provides cells, including prokaryotic and eukaryotic cells, comprising the nucleic acids. The eukaryotic cells may be yeast cells or mammalian cells.

In another related aspect, the invention features a transgenic mammal having a methionine synthase transgene. The gene may be wild-type, or may contain a mutation or polymorphism. The mammal may have a mutation associated with hyperhomocysteinemia in its methionine synthase gene in an expressible genetic construction or may have a deletion or knockout mutation in one or both alleles sufficient to abolish methionine synthase expression from the locus. In addition, or as a replacement, the mammal may have the methionine synthase gene from another species. For example, in one preferred embodiment the transgenic mammal is a rodent such as a mouse and the transgene is from a human. Cells from these transgenic or knockout animals are also provided by the invention. Such transgenic mammals may be used to screen for drugs for the treatment of diseases related to hyperhomocysteinemia.

In a sixth aspect, the invention features a method for treating patients with neural tube defects, colon cancer or related cancers by the delivery of antisense methionine synthase nucleic acid sufficient to lower the levels of methionine synthase polypeptide biological activity.

In a related aspect, the invention provides a method for treating or preventing cardiovascular disease, neural tube defects and cancer. The method comprises detecting an altered risk of such defects by analyzing methionine synthase nucleic acid, potential test subjects being a mammal, a potential parent, either male or female, a pregnant mammal, or a developing embryo or fetus, and then by exposing the subject (e.g., patient or pregnant mammal) to metabolites or cofactors such as, but not limited to, folate, cobalamin, S-adenosyl methionine, betaine, or methionine. In another related aspect, the invention features a method of pretreating or treating colon cancer or neural tube defects by inhibiting or activating methionine synthase biological activity in a mammal, pregnant mammal, embryo, or fetus. In preferred embodiments, this inhibiting or activating may be effected by exposing the subject to nucleic acids, peptides or small molecule-based inhibitors or activators of methionine synthase or substrates. The exposure is to quantities of the compound sufficient to reduce the probability of the subject developing the disease or to confer an increased likelihood of a decrease in the disease symptoms of the subject.

By “methionine synthase,” “methionine synthase protein,” or “methionine synthase polypeptide” is meant a polypeptide, or fragment thereof, which has at least 50% amino acid identity to boxes 1-4 of the human methionine synthase polypeptide (SEQ ID NO: 2) (see FIG. 1). It is understood that polypeptide products from splice variants of methionine synthase gene sequences are also included in this definition. Preferably, the methionine synthase protein is encoded by nucleic acid having a sequence which hybridizes to a nucleic acid sequence present in SEQ ID NO: 1 (human methionine synthase cDNA) under stringent conditions. Even more preferably the encoded polypeptide also has methionine synthase biological activity.

By “methionine synthase nucleic acid” or “methionine synthase gene” is meant a nucleic acid, such as genomic DNA, cDNA, or mRNA, that encodes methionine synthase, a methionine synthase protein, methionine synthase polypeptide, or portion thereof, as defined above. A methionine synthase nucleic acid also may be a methionine synthase primer or probe, or antisense nucleic acid that is complementary to a methionine synthase nucleic acid.

By “wild-type methionine synthase” is meant a methionine synthase nucleic acid or methionine synthase polypeptide having the nucleic acid and/or amino acid sequence most often observed among members of a given animal species and not statistically associated with a disease phenotype. Wild-type methionine synthase is biologically active methionine synthase. A wild-type methionine synthase is, for example, a human methionine synthase polypeptide having the sequence of SEQ ID NO: 1.

By “mutant methionine synthase,” “methionine synthase mutation(s),” “mutations in methionine synthase,” “polymorphic methionine synthase,” “methionine synthase polymorphism(s),” “polymorphisms in methionine synthase,” is meant a methionine synthase polypeptide or nucleic acid having a sequence that deviates from the wild-type sequence in a manner sufficient to confer an altered risk for a disease phenotype, or enhanced protection against a disease, in at least some genetic and/or environmental backgrounds. Such is mutations may be naturally occurring or artificially induced. They may be, without limitation, insertion, deletion, frameshift, or missense mutations. A mutant methionine synthase protein may have one or more mutations, and such mutations may affect different aspects of methionine synthase biological activity (protein function), to various degrees. Alternatively, a methionine synthase mutation may indirectly affect methionine synthase biological activity by influencing, for example, the transcriptional activity of a gene encoding methionine synthase, or the stability of methionine synthase mRNA. For example, a mutant methionine synthase gene may be a gene which expresses a mutant methionine synthase protein or may be a gene which alters the level of methionine synthase protein in a manner sufficient to confer a disease phenotype in at least some genetic and/or environmental backgrounds.

By “biologically active” methionine synthase is meant a methionine synthase protein or methionine synthase gene that provides at least one biological function equivalent to that of the wild-type methionine synthase polypeptide or methionine synthase gene. Biological activities of a methionine synthase polypeptide include, and are not limited to, the ability to catalyze the methylation of homocysteine to generate methionine. Preferably, a biologically active methionine synthase will display activity equivalent to at least 35% of wild-type activity, more preferably, a biologically active methionine synthase will display at least 40-55% of wild-type activity, still more preferably, a biologically active methionine synthase will display at least 60-75% of wild-type activity, and most preferably, a biologically active methionine synthase will display at least 80-90% of wild-type activity. A biologically active methionine synthase also may display more than 100% of wild-type activity. Preferably, the biological activity of the wild-type methionine synthase is determined using the methionine synthase nucleic acid of SEQ ID NO: 1 or methionine synthase polypeptide of SEQ ID NO: 2. The degree of methionine synthase biological activity may be intrinsic to the methionine synthase polypeptide itself, or may be modulated by increasing or decreasing the number of methionine synthase polypeptide molecules present intracellularly.

By “high stringency conditions” is meant hybridization in 2×SSC at 40° C. with a DNA probe length of at least 40 nucleotides. For other definitions of high stringency conditions, see F. Ausubel et al., Current Protocols in Molecular Biology, pp. 6.3.1-6.3.6, John Wiley & Sons, New York, N.Y., 1994, hereby incorporated by reference.

By “analyzing” or “analysis” is meant subjecting a methionine synthase nucleic acid or methionine synthase polypeptide to a test procedure that allows the determination of whether a methionine synthase gene is wild-type or mutant. For example, one could analyze the methionine synthase genes of an animal by amplifying genomic DNA using the polymerase chain reaction, and then determining the DNA sequence of the amplified DNA.

By “probe” or “primer” is meant a single- or double-stranded DNA or RNA molecule of defined sequence that can base pair to a second DNA or RNA molecule that contains a complementary sequence (the “target”). The stability of the resulting hybrid depends upon the extent of the base pairing that occurs. The extent of base-pairing is affected by parameters such as the degree of complementarity between the probe and target molecules, and the degree of stringency of the hybridization conditions. The degree of hybridization stringency is affected by parameters such as temperature, salt concentration, and the concentration of organic molecules such as formamide, and is determined by methods known to one skilled in the art Probes or primers specific for methionine synthase nucleic acid preferably will have at least 35% sequence identity, more preferably at least 45-55% sequence identity, still more preferably at least 60-75% sequence identity, still more preferably at least 80-90% sequence identity, and most preferably 100% sequence identity. Probes may be detectably-labelled, either radioactively, or non-radioactively, by methods well-known to those skilled in the art. Probes are used for methods involving nucleic acid hybridization, such as: nucleic acid sequencing, nucleic acid amplification by the polymerase chain reaction, single stranded conformational polymorphism (SSCP) analysis, restriction fragment polymorphism (RFLP) analysis, Southern hybridization, Northern hybridization, in situ hybridization, electrophoretic mobility shift assay (EMSA).

By “pharmaceutically acceptable carrier” means a carrier which is physiologically acceptable to the treated mammal while retaining the therapeutic properties of the compound with which it is administered. One exemplary pharmaceutically acceptable carrier is physiological saline. Other physiologically acceptable carriers and their formulations are known to one skilled in the art and described, for example, in Remington's Pharmaceutical Sciences, (18 ^thedition), ed. A. Gennaro, 1990,, Mack Publishing Company, Easton, Pa.

By “substantially identical” is meant a polypeptide or nucleic acid exhibiting at least 50%, preferably 85%, more preferably 90%, and most preferably 95% identity to a reference amino acid or nucleic acid sequence. For polypeptides, the length of comparison sequences will generally be at least 16 amino acids, preferably at least 20 amino acids, more preferably at least 25 amino acids, and most preferably 35 amino acids. For nucleic acids, the length of comparison sequences will generally be at least 50 nucleotides, preferably at least 60 nucleotides, more preferably at least 75 nucleotides, and most preferably 110 nucleotides.

Sequence identity is typically measured using sequence analysis software with the default parameters specified therein (e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705). This software program matches similar sequences by assigning degrees of homology to various substitutions, deletions, and other modifications. Conservative nucleotide substitutions typically include substitutions which generate changes within the following groups: glycine, alanine, valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.

By “substantially pure polypeptide” is meant a polypeptide that has been separated from the components that naturally accompany it. Typically, the polypeptide is substantially pure when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the polypeptide is a methionine synthase polypeptide that is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, pure. A substantially pure methionine synthase polypeptide may be obtained, for example, by extraction from a natural source (e.g., a fibroblast or liver cell) by expression of a recombinant nucleic acid encoding a methionine synthase polypeptide, or by chemically synthesizing the protein. Purity can be measured by any appropriate method, e.g., by column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.

A protein is substantially free of naturally associated components when it is separated from those contaminants which accompany it in its natural state. Thus, a protein which is chemically synthesized or produced in a cellular system different from the cell from which it naturally originates will be substantially free from its naturally associated components. Accordingly, substantially pure polypeptides not only includes those derived from eukaryotic organisms but also those synthesized in E. coli or other prokaryotes.

By “substantially pure DNA” is meant DNA that is free of the genes which, in the naturally-occurring genome of the organism from which the DNA of the invention is derived, flank the gene. The term therefore includes, for example, a recombinant DNA which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or which exists as a separate molecule (e.g., a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. It also includes a recombinant DNA which is part of a hybrid gene encoding additional polypeptide sequence.

By “transgene” is meant any piece of DNA which is inserted by artifice into a cell, and becomes part of the genome of the organism which develops from that cell. Such a transgene may include a gene which is partly or entirely heterologous (i.e., foreign) to the transgenic organism, or may represent a gene homologous to an endogenous gene of the organism.

By “transgenic” is meant any cell which includes a DNA sequence which is inserted by artifice into a cell and becomes part of the genome of the organism which develops from that cell. As used herein, the transgenic organisms are generally transgenic mammals (e.g., rodents such as rats or mice) and the DNA (transgene) is inserted by artifice into the nuclear genome. Preferably the inserted DNA encodes a protein in at least some cells of the organism.

By “knockout mutation” is meant an alteration in the nucleic acid sequence that reduces the biological activity of the polypeptide normally encoded therefrom by at least 80% relative to the unmutated gene. The mutation may, without limitation, be an insertion, deletion, frameshift mutation, or a missense mutation. Preferably, the mutation is an insertion or deletion, or is a frameshift mutation that creates a stop codon.

By “transformation” is meant any method for introducing foreign molecules into a cell. Lipofection, DEAE-dextran-mediated transfection, microinjection, protoplast fusion, calcium phosphate precipitation, retroviral delivery, electroporation, and biolistic transformation are just a few of the methods known to those skilled in the art which may be used. For example, biolistic transformation is a method for introducing foreign molecules into a cell using velocity driven microprojectiles such as tungsten or gold particles. Such velocity-driven methods originate from pressure bursts which include, but are not limited to, helium-driven, air-driven, and gunpowder-driven techniques. Biolistic transformation may be applied to the transformation or transfection of a wide variety of cell types and intact tissues including, without limitation, intracellular organelles (e.g., and mitochondria and chloroplasts), bacteria, yeast, fungi, algae, animal tissue, and cultured cells.

By “transformed cell” is meant a cell into which (or into an ancestor of which) has been introduced, by means of recombinant DNA techniques, a DNA molecule encoding (as used herein) a methionine synthase polypeptide.

By “positioned for expression” is meant that the DNA molecule is positioned adjacent to a DNA sequence which directs transcription and translation of the sequence (i.e., facilitates the production of, e.g., a methionine synthase polypeptide, a recombinant protein or a RNA molecule).

By “promoter” is meant a minimal sequence sufficient to direct transcription. Also included in the invention are those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell type-specific, tissue-specific, temporal-specific, or inducible by external signals or agents; such elements may be located in the 5′ or 3′ or intron sequence regions of the native gene.

By “operably linked” is meant that a gene and one or more regulatory sequences are connected in such a way as to permit gene expression when the appropriate molecules (e.g., transcriptional activator proteins) are bound to the regulatory sequences.

By “conserved region” is meant any stretch of six or more contiguous amino acids exhibiting at least 30%, preferably 50%, and most preferably 70% amino acid sequence identity between two or more of the methionine synthase family members, (e.g., between human and bacterial methionine synthase). Examples of conserved regions within methionine synthase are Boxes 1-4 (FIG. 1).

By “detectably-labeled” is meant any means for marking and identifying the presence of a molecule, e.g., an oligonucleotide probe or primer, a gene or fragment thereof, or a cDNA molecule. Methods for detectably-labeling a molecule are well known in the art and include, without limitation, radioactive labeling (e.g., with an isotope such as ³²P or ³⁵S) and nonradioactive labeling (e.g., chemiluminescent labeling, e.g., fluorescein labeling).

By “antisense” as used herein in reference to nucleic acids, is meant a nucleic acid sequence that is complementary to the coding strand of a gene, preferably, a methionine synthase gene. An antisense nucleic acid is capable of preferentially lowering the activity of a mutant methionine synthase polypeptide encoded by a mutant methionine synthase gene.

By “purified antibody” is meant antibody which is at least 60%, by weight, free from proteins and naturally occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably 90%, and most preferably at least 99%, by weight, antibody, e.g., a methionine synthase amino-terminus-specific antibody. A purified antibody may be obtained, for example, by affinity chromatography using recombinantly-produced protein or conserved motif peptides and standard techniques.

By “specifically binds” is meant an antibody that recognizes and binds a human methionine synthase polypeptide but that does not substantially recognize and bind other non-methionine synthase molecules in a sample, e.g., a biological sample, that naturally includes protein. A preferred antibody binds to the methionine synthase polypeptide sequence of SEQ ID NO: 2 (FIG. 3).

By “neutralizing antibodies” is meant antibodies that interfere with any of the biological activities of a wild-type or mutant methionine synthase polypeptide, for example, the ability of methionine synthase to catalyze the transfer of a methyl group to homocysteine. The neutralizing antibody may reduce the ability of a methionine synthase polypeptide to catalyze the transfer preferably by 10% or more, more preferably by 25% or more, still more preferably by 50% or more, yet preferably by 70% or more, and most preferably by 90% or more.

Any standard assay for the biological activity of methionine synthase, may be used to assess potentially neutralizing antibodies that are specific for methionine synthase.

By “expose” is meant to allow contact between an animal, cell, lysate or extract derived from a cell, or molecule derived from a cell, and a test compound.

By “treat” is meant to submit or subject an animal (e.g. a human), cell, lysate or extract derived from a cell, or molecule derived from a cell to a test compound.

By “test compound” is meant a chemical, be it naturally-occurring or artificially-derived, that is surveyed for its ability to modulate an alteration in reporter gene activity or protein levels, by employing one of the assay methods described herein. Test compounds may include, for example, peptides, polypeptides, synthesized organic molecules, naturally occurring organic molecules, nucleic acid molecules, and components thereof.

By “assaying” is meant analyzing the effect of a treatment, be it chemical or physical, administered to whole animals or cells derived therefrom. The material being analyzed may be an animal, a cell, a lysate or extract derived from a cell, or a molecule derived from a cell. The analysis may be for the purpose of detecting altered protein biological activity, altered protein stability, altered protein levels, altered gene expression, or altered RNA stability. The means for analyzing may include, for example, for example, the detection of the product of an enzymatic reaction, (e.g., the formation of methionine as a result of methionine synthase activity), antibody labeling, immunoprecipitation, and methods known to those skilled in the art for detecting nucleic acids.

By “modulating” is meant changing, either by decrease or increase, in biological activity.

By “a decrease” is meant a lowering in the level of biological activity, as measured by a lowering/increasing of: a) the formation of methionine as a result of methionine synthase activity; b) protein, as measured by ELISA; c) reporter gene activity, as measured by reporter gene assay, for example, lacZ/β-galactosidase, green fluorescent protein, luciferase, etc.; or d) mRNA, levels of at least 30%, as measured by PCR relative to an internal control, for example, a “housekeeping” gene product such as β-actin or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) or an externally added nucleic acid standard. In all cases, the lowering is preferably by at least 10% more preferably by at least 25%, still more preferably by at least 50%, and even more preferably by at least 70%.

By “an increase” is meant a rise in the level of biological activity, as measured by a lowering/increasing of: a) the formation of methionine as a result of methionine synthase activity; b) protein, as measured by ELISA; c) reporter gene activity, as measured by reporter gene assay, for example, lacZ/β-galactosidase, green fluorescent protein, luciferase, etc.; or d) mRNA, levels of at least 30%, as measured by PCR relative to an internal control, for example, a “housekeeping” gene product such as β-actin or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) or an externally added nucleic acid standard. Preferably, the increase is by 10% or more, more preferably by 25% or more, even more preferably by 2-fold, and most preferably by at least 3-fold.

By “alteration in the level of gene expression” is meant a change in gene activity such that the amount of a product of the gene, i.e., mRNA or polypeptide, is increased or decreased, or that the stability of the mRNA or the polypeptide is increased or decreased.

By “reporter gene” is meant any gene which encodes a product whose expression is detectable and/or quantitatable by immunological, chemical, biochemical or biological assays. A reporter gene product may, for example, have one of the following attributes, without restriction: fluorescence (e.g., green fluorescent protein), enzymatic activity (e.g., lacZ/β-galactosidase, luciferase, chloramphenicol acetyltransferase), toxicity (e.g., ricin A), or an ability to be specifically bound by a second molecule (e.g., biotin or a detectably labelled antibody). It is understood that any engineered variants of reporter genes, which are readily available to one skilled in the art, are also included, without restriction, in the forgoing definition.

By “protein” or “polypeptide” or “polypeptide fragment” is meant any chain of more than two amino acids, regardless of post-translational modification (e.g., glycosylation or phosphorylation), constituting all or part of a naturally-occurring polypeptide or peptide, or constituting a non-naturally occurring polypeptide or peptide.

By “missense mutation” is meant the substitution of one purine or pyrimidine base (i.e. A, T, G, or C) by another within a nucleic acid sequence, such that the resulting new codon encodes an amino acid distinct from the amino acid originally encoded by the reference (e.g. wild-type) codon.

By “deletion mutation” is meant the deletion of at least one nucleotide within a polynucleotide coding sequence. A deletion mutation alters the reading frame of a coding region unless the deletion consists of one or more contiguous 3-nucleotide stretches (i.e. “codons”). Deletion of a codon from a nucleotide coding region results in the deletion of an amino acid from the resulting polypeptide.

By “frameshift mutation” is meant the insertion or deletion of at least one nucleotide within a polynucleotide coding sequence. A frameshift mutation alters the codon reading frame at and/or downstream from the mutation site. Such a mutation results either in the substitution of the encoded wild-type amino acid sequence by a novel amino acid sequence, or a premature termination of the encoded polypeptide due to the creation of a stop codon, or both.

DETAILED DESCRIPTION OF THE DRAWINGS

The drawings will first be briefly described. [0058]
FIG. 1 is a diagram showing four homologous regions among methionine synthases. [0059] Boxes 1 to 4 were used to design degenerate oligonucleotides for the initial cloning experiments. Ec: Escherichia coli, accession number J04975; Ss: Synechocystis sp., accession number D64002; Ml1 and Ml2: Mycobacterium leprae, accession number U000175 (see Drennan et al., 1994); Hi: Haemophilus influenzae, accession number U32730; Ce: Caenorhabditis elegans, accession number Z46828; Hs: Homo sapiens, this work. Identical residues are indicated by a star above the alignment. Amino acid position for each protein is shown at left.
FIG. 2 is a diagram showing overlapping PCR fragments generated to clone human methionine synthase. Oligonucleotides are described in Table 1. [0060]
Primers in parentheses designate mispriming outcomes that generated valid internal sequence. iPCRc: inverse PCR on cDNA, iPCRg: inverse PCR on genomic DNA. [0061]
FIG. 3 is a diagram showing nucleotide sequence (SEQ ID NO: 1) and deduced amino acid sequence (SEQ ID NO: 2) of human methionine synthase. The nucleotide residue numbering is shown in the left margin, and the amino acid residue numbering is shown in the right margin. [0062]
FIG. 4 is a photograph showing mapping of the human methionine synthase gene using FISH. Signals are clearly visible at 1q43 (arrows). [0063]
FIGS. [0064] 5A-5C is a series of photographs showing diagnostic tests for mutations in the methionine synthase gene. Numbers above the gel lanes correspond to patients cell lines whereas the letter “c” identifies wild-type controls. FIG. 5A: HaeIII restriction analysis of genomic DNA PCR products using primers #1796 and #305A. The 2756A-G change creates a HaeIII site. Expected fragments, 2756A allele: 189 bp, 2756G allele: 159 and 30 bp (the 30 bp fragment was run off the gel). FIG. 5B: Heteroduplex analysis of PCR products amplified from RT reactions of patient 1892 and 3 controls. RT-PCR was done with primers #1772 and #1773. Expected PCR product: 338 bp, heteroduplexes can be seen above this band in patient 1892 (heterozygous for Δ2640-2642). C. Sau96I restriction analysis of genomic DNA PCR products. PCR was done as in (A). The 2758C→G mutation abolishes a Sau96I restriction endonuclease site in patient 2290. Expected fragments, control allele: 159, 30 bp, mutant allele: 189 bp (the 30 bp fragment has been run off the gel).
FIG. 6. shows an amino acid sequence comparison among methionine synthases in the [0065] Box 2 region. Identical residues are indicated by a star above the alignment. Dots show partially conserved residues, for which at least {fraction (6/7)} identical or similar residues can be aligned (A,G,S,T; D,E,N,Q; V,L,I,M; K,R; and F,W,Y (Bordo,D. and Argos,P. (1991) J. Molec. Biol., 217, 721-729)). Mutations identified in this work are shown below the alignment. For abbreviations, see FIG. 1; Mm: Mus musculus. The seven amino acids conserved in cobalamin-binding proteins (Drennan, C. L., Huang, S., Drummond, J. T., Matthews, R. G., and Ludwig, M. L. (1994) Science, 266, 1669-1674) are underlined.

DETAILED DESCRIPTION

We used specific regions of homology within the methionine synthase sequences of several lower organisms to clone a human methionine synthase cDNA (SEQ ID NO:1) by a combination of RT-PCR and inverse PCR. The enzyme (SEQ ID NO:2) is 1265 amino acids in length and contains the seven residue structure-based sequence fingerprint identified for cobalamin-containing enzymes. The gene was localized to chromosome 1q43 by the FISH technique. We have identified one missense mutation and a 3 base pair deletion in patients of the cblG complementation group of inherited homocysteine/folate disorders by SSCP and sequence analysis, as well as an amino acid substitution present in high frequency in the general population. [0066]
We conclude that the cDNA that we have identified corresponds to human methionine synthase on the basis of homology to known methionine synthases and by the identification of mutations in patients with a deficiency of enzyme activity. The most striking sequence conservation was found in four boxes of 9-13 amino acids. [0067] Box 2 has been proposed to correspond to part of the cobalamin binding domain (Drennan, C. L., Huang, S., Drummond, J. T., Matthews, R. G., and Ludwig, M. L. (1994) Science, 266, 1669-1674). It contains 13 consecutive residues that are identical in all known methionine synthases. Three amino acids within box 2 and four others C-terminal to it correspond to residues proposed by Drennan et al. (Drennan, C. L., Huang, S., Drummond, J. T., Matthews, R. G., and Ludwig, M. L. (1994) Science, 266, 1669-1674) as a structure-based sequence fingerprint for cobalamin binding. The three amino acids appear to make direct contact with the lower face of the corrin ring and dimethylbenzimidazole tail of cobalamin, determined from the crystal structure of the E. coli enzyme at 3 Å resolution (Drennan, C. L., Huang, S., Drummond, J. T., Matthews, R. G., and Ludwig, M. L. (1994) Science, 266, 1669-1674). All seven residues are identical in the human sequence (FIG. 6).
A survey of the NCBI databases for homology to the human methionine synthase using BLASTP yielded the various methionine synthases listed in FIG. 1, as well as the glutamate mutase (S41332, Q05488) and methylmalonyl-CoA mutase (P11653)(adenosyl-cobalamin dependent mutases) used to deduce the sequence fingerprint for cobalamin binding (Drennan, C. L., Huang, S., Drummond, J. T., Matthews, R. G., and Ludwig, M. L. (1994) [0068] Science, 266, 1669-1674). Homology was also found with the cobalamin binding region of the corrinoid: coenzyme M methyltransferase of Methanosarcina barkeri (U36337), the 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase of Clostridium thermoaceticum (L34780) and the B12-dependent 2-methyleneglutarate mutase of Clostridium barkeri (S43552, S43237). Further, homology was found with the B12-binding site domain of the recently identified putative methionine synthase of Agrobacterium tumefaciens (U48718; partial N-terminal sequence is given, up to region of box 4). Significantly, homology with the B12-binding site domain was also found in the Hg resistance protein of Myxococcus xanthus (Z21955). This protein has not been described as having a cobalamin prosthetic group.
The two mutations we have identified as candidates for causing cblG disease are located in the vicinity of the cobalamin binding domain by comparison with [0069] E. coli methionine synthase (FIG. 6). Ile881 corresponds by sequence alignment to Val855 in the E. coli enzyme. Val855 is within a beta sheet strand that is part of an α/β domain that is a variant of the Rossmann nucleotide binding fold. The H920D substitution is found in a region which, in the E. coli enzyme, is in an α helix at the C-terminal end of the α/β domain. It is interesting that the polymorphism we have identified is at the adjacent residue (D919G). The functional role of the polymorphism and deleterious mutations will have to be examined in expression experiments to confirm their precise effect on the protein.
Through the cloning of a cDNA for human methionine synthase and mutations therein, we can now determine the properties of the human enzyme and complete the characterization of mutations in patients with severe synthase deficiency. This analysis has allowed us to tie mutations in the gene to disturbances in homocysteine metabolism which are known to result in hyperhomocysteinemia is a risk factor for cardiovascular disease (Boushey, C. J., Beresford, S. A., Omenn, G. S., and Motulsky, A. G. (1995) [0070] JAMA, 274, 1049-1057) and neural tube defects (Steegers-Theunissen, R. P., Boers, G. H., Trijbels, F. J., Finkelstein, J. D., Blom, H. J., Thomas, C. M., Borm, G. F., Wouters, M. G., and Eskes, T. K. (1994) Metab. Clin. Exp., 43, 1475-1480; and Mills, J. L., McPartlin, J. M., Kirke, P. N., Lee, Y. J., Conley, M. R., Weir, D. G. and Scott, J. M. (1995) Lancet, 345, 149-151).
Our observations indicate the importance of methionine synthase as one of several genes involved in homocysteine metabolism. Results with other pathway genes underscores the significance of our findings. For example, a recently-identified mutation in methylenetetrahydrofolate reductase, the enzyme that synthesizes the 5-methyltetrahydrofolate substrate for the methionine synthase reaction, results in mild hyperhomocysteinemia (Frosst,P., Blom,H. J., Milos,R., Goyette,P., Sheppard,C. A., Matthews,R. G., Boers,G. J., den Heijer,M., Kluijtmans,L. A., van den Heuvel,L. P., et al. (1995) [0071] Nat. Genet., 10, 111-113). Evidence is accumulating that this mutation, present in 35-40% of alleles, is a risk factor in both cardiovascular disease and neural tube defects (Rozen,R. (1996) Clin. Invest. Med., 19, 171-178). We believe that genetic variants of methionine synthase similarly lead to mild hyperhomocysteinemia with consequent impact on these two multifactorial disorders.
We used specific regions of homology within the methionine synthase sequences, including a portion of the cobalamin binding site determined from the [0072] E. coli enzyme, to design degenerate oligonucleotides for RT-PCR-dependent cloning of human methionine synthase. We confirmed the identification of the cDNA sequences for human methionine synthase by the high degree of homology to the enzymes in other species and the identification of mutations in patients from the cblG complementation group. We also mapped the gene to human chromosome 1.
The assays described herein can be used to test for compounds that modulate methione synthase activity and hence may have therapeutic value in the prevention of neural tube defects, prevention and/or treatment of colon cancer, cardiovascular disease, hyperhomocysteinemia, and megaloblastic anemia without methylmalonic aciduria. [0073]

Screens for Compounds that Modulate Methionine Synthase Enzymatic Activity

Screens for potentially useful therapeutic compounds that modulate methionine synthase activity may be readily performed, for example, by assays that measure the incorporation of [14C]5-methyltetrahydrofolate into methionine or protein, or assays that measure the conversion of [14C]-homocysteine into methionine or protein. Examples of such assays, which employ whole cells or cell lysates, are well-known to those skilled in the art (see, e.g., Schuh, S., et al., [0074] N. Engl. J. Med. 1984, 310:686-69; Rosenblatt, D. S., et al., J. Clin. Invest. 1984, 74:2149-2156; Watkins, D., and Rosenblatt, D. S., J. Clin. Invest. 1988, 81:1690-1694; and Watkins, D., and Rosenblatt, D. S., Am. J. Med. Genet. 1989, 34:427-434), and may be readily adapted for high throughput screening.

ELISA for the Detection of Compounds that Modulate Methionine Synthase Expression

Enzyme-linked immunosorbant assays (ELISAs) are easily incorporated into high-throughput screens designed to test large numbers of compounds for their ability to modulate levels of a given protein. When used in the methods of the invention, changes in a given protein level of a sample, relative to a control, reflect changes in the methionine synthase expression status of the cells within the sample. Protocols for ELISA may be found, for example, in Ausubel et al.,[0075] Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., 1997. Lysates from cells treated with potential modulators of methionine synthase expression are prepared (see, for example, Ausubel et al., supra), and are loaded onto the wells of microtiter plates coated with “capture” antibodies specific for methionine synthase. Unbound antigen is washed out, and a methionine synthase-specific antibody, coupled to an agent to allow for detection, is added. Agents allowing detection include alkaline phosphatase (which can be detected following addition of colorimetric substrates such as p-nitrophenolphosphate), horseradish peroxidase (which can be detected by chemiluminescent substrates such as ECL, commercially available from Amersham) or fluorescent compounds, such as FITC (which can be detected by fluorescence polarization or time-resolved fluorescence). The amount of antibody binding, and hence the level of a methionine synthase polypeptide within a lysate sample, is easily quantitated on a microtiter plate reader.
As a baseline control for methionine synthase expression, a sample that is not exposed to test compound is included. Housekeeping proteins are used as internal standards for absolute protein levels. A positive assay result, for example, identification of a compound that decreases methionine synthase expression, is indicated by a decrease in methionine synthase polypeptide within a sample, relative to the methionine synthase level observed in cells which are not treated with a test compound. [0076]

Reporter Gene Assays for Compounds that Modulate Methionine Synthase Expression

Assays employing the detection of reporter gene products are extremely sensitive and readily amenable to automation, hence making them ideal for the design of high-throughput screens. Assays for reporter genes may employ, for example, colorimetric, chemiluminescent, or fluorometric detection of reporter gene products. Many varieties of plasmid and viral vectors containing reporter gene cassettes are easily obtained. Such vectors contain cassettes encoding reporter genes such as lacZ/β-galactosidase, green fluorescent protein, and luciferase, among others. Cloned DNA fragments encoding transcriptional control regions of interest (e.g. that of the mammalian methionine synthase gene) are easily inserted, by DNA subcloning, into such reporter vectors, thereby placing a vector-encoded reporter gene under the transcriptional control of any gene promoter of interest. The transcriptional activity of a promoter operatively linked to a reporter gene can then be directly observed and quantitated as a function of reporter gene activity in a reporter gene assay. [0077]
Cells are transiently- or stably-transfected with methionine synthase control region/reporter gene constructs by methods that are well known to those skilled in the art. Transgenic mice containing methionine synthase control region/reporter gene constructs are used for late-stage screens in vivo. Cells containing methionine synthase/reporter gene constructs are exposed to compounds to be tested for their potential ability to modulate methionine synthase expression. At appropriate timepoints, cells are lysed and subjected to the appropriate reporter assays, for example, a colorimetric or chemiluminescent enzymatic assay for lacZ/β-galactosidase activity, or fluorescent detection of GFP. Changes in reporter gene activity of samples treated with test compounds, relative to reporter gene activity of appropriate control samples, indicate the presence of a compound that modulates methionine synthase expression. [0078]

Quantitative PCR of Methionine Synthase mRNA as an Assay for Compounds that Modulate Methionine Synthase Expression

The polymerase chain reaction (PCR), when coupled to a preceding reverse transcription step (rtPCR), is a commonly used method for detecting vanishingly small quantities of a target mRNA. When performed within the linear range, with an appropriate internal control target (employing, for example, a housekeeping gene such as actin), such quantitative PCR provides an extremely precise and sensitive means of detecting slight modulations in mRNA levels. Moreover, this assay is easily performed in a 96-well format, and hence is easily incorporated into a high-throughput screening assay. Cells are treated with test compounds for the appropriate time course, lysed, the mRNA is reverse-transcribed, and the PCR is performed according to commonly used methods, (such as those described in Ausubel et al., [0079] Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., 1997), using oligonucleotide primers that specifically hybridize with methionine synthase nucleic acid. Changes in product levels of samples exposed to test compounds, relative to control samples, indicate test compounds that modulate methionine synthase expression.

Secondary Screens of Test Compounds that Appear to Modulate Methionine Synthase Activity

After test compounds that appear to have methionine synthase-modulating activity are identified, it may be necessary or desirable to subject these compounds to further testing. At late stages testing will be performed in vivo to confirm that the compounds initially identified to affect methionine synthase activity will have the predicted effect in vivo. [0080]

Test Compounds

In general, novel drugs for prevention of neural tube defects, or prevention and/or treatment of colon cancer or cardiovascular disease are identified from large libraries of both natural product or synthetic (or semi-synthetic) extracts or chemical libraries according to methods known in the art. Those skilled in the field of drug discovery and development will understand that the precise source of test extracts or compounds is not critical to the screening procedure(s) of the invention. Accordingly, virtually any number of chemical extracts or compounds can be screened using the exemplary methods described herein. Examples of such extracts or compounds include, but are not limited to, plant-, fungal-, prokaryotic- or animal-based extracts, fermentation broths, and synthetic compounds, as well as modification of existing compounds. Numerous methods are also available for generating random or directed synthesis (e.g., semi-synthesis or total synthesis) of any number of chemical compounds, including, but not limited to, saccharide-, lipid-, peptide-, and nucleic acid-based compounds. Synthetic compound libraries are commercially available from Brandon Associates (Merrimack, N.H.) and Aldrich Chemical (Milwaukee, Wis.). Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant, and animal extracts are commercially available from a number of sources, including Biotics (Sussex, UK), Xenova (Slough, UK), Harbor Branch Oceangraphics Institute (Ft. Pierce, Fla.), and PharmaMar, U.S.A. (Cambridge, Mass.). In addition, natural and synthetically produced libraries are produced, if desired, according to methods known in the art, e.g., by standard extraction and fractionation methods. Furthermore, if desired, any library or compound is readily modified using standard chemical, physical, or biochemical methods. [0081]
In addition, those skilled in the art of drug discovery and development readily understand that methods for dereplication (e.g., taxonomic dereplication, biological dereplication, and chemical dereplication, or any combination thereof) or the elimination of replicates or repeats of materials already known for their therapeutic activities for homocysteinemia, megaloblastic anemia without methylmalonic aciduria, cardiovasular disease, colon cancer, and neural tube defects should be employed whenever possible. [0082]
When a crude extract is found to modulate methionine synthase biological activity, further fractionation of the positive lead extract is necessary to isolate chemical constituents responsible for the observed effect. Thus, the goal of the extraction, fractionation, and purification process is the careful characterization and identification of a chemical entity within the crude extract that modulates methionine synthase biological activity. The same assays described herein for the detection of activities in mixtures of compounds can be used to purify the active component and to test derivatives thereof. Methods of fractionation and purification of such heterogenous extracts are known in the art. If desired, compounds shown to be useful agents for treatment are chemically modified according to methods known in the art. Compounds identified as being of therapeutic value may be subsequently analyzed using mammalian models of homocysteinemia, megaloblastic anemia without methylmalonic aciduria, cardiovasular disease, colon cancer, and neural tube defects. [0083]

Therapy

Compounds identified using any of the methods disclosed herein, may be administered to patients or experimental animals with a pharmaceutically-acceptable diluent, carrier, or excipient, in unit dosage form. Conventional pharmaceutical practice may be employed to provide suitable formulations or compositions to administer such compositions to patients or experimental animals. Although intravenous administration is preferred, any appropriate route of administration may be employed, for example, parenteral, subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intracisternal, intraperitoneal, intranasal, aerosol, or oral administration. Therapeutic formulations may be in the form of liquid solutions or suspensions; for oral administration, formulations may be in the form of tablets or capsules; and for intranasal formulations, in the form of powders, nasal drops, or aerosols. [0084]
Methods well known in the art for making formulations are found in, for example, “Remington's Pharmaceutical Sciences.” Formulations for parenteral administration may, for example, contain excipients, sterile water, or saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated naphthalenes. Biocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compounds. Other potentially useful parenteral delivery systems for antagonists or agonists of the invention include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation may contain excipients, for example, lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate and deoxycholate, or may be oily solutions for administration in the form of nasal drops, or as a gel. [0085]

EXAMPLES

The following examples are to illustrate, not limit the invention. [0086]

Example 1

Cloning Human Methionine Synthase cDNA

An initial survey of the NCBI databases yielded several sequences corresponding to methionine synthase from different organisms. Comparison of these sequences generated four very conserved regions identified as Boxes 1-4 in FIG. 1 (SEQ ID Nos:3-25). Degenerate oligonucleotides (SEQ ID Nos:26-66) were synthesized corresponding to these conserved sequences (Table 1). These were used as primers for RT-PCR with human and mouse mRNA. These experiments yielded PCR products which were subcloned, sequenced and aligned as shown in FIG. 2. In subsequent experiments, oligonucleotide primers were specified from the non-degenerate internal sequences of the subclones and additional PCR products encompassing the conserved boxes were obtained. In later experiments, additional sequences were obtained by inverse PCR (“PCR”, FIG. 2) to obtain upstream or downstream sequences from those already determined. At the 3′ end, a mouse sequence was obtained from the dbEST database (Accession Number W33307). This sequence was used as the source of primers for additional PCR experiments. Throughout the experiments, the sequences of the PCR products were considered provisionally authentic if they were homologous to the methionine synthase sequences obtained from the databases. The sequences were taken as error free by comparison of the sequences of at least two, and usually three, independent PCR reactions. Sequences were linked into a common sequence if RT-PCRs bridging independently isolated sequences were successful. Through this approach the complete coding sequence was determined through exclusive use of PCR reactions. [0087]
The coding sequence of human methionine synthase contains 3795 bp (SEQ ID NO:1) encoding a polypeptide of 1265 amino acids in length (SEQ ID NO:2) (FIG. 3), exceeding the length of published methionine synthases by 11-29 residues. The putative initiation codon is in a sequence of good context for the initiation of translation in eukaryotic cells ([0088] GACAACATGT, underlined nucleotides matching Kozak consensus (Kozak,M. (1991) J. Biol. Chem., 266, 19867-19870)). The predicted MW of methionine synthase is 141,000, comparing favorably with the published size of 151,000 based on SDS-polyacrylamide electrophoresis of the pig enzyme (Chen, Z., Crippen, K., Gulati, S., and Baneijee, R. (1994) J. Biol. Chem., 269, 27193-27197). It shares 58% identity with the E. coli and 65% identity with the C. elegans enzyme.

Example 2

Chromosomal Location

Using FISH, the gene encoding methionine synthase was mapped to chromosome band 1q43, close to the telomeric region of the long arm (FIG. 4). A total of 50 cells with at least one signal were observed. A signal was seen on 1 chromatid in 26 cells, on two chromatids in 14 cells, on 3 chromatids in 7 cells, and on 4 chromatids in 3 cells. These results confirm the previous assignment of the gene to [0089] chromosome 1 by Mellman et al. (Mellman, I. S., Lin, P. F., Ruddle, F. H., and Rosenberg, L. E. (1979) Proc. Natl. Acad. Sci. USA, 76, 405-409), who used cobalamin binding as a marker for the enzyme in human-hamster hybrids.

Example 3

Mutations in the cblG Complementation Group

Patients with deficiency of methionine synthase activity have been grouped into the cblG complementation group in cell fusion experiments (Watkins, D. and Rosenblatt, D. S. (1988) [0090] J. Clin. Invest., 81, 1690-1694). Fibroblast cultures from patients assigned to cblG were examined by RT-PCR based SSCP analysis. Three mutations were identified by sequencing PCR fragments showing band shifts by SSCP (FIG. 5). In each case, the change was confirmed by an independent diagnostic test on genomic DNA or a separate preparation of cDNA from patient fibroblasts. One of the mutations, 2756A→G (D919G), was confirmed by a diagnostic test that monitored the presence of a HaeIII site created by the mutation (FIG. 5A). Using this test, it was identified as a polymorphism since it was seen in 8 of 52 control alleles (15%). In two other cases, candidate deleterious mutations were identified. One is a 3 bp deletion, bp 2640-2642, that results in the deletion of an isoleucine codon (ΔIle881). It was confirmed by heteroduplex analysis of cDNA generated by RT-PCR (FIG. 5B). The second is a point mutation, 2758C→G. It results in the amino acid substitution H920D. It was confirmed in genomic DNA by the loss of a Sau96I site (FIG. 5C). The latter two mutations were heterozygous in the patient cell lines. Their second mutation has not been identified. The candidate deleterious mutations were not seen in panels of 68 or 52 control alleles, respectively.

Example 4

Additional Roles for Methionine Synthase Polymorphism (Asp919Gly or D919G) in Disease

The following data suggest that the D919G polymorphism contributes to altered metabolism of homocysteine, methionine, folates, Vit. B12, and S-adenosylmethionine. [0091]
First in a Montreal study (n=303), in which mother-child pairs (cases and controls) were examined, we observed that infants who were homozygous for the polymorphism (Gly/Gly; Table 2) were at decreased risk for NTD. [0092]
Measurements of serum folate, RBC folate, plasma homocysteine and serum cobalamin did not give any statistically significant differences, except the trend was toward low folate levels in Gly/Gly individuals (cases and controls). [0093]
A second study (n=255) in California also examined the methionine synthase polymorphism as a risk factor for neural tube defects (Table 3). This study shows a similar decreased risk of neural tube defects in children homozygous for Gly/Gly. Since the study encompassed a mix of whites and Hispanics, the data were reexamined stratified according to ethnic origin. Both groups showed a protective effect of Gly/Gly. [0094]
In summary, two independent studies suggest a protective effect of Gly/Gly against the risk of neural tube defects. This is likely to be mediated by a mild reduction in methionine synthase activity. [0095]
Next, in a study of colon cancer, (212 cases and 345 controls), we observed a decreased risk for colon cancer in the individuals who were homozygous for the polymorphism (relative risk=0.62); see Table 4. In the same study, we observed significantly decreased levels of plasma folate in individuals who were homozygous for the polymorphism; see Table 5. [0096]
The Boston study described in Tables 4 and 5 is presented again in Table 6 with the data stratified according to alcohol intake. As shown in the table, Gly/Gly individuals with a low to medium alcohol intake had a relative risk associated with colon cancer of 0.11. The combined data (low+high alcohol) gave a risk level of 0.62 (Table 6). [0097]
In summary, drug therapy targeted to a reduction in methionine synthase activity may be protective in individuals at risk for colon cancer or at risk for neural tube defects. Additional polymorphisms or mutations may also exert a protective effect against the risk of neural tube defects or colon cancer. Conversely, it is understood that some polymorphisms and/or mutations may enhance the risk of neural tube defects or colon cancer, for example, by increasing methionine synthase activity. [0098]

Example 5

Role of Polymorphism on Homocysteine and Folate Levels

Third, in a study of individuals participating in the U.S. NHLBI Family Heart Study, we observed both an increase in plasma homocysteine following a methionine load and a decrease in plasma folate in individuals who were homozygous for this polymorphism; see Table 7. [0099]

Example 6

Methionine Synthase Assays for the Detection of Compounds that Modulate Methionine Synthase Activity and Expression

Potentially useful therapeutic compounds that modulate (e.g. increase or decrease) methionine synthase activity or expression may be isolated by various screens that are well-known to those skilled in the art. Such compounds may modulate methionine synthase expression at the pre- or post-transcriptional level, or at the pre- or post-translational level. [0100]

Example 7

Materials and Methods

Cell lines. The skin fibroblast lines are from patients with methionine synthase deficiency. They were assigned to the cblG complementation group in cell fusion experiments assayed by [0101] ¹⁴C-methyltetrahydrofolate incorporation into cellular macromolecules (Watkins, D. and Rosenblatt, D. S. (1988) J. Clin. Invest., 81, 1690-1694). Control fibroblasts were from other laboratory stocks or the Montreal Children's Hospital Cell Repository for Mutant Human Cell Strains. Of the patients for which non-polymorphic mutations were found, WG 1892, a Caucasian male, was diagnosed at the age of 4 years with developmental delay, tremors, gait instability, megaloblastic anemia and homocystinuria; and WG2290, also a Caucasian male, was diagnosed at age 3 months with failure to thrive, severe eczema, megaloblastic anemia and surprisingly both homocystinuria and methylmalonic aciduria.
Materials. The T/A cloning kit was from Invitrogen. The Geneclean III Kit was obtained from Bio 101 Inc. and the Wizard Mini-Preps were from Promega. The random-primed DNA labelling kit was from Boehringer-Mannheim. Taq polymerase, Superscript II reverse transcriptase, AMV reverse transcriptase, Trizol reagent, DNAzol reagent, T4 DNA ligase, and restriction enzymes were purchased from Gibco BRL. The Sequenase kit for manual sequencing was from United States Biochemicals. The α-[[0102] ³⁵S]dATP (12.5 Ci/mole) was from Dupont or ICN. The oligonucleotide primers were synthesized by R. Clarizio of the Montreal Children's Hospital Research Institute Oligonucleotide Synthesis Facility or the Sheldon Biotechnology Centre, McGill University.
Homology matches. Comparisons were made between the published [0103] E. coli cobalamin-dependent methionine synthase sequence and sequences in the NCBI databases (dbEST and GenBank) using the BLAST programs.
PCR cloning and DNA sequencing. DNA was prepared from fibroblast pellets by the method of Hoar et al. (Hoar,D. I., Haslam,D. B., and Starozik,D. M. (1984) [0104] Prenat. Diag., 4, 241-247). Total cellular RNA was isolated by the method of Chirgwin et al. (Chirgwin,J. M., Przybyla,A. E., MacDonald,R. J., and Rutter,W. J. (1979) Biochemistry, 18, 5294-5299) and is reverse-transcribed using oligo-dT₁₅as primer. PCR was conducted using degenerate oligonucleotides as primers, paired so as to link the sequences of different homology boxes. The PCRs were conducted as described previously (Triggs-Raine,B. L., Akerman,B. R., Clarke,J. T., and Gravel,R. A. (1991) Am. J. Hum. Genet., 49, 1041-1054) except that the temperature of incubation was modified to accommodate the use of reduced temperatures in the annealing step or by step-down PCR (Hecker,K. H. and Roux,K. H. (1996) Biotechniques, 20, 478-485. (Abstract)). In some experiments, inverse PCR was used to determine sequence upstream or downstream of known sequence (Ochman,H., Medhora,M. M., Garza,D., and Hartl,D. L. (1990) PCR Protocols: A Guide to Methods and Applications, Academic Press, San Diego, pp. 219-227). In these instances, genomic DNA or cDNA prepared by reverse transcription of RNA was digested with different four base restriction endonucleases, ligated with T4 DNA ligase, and amplified by PCR using adjacent oligonucleotides priming in opposite directions. Templates for inverse PCR at the cDNA level were generated with 12.5 μg RNA reversed transcribed using AMV-RT. Second strand synthesis was carried out using the random-primed DNA labelling kit adding 1 μl of each dNTP. Samples were incubated 30 min. at 37° C. Template was then treated as genomic DNA for digestion and ligation. Inverse PCR was used to obtain the 5′ and 3′ ends of the cDNA and to define an intron sequence adjacent to a splice junction for the design of a mutation diagnostic test. The PCR products were purified with Geneclean and were subcloned in the pCR2.1 vector and transformed into E. coli as per the supplier's protocol (TA Cloning Kit). The candidate clones were sequenced manually or by the DNA Core Facility of the Canadian Genetic Diseases Network or the McGill University Sheldon Biotechnology Centre.
Mutation analysis. Genomic DNA and RNA were isolated from control or patient fibroblast pellets using the DNAzol or Trizol reagents, respectively, as per the manufacturer. The cDNA template for PCR was prepared by reverse transcription of 3-5 μg total RNA in reactions containing 400 U of Superscript II reverse transcriptase and 100 ng random hexamers in a total reaction volume of 20 ul. SSCP analysis was performed as described previously (Triggs-Raine,B. L., Akerman,B. R., Clarke,J. T., and Gravel,R. A. (1991) [0105] Am. J. Hum. Genet., 49, 1041-1054) in reactions containing 4 μl of template, 1 μl of each dTTP, dCTP, dGTP (0.625 mM), 0.5 μl of dATP (0.625 mM), 1 μl α-[³⁵S]-dATP (12.5 Ci/mole). The radio labelled PCR products mixed with sequencing stop solution were heat denatured and quick chilled on ice prior to loading (Triggs-Raine,B. L., Akerman,B. R., Clarke,J. T., and Gravel,R. A. (1991) Am. J. Hum. Genet., 49, 1041-1054). As well, an aliquot of each sample was run without prior heating to identify the duplex product. The fragments were subjected to electrophoresis in a 6% acrylamide/10% glycerol gel in 1×TBE for 18 hrs at 8 watts at room temperature. The gel was dried and exposed to Biomax film (Kodak). Fragments that displayed band shifts were sequenced directly.
Two mutations were confirmed directly in PCR amplification products from genomic DNA and one mutation was confirmed in reversed transcribed mRNA. The PCR reactions for mutation confirmation were performed using 4 μl of cDNA template or 500 ng genomic DNA, 500 ng of specific primers, 2.5 U Taq polymerase and 1.5 mM MgCl2 in a 50 μl volume. Heteroduplex analysis was accomplished by preheating PCR products to 95° C. for five minutes and subjecting the samples to electrophoresis in a 9% polyacrylamide gel (Triggs-Raine,B. L., Akerman,B. R., Clarke,J. T., and Gravel,R. A. (1991) [0106] Am. J. Hum. Genet., 49, 1041-1054). Other diagnostic assays were accomplished by digesting a 15 μl sample of the PCR products with the indicated restriction endonuclease prior to electrophoresis.

Chromosomal localization. Human metaphase spreads were obtained from short-term cultures of phytohemaglutinin-stimulated peripheral blood lymphocytes. The cells were synchronized with thymidine and treated with BrdU during the late S-phase before harvesting for simultaneous observation of the hybridized sites and chromosome banding. The protocol for FISH was essentially as described previously (Lemieux, N., Malfoy, B., and Forrest, G. L. (1993) Genomics, 15, 169-172; Zhang, X. X., Rozen, R., Hediger, M. A., Goodyer, P., and Eydoux, P. (1994) Genomics, 24, 413-414). Briefly, a 5 kb DNA fragment of the methionine synthase genomic DNA (generated by PCR using oligonucleotides #1782 and #1780) was labelled by nick translation with biotin-16-dUTP (Boehringer-Mannheim), ethanol precipitated and dissolved in hybridization buffer at a final concentration of 8 ng/μl. The slides were denatured in 70% formamide, 2×SSC at 70° C. for 2 min. The biofinylated probe was denatured in the hybridization buffer at 95° C. for 10 min, quickly cooled on ice, then applied on slides. Post-washing was done by rinsing in 50% formamide, 2×SSC at 37° C. The slides were incubated with rabbit antibiotin antibody (Enzo Biochemicals), biotinylated goat anti-rabbit antibodies (BRL) and streptavidin-FITC. They were stained with propidium iodide and mounted in p-phenylenediamine, pH 11. Cells were observed under the microscope (Zeiss), then captured through a CCD camera and processed using a FISH software (Applied Imaging).

TABLE 1


Oligonucleotides used for cDNA cloning, chromosome mapping and mutation
detection.

Oligonucleotides^a	Sequence	Location^b

D1729	5′-GAYGGNGCNATGGGNACNATGATHCA	(SEQ ID NO:26)	100-125

D1730	5′-GCNACNGTNAARGGNGAYGTNCAYGAYAT	(SEQ ID NO:27)	2332-2360

D1731	5′-RTTYTTNCCDATRTCRTGNACRTCNCCYTT	(SEQ ID NO:28)	2370-2341

D1733	5′-RTGNAGRTAYTCNGCRAANGCYTCNGC	(SEQ ID NO:29)	3426-3400

D1754	5′-ATRTGRTCNGGNGTNGTNCCRCARCANCCNCC	(SEQ ID NO:30)	992-961

D1755	5′-GGNGGNTGYTGYGGNACNACNCCNGAYCAYAT	(SEQ ID NO:31)	961-992

M1806A	5′-GTCTGTGTCATAGCCCAGAATGGG	(SEQ ID NO:32)	3795-3772

M1806B	5′-TCAGTCTGTGTCATAGCCCAGAAT	(SEQ ID NO:33)	3798-3775

305A	5′-GAACTAGAAGACAGAAATTCTCTA	(SEQ ID NO:34)	(intronic)

407A	5′-TTCCGAGGTCAGGAATTTAAAGATCA	(SEQ ID NO:35)	151-176

407B	5′-GTGTTCTTCGTTTAGCTTCTCCCG	(SEQ ID NO:36)	150-127

407D	5′-CCCCAGCCAGCAAGTATTCCTTAT	(SEQ ID NO:37)	268-245

1107A	5′-CTAGGTTGTATTTCCTTGAGGATC	(SEQ ID NO:38)	3856-3833

1406D	5′-GGAGCTGGAAAAATGTTTCTACCTC	(SEQ ID NO:39)	2170-2194

1406E	5′-ACAGGAGGGAAGAAAGTCATTCAG	(SEQ ID NO:40)	1963-1986

1706A	5′-CCTTCAATTATATTGAGAGGTCGGG	(SEQ ID NO:41)	2129-2105

1707A	5′-CAACCCGAAGGTCTGAAGAAAACC	(SEQ ID NO:42)	28-51

1707B	5′-CCCGCGCTCCAAGACCTGTCG	(SEQ ID NO:43)	7-27

1707C	5′-CGACAGGTCTTGGAGCGCGGG	(SEQ ID NO:44)	27-7

1758	5′-GGAGTCATGACTCCTAAATCAATAACTC	(SEQ ID NO:45)	2432-2405

1760	5′-GACGACTACAGCAGCATCATGGT	(SEQ ID NO:46)	3355-3377

1766	5′-AAAAATCATTTCATCCAGGGAA	(SEQ ID NO:47)	2526-2505

1772	5′-ATAGGCAAGAACATAGTTGGAGTAGT	(SEQ ID NO:48)	2359-2384

1773	5′-TTTCATCTAACAGCTGGGAACACAC	(SEQ ID NO:49)	2698-2674

1774	5′-TGCCTCTCAGACTTCATCGCTCCC	(SEQ ID NO:50)	3241-3264

1780	5′-TGCAGCCTGGGGCACAGCAGC	(SEQ ID NO:51)	3168-3148

1782	5′-ATGGATTGGCTGTCTGAACCTCAC	(SEQ ID NO:52)	2824-2847

1796	5′-CATGGAAGAATATGAAGATATTAGAC	(SEQ ID NO:53)	2727-2752

1803	5′-ACCATCATCCTCATAGGCCTTGCT	(SEQ ID NO:54)	3354-3331

1806C	5′-CAGACCTGCGAAGGTTGCGGTAC	(SEQ ID NO:55)	3482-3504

1806F	5′-GAAGTGGTTGCTCCTCCAATCAAC	(SEQ ID NO:56)	2591-2568

1808	5′-GAGCAGCTTTCAGTATCTTATCACAT	(SEQ ID NO:57)	2458-2433

1827	5′-ACAAGTTGTGTTCCTCCATTCCAGT	(SEQ ID NO:58)	1657-1633

1828	5′-AGAGCGCTGTAATGTTGCAGGATCA	(SEQ ID NO:59)	1125-1149

1907B	5′-TGTTTTTCAATGCCCTTCACAAGGG	(SEQ ID NO:60)	2057-2033

1907C	5′-TAAAAAGTATGGAGCTGCTATGGTG	(SEQ ID NO:61)	1464-1488

2606A	5′-GACCAGACAGTAACATATGTCCTTC	(SEQ ID NO:62)	1078-1054

2606B	5′-ACATTACAGCGCTCTCCAATGTTAAC	(SEQ ID NO:63)	1139-1114

2706A	5′-TGAGGTTGAGAAATGGCTTGGACC	(SEQ ID NO:64)	3750-3773

2706B	5′-GCCACAGATATGTTCTTCCTCAATG	(SEQ ID NO:65)	3749-3725

3107A	5′-TGTGGAGAGCACGTCTTCTCTGCC	(SEQ ID NO:66)	−55-−32

[0108]

TABLE 2

MS Polymorphism in Neural Tube Defects - Montreal Study

Case Con- Control

Cases mothers trols mothers Odds

Genotype N % N % N % N % ratio* 95% C.I.

Asp/Asp 38 69 40 66 59 61 55 61

Asp/Gly 17 31 20 33 28 29 34 38

Gly/Gly 0 0.9 1 2 10 10 1 1 0.07 0.004-1.29

N 55 61 97 90

TABLE 3


MS Polymorphisms in Neural Tube Defects - California Study

Genotype

Cases

Controls

Odds

Ethnic Group	2756A-G	N	%	N	%	ratio*	95% C.I.

Overall	Asp/Asp	64	67	104	64	1.0
	Asp/Gly	30	32	49	30	0.99	0.56-1.72
	Gly/Gly	1	1	7	4	0.23	0.05-1.92
White only	Asp/Asp	21	66	38	66	2.0
	Asp/Gly	10	31	16	28	1.1	0.44-2.9
	Gly/Gly	1	3	3	5	0.60	0.11-5.6
Hispanic only	Asp/Asp	43	68	66	63	1.0
	Asp/Gly	20	32	33	31	0.9	0.45-1.8
	Gly/Gly	0	0	4	4	0

[0110]

TABLE 4

Frequency of MS genotype and relative risk (RR) of colorectal cancer by

MS genotype

Cases Controls

MS Genotype n % n % RR 95% CI

Asp/Asp 145 (68) 234 (68) 1.0

Asp/Gly 61 (29) 95 (28) 1.02 0.69-1.50

Gly/Gly 6 (3) 16 (5) 0.62 0.24-1.64

Total 212 345
[0111]

TABLE 5

Mean of homocysteine and folate (geometric) by case control status and

MS Genotype in a colon cancer study

Cases &

Cases Controls Controls

MS genotype n mean n mean n mean

Folate (Bio-Kit) ng/ml

Asp/Asp 115 3.8 201 3.9 * 316 3.9 **

Asp/Gly 49 4.1 * 80 3.8 * 129 3.9 **

Gly/Gly 6 2.1 12 2.3 18 2.2

Homocysteine (μM)

Asp/Asp 66 12.5 160 12.1 226 12.3

Asp/Gly 30 10.8 50 11.6 80 11.2

Gly/Gly 4 13.4 9 11.7 13 12.5

TABLE 6


Age Adjusted Relative Risk of Colon Cancer According to MS
Polymorphism and Alcohol Intake Status Among US Physicians

	Genotype
	2756A−>G	Cases	Controls	Odds
Alcohol intake	Asp919Gly	N	N	ratio	95% C.I.

Low-Medium	Asp/Asp	1013	2e+09	1.0
0-0.8 drinks/day	Asp/Gly	7113		0.87	0.54-1.4
	Gly/Gly	9		0.11	0.01-0.82
	N
High	Asp/Asp	3721	7e+06	0.74	0.46-1.19
1-2+ drinks/day	Asp/Gly	563		1.15	0.60-2.18
	Gly/Gly			3.83	0.72-20.47
	N

TABLE 7


Mean Homocysteine and Folate Status by MS Genotype
(Date of Analysis: Feb. 18, 1997)

Methionine Synthase Genotype

Asp/Asp

Asp/Gly

Gly/Gly

	Result	Result	P	Result	P

N	252	111		17
Fasting Hcy (μM)	8.5	8.4	0.76	8.7
post-methionine load	17.9	19.6		0.74
Hcy
(μM)	7.4	0.05*	6.9	22.3
Folate (microb test)		0.37		0.03*
				6.3
				0.37

[0114]
1 76 1 3919 DNA Homo sapiens Other (1)...(3919) Entire cloned cDNA encoding wild type methionine synthase. 1 ggtcacctgt ggagagcacg tcttctctgc cgcgccctct gcgcaaggag gagactcgac 60 aacatgtcac ccgcgctcca agacctgtcg caacccgaag gtctgaagaa aaccctgcgg 120 gatgagatca atgccattct gcagaagagg attatggtgc tggatggagg gatggggacc 180 atgatccagc gggagaagct aaacgaagaa cacttccgag gtcaggaatt taaagatcat 240 gccaggccgc tgaaaggcaa caatgacatt ttaagtataa ctcagcctga tgtcatttac 300 caaatccata aggaatactt gctggctggg gcagatatca ttgaaacaaa tacttttagc 360 agcactagta ttgcccaagc tgactatggc cttgaacact tggcctaccg gatgaacatg 420 tgctctgcag gagtggccag aaaagctgcc gaggaggtaa ctctccagac aggaattaag 480 aggtttgtgg caggggctct gggtccgact aataagacac tctctgtgtc cccatctgtg 540 gaaaggccgg attataggaa catcacattt gatgagcttg ttgaagcata ccaagagcag 600 gccaaaggac ttctggatgg cggggttgat atcttactca ttgaaactat ttttgatact 660 gccaatgcca aggcagcctt gtttgcactc caaaatcttt ttgaggagaa atatgctccc 720 cggcctatct ttatttcagg gacgatcgtt gataaaagtg ggcggactct ttccggacag 780 acaggagagg gatttgtcat cagcgtgtct catggagaac cactctgcat tggattaaat 840 tgtgctttgg gtgcagctga gatgagacct tttattgaaa taattggaaa atgtacaaca 900 gcctatgtcc tctgttatcc caatgcaggt cttcccaaca cctttggtga ctatgatgaa 960 acgccttcta tgatggccaa gcacctaaag gattttgcta tggatggctt ggtcaatata 1020 gttggaggat gctgtgggtc aacaccagat catatcaggg aaattgctga agctgtgaaa 1080 aattgtaagc ctagagttcc acctgccact gcttttgaag gacatatgtt actgtctggt 1140 ctagagccct tcaggattgg accgtacacc aactttgtta acattggaga gcgctgtaat 1200 gttgcaggat caaggaagtt tgctaaactc atcatggcag gaaactatga agaagccttg 1260 tgtgttgcca aagtgcaggt ggaaatggga gcccaggtgt tggatgtcaa catggatgat 1320 ggcatgctag atggtccaag tgcaatgacc agattttgca acttaattgc ttccgagcca 1380 gacatcgcaa aggtaccttt gtgcatcgac tcctccaatt ttgctgtgat tgaagctggg 1440 ttaaagtgct gccaagggaa gtgcattgtc aatagcatta gtctgaagga aggagaggac 1500 gacttcttgg agaaggccag gaagattaaa aagtatggag ctgctatggt ggtcatggct 1560 tttgatgaag aaggacaggc aacagaaaca gacacaaaaa tcagagtgtg cacccgggcc 1620 taccatctgc ttgtgaaaaa actgggcttt aatccaaatg acattatttt tgaccctaat 1680 atcctaacca ttgggactgg aatggaggaa cacaacttgt atgccattaa ttttatccat 1740 gcaacaaaag tcattaaaga aacattacct ggagccagaa taagtggagg tctttccaac 1800 ttgtccttct ccttccgagg aatggaagcc attcgagaag caatgcatgg ggttttcctt 1860 taccatgcaa tcaagtctgg catggacatg gagatagtga atgctggaaa cctccctgtg 1920 tatgatgata tccataagga acttctgcag ctctgtgaag atctcatctg gaataaagac 1980 cctgaggcca ctgagaagct cttacgttat gcccagactc aaggcacagg agggaagaaa 2040 gtcattcaga ctgatgagtg gagaaatggc cctgtcgaag aacgccttga gtatgccctt 2100 gtgaagggca ttgaaaaaca tattattgag gatactgagg aagccaggtt aaaccaaaaa 2160 aaatatcccc gacctctcaa tataattgaa ggacccctga tgaatggaat gaaaattgtt 2220 ggtgatcttt ttggagctgg aaaaatgttt ctacctcagg ttataaagtc agcccgggtt 2280 atgaagaagg ctgttggcca ccttatccct ttcatggaaa aagaaagaga agaaaccaga 2340 gtgcttaacg gcacagtaga agaagaggac ccttaccagg gcaccatcgt gctggccact 2400 gttaaaggcg acgtgcacga cataggcaag aacatagttg gagtagtcct tggctgcaat 2460 aatttccgag ttattgattt aggagtcatg actccatgtg ataagatact gaaagctgct 2520 cttgaccaca aagcagatat aattggcctg tcaggactca tcactccttc cctggatgaa 2580 atgatttttg ttgccaagga aatggagaga ttagctataa ggattccatt gttgattgga 2640 ggagcaacca cttcaaaaac ccacacagca gttaaaatag ctccgagata cagtgcacct 2700 gtaatccatg tcctggacgc gtccaagagt gtggtggtgt gttcccagct gttagatgaa 2760 aatctaaagg atgaatactt tgaggaaatc atggaagaat atgaagatat tagacaggac 2820 cattatgagt ctctcaagga gaggagatac ttacccttaa gtcaagccag aaaaagtggt 2880 ttccaaatgg attggctgtc tgaacctcac ccagtgaagc ccacgtttat tgggacccag 2940 gtctttgaag actatgacct gcagaagctg gtggactaca ttgactggaa gcctttcttt 3000 gatgtctggc agctccgggg caagtacccg aatcgaggct tccccaagat atttaacgac 3060 aaaacagtag gtggagaggc caggaaggtc tacgatgatg cccacaatat gctgaacaca 3120 ctgattagtc aaaagaaact ccgggcccgg ggtgtggttg ggttctggcc agcacagagt 3180 atccaagacg acattcacct gtacgcagag gctgctgtgc cccaggctgc agagcccata 3240 gccactttct atgggttaag gcaacaggct gagaaggact ctgccagcac ggagccatac 3300 tactgcctct cagacttcat cgctcccttg cattctggca tccgtgacta cctgggcctg 3360 tttgccgttg cctgctttgg ggtagaagag ctgagcaagg cctatgagga tgatggtgac 3420 gactacagca gcatcatggt caaggcgctg ggggaccggc tggcagaggc ctttgcagaa 3480 gagctccatg aaagagttcg ccgagaactg tgggcctact gtggcagtga gcagctggac 3540 gtcgcagacc tgcgaaggtt gcggtacaag ggcatccgcc cggctcctgg ctaccccagc 3600 cagcccgacc acaccgagaa gctcaccatg tggagactcg cagacatcga gcagtctaca 3660 ggcattaggt taacagaatc attagcaatg gcacctgctt cagcagtctc aggcctctac 3720 ttctccaatt tgaagtccaa atattttgct gtggggaaga tttccaagga tcaggttgag 3780 gattatgcat tgaggaagaa catatctgtg gctgaggttg agaaatggct tggacccatt 3840 ttgggatatg atacagacta actttttttt ttttttttgc cttttttatc ttgatgatcc 3900 tcaaggaaat acaacctag 3919 2 1265 PRT Homo sapiens VARIANT (1)...(1265) Wild type methionine synthase polypeptide. 2 Met Ser Pro Ala Leu Gln Asp Leu Ser Gln Pro Glu Gly Leu Lys Lys 1 5 10 15 Thr Leu Arg Asp Glu Ile Asn Ala Ile Leu Gln Lys Arg Ile Met Val 20 25 30 Leu Asp Gly Gly Met Gly Thr Met Ile Gln Arg Glu Lys Leu Asn Glu 35 40 45 Glu His Phe Arg Gly Gln Glu Phe Lys Asp His Ala Arg Pro Leu Lys 50 55 60 Gly Asn Asn Asp Ile Leu Ser Ile Thr Gln Pro Asp Val Ile Tyr Gln 65 70 75 80 Ile His Lys Glu Tyr Leu Leu Ala Gly Ala Asp Ile Ile Glu Thr Asn 85 90 95 Thr Phe Ser Ser Thr Ser Ile Ala Gln Ala Asp Tyr Gly Leu Glu His 100 105 110 Leu Ala Tyr Arg Met Asn Met Cys Ser Ala Gly Val Ala Arg Lys Ala 115 120 125 Ala Glu Glu Val Thr Leu Gln Thr Gly Ile Lys Arg Phe Val Ala Gly 130 135 140 Ala Leu Gly Pro Thr Asn Lys Thr Leu Ser Val Ser Pro Ser Val Glu 145 150 155 160 Arg Pro Asp Tyr Arg Asn Ile Thr Phe Asp Glu Leu Val Glu Ala Tyr 165 170 175 Gln Glu Gln Ala Lys Gly Leu Leu Asp Gly Gly Val Asp Ile Leu Leu 180 185 190 Ile Glu Thr Ile Phe Asp Thr Ala Asn Ala Lys Ala Ala Leu Phe Ala 195 200 205 Leu Gln Asn Leu Phe Glu Glu Lys Tyr Ala Pro Arg Pro Ile Phe Ile 210 215 220 Ser Gly Thr Ile Val Asp Lys Ser Gly Arg Thr Leu Ser Gly Gln Thr 225 230 235 240 Gly Glu Gly Phe Val Ile Ser Val Ser His Gly Glu Pro Leu Cys Ile 245 250 255 Gly Leu Asn Cys Ala Leu Gly Ala Ala Glu Met Arg Pro Phe Ile Glu 260 265 270 Ile Ile Gly Lys Cys Thr Thr Ala Tyr Val Leu Cys Tyr Pro Asn Ala 275 280 285 Gly Leu Pro Asn Thr Phe Gly Asp Tyr Asp Glu Thr Pro Ser Met Met 290 295 300 Ala Lys His Leu Lys Asp Phe Ala Met Asp Gly Leu Val Asn Ile Val 305 310 315 320 Gly Gly Cys Cys Gly Ser Thr Pro Asp His Ile Arg Glu Ile Ala Glu 325 330 335 Ala Val Lys Asn Cys Lys Pro Arg Val Pro Pro Ala Thr Ala Phe Glu 340 345 350 Gly His Met Leu Leu Ser Gly Leu Glu Pro Phe Arg Ile Gly Pro Tyr 355 360 365 Thr Asn Phe Val Asn Ile Gly Glu Arg Cys Asn Val Ala Gly Ser Arg 370 375 380 Lys Phe Ala Lys Leu Ile Met Ala Gly Asn Tyr Glu Glu Ala Leu Cys 385 390 395 400 Val Ala Lys Val Gln Val Glu Met Gly Ala Gln Val Leu Asp Val Asn 405 410 415 Met Asp Asp Gly Met Leu Asp Gly Pro Ser Ala Met Thr Arg Phe Cys 420 425 430 Asn Leu Ile Ala Ser Glu Pro Asp Ile Ala Lys Val Pro Leu Cys Ile 435 440 445 Asp Ser Ser Asn Phe Ala Val Ile Glu Ala Gly Leu Lys Cys Cys Gln 450 455 460 Gly Lys Cys Ile Val Asn Ser Ile Ser Leu Lys Glu Gly Glu Asp Asp 465 470 475 480 Phe Leu Glu Lys Ala Arg Lys Ile Lys Lys Tyr Gly Ala Ala Met Val 485 490 495 Val Met Ala Phe Asp Glu Glu Gly Gln Ala Thr Glu Thr Asp Thr Lys 500 505 510 Ile Arg Val Cys Thr Arg Ala Tyr His Leu Leu Val Lys Lys Leu Gly 515 520 525 Phe Asn Pro Asn Asp Ile Ile Phe Asp Pro Asn Ile Leu Thr Ile Gly 530 535 540 Thr Gly Met Glu Glu His Asn Leu Tyr Ala Ile Asn Phe Ile His Ala 545 550 555 560 Thr Lys Val Ile Lys Glu Thr Leu Pro Gly Ala Arg Ile Ser Gly Gly 565 570 575 Leu Ser Asn Leu Ser Phe Ser Phe Arg Gly Met Glu Ala Ile Arg Glu 580 585 590 Ala Met His Gly Val Phe Leu Tyr His Ala Ile Lys Ser Gly Met Asp 595 600 605 Met Glu Ile Val Asn Ala Gly Asn Leu Pro Val Tyr Asp Asp Ile His 610 615 620 Lys Glu Leu Leu Gln Leu Cys Glu Asp Leu Ile Trp Asn Lys Asp Pro 625 630 635 640 Glu Ala Thr Glu Lys Leu Leu Arg Tyr Ala Gln Thr Gln Gly Thr Gly 645 650 655 Gly Lys Lys Val Ile Gln Thr Asp Glu Trp Arg Asn Gly Pro Val Glu 660 665 670 Glu Arg Leu Glu Tyr Ala Leu Val Lys Gly Ile Glu Lys His Ile Ile 675 680 685 Glu Asp Thr Glu Glu Ala Arg Leu Asn Gln Lys Lys Tyr Pro Arg Pro 690 695 700 Leu Asn Ile Ile Glu Gly Pro Leu Met Asn Gly Met Lys Ile Val Gly 705 710 715 720 Asp Leu Phe Gly Ala Gly Lys Met Phe Leu Pro Gln Val Ile Lys Ser 725 730 735 Ala Arg Val Met Lys Lys Ala Val Gly His Leu Ile Pro Phe Met Glu 740 745 750 Lys Glu Arg Glu Glu Thr Arg Val Leu Asn Gly Thr Val Glu Glu Glu 755 760 765 Asp Pro Tyr Gln Gly Thr Ile Val Leu Ala Thr Val Lys Gly Asp Val 770 775 780 His Asp Ile Gly Lys Asn Ile Val Gly Val Val Leu Gly Cys Asn Asn 785 790 795 800 Phe Arg Val Ile Asp Leu Gly Val Met Thr Pro Cys Asp Lys Ile Leu 805 810 815 Lys Ala Ala Leu Asp His Lys Ala Asp Ile Ile Gly Leu Ser Gly Leu 820 825 830 Ile Thr Pro Ser Leu Asp Glu Met Ile Phe Val Ala Lys Glu Met Glu 835 840 845 Arg Leu Ala Ile Arg Ile Pro Leu Leu Ile Gly Gly Ala Thr Thr Ser 850 855 860 Lys Thr His Thr Ala Val Lys Ile Ala Pro Arg Tyr Ser Ala Pro Val 865 870 875 880 Ile His Val Leu Asp Ala Ser Lys Ser Val Val Val Cys Ser Gln Leu 885 890 895 Leu Asp Glu Asn Leu Lys Asp Glu Tyr Phe Glu Glu Ile Met Glu Glu 900 905 910 Tyr Glu Asp Ile Arg Gln Asp His Tyr Glu Ser Leu Lys Glu Arg Arg 915 920 925 Tyr Leu Pro Leu Ser Gln Ala Arg Lys Ser Gly Phe Gln Met Asp Trp 930 935 940 Leu Ser Glu Pro His Pro Val Lys Pro Thr Phe Ile Gly Thr Gln Val 945 950 955 960 Phe Glu Asp Tyr Asp Leu Gln Lys Leu Val Asp Tyr Ile Asp Trp Lys 965 970 975 Pro Phe Phe Asp Val Trp Gln Leu Arg Gly Lys Tyr Pro Asn Arg Gly 980 985 990 Phe Pro Lys Ile Phe Asn Asp Lys Thr Val Gly Gly Glu Ala Arg Lys 995 1000 1005 Val Tyr Asp Asp Ala His Asn Met Leu Asn Thr Leu Ile Ser Gln Lys 1010 1015 1020 Lys Leu Arg Ala Arg Gly Val Val Gly Phe Trp Pro Ala Gln Ser Ile 1025 1030 1035 1040 Gln Asp Asp Ile His Leu Tyr Ala Glu Ala Ala Val Pro Gln Ala Ala 1045 1050 1055 Glu Pro Ile Ala Thr Phe Tyr Gly Leu Arg Gln Gln Ala Glu Lys Asp 1060 1065 1070 Ser Ala Ser Thr Glu Pro Tyr Tyr Cys Leu Ser Asp Phe Ile Ala Pro 1075 1080 1085 Leu His Ser Gly Ile Arg Asp Tyr Leu Gly Leu Phe Ala Val Ala Cys 1090 1095 1100 Phe Gly Val Glu Glu Leu Ser Lys Ala Tyr Glu Asp Asp Gly Asp Asp 1105 1110 1115 1120 Tyr Ser Ser Ile Met Val Lys Ala Leu Gly Asp Arg Leu Ala Glu Ala 1125 1130 1135 Phe Ala Glu Glu Leu His Glu Arg Val Arg Arg Glu Leu Trp Ala Tyr 1140 1145 1150 Cys Gly Ser Glu Gln Leu Asp Val Ala Asp Leu Arg Arg Leu Arg Tyr 1155 1160 1165 Lys Gly Ile Arg Pro Ala Pro Gly Tyr Pro Ser Gln Pro Asp His Thr 1170 1175 1180 Glu Lys Leu Thr Met Trp Arg Leu Ala Asp Ile Glu Gln Ser Thr Gly 1185 1190 1195 1200 Ile Arg Leu Thr Glu Ser Leu Ala Met Ala Pro Ala Ser Ala Val Ser 1205 1210 1215 Gly Leu Tyr Phe Ser Asn Leu Lys Ser Lys Tyr Phe Ala Val Gly Lys 1220 1225 1230 Ile Ser Lys Asp Gln Val Glu Asp Tyr Ala Leu Arg Lys Asn Ile Ser 1235 1240 1245 Val Ala Glu Val Glu Lys Trp Leu Gly Pro Ile Leu Gly Tyr Asp Thr 1250 1255 1260 Asp 1265 3 9 PRT Escherichia coli 3 Asp Gly Gly Met Gly Thr Met Ile Gln 1 5 4 9 PRT Cyanobacterium synechocystis 4 Asp Gly Ala Met Gly Thr Asn Leu Gln 1 5 5 9 PRT Mycobacterium leprae 5 Asp Gly Ala Met Gly Thr Gln Leu Gln 1 5 6 9 PRT Hemophilus influenzae 6 Asp Gly Ala Met Gly Thr Met Ile Gln 1 5 7 9 PRT Caenorrhabditis elegans 7 Asp Gly Ala Met Gly Thr Met Ile Gln 1 5 8 9 PRT Homo sapiens 8 Asp Gly Gly Met Gly Thr Met Ile Gln 1 5 9 13 PRT Escherichia coli 9 Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn 1 5 10 10 13 PRT Cyanobacterium synechocystis 10 Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn 1 5 10 11 13 PRT Mycobacterium leprae 11 Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn 1 5 10 12 13 PRT Hemophilus influenzae 12 Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn 1 5 10 13 13 PRT Caenorrhabditis elegans 13 Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn 1 5 10 14 13 PRT Homo sapiens 14 Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn 1 5 10 15 10 PRT Escherichia coli 15 Leu Ala Glu Ala Phe Ala Glu Tyr Leu His 1 5 10 16 10 PRT Cyanobacterium synechocystis 16 Met Ala Glu Ala Leu Ala Glu Trp Thr His 1 5 10 17 10 PRT Mycobacterium leprae 17 Leu Thr Glu Ala Leu Ala Glu Tyr Trp His 1 5 10 18 10 PRT Hemophilus influenzae 18 Leu Ala Glu Ala Met Ala Glu Tyr Leu His 1 5 10 19 10 PRT Caenorrhabditis elegans 19 Leu Ala Glu Ala Tyr Ala Glu Tyr Leu His 1 5 10 20 10 PRT Homo sapiens 20 Leu Ala Glu Ala Phe Ala Glu Glu Leu His 1 5 10 21 11 PRT Escherichia coli 21 Gly Gly Cys Cys Gly Thr Thr Pro Gln His Ile 1 5 10 22 11 PRT Cyanobacterium synechocystis 22 Gly Gly Cys Cys Gly Thr Arg Pro Asp His Ile 1 5 10 23 11 PRT Mycobacterium leprae 23 Gly Gly Cys Cys Gly Thr Thr Pro Asp His Ile 1 5 10 24 11 PRT Caenorrhabditis elegans 24 Gly Gly Cys Cys Gly Thr Thr Pro Asp His Ile 1 5 10 25 11 PRT Homo sapiens 25 Gly Gly Cys Cys Gly Ser Thr Pro Asp His Ile 1 5 10 26 26 DNA Homo sapiens variation (1)...(26) n is a, t, g, or c; h is a, c, or t; d is a, g, or t; and r is a or g; 26 gayggngcna tgggnacnat gathca 26 27 29 DNA Homo sapiens variation (1)...(29) n is a, t, g, or c; h is a, c, or t; d is a, g, or t; and r is a or g; 27 gcnacngtna arggngaygt ncaygayat 29 28 30 DNA Homo sapiens variation (1)...(30) n is a, t, g, or c; h is a, c, or t; d is a, g, or t; and r is a or g; 28 rttyttnccd atrtcrtgna crtcnccytt 30 29 27 DNA Homo sapiens variation (1)...(27) n is a, t, g, or c; h is a, c, or t; d is a, g, or t; and r is a or g; 29 rtgnagrtay tcngcraang cytcngc 27 30 32 DNA Homo sapiens variation (1)...(32) n is a, t, g, or c; h is a, c, or t; d is a, g, or t; and r is a or g; 30 atrtgrtcng gngtngtncc rcarcanccn cc 32 31 32 DNA Homo sapiens variation (1)...(32) n is a, t, g, or c; h is a, c, or t; d is a, g, or t; and r is a or g; 31 ggnggntgyt gyggnacnac nccngaycay at 32 32 24 DNA Mus musculus 32 gtctgtgtca tagcccagaa tggg 24 33 24 DNA Mus musculus 33 tcagtctgtg tcatagccca gaat 24 34 24 DNA Homo sapiens 34 gaactagaag acagaaattc tcta 24 35 26 DNA Homo sapiens 35 ttccgaggtc aggaatttaa agatca 26 36 24 DNA Homo sapiens 36 gtgttcttcg tttagcttct cccg 24 37 24 DNA Homo sapiens 37 ccccagccag caagtattcc ttat 24 38 24 DNA Homo sapiens 38 ctaggttgta tttccttgag gatc 24 39 25 DNA Homo sapiens 39 ggagctggaa aaatgtttct acctc 25 40 24 DNA Homo sapiens 40 acaggaggga agaaagtcat tcag 24 41 25 DNA Homo sapiens 41 ccttcaatta tattgagagg tcggg 25 42 24 DNA Homo sapiens 42 caacccgaag gtctgaagaa aacc 24 43 21 DNA Homo sapiens 43 cccgcgctcc aagacctgtc g 21 44 21 DNA Homo sapiens 44 cgacaggtct tggagcgcgg g 21 45 28 DNA Homo sapiens 45 ggagtcatga ctcctaaatc aataactc 28 46 23 DNA Homo sapiens 46 gacgactaca gcagcatcat ggt 23 47 22 DNA Homo sapiens 47 aaaaatcatt tcatccaggg aa 22 48 26 DNA Homo sapiens 48 ataggcaaga acatagttgg agtagt 26 49 25 DNA Homo sapiens 49 tttcatctaa cagctgggaa cacac 25 50 24 DNA Homo sapiens 50 tgcctctcag acttcatcgc tccc 24 51 21 DNA Homo sapiens 51 tgcagcctgg ggcacagcag c 21 52 24 DNA Homo sapiens 52 atggattggc tgtctgaacc tcac 24 53 26 DNA Homo sapiens 53 catggaagaa tatgaagata ttagac 26 54 24 DNA Homo sapiens 54 accatcatcc tcataggcct tgct 24 55 23 DNA Homo sapiens 55 cagacctgcg aaggttgcgg tac 23 56 24 DNA Homo sapiens 56 gaagtggttg ctcctccaat caac 24 57 26 DNA Homo sapiens 57 gagcagcttt cagtatctta tcacat 26 58 25 DNA Homo sapiens 58 acaagttgtg ttcctccatt ccagt 25 59 25 DNA Homo sapiens 59 agagcgctgt aatgttgcag gatca 25 60 25 DNA Homo sapiens 60 tgtttttcaa tgcccttcac aaggg 25 61 25 DNA Homo sapiens 61 taaaaagtat ggagctgcta tggtg 25 62 25 DNA Homo sapiens 62 gaccagacag taacatatgt ccttc 25 63 26 DNA Homo sapiens 63 acattacagc gctctccaat gttaac 26 64 24 DNA Homo sapiens 64 tgaggttgag aaatggcttg gacc 24 65 25 DNA Homo sapiens 65 gccacagata tgttcttcct caatg 25 66 24 DNA Homo sapiens 66 tgtggagagc acgtcttctc tgcc 24 67 50 PRT Homo sapiens 67 Leu Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn Ile Val 1 5 10 15 Gly Val Val Leu Gly Cys Asn Asn Phe Arg Val Ile Asp Leu Gly Val 20 25 30 Met Thr Pro Cys Asp Lys Ile Leu Lys Ala Ala Leu Asp His Lys Ala 35 40 45 Asp Ile 50 68 50 PRT Mus musculus 68 Leu Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn Ile Val 1 5 10 15 Gly Val Val Leu Ala Cys Asn Asn Phe Arg Val Ile Asp Leu Gly Val 20 25 30 Met Thr Pro Cys Asp Lys Ile Leu Gln Ala Ala Leu Asp His Lys Ala 35 40 45 Asp Ile 50 69 50 PRT Cyanobacterium synechocystis 69 Ile Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn Leu Val 1 5 10 15 Asp Ile Ile Leu Ser Asn Asn Gly Tyr Arg Val Val Asn Leu Gly Ile 20 25 30 Lys Gln Pro Val Glu Asn Ile Ile Glu Ala Tyr Lys Lys His Arg Pro 35 40 45 Asp Cys 50 70 50 PRT Mycobacterium leprae 70 Leu Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn Leu Val 1 5 10 15 Asp Ile Ile Leu Ser Asn Asn Gly Tyr Glu Val Val Asn Leu Gly Ile 20 25 30 Lys Gln Pro Ile Thr Asn Ile Leu Glu Val Ala Glu Asp Lys Ser Ala 35 40 45 Asp Val 50 71 50 PRT Caenorrhabditis elegans 71 Ile Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn Ile Val 1 5 10 15 Ser Val Val Leu Gly Cys Asn Asn Phe Lys Val Val Asp Leu Gly Val 20 25 30 Met Thr Pro Cys Glu Asn Ile Ile Lys Ala Ala Ile Glu Glu Lys Ala 35 40 45 Asp Phe 50 72 50 PRT Hemophilus influenzae 72 Ile Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn Ile Val 1 5 10 15 Ser Val Val Met Gln Cys Asn Asn Phe Glu Val Ile Asp Leu Gly Val 20 25 30 Met Val Pro Ala Asp Lys Ile Ile Gln Thr Ala Ile Asn Gln Lys Thr 35 40 45 Asp Ile 50 73 50 PRT Escherichia coli 73 Ile Ala Thr Val Lys Gly Asp Val His Asp Ile Gly Lys Asn Ile Val 1 5 10 15 Gly Val Val Leu Gln Cys Asn Asn Tyr Glu Ile Val Asp Leu Gly Val 20 25 30 Met Val Pro Ala Glu Lys Ile Leu Arg Thr Ala Lys Glu Val Asn Ala 35 40 45 Asp Leu 50 74 1265 PRT Homo sapiens VARIANT (1)...(1265) Xaa at position 881 is either Ile or no amino acid; Xaa at position 919 is either Asp or Gly; Xaa at position 920 is either His or Asp. 74 Met Ser Pro Ala Leu Gln Asp Leu Ser Gln Pro Glu Gly Leu Lys Lys 1 5 10 15 Thr Leu Arg Asp Glu Ile Asn Ala Ile Leu Gln Lys Arg Ile Met Val 20 25 30 Leu Asp Gly Gly Met Gly Thr Met Ile Gln Arg Glu Lys Leu Asn Glu 35 40 45 Glu His Phe Arg Gly Gln Glu Phe Lys Asp His Ala Arg Pro Leu Lys 50 55 60 Gly Asn Asn Asp Ile Leu Ser Ile Thr Gln Pro Asp Val Ile Tyr Gln 65 70 75 80 Ile His Lys Glu Tyr Leu Leu Ala Gly Ala Asp Ile Ile Glu Thr Asn 85 90 95 Thr Phe Ser Ser Thr Ser Ile Ala Gln Ala Asp Tyr Gly Leu Glu His 100 105 110 Leu Ala Tyr Arg Met Asn Met Cys Ser Ala Gly Val Ala Arg Lys Ala 115 120 125 Ala Glu Glu Val Thr Leu Gln Thr Gly Ile Lys Arg Phe Val Ala Gly 130 135 140 Ala Leu Gly Pro Thr Asn Lys Thr Leu Ser Val Ser Pro Ser Val Glu 145 150 155 160 Arg Pro Asp Tyr Arg Asn Ile Thr Phe Asp Glu Leu Val Glu Ala Tyr 165 170 175 Gln Glu Gln Ala Lys Gly Leu Leu Asp Gly Gly Val Asp Ile Leu Leu 180 185 190 Ile Glu Thr Ile Phe Asp Thr Ala Asn Ala Lys Ala Ala Leu Phe Ala 195 200 205 Leu Gln Asn Leu Phe Glu Glu Lys Tyr Ala Pro Arg Pro Ile Phe Ile 210 215 220 Ser Gly Thr Ile Val Asp Lys Ser Gly Arg Thr Leu Ser Gly Gln Thr 225 230 235 240 Gly Glu Gly Phe Val Ile Ser Val Ser His Gly Glu Pro Leu Cys Ile 245 250 255 Gly Leu Asn Cys Ala Leu Gly Ala Ala Glu Met Arg Pro Phe Ile Glu 260 265 270 Ile Ile Gly Lys Cys Thr Thr Ala Tyr Val Leu Cys Tyr Pro Asn Ala 275 280 285 Gly Leu Pro Asn Thr Phe Gly Asp Tyr Asp Glu Thr Pro Ser Met Met 290 295 300 Ala Lys His Leu Lys Asp Phe Ala Met Asp Gly Leu Val Asn Ile Val 305 310 315 320 Gly Gly Cys Cys Gly Ser Thr Pro Asp His Ile Arg Glu Ile Ala Glu 325 330 335 Ala Val Lys Asn Cys Lys Pro Arg Val Pro Pro Ala Thr Ala Phe Glu 340 345 350 Gly His Met Leu Leu Ser Gly Leu Glu Pro Phe Arg Ile Gly Pro Tyr 355 360 365 Thr Asn Phe Val Asn Ile Gly Glu Arg Cys Asn Val Ala Gly Ser Arg 370 375 380 Lys Phe Ala Lys Leu Ile Met Ala Gly Asn Tyr Glu Glu Ala Leu Cys 385 390 395 400 Val Ala Lys Val Gln Val Glu Met Gly Ala Gln Val Leu Asp Val Asn 405 410 415 Met Asp Asp Gly Met Leu Asp Gly Pro Ser Ala Met Thr Arg Phe Cys 420 425 430 Asn Leu Ile Ala Ser Glu Pro Asp Ile Ala Lys Val Pro Leu Cys Ile 435 440 445 Asp Ser Ser Asn Phe Ala Val Ile Glu Ala Gly Leu Lys Cys Cys Gln 450 455 460 Gly Lys Cys Ile Val Asn Ser Ile Ser Leu Lys Glu Gly Glu Asp Asp 465 470 475 480 Phe Leu Glu Lys Ala Arg Lys Ile Lys Lys Tyr Gly Ala Ala Met Val 485 490 495 Val Met Ala Phe Asp Glu Glu Gly Gln Ala Thr Glu Thr Asp Thr Lys 500 505 510 Ile Arg Val Cys Thr Arg Ala Tyr His Leu Leu Val Lys Lys Leu Gly 515 520 525 Phe Asn Pro Asn Asp Ile Ile Phe Asp Pro Asn Ile Leu Thr Ile Gly 530 535 540 Thr Gly Met Glu Glu His Asn Leu Tyr Ala Ile Asn Phe Ile His Ala 545 550 555 560 Thr Lys Val Ile Lys Glu Thr Leu Pro Gly Ala Arg Ile Ser Gly Gly 565 570 575 Leu Ser Asn Leu Ser Phe Ser Phe Arg Gly Met Glu Ala Ile Arg Glu 580 585 590 Ala Met His Gly Val Phe Leu Tyr His Ala Ile Lys Ser Gly Met Asp 595 600 605 Met Glu Ile Val Asn Ala Gly Asn Leu Pro Val Tyr Asp Asp Ile His 610 615 620 Lys Glu Leu Leu Gln Leu Cys Glu Asp Leu Ile Trp Asn Lys Asp Pro 625 630 635 640 Glu Ala Thr Glu Lys Leu Leu Arg Tyr Ala Gln Thr Gln Gly Thr Gly 645 650 655 Gly Lys Lys Val Ile Gln Thr Asp Glu Trp Arg Asn Gly Pro Val Glu 660 665 670 Glu Arg Leu Glu Tyr Ala Leu Val Lys Gly Ile Glu Lys His Ile Ile 675 680 685 Glu Asp Thr Glu Glu Ala Arg Leu Asn Gln Lys Lys Tyr Pro Arg Pro 690 695 700 Leu Asn Ile Ile Glu Gly Pro Leu Met Asn Gly Met Lys Ile Val Gly 705 710 715 720 Asp Leu Phe Gly Ala Gly Lys Met Phe Leu Pro Gln Val Ile Lys Ser 725 730 735 Ala Arg Val Met Lys Lys Ala Val Gly His Leu Ile Pro Phe Met Glu 740 745 750 Lys Glu Arg Glu Glu Thr Arg Val Leu Asn Gly Thr Val Glu Glu Glu 755 760 765 Asp Pro Tyr Gln Gly Thr Ile Val Leu Ala Thr Val Lys Gly Asp Val 770 775 780 His Asp Ile Gly Lys Asn Ile Val Gly Val Val Leu Gly Cys Asn Asn 785 790 795 800 Phe Arg Val Ile Asp Leu Gly Val Met Thr Pro Cys Asp Lys Ile Leu 805 810 815 Lys Ala Ala Leu Asp His Lys Ala Asp Ile Ile Gly Leu Ser Gly Leu 820 825 830 Ile Thr Pro Ser Leu Asp Glu Met Ile Phe Val Ala Lys Glu Met Glu 835 840 845 Arg Leu Ala Ile Arg Ile Pro Leu Leu Ile Gly Gly Ala Thr Thr Ser 850 855 860 Lys Thr His Thr Ala Val Lys Ile Ala Pro Arg Tyr Ser Ala Pro Val 865 870 875 880 Xaa His Val Leu Asp Ala Ser Lys Ser Val Val Val Cys Ser Gln Leu 885 890 895 Leu Asp Glu Asn Leu Lys Asp Glu Tyr Phe Glu Glu Ile Met Glu Glu 900 905 910 Tyr Glu Asp Ile Arg Gln Xaa Xaa Tyr Glu Ser Leu Lys Glu Arg Arg 915 920 925 Tyr Leu Pro Leu Ser Gln Ala Arg Lys Ser Gly Phe Gln Met Asp Trp 930 935 940 Leu Ser Glu Pro His Pro Val Lys Pro Thr Phe Ile Gly Thr Gln Val 945 950 955 960 Phe Glu Asp Tyr Asp Leu Gln Lys Leu Val Asp Tyr Ile Asp Trp Lys 965 970 975 Pro Phe Phe Asp Val Trp Gln Leu Arg Gly Lys Tyr Pro Asn Arg Gly 980 985 990 Phe Pro Lys Ile Phe Asn Asp Lys Thr Val Gly Gly Glu Ala Arg Lys 995 1000 1005 Val Tyr Asp Asp Ala His Asn Met Leu Asn Thr Leu Ile Ser Gln Lys 1010 1015 1020 Lys Leu Arg Ala Arg Gly Val Val Gly Phe Trp Pro Ala Gln Ser Ile 1025 1030 1035 1040 Gln Asp Asp Ile His Leu Tyr Ala Glu Ala Ala Val Pro Gln Ala Ala 1045 1050 1055 Glu Pro Ile Ala Thr Phe Tyr Gly Leu Arg Gln Gln Ala Glu Lys Asp 1060 1065 1070 Ser Ala Ser Thr Glu Pro Tyr Tyr Cys Leu Ser Asp Phe Ile Ala Pro 1075 1080 1085 Leu His Ser Gly Ile Arg Asp Tyr Leu Gly Leu Phe Ala Val Ala Cys 1090 1095 1100 Phe Gly Val Glu Glu Leu Ser Lys Ala Tyr Glu Asp Asp Gly Asp Asp 1105 1110 1115 1120 Tyr Ser Ser Ile Met Val Lys Ala Leu Gly Asp Arg Leu Ala Glu Ala 1125 1130 1135 Phe Ala Glu Glu Leu His Glu Arg Val Arg Arg Glu Leu Trp Ala Tyr 1140 1145 1150 Cys Gly Ser Glu Gln Leu Asp Val Ala Asp Leu Arg Arg Leu Arg Tyr 1155 1160 1165 Lys Gly Ile Arg Pro Ala Pro Gly Tyr Pro Ser Gln Pro Asp His Thr 1170 1175 1180 Glu Lys Leu Thr Met Trp Arg Leu Ala Asp Ile Glu Gln Ser Thr Gly 1185 1190 1195 1200 Ile Arg Leu Thr Glu Ser Leu Ala Met Ala Pro Ala Ser Ala Val Ser 1205 1210 1215 Gly Leu Tyr Phe Ser Asn Leu Lys Ser Lys Tyr Phe Ala Val Gly Lys 1220 1225 1230 Ile Ser Lys Asp Gln Val Glu Asp Tyr Ala Leu Arg Lys Asn Ile Ser 1235 1240 1245 Val Ala Glu Val Glu Lys Trp Leu Gly Pro Ile Leu Gly Tyr Asp Thr 1250 1255 1260 Asp 1265 75 3856 DNA Homo sapiens variation (1)...(3856) nnn at positions 2640-2642 is either AAT or no nucleotides; n at position 2756 is either A or G; n at position 2758 is either C or G. 75 atgtcacccg cgctccaaga cctgtcgcaa cccgaaggtc tgaagaaaac cctgcgggat 60 gagatcaatg ccattctgca gaagaggatt atggtgctgg atggagggat ggggaccatg 120 atccagcggg agaagctaaa cgaagaacac ttccgaggtc aggaatttaa agatcatgcc 180 aggccgctga aaggcaacaa tgacatttta agtataactc agcctgatgt catttaccaa 240 atccataagg aatacttgct ggctggggca gatatcattg aaacaaatac ttttagcagc 300 actagtattg cccaagctga ctatggcctt gaacacttgg cctaccggat gaacatgtgc 360 tctgcaggag tggccagaaa agctgccgag gaggtaactc tccagacagg aattaagagg 420 tttgtggcag gggctctggg tccgactaat aagacactct ctgtgtcccc atctgtggaa 480 aggccggatt ataggaacat cacatttgat gagcttgttg aagcatacca agagcaggcc 540 aaaggacttc tggatggcgg ggttgatatc ttactcattg aaactatttt tgatactgcc 600 aatgccaagg cagccttgtt tgcactccaa aatctttttg aggagaaata tgctccccgg 660 cctatcttta tttcagggac gatcgttgat aaaagtgggc ggactctttc cggacagaca 720 ggagagggat ttgtcatcag cgtgtctcat ggagaaccac tctgcattgg attaaattgt 780 gctttgggtg cagctgagat gagacctttt attgaaataa ttggaaaatg tacaacagcc 840 tatgtcctct gttatcccaa tgcaggtctt cccaacacct ttggtgacta tgatgaaacg 900 ccttctatga tggccaagca cctaaaggat tttgctatgg atggcttggt caatatagtt 960 ggaggatgct gtgggtcaac accagatcat atcagggaaa ttgctgaagc tgtgaaaaat 1020 tgtaagccta gagttccacc tgccactgct tttgaaggac atatgttact gtctggtcta 1080 gagcccttca ggattggacc gtacaccaac tttgttaaca ttggagagcg ctgtaatgtt 1140 gcaggatcaa ggaagtttgc taaactcatc atggcaggaa actatgaaga agccttgtgt 1200 gttgccaaag tgcaggtgga aatgggagcc caggtgttgg atgtcaacat ggatgatggc 1260 atgctagatg gtccaagtgc aatgaccaga ttttgcaact taattgcttc cgagccagac 1320 atcgcaaagg tacctttgtg catcgactcc tccaattttg ctgtgattga agctgggtta 1380 aagtgctgcc aagggaagtg cattgtcaat agcattagtc tgaaggaagg agaggacgac 1440 ttcttggaga aggccaggaa gattaaaaag tatggagctg ctatggtggt catggctttt 1500 gatgaagaag gacaggcaac agaaacagac acaaaaatca gagtgtgcac ccgggcctac 1560 catctgcttg tgaaaaaact gggctttaat ccaaatgaca ttatttttga ccctaatatc 1620 ctaaccattg ggactggaat ggaggaacac aacttgtatg ccattaattt tatccatgca 1680 acaaaagtca ttaaagaaac attacctgga gccagaataa gtggaggtct ttccaacttg 1740 tccttctcct tccgaggaat ggaagccatt cgagaagcaa tgcatggggt tttcctttac 1800 catgcaatca agtctggcat ggacatggag atagtgaatg ctggaaacct ccctgtgtat 1860 gatgatatcc ataaggaact tctgcagctc tgtgaagatc tcatctggaa taaagaccct 1920 gaggccactg agaagctctt acgttatgcc cagactcaag gcacaggagg gaagaaagtc 1980 attcagactg atgagtggag aaatggccct gtcgaagaac gccttgagta tgcccttgtg 2040 aagggcattg aaaaacatat tattgaggat actgaggaag ccaggttaaa ccaaaaaaaa 2100 tatccccgac ctctcaatat aattgaagga cccctgatga atggaatgaa aattgttggt 2160 gatctttttg gagctggaaa aatgtttcta cctcaggtta taaagtcagc ccgggttatg 2220 aagaaggctg ttggccacct tatccctttc atggaaaaag aaagagaaga aaccagagtg 2280 cttaacggca cagtagaaga agaggaccct taccagggca ccatcgtgct ggccactgtt 2340 aaaggcgacg tgcacgacat aggcaagaac atagttggag tagtccttgg ctgcaataat 2400 ttccgagtta ttgatttagg agtcatgact ccatgtgata agatactgaa agctgctctt 2460 gaccacaaag cagatataat tggcctgtca ggactcatca ctccttccct ggatgaaatg 2520 atttttgttg ccaaggaaat ggagagatta gctataagga ttccattgtt gattggagga 2580 gcaaccactt caaaaaccca cacagcagtt aaaatagctc cgagatacag tgcacctgtn 2640 nnccatgtcc tggacgcgtc caagagtgtg gtggtgtgtt cccagctgtt agatgaaaat 2700 ctaaaggatg aatactttga ggaaatcatg gaagaatatg aagatattag acaggncnat 2760 tatgagtctc tcaaggagag gagatactta cccttaagtc aagccagaaa aagtggtttc 2820 caaatggatt ggctgtctga acctcaccca gtgaagccca cgtttattgg gacccaggtc 2880 tttgaagact atgacctgca gaagctggtg gactacattg actggaagcc tttctttgat 2940 gtctggcagc tccggggcaa gtacccgaat cgaggcttcc ccaagatatt taacgacaaa 3000 acagtaggtg gagaggccag gaaggtctac gatgatgccc acaatatgct gaacacactg 3060 attagtcaaa agaaactccg ggcccggggt gtggttgggt tctggccagc acagagtatc 3120 caagacgaca ttcacctgta cgcagaggct gctgtgcccc aggctgcaga gcccatagcc 3180 actttctatg ggttaaggca acaggctgag aaggactctg ccagcacgga gccatactac 3240 tgcctctcag acttcatcgc tcccttgcat tctggcatcc gtgactacct gggcctgttt 3300 gccgttgcct gctttggggt agaagagctg agcaaggcct atgaggatga tggtgacgac 3360 tacagcagca tcatggtcaa ggcgctgggg gaccggctgg cagaggcctt tgcagaagag 3420 ctccatgaaa gagttcgccg agaactgtgg gcctactgtg gcagtgagca gctggacgtc 3480 gcagacctgc gaaggttgcg gtacaagggc atccgcccgg ctcctggcta ccccagccag 3540 cccgaccaca ccgagaagct caccatgtgg agactcgcag acatcgagca gtctacaggc 3600 attaggttaa cagaatcatt agcaatggca cctgcttcag cagtctcagg cctctacttc 3660 tccaatttga agtccaaata ttttgctgtg gggaagattt ccaaggatca ggttgaggat 3720 tatgcattga ggaagaacat atctgtggct gaggttgaga aatggcttgg acccattttg 3780 ggatatgata cagactaact tttttttttt tttttgcctt ttttatcttg atgatcctca 3840 aggaaataca acctag 3856 76 10 DNA Homo sapiens 76 gacaacatgt 10

Claims

What is claimed is:

1. A substantially pure human nucleic acid comprising at least 40 nucleotides that hybridizes under high stringency conditions to a sequence found within the nucleic acid of SEQ ID NO:1.

2. The nucleic acid of claim 1, wherein said sequence has a sequence complementary to at least 50% of at least 60 contiguous nucleotides of the nucleic acid encoding the methionine synthase polypeptide, said sequence sufficient to allow nucleic acid hybridization under high stringency conditions.

3. The nucleic acid of claim 1, wherein said nucleic acid comprises a mutation or a polymorphism, wherein said nucleic acid probe detects a mutation or polymorphism selected from the group consisting of D919G, H920D, and ΔIle881.

4. The nucleic acid of claim 3, wherein said sequence of said nucleic acid comprises the cobalamin binding domain of the human methionine synthase gene.

5. The nucleic acid of claim 2, wherein at least 18 contiguous nucleotides of said sequence are complementary to at least 90% of the corresponding nucleotides of the nucleic acid encoding the methionine synthase polypeptide.

6. The nucleic acid of claim 1, wherein said high stringency conditions comprise hybridization in 2×SSC at 40° C.

7. A substantially pure human nucleic acid, wherein the sequence of said nucleic acid is at least 75% identical to the corresponding region of at least 50 contiguous base pairs of the nucleic acid of SEQ ID NO:1.

8. A substantially pure human nucleic acid, wherein the sequence of said nucleic acid is at least 35% identical to the corresponding region of at least 50 contiguous base pairs of the nucleic acid of SEQ ID NO:1.

9. A kit for the analysis of a human methionine synthase nucleic acid, said kit comprising a nucleic acid probe useful for detecting in the nucleic acids of a human a mutation or polymorphism in said methionine synthase nucleic acid, wherein said mutation or polymorphism is selected from the group consisting of D919G, H920D, and ΔIle881.

10. The kit of claim 9, wherein said probe comprises at least 40 nucleotides that hybridizes at high stringency to a sequence found within the nucleic acid of SEQ ID NO:1.