High specificity homocysteinases and genes therefor

FIELD OF THE INVENTION
The present invention relates to the assay of homocysteine in biological fluids such as urine, whole blood, and blood plasma. More particularly, the invention relates to the use of enzyme preparations that comprise one or more homocysteinase enzymes and diagnostic kits containing these enzymes. In the preferred practice of the invention, homocysteine concentration is determined by measurement of hydrogen sulfide produced therefrom.
K. S. McCully et al. (American Journal of Pathology, 56, pp. 111-128, 1969) first reported the association of blood plasma homocysteine levels with risk from cardiovascular disease. McCully et al. identified a correlation between elevated plasma homocysteine concentrations and arteriosclerotic disease. More recent studies have determined that even moderately elevated plasma homocysteine levels are indicative of substantially increased risk to coronary heart disease, cerebrovascular disease, and peripheral vascular disorders. See, for example, J. Selhub et al., New England Journal of Medicine, 32, pp. 286-291, 1995, and S. Kang et al., Annual Review of Nutrition. 12, pp. 279-298, 1992.
With respect to assessing risk to cardiovascular disease, there is substantial evidence that elevated homocysteine levels may be a better predictor of risk than elevated cholesterol levels. For example, in one study, plasma homocysteine concentrations only 12% above the upper limit of normal were associated with a 3.4-fold increase in risk for myocardial infarction (M. Stampfer et al., Journal of the American Medical Association, 268, pp. 877-881, 1992). In another case study where blood was drawn before cardiovascular disease was diagnosed, a group of 271 men (who later suffered myocardial infarctions) presented significantly higher levels of homocysteine than control patients who did not later suffer infarctions (see P. Ueland et al., Cardiovascular Disease, Hemostasis and Endothelial Function, 1992, at pages 183-236, Marcel Dekker, New York).
Nygard et al., New England Journal of Medicine, 337(4), pp. 230-236 (1997) report that total plasma homocysteine is a strong predictor of mortality in patients with confirmed coronary artery disease.
A detailed understanding of the molecular mechanisms whereby homocysteine participates in cardiovascular disease processes has not yet been achieved. It has been suggested that homocysteine participates in reactions resulting, for example, in overproduction of oxygen free radicals, elastase activation, and calcium deposition (i.e. plaque formation). For a review of current theories, see K. McCully, Nature Medicine, 2(4), pp. 386-389 (1996) and K. S. McCully, Annals of Clinical and Laboratory Science, 23(6), pp. 477-493 (1993). Elevated levels of circulating homocysteine may also affect the coagulation process directly (see O. Nygard et al., above, and references cited therein).
Accordingly, there is a need to develop accurate methods to determine homocysteine levels in patients, and to make such assays a recognized part of standard medical practice. As described below, there is also a critical need to make available widespread screening of infants for diseases involving abnormal homocysteine metabolism, such as homocystinvria.
REPORTED DEVELOPMENTS
A. Araki et al., Journal of Chromatogtraphy. 422, pp. 43-52 (1987) describe a detection method for free and protein bound homocysteine in plasma that utilizes reaction with a thiol specific fluorogenic agent, followed by detection with high pressure liquid chromotogaphy (HPLC) to separate other thiol species. See also N. P. B. Dudman et al., Clinical Chemistry, 42(12), pp. 2028-2032 (1996). Disadvantages of such methods for clinical application may include the inherent limits on the number of samples that can be processed by HPLC, that use of HPLC may not permit high through-put screening, and that appropriate HPLC machines may not be present in clinical labs.
Shipchandler et al. (see Clinical Chemistry. 41(7), pp. 991-994, 1995) have recently described a fluorescence polarization immunoassay for detection of homocysteine, and of homocystine (the disulfide dimer of homocysteine). The assay was stated to evidence little cross reactivity toward cysteine and methionine. The assay involves conversion of homocysteine to S-adenosylhomocysteine, and detection is based on use of a monoclonal antibody that recognizes S-adenosylhomocysteine, and also a fluorescein analog thereof However, potential disadvantages of this detection technology may include cost associated with monoclonal antibody production and "nonspecificity" of the antibody, that is, cross reactivity toward, for example, S-adenosyl methionine. Additionally, it appears that this method can only be practiced with particular patented instrumentation available from only once source.
K-W. Thong et al. (Experimental Parasitology. 63, pp. 143-151, 1987) describe enzymatic conversion of homocysteine to alpha-ketobutyrate, hydogen sulfide and ammonia followed by determination of the hydrogen sulfide with lead acetate (see also K.-W. Thong et al., IRCS Medical Science, 13, pp. 493-494, and pp. 495-496, 1985) However, there is no suggestion of use of the involved enzyme (for example, from the parasite Trichomonas vaginalis) for clinical diagnosis. Additionally, in a clinical context, the disclosed procedure does not distinguish homocysteine from cysteine, nor does it account for that fraction of homocysteine molecules in biological samples that is disulfide bonded, or bonded to protein.
An additional procedure for detection of homocysteine that involves use of a microbial enzyme from the bacterium Pseudomonas ovalis is disclosed in Yamaguchi et al., Annual Report of Sapporo City Institute of Public Health, No. 20, pp. 67-74, 1993. The authors focused on detection of the amino acid methionine as an indirect method to determine homocysteine levels (such as for homocystinuria patients), since homocysteine was considered unstable, for example being prone to disulfide bonding with proteins.
As an indirect measure of homocysteine, it is possible that the method is less accurate, and determination of product ammonia instead of product hydrogen sulfide may be less sensitive given the high background levels of ammonia in biological fluids. It is noted also that ammonia assays are adversely affected by the presence of contaminating deaminases, a potentially pervasive problem. Similarly, assay of product alpha-keto butyrate is expected to be ineffective given the high background level in biological samples (for an assay procedure, see Y. Tan et al., Protein Expression and Purification, 9, pp. 233-245, 1997).
An additional reference of relevance to the practice of the invention is U.S. Pat. No. at 5,631,127 to Sundrehagen, issued May 20, 1997.
Given the increasing awareness of the role of homocysteine in cardiovascular disease, and the public health goal to screen patients for risk from cardiovascular disease, there is a critical need for novel analytical procedures that can be used to accurately determine homocysteine levels in patients. Such procedures are expected to provide considerable medical benefit both in those cases where elevated homocysteine concentrations are a cause of a particular disease state, and in cases where elevated homocysteine concentrations are a detectable byproduct of an exisiting disease state.
Such analytical procedures would also provide great benefit by predicting a patient's susceptibility to cardiovascular disease before onset can be detected by other procedures. In this regard, great benefit would be achieved by adapting such procedures to the widespread screening of the general population, and in particular, to all infants. The present invention provides for such methods, including diagnostic kits for use in the clinical setting.
In connection with the design of such improved analytical procedures, it would be of great value to develop enzymes useful to measure homocysteine in single step assay, but which are substantially non-reactive toward the interfering concentrations of cysteine and methionine that are typically present in biological samples. As described below, the present invention provides for homocysteinase enzymes which have such specificity.
SUMMARY OF THE INVENTION
The present invention provides for novel methods to determine the concentration of homocysteine in biological fluids. In a preferred embodiment of the invention, the biological fluid is a urine, tissue fluid, blood, blood serum, or blood plasma sample from a patient, and the methods of the invention are useful to assess risk for cardiovascular disease. In particular, the present invention provides novel methods to determine homocysteine concentrations in biological fluids while avoiding detection of related but interferring substances, most particularly cysteine and methionine.
Accordingly, there is provided a method for determining the amount of homocysteine that is present in a biological sample containing, for example, homocysteine and cysteine, that comprises contacting said sample with an enzyme preparation capable of producing hydrogen sulfide from homocysteine and cysteine, and determining the amount of homocysteine in said sample by measuring the amount of hydrogen sulfide produced from homocysteine.
Said enzyme preparation comprises an enzyme referred to as a homocysteinase, and which may be referred to by other names as described below.
According to a preferred aspect of the invention, it is recognized that the total concentration of homocysteine present in biological samples, for example in body fluids, includes homocysteine molecules that are not present in free form, being instead covalently coupled to other molecules. The methods of the invention provide further steps for releasing this homocysteine prior to measuring of homocysteine-derived hydrogen sulfide.
It should be noted, however, that since the methodology of the present invention provides for accurate measurement of free homocysteine levels absent interference from related substances (for example, cysteine), valuable information is provided to the clinician even if only free homocysteine is detected. Among many uses, it is expected that such information is very useful as a fast initial diagnostic tool, for example, in the testing of all newborn infants.
Additional embodiments of the invention include methods to distinguish homocysteine from any cysteine that may be present in said biological sample. Representative of such methods are:
(I) a procedure wherein hydrogen sulfide produced from homocysteine is distinguished from hydrogen sulfide produced from cysteine by including in said method the additional initial steps of:
(a) contacting said biological sample with a reagent that protects homocysteine from said enzyme preparation;
(b) permitting said enzyme preparation to produce hydrogen sulfide from cysteine present in said sample;
(c) removing said hydrogen sulfide; and
(d) deprotecting said homocysteine, and adding a further amount of enzyme preparation to produce hydrogen sulfide therefrom; and
(II) a procedure that includes the additional initial steps of:
(a) contacting homocysteine that is present in said biological sample with a further enzyme preparation capable of converting it to a compound that can be isolated;
(b) isolating said compound;
(c) contacting said compound with an enzyme preparation or other reagent under conditions where said compound is converted back to homocysteine; and
(d) contacting the homocysteine so produced with said enzyme preparation capable of producing hydrogen sulfide therefrom;
(III) a procedure wherein said biological sample is pretreated with an agent that renders cysteine non-reactive to said enzyme preparation; and
(IV) a procedure wherein hydrogen sulfide produced from homocysteine is distinguished from hydrogen sulfide produced from cysteine, that includes the steps of:
(a) permitting an enzyme preparation to produce hydrogen sulfide from both if homocysteine and cysteine present in said sample, wherein said enzyme also produces pyruvate from cysteine in an amount equal to the amount of hydrogen sulfide produced therefrom;
(b) determine the amount of pyruvate so produced; and
(c) calculate the amount of homocysteine from the amount of hydrogen sulfide attributed thereto, wherein said sample is, or optionally is not, divided into a first part and a second part in order to conduct said assays.
In a particularly preferred embodiment of the invention that is readily adapted to the rapid testing of samples from a large number of patient samples, there is provided a method for determining the amount of homocysteine that is present in a biological sample containing homocysteine and cysteine, comprising the steps of:
(a) dividing said sample into 2 parts, part 1 and part 2;
(b) contacting part 1 with a first enzyme preparation that is capable of converting homocysteine to a substance that is not a substrate for homocysteinase, wherein said first enzyme preparation does not recognize cysteine as a substrate;
(c) independently contacting part 1 and part 2 with a second enzyme preparation that comprises a homocysteinase capable of producing hydrogen sulfide from both homocysteine and cysteine;
(d) measuring the amount of hydrogen sulfide produced in part 1 and part 2; and
(e) calculating the amount of homocysteine in said biological sample by subtracting the hydrogen sulfide measurement of part 1 from that of part 2, and doubling the result.
For the clinical practice of the invention, there is provided a diagnostic kit for use in determining the amount of homocysteine in a biological sample, and wherein the homocysteinase included therewith is obtained from one of several sources. In a preferred embodiment, the diagnostic kit comprises:
(a) a homocysteinase from Trichomonas vaginalis, or Pseudomonas (such as species ovalis or putida), and
(b) at least one reagent capable of being used to determine the amount of hydrogen sulfide formed in the homocysteinase reaction.
In a further aspect of the invention, there is provided a chimeric nucleotide sequence (whether of DNA or RNA), derived from more than one gene, or other polynucletide, that codes for a homocysteinase, wherein expression of such sequence leads to the production of a chimeric homocysteinase. Such homocysteinases have valuable properties with respect to the practice of the invention, and a preferred example thereof includes a chimeric enzyme that comprises amino acid sequences derived from both Trichomonas vaginalis and Pseudomonas putida homocysteinases.
Thus the present invention provides two basic approaches in the design of clinical assays for homocysteine: (1) to enhance detection of homocysteine in biological samples using novel assay techniques to detect homocysteinase reaction products, and (2) to further enhance the sensitivity of such assays by designing homocysteinase enyzmes that have substantially enhanced reactivity toward homocysteine, in comparison with other sulfur-containing amino acids.
With respect to approach (2) above, use of the protein encoded by SEQ ID NO:10 is representative. Such a homocysteinase enzyme is sufficiently non-reactive toward cysteine or methionine that the concentration of homocysteine that is present, for example, in a sample of tissue fluid, urine, blood, blood serum, or blood plasma of a subject may be determined in a single step assay, wherein is measured the amount of one or more products resulting from reaction of said homocysteinease on homocysteine in said sample, and wherein said measurement is substantially unaffected by the concentration of cysteine or methionine therein.
In a preferred aspect, such a homocysteinase is patterned on a homocysteinase from Pseudomonas, Clostridium, Aeromonas or Trichomonas, and in an example thereof, one or more peptide sequences of such an enzyme are correspondingly replaced by one or more homologous peptide sequences of SEQ ID NO:10, for example, those selected from the group consisting of:
(a) Gly-Gly-Asn-Arg-Leu-Ala-Gly-Gln-Glu, (see residues 43-51 of SEQ ID NO: 10);
(b) a subset of (a) that comprises Leu;
(c) Arg-Val-Cys-Lys-Glu-Ala-His-Ser-Gln, (see residues 168-176 of SEQ ID NO:10);
(d) a subset of (c) that comprises Glu;
(e) Gln-Met-Arg-Met-Tyr-Gly-Ser-Met-Ile, (see residues 304-312 of SEQ ID NO:10); and
(f) a subset of (e) that comprises Tyr.
In a preferred aspect, such a homocysteinase is a substitution variant, addition variant, deletion variant, or derivative of SEQ ID NO: 10, wherein said variant or derivative has one or both of the following properties:
(a) at least about 10% of the activity of SEQ ID NO:10 toward homocysteine in a suitable assay; and/or
(b) no more than about 1000 % of the activity of SEQ ID NO:10 toward cysteine (or methionine) in a suitable assay.
Additional aspects of the invention therefore include: (1) a purified and isolated DNA molecule that comprises a nucleotide sequence coding for a homocysteinase having such specificity, and wherein said coding sequence is operably linked to control sequences capable of directing expression therefrom in a host cell; and (2) appropriately transfected host cells.
Further representative and additional aspects of the invention are described according to the Detailed Description of the Invention which follows directly. It should be recognized also that the practice of the present invention should not be seen as dependent on, or limited by, any particular theory concerning the role of homocysteine in pathological processes.

BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 (panels A and B) provides a comparison of the amino acid sequence of Trichomonas vaginalis homocysteinase encoded by the mgl1 gene with that encoded by the Trichomonas vaginalis pAC2-1 clone.
FIG. 2 shows the comparative specific activities (units/mg crude E. coli extract) corresponding to homocysteinase of the pAC2-1 clone for cysteine, methionine, and homocysteine.
FIG. 3 shows the comparative specific activities of homocysteinase (pAC2-1 clone, purified using a DEAE-Fast Flow procedure) for cysteine, methionine, and homocysteine.
FIG. 4 shows the comparative specific activities of homocysteinase (pAC2-1 clone, purified using a nickel cation affinity reagent) for cysteine, methionine, and homocysteine.
FIG. 5 shows determined K.sub.cat values of homocysteinase (pAC2-1 clone) for cysteine, methionine, and homocysteine.

DETAILED DESCRIPTION OF THE INVENTION
Elevated blood plasma homocysteine levels are recognized as a risk factor for vascular disease. The atherogenic properties of homocysteine were first noted in association with a rare group of genetic diseases referred to collectively as homocystinuria. The disease state is characterized by a level of circulating homocysteine that is typically 10-fold (or greater) above that in normal blood. Under these circumstances, homocysteine is also detected in the urine. Premature vascular disease is strongly correlated with this condition. For example, if homocystinuria is left untreated, about 50% of patients suffer thromboembolic events, and mortality by the age of 30 is approximately 20% (see, for example, S. H. Mudd et al., American Journal of Human Genetics, 37, pp. 1-31, 1985).
Given that more than 75 epidemiologic or clinical studies have now shown a relation between total homocysteine levels and coronary and peripheral arterial diseases, stroke, and venous thrombosis, there is a clear medical need for diagnostic procedures that can accurately determine homocysteine levels in, for example, blood plasma. It would be highly advantageous also if such methods could be adapted to mass screenings of large populations of patients, or of the general population or newborn infants. The development of such assay procedures has been hindered principally by two interrelated difficulties:
(1) the chemical and biochemical properties of homocysteine are intimately related to those of other sulfhydryl-containing biomolecules, including the amino acids methionine and cysteine, and thus improved assay procedures for homocysteine must be uniquely responsive to homocysteine.
(2) homocysteine is highly reactive and exists under physiological conditions in many forms besides the free homocysteine molecule, for example, as a disulfide-linked dimer, as a disulfide-linked heterodimer with free cysteine, as a disulfide-linked conjugate with cysteine residues of blood plasma proteins, and bonded (often as an N-Acyl derivative) to the R groups of other protein amino acids (for example, to the epsilon amino group of protein lysine). These conjugated forms contribute very substantially to the total amount of homocysteine that may participate in pathological processes. Given also that only minor increases, beyond the normal range, in plasma homocysteine concentrations lead to satistically significant disease risk (see, O. Nygard et al. above), it is useful that clinical assays provide the capability to detect the total homocysteine content of biological fluids. This said, the reproducible detection of free homocysteine (or of any of the other forms in which homocysteine is found), but absent interference from such other substances as methionine and cysteine, also provides valuable information to the clinician.
The present invention is thus directed to the development of homocysteine assay procedures, and the selection of reagents therefor, that overcome the above complexities under conditions where large scale screening of patient samples is practicable.
Homocysteinase Enzymes Useful in the Practice of the Invention
According to the practice of the invention, homocysteine concentrations in biological samples are determined enzymatically with enzymes hereinafter referred to as "homocysteinases", which are defined as enzymes capable of catalyzing reactions whereby hydrogen sulfide is produced from homocysteine. In the typical case, ammonia and alpha-ketobutyrate are also produced. As described herein, it is preferred to detect product hydrogen sulfide, although product ammonia and/or alpha-ketobutyrate or other products may also be detected. Homocysteinases, as defined herein, may catalzye other reactions involving other sulfhydryl compounds and have acquired multiple names in the literature; however, they are generally useful in the practice of the present invention if they possess the property of catalyzing production of hydrogen sulfide from homocysteine.
A first homocysteinase that is preferred in the practice of the invention is L-methionine-alpha-dearnino-gamma-mercaptomethane lyase (methionine lyase) derived from the bacterial source, Pseudomonas putida. The enzyme has been purified by S. Ito et al., Journal of Biochemistr , 79, pp.1263-1272 (1976), and determined to have a molecular weight of about 170 kDa. In the context studied by S. Ito, the enzyme carried out the alpha-gamma elimination of methionine to alpha-keto butyrate, methanethiol, and ammonia. If homocysteine is the substrate, then alpha-keto butyrate, hydrogen sulfide, and ammonia would be the resultant products. The homologous enzyme has been isolated from Pseudomonas ovalis, H. Tanaka et al., Biochemistry ,16, pp.100-106 (1977). Methods for the recombinant production of this Pseudomonas enzyme have also been developed (see Y. Tan et al., Protein Expression and Purification, 9, pp. 233-245, 1997), and use of recombinant enzyme in the clinical practice of the present invention is expected to provide advantages in terms of diagnostic kit cost and assay reproducibility.
The substrate specificity of the P. putida enzyme has also been determined. For example, N. Esaki et al. Methods in Enzvrnology 143, pp. 459-465 (1987) report that on a relative activity scale where activity toward methionine is assigned 100, cysteine is 10, and homocysteine is 180. That the enzyme is reactive to all three sulfhydryl-containing amino acids underscores the need to define clinical assays for which the source of hydrogen sulfide can be properly determined. It should be noted that the apparent 10-fold preference of the enzyme for homocysteine over cysteine does not take into account that the concentration of cysteine in a biological sample may be high--in fact much higher than the concentration of homocysteine. Homocysteinase enzymes of suitable catalytic activity can be derived from other Pseudomonas species, or from other bacteria, using routine screening procedures and assays that are recognized in the art.
An additional group of organisms that are a source of homocysteinase useful in the practice of the invention are species of the Trichomonad parasites and related protozoans.
Trichomonads are important parasites of the urogenital tract and are aerotolerant (but nonetheless anaerobic) flagellate protozoa. Use of homocysteinase from Trichomonas vaginalis is preferred according to the practice of the invention.
Trichomonas species are believed to use their capabilities for thiol metabolism in order to counter oxygen toxicity in host tissues, see K-W Thong et al., Experimental Parasitolog, 63, pp.143-151 (1987), and papers cited therein. Although considerable variation in homocysteinase activity (termed homocysteine desulphurase activity therein) was found between Trichomonas species, it is routine to screen available species for acceptable levels of enzyme activity. Generally speaking, it is preferred that a homocysteinase should have a specific activity of at least about 1 unit/mg purified protein for use in the below-described assays, although it is well within the skill of those familiar with the relevant art to design variations on these assays that use greater or lesser amounts of enzyme or enzyme preparations with differing enzyme activity. It is noted that highly purified and active P. putida enzyme has a specific activity of about 20 units/mg (a unit of enzyme activity may be described as 1 micromole of substrate converted per minute under standard conditions (see Y. Tan et al. above).
The "homocysteine desulphurase activity" reported by K-W. Thong et al. (1987) above appears to result from the same enzyme responsible for methionine catabolizing activity in Trichomonas, and later termed methionine-gamma-lyase by B. C. Lockwood and G. H. Coombs (Biochemical Journal, 279, pp. 675-682, 1991) wherein is also described purification of this enzyme. As aforementioned, use of methionine-gamma-lyase (a homocysteinase) from Trichomonas vaginalis is preferred in the practice of the present invention.
Use of a recombinant version of the T. vaginalis enzyme is also preferred. One potential cloning strategy follows the observations by A. Marcos et al., FEMS Microbiology Letters, 135, pp. 259-264 (1996), that T. vapinalis genes may have few introns. Accordingly, a genomic library would be constructed (see D. E. Riley et al. Molecular and Biochemical Parasitology, 51, pp. 161-164, 1992) and screened with DNA fragments corresponding to the Psuedomonas putida enzyme, and which are expected to reflect some partially conserved sequence.
Lockwood et al. also list other reports of bacteria having methionine-gamma-lyase activity involving species of Pseudomonas, Clostridium, and Aeromonas.
It is expected that such species are sources of homocysteinase activity useful in the practice of the present invention. Additional organisms that are expected to provide useful homocysteinase enzymes are certain marine algae (see, for example, D. A. Gage et al. Nature, 387, pp.891-897, (1997) describing species with extensive methionine-related metabolism); sulfur bacteria; and geomicrobes or other microbes living under extreme environmental conditions (see, for example, R. A. Kerr, Science, 276, pp.703-704, 1997 and E. Pennist, Science, 276, pp.705-706, 1997). Additional examples of microorganisms that may be useful sources for homocysteinase-type enzymes include bacteria involved in periodontal disease, such as are capable of forming volatile sulfur compounds from cysteine. In this regard, see S. Persson et al., Oral Microbiologa and Immunologvy 5(4), pp.195-201, 1990.
Finally, with respect to the definition of "homocysteinases" that are usefull in the practice of the invention, it should not be viewed as a limitation herein that hydrogen sulfide necessarily be a product of such enzymes. Broadly speaking, the present invention provides for high through-put diagnostic procedures, permitting the cost effective analysis of a very large number of homocysteine-containing samples while avoiding detection of interfering substances.
Accordingly, it is expected that other enzymes that metabolize homocysteine are useful in the practice of the invention if methods exists to detect such metabolites under conditions where interference from substances similar to homocysteine (such as cysteine) can be avoided. The following examples describe a considerable spectrum of techniques to accurately measure homocysteine while avoiding detection of interfering substances. Accordingly, it will be appreciated that the techniques disclosed below can be adapted by those skilled in the art to detection methods using many other enzymes that act on homocysteine.
Chimeric Homocysteinases
As aforementioned, in a preferred aspect of the invention there is provided a chimeric nucleotide sequence (whether of DNA or RNA), derived from more than one gene (or other polynucleotide such as a cDNA or other intron-less sequence), that codes for a chimeric homocysteinase enzyme.
Such homocysteinases have properties that are very useful with respect to the practice of the invention, and a preferred example thereof includes a chimeric enzyme that comprises amino acid sequences corresponding to both Trichomonas vaginalis and Pseudomonas putida homocysteinases.
It is believed that P. putida homocysteinase is more stable than the T. vaginalis enzyme under a variety of conditions. As one probable consequence thereof (see B. Lockwood et al., Biochemical Journal, 279, pp. 675-682, (1991), recovery of the T. Vaginalis enzyme during purification was very low (see p. 679 at Table 2, referring to "methionine .gamma. lyase"). Thus in the practice of the present invention, it is preferred to include P.putida sequences in chimeric enzymes in order to take advantage of this enhanced stability.
As discussed above, different homocysteinases have different respective reactivities toward their various sulfur-containing substrates, for example, cysteine, methionine, and homocysteine. Although the selection of particular reaction conditions may affect apparent reactivities under particular circumstances, evidence indicates that the T. Vaginalis enzyme has a higher reactivity toward homocysteine as substrate than does the P. putida enzyme, which may show greater reactivity toward cysteine, or methionine as substrate. In this regard, the results reported by Lockwood et al., 1991 at Table 4 thereof) are of note in that relative activity data for the T. vaginalis enzyme evidence a very pronounced "preference" for homocysteine as substrate (see also the K.sub.m data reported on page 678 thereof). This is in contrast to the data reported by N. Esaki et al. above with respect to the P. putida enzyme.
Thus, the properties of homocysteinease for use in the clinical diagnostic applications of the present invention can be improved by providing the enzyme as a chimeric molecule that draws upon functional features contributed to the chimeric protein from both of its component species. In particular, it is preferred to select for inclusion in the chimeric homocysteinases of the invention regions of the P. putida enzyme that contribute substantially to the stability thereof, while including also regions of the T. vaginalis enzyme that preferentially enhance reactivity toward homocysteine as substrate.
In connection with the design of such enzymes, a recent report that T. Vaginalis homocysteinase actually represents two protein species derived from two genes is of note (see J. C. Mottram, direct submission of sequences to Gene Bank, submitted Jul. 17, 1997, as T. vaginalis mgl1 gene, accession number AJ000486, NID g2330884, and T. vaginalis mgl2 gene, accession number AJ000487, NID g2330886), the complete sequences of which are fully incorporated by reference herein, as if directly set forth. It should be noted also that the depositors have submitted a manuscript concerning the above sequences, apparently entitiled "Two methionine gamma lyase genes from the anaerobic protozoan parasite Trichomonas vaginalis", to an unspecified journal, but to which the practitioner is directed in due course.
The present invention therefore provides for a purified and isolated DNA molecule comprising a chimeric nucleotide sequence that encodes amino acid sequence of Pseudomonas putida homocysteinase, and amino acid sequence of Trichomonas vaginalis homocysteinase (derived from either mgl1, or mgl2, or both) from which can be expressed a functional protein having homocysteinase activity. In a preferred aspect, the nucleotide construct (or corresponding amino acid construct) corresponds predominantly to that of P. putida, and thus there is provided a DNA molecule that comprises an encoding nucleotide sequence for Pseudomonas putida homocysteinase, wherein one or more subsequences thereof that encode one or more amino acids of said enzyme are correspondingly replaced by one or more nucleotide subsequences that encode the corresponding amino acids of a Trichomonas vaginalis homocysteinase. In the practice of the present invention, the T. vaginalis enzyme encoded by the mgl 1 gene is hereinafter referred to as the T1 protein, and that encoded by the mgl2 gene is referred to as the T2 protein.
In connection with the selection of chimeric polypeptides and encoding polynucleotides, the following considerations are of note. The T 1 and T2 proteins are encoded by remarkably similar DNA sequences. Accordingly, it is generally expected to be the case that substitution of an mgll-encoding subsequence into a P.putida backbone will have substantially the same effect, and generate improvements substantially similar to those resultant from an equivalent mgl2 subsequence substitution.
However, it is noted that there are a limited number of subregions where the T1 and T2 sequences differ substantially, while at the same time, the T1 sequence (less so the T2 sequence) shows substantial homology with the published P. putida sequence. Indeed, the published P.putida sequence shows considerable homology with the T1 sequence.
Thus, in a further preferred aspect of the invention, there are identified regions of the encoding sequence for T. vaginalis enzyme where the T2 sequence and corresponding T1 sequence are very different from each other, and yet the T1 sequence is substantially similar to that of P.putida. Without being limited as to theory, it is believed that these encoding subregions of T2 present unique opportunities to insert into the a P. putida encoding polynucleotide, amino acid sequence domains that provide enhanced reactivity of the chimeric species toward homocysteine, thereby facilitating the diagnostic procedures of the invention.
The invention therefore provides for a DNA molecule that comprises an encoding sequence for Pseudomonas putida homocysteinase, wherein one or more subsequences thereof, that each encode one or more amino acids of said enzyme, are correspondingly replaced by one or more nucleotide subsequences than each encode the one or more corresponding amino acids of a Trichomonas vaginalis homocysteinase, and wherein said resultant amino acid replacements are selected from the group consisiting of:
(a) Cys-Ser-Arg-Ala-Asp-Ile-fle-Ala-Lys-Val-Lys-Ser (SEQ ID NO: 1), or any subset thereof, from Trichomonas vaginalis (T2) for Val-Gly-Ser-Gln-Ala-Leu-Val-Asp-Arg-Ile-Arg-Leu (SEQ ID NO: 2), or any subset thereof, from Pseudomonas putida;
(b) Asp-Val-Asp (SEQ ID NO: 3), or any subset thereof, from Trichomonas vaginalis (T2) for Glu-Leu-Lys (SEQ ID NO: 4), or any subset thereof, from Pseudomonas putida;
(c) Cys-His-Val-Val (SEQ ID NO: 5), or any subset thereof, from Trichornonas vaginalis (T2) for Ala-Leu-Gln-Leu (SEQ ID NO: 6), or any subset thereof, from Pseudomonas putida;
(d) Cys-Glu-Asn-Val-Gln-Asp-Ile-Ile-Asp-Asp (SEQ ID NO: 7), or any subset thereof, from Trichomonas vaginalis (T2) for Gly-Leu-Glu-Asp-Ile-Asp-Asp-Leu-Leu-Ala (SEQ ID NO: 8), or any subset thereof, from Pseudomonas putida; and
(e) any combination involving one, two, three or four of the replacements provided for by groups (a), (b), (c), and (d) above.
With respect to the above-listed Trichomonas vagnalis mgl2 ("T2") amino acid subsequences it should be noted they correspond approximately to the following amino acid sequence positions:
Cys-Ser-Arg-Ala-Asp-Ile-Ile-Ala-Lys-Val-Lys-Ser (SEQ ID NO: 1), approximately 226-237;
Asp-Val-Asp (SEQ IID NO:3), approximately 318-320;
Cys-His-Val-Val (SEQ ID NO:5), approximately 331-335; and
Cys-Glu-Asn-Val-Gln-Asp-Ile-Ile-Asp-Asp (SEQ ID NO: 7), approximately 381-390.
In connection with the practice of this aspect of the invention, the above-listed T. vaginalis subsequences can be additionally modified to accept conservative amino acid substitutions. Additionally, the T. vaginalis subsequences need not correspondingly replace the above listed P. putida sequences so that, for example, the T. vaginalis subsequences may be inserted nearby (i.e. up to about 10 amino acid positions distant therefrom), while the targeted P. putida sequences remaining in place, in whole or in part. Additionally, the T. vaginalis inserts may comprise transfer of additional amino acids found on the N-termnal or C-terminal side of the above-depicted sequences thereof, as long as the benefit of increased reactivity toward homocysteine is not compromised owing to decreased enzyme stability.
The construction of appropriate chimeric encoding polynucleotides is straightforward for those familiar with the art, and may involve techniques of site directed or loop out mutagenesis, or use of PCR technology. Appropriate host cells for the expression of such encoding polynucleotides are described, for example, in Y. Tan et al., Protein Expression and Purification, 9, pp. 233-245, 1997.
Homocysteinases for One Step Assays that Lack Reactivity Toward Cysteine and Methionine
According to the practice of the invention, there are also provided novel homocysteinase enzymes that are essentially non-reactive toward cysteine or methionine; that is, any such reactivity is sufficiently low that the amount of homocysteine present in a sample of tissue fluid, urine, blood, blood serum, or blood plasma, or other biological fluids or samples from human subjects, may be determined in a single step assay--absent the need to correct for the concentrations of cysteine and/or of methionine that are also present in the sample. The significance of these discoveries will be immediately apparent to the clinician, given the widespread public health need for simple and fast homocysteine assays, when it is recognized that the concentration of cysteine and/or of methionine in such biological samples is generally much higher than that of homocysteine, and particularly so in certain disease states.
In this regard, the activity of the novel Trichomonas vaginalis homocysteinase represented by SEQ ID NO: 10 is of particular note (see Example 8, and FIGS. 2 through 4, as discussed further below). The relative activity of this enzyme toward homocysteine, compared to cysteine or methionine, will readily permit homocysteine measurements without the need to correct for any cysteine or methionine present in the biological test sample.
In a preferred example of the invention, such novel enzymes are patterned on homocysteinases found in various microorganisms including Pseudomnonas, Clostridium, Aeromonas or Trichomonas, and particularly preferred homocysteinases are derived from T vaginalis, including that expressed from the mgl1 gene (SEQ ID NO: I 1), or the mgl2 gene thereof
In FIG. 1 (panels A and B) are depicted the amino acid sequences of two Trichomonas vaginalis homocysteinases, the first derived from a novel clone (pAC2-1) of the present invention, and the second, the enzyme derived from the known mgll gene (see also SEQ ID NOS:10 and 12 for comparison of amino acids; SEQ ID NOS: 9 and 11 for comparison of encoding DNAs). It will be seen that pAC2-1 is characterized by the existence of three differences (mutations), compared to mgl 1:
Phe to Leu at amino acid position 47,
Asp to Glu at amino acid position 172, and
Ser to Tyr at amino acid position 308.
Modified homocysteinase amino acid sequences, made by incorporating amino acid substitutions that include one or more of these mutations, are particularly useful in the practice of the invention. Accordingly, a preferred example of the invention involves providing a homocysteinase to contain one or more peptide (sub)sequences of SEQ ID NO: 10 that are selected from the group consisting of:
(a) Gly-Gly-Asn-Arg-Leu-Ala-Gly-Gln-Glu, (see residues 43-51 of SEQ ID NO: 10);
(b) a subset of (a) that comprises Leu;
(c) Arg-Val-Cys-Lys-Glu-Ala-His-Ser-Gln, (see residues 168-176 of SEQ ID NO: 10);
(d) a subset of (c) that comprises Glu;
(e) Gln-Met-Arg-Met-Tyr-Gly-Ser-Met-Ile; (see residues 304-312 of SEQ ID NO: 10); and
(f) a subset of (e) that comprises Tyr.
In a representative example, the homocysteinase is patterned on an enzyme from Pseudomonas, Clostridium, Aeromonas or Trichomonas wherein one or more peptide (sub)sequences of the original polypeptide sequence(s) thereof are correspondingly replaced by one or more homologous peptide sequences of SEQ ID NO: 10 that are selected from the group consisting of:
(a) Gly-Gly-Asn-Arg-Leu-Ala-Gly-Gln-Glu, (see residues 43-51 of SEQ ID NO: 10);
(b) a subset of (a) that comprises Leu;
(c) Arg-Val-Cys-Lys-Glu-Ala-His-Ser-Gln, (see residues 168-176 of SEQ ID NO: 10);
(d) a subset of (c) that comprises Glu;
(e) Gln-Met-Arg-Met-Tyr-Gly-Ser-Met-Ile, (see residues 304-312 of SEQ ID NO:10); and
(f) a subset of (e) that comprises Tyr.
In this regard, use of the term "homologous" is not intented to suggest that such homology is exact, but rather, that a comparison of such sequences using generally recognized models would suggest that such sequences, even if now signficantly different, may have evolved from a common ancestor gene or subset thereof Similarly, the term "mutation" as used herein, should be broadly understood to include modifications that arise by whatever means, whether natural, or experimental and the like.
Accordingly, a generally preferred example includes a chimeric homocysteinase patterned on a first Trichomonas homocysteinase wherein one or more amino acids thereof, that correspond to the Leu.sup.47, Glu.sup.172, and Tyr.sup.308 residues of a second Trichomonas homocysteinase (that from pAC2-1, as depicted in SEQ ID NO: 10), are correspondingly replaced by one or more of said Leu.sup.47, Glu.sup.172, and Tyr.sup.308.
An additional example of the invention is defined by a homocysteinase that is a substitution variant, addition variant, deletion variant, or other derivative of SEQ ID NO: 10, wherein said variant or derivative has one or both of the following properties:
(a) at least about 10%, preferably about 25%, more preferably at least 50% of the activity of SEQ ID NO: 10 toward homocysteine in a suitable assay (such as described in Example 8); and/or
(b) no more than about 1000%, preferably less than 500%, more preferably less than 200% of the activity of SEQ ID NO: 10 toward cysteine or methionine in a suitable assay (such as described in Example 8).
Such a range of properties is generally believed to maintain sufficiently enhanced activity of the enzyme with respect to homocysteine, in comparison with cysteine or methionine, that single step methodology is still practical, although it will be appreciated that the exclinical application. For exaative sensitivity may be readily determined in each clinical application. For example, cysteine would generally be expected to be at low concentration in a urine sample, at least with respect to a non-diseased patient. With respect to the provision of mutant homocysteinases from other organisms, as produced for example by appropriate recombinant methods, the above relative guidelines are expected to prove useful. The enzyme represented by SEQ ID NO: 10 is a particularly useful example given that the apparent activity of this homocysteinase for homocysteine is at least about 100-fold greater than for cysteine and methionine.
In a representative example whereby a homocysteinase is modified to improve its usefulness for single-step assay methodology, the wild type T. vaginals amino acid sequence (from mgl1, see SEQ ID NOS: 11 and 12) is altered (generally of course by modification of an appropriate encoding DNA) as follows:
one or more of Phe.sup.47, Asp.sup.172, and Ser.sup.308 thereof is deleted, or is replaced according to the following formula:
(1) for Phe.sup.47, replace with Leu, Ile, Val, Ala, Gly, Met, and Trp;
(2) for Asp.sup.172, replace with Glu, Gln, or Asn;
(3) for Ser.sup.308, replace with Tyr, Phe, Met, Trp, Gln, Thr, or Asn, wherein are suggested relatively conservative amino acid substitutions, as is recognized in the art, and whose efficacy in this regard can be determined by routine experimentation.
As further described below (see Example 7), nickel-NTA affinity purification procedures (available from the Qiagen Company, Germany) can be used to facilitate purification of homocysteinase from E. coli or other host cells transfected with an appropriate homocysteinase-encoding DNA sequence. These procedures take advantage of the selective binding of protein imidazole groups to nickel cations immobilized in the NTA resin matrix. In a preferred example of this aspect of the invention, by modification of an appropriate encoding DNA (see SEQ ID NOS:9 and 10), an amino terminal tag that contains, for example, 6 consecutive histidine residues is introduced into the homocysteinase, thereby facilitating its purification from host cell materials.
Homocysteinease SEQ ID NO: 10 (see also FIG. 1 AB), is representative of modified homocysteinase enzymes that comprise one or more histidine residues positioned on the N-terminal side of the natural Met.sup.1 of said proteins, said modified enzymes being sufficiently non reactive toward cysteine or methionine that the concentration of homocysteine that is present in a sample of tissue fluid, urine, blood, blood serum, or blood plasma of a subject may be determined by use of such enzymes in a single step assay. In such an assay, the amount of one or more products resulting from reaction of said modified homocysteinease on homocysteine are measured, and such measurements are substantially unaffected by the concentration of cysteine or methionine in the sample. According to this aspect of the disclosure, a homocysteinase that is useful in the practice of the invention comprises one or more, preferably 2-15, and most preferably 5-8 histidine residues consecutively positioned on the N-terminal side of the natural homocysteinase Met.sup.1.
Examples
Example 1
Detection of Homocysteine by Double Enzymatic Subtraction in a Saqple Containing Cysteine
The concentration of free homocysteine in a blood plasma sample is determined as follows. Blood samples (0.1 to 5.0 mL) are collected with a standard vacutainer using EDTA as anticoagulant, and plasma is then prepared by centrifugation.
A stock homocysteinase solution of 150 units/ml Trichomonas vaginalis enzyme is also prepared. Stock solutions of enzyme generally range from 1-1000 units/ml, and preferably 100-200 units/ml, although the exact activity is subject to selection by the practitioner, depending on various factors, including the concentration of homocysteine in the samples.
As described above, use of P. putida enzyme is also preferred, at similar activity levels.
The plasma sample, at an appropriate dilution in buffer, is divided into two equal volumes, Parts 1 and 2. To Part 1 is added a suitable amount of S-adenosylhomocysteine hydrolase ("SAHH") and also a quantity of adenosine (SAHH is available from both eukaryotic and prokaryotic sources, and a procedure for cloning it in T. vaginalis has been presented, Bagnara et al. Molecular and Biochemical Parasitology. 81, pp. 1-11, 1996). In the presence of sufficient adenosine, the plasma homocysteine is converted to S-adenosylhomocysteine. The Part 2 volume is not reacted with SAHH.
Trichomonas vaginalis homocysteinase is then added to the Part 1 and Part 2 samples and reacted for about 10-30 minutes. A final concentration of homocysteinase in the range of 0.5-1 unit/mL is preferred, although the exact amount may be adjusted as needed. It is noted that the adenosine remaining in the Part 1 sample prevents the hydrolyase reaction from running in reverse, and so its initial concentration should be chosen with this in mind. The amount needed may depend on the SAHH selected, but a useful starting point is a concentration not less than that of the homocysteine present. Hydrogen sulfide is then measured in both Part 1 and Part 2, and the amount of homocysteine present in the original sample is calculated by subtracting the hydrogen sulfide measurement of part 1 from that of part 2, and doubling the result. The hydrogen sulfide measurement is performed by adding lead acetate to the samples in the range of about 0.1 to 1.0 Molar, thus precipitating the sulfide. The precipitate is measured in a standard spectrophotometer at 360 nm, or other suitable wavelength (such as in the visible range) at which the insoluble precipitate can be determined. This procedure is readily automated.
An additional enzyme useful in the practice of the double enzymatic subtraction approach is cystathionine .beta.-synthase, which catalyzes production in the body of cystathionine from homocysteine and serine. For blood serum or plasma samples, the reaction may be driven in the direction of cystathionine by taking advantage of the relatively high concentration of serine in the blood. Suitable sources of this enzyme include material isolated from Trichomonas, from Pseudomonas, or from mammalian tissues including, for example, liver. The enzyme may be used in an amount that provides a unitslml equivalent to the range described above for S-adenosylhomocysteine hydrolase. As mentioned above in connection with the use of SAHH, it is preferable that steps be taken to prevent this enzymatic reaction from running backwards, which may lead to inaccurate data. The reaction may be driven, and then maintained, in the direction of cystathionine by adding exogenous serine to the reaction samples, or by irreversibly inhibiting the enzyme once conversion to cystathionine has been accomplished. Suitable inhibitors include serine analogs of high affinity for the active site.
A further additional procedure based on the double enzymatic subtraction approach may be available. Recent published work may indicate that the enzyme methionine tRNA synthetase (methionine tRNA synthase) is capable of accepting homocysteine as a reactant (see H. Jakubowsky et al., FEBS Letters, 317, pp. 237-246, 1993). Thus it may be possible to reproduce the above result using this enzyme.
Example 2
Alternate S-adenosylhomocysteine hydrolase procedure
S-adenosylhomocysteine produced according to Example 1 is subjected to the following manipulations: following its production it is isolated, and contacted with a further amount of S-adenosylhomocysteine hydrolase under conditions where S-adenosylhomocysteine is converted back to homocysteine; after which the homocysteine so produced with said enzyme preparation is contacted with homocysteinase to produce hydrogen sulfide therefrom.
Example 3
Detection of Homocysteine by a Direct Enzymatic Subtraction in a Sample Containing Cysteine
Following the initial procedures of Example 1, a blood plasma sample containing both homocysteine and cysteine is prepared. The sample is not divided into parts; instead, a sample of the enzyme cysteine tRNA synthetase is added under conditions that cysteine present is combined with tRNA. The enzyme selected may be of eukaryotic or prokaryotic origin, and conditions for its reaction are well known in the art.
The cysteine-depleted sample is then reacted with homocysteinase as aforementioned, and the homocysteine concentration is determined directly from the hydrogen sulfide measurement.
Example 4
Methods to Detect Homocysteine Bonded to Other Biomolecules
As aforementioned, homocysteine exists in biological fluids bonded to other biomolecules, and homocysteine "stored" in such forms is believed to contribute to pathological processes. Thus it is desireable to determine total homocysteine, and this includes (1) homocysteine dimers, (2) homocysteine/cysteine heterodimers, (3) conjugates of homocysteine and protein wherein homocysteine is attached by way of disulfide bonds to protein cysteine, and also (4) conjugates of homocysteine and protein wherein homocysteine (including N-Acylated forms thereof ) is bonded to protein amino acid R groups, most notably to the epsilon amino group of protein lysine.
With respect to forms (1) through (3), reducing solutions are used to release the covalently bound homocysteine. Accordingly, a stock sodium borohydride or sodium cyanoborohydride solution is prepared at about 0.1 M or less. The reaction is carried out by adding the borohydride to the plasma sample (prepared following the intitial procedure of Example 1) at pH 6 to 8 for 5-10 minutes at room temperature. The excess borohydride is destroyed, and the sample may then be subjected to the enzymatic procedures of Examples 1 or 3. Alternatively, the borohydride may be neutralized with HCl if the sample is further manipulated according to the following procedure.
Example 5
Manipulations under Acid Conditions
With respect to form (4) above, 6 N HCl can be used by dilution at about 50/50 with the protein sample. Following reflux at boiling temperature for 1-2 hours under nitrogen, water is removed from the sample under vacuum to complete dryness. This liberates homocysteine if bonded to other amino acids, and also completes the homocysteine lactonization process. At the point of dryness, sodium acetate (1M) and acetic anhydride (10M) are added. This is refluxed for one further hour at boiling temperature to create acetylated homocysteine thiolactone.
The anhydride is removed by evaporation to dryness. The N-acetylated homocysteine thiolactone is selectively extracted with ether. The ether is then evaporated at 35 degrees C under vacuum. Physiologically buffered water (phosphate buffered saline, pH 7.5) is then added which then opens the thiolactone ring. At this point, either of two reactions is carried out. Homocysteinase may then be added and reacted for 10-30 minutes followed by detection of hydrogen sulfide as above, or preferrably a hog-kidney deacetylase is added to deacylate the homocysteine with subsequent addition of the homocysteinase.
Example 6
Additional Methods for Detection of Homocysteine by a Direct Enzymatic Subtraction in a Sample That Also Contains Cysteine
Generally speaking, this additional method takes advantage of the fact that pyruvate produced from cysteine by the action of homocysteinases may be detected independently of the hydrogen sulfide that is generated by the action of homocysteinases on both homocysteine and cysteine present in biological samples, such as blood plasma. Thus determination of homocysteine may be made by simple subtraction. According to this method, pyruvate can be determined enzymatically by any number of enzymes that generate a detectable product therefrom.
The two principal processes of the method, detection of pyruvate and detection of hydrogen sulfide, may be conducted simultaneously in a single sample, or they may be conducted separately in parallel samples, in either case with appropriate controls.
In a preferred example, the enzyme used to detect pyruvate is a mammalian lactate dehydrogenase, and determinations of both pyruvate and total hydrogen sulfide are performed in a single cuvette, using a standard spectrophotometer. Following the initial procedures of Example 1, a blood plasma sample containing both homocysteine and cysteine is prepared. The sample is not divided into parts, instead a sample of a homocysteinase (from Trichomonas vaginalis or P. putida) is added under conditions such that hydrogen sulfide, ammonia, and a-keto butyrate are produced from homocysteine, and additionally, hydrogen sulfide, ammonia and pyruvate are produced from cysteine. A sample of the enzyme lactate dehydrogenase (at an amount of units/ml comparable to that used in previous examples) is also added under conditions such that it will react with the pyruvate produced from cysteine, which reaction is then monitored at or in the vicinity of 340 nm (for NADH), per well known procedures.
The total concentration of both homocysteine and cysteine in a sample may be determined calorimetrically, as before (see Example 1), by measuring the total hydrogen sulfide produced from homocysteinase, and at any suitable wavelength at which the precipitating colored lead salt can be detected, such as in the visible range, or also at or near, for example, 360 nm. Hydrogen sulfide may also be detected based on formation of other chromophoric metal salts, as is known in the art. The homocysteine concentration in the original sample is determined by comparison of the total hydrogen sulfide produced (from cysteine and homocysteine) with the total pyruvate produced (from cysteine only). This procedure is also readily automated, and both detection wavelengths can be monitored simultaneoulsy.
Although use of lactate dehydrogenase to detect pyruvate in blood, or in solutions derived from blood, may follow one of several art-recognized procedures, certain precautions should be repeated. Pyruvate is very unstable in blood, and in materials derived therefrom, and it may even polymerize. Accordingly, it may be desirable to conduct pyruvate determinations on protein-free filtrates of recovered samples, and on such samples only when processed with metaphosphoric acid, as is known in the art.
Example 7
Production of the E. coli BL21 (DE3) pAC2-1 clone
The cloning of the pAC2-1 homocysteinase gene of Trichomonas vaginalis was accomplished as described below. Generally speaking, recombinant methodology recognized as applicable in other microorganisms is useful with respect to manipulation of Trichomonas DNA, particularly so since many Trichomonas genes, as aforementioned, lack introns. Useful reference may therefore be made to Y. Tan et al., Protein Expression and Purification, 9, pp. 233-245, (1997) and International Patent publication number WO 96/40284 of Y. Tan et al., published December 19, 1996.
Genomic DNA from Trichomonas vaginalis was isolated by standard procedures (Wizard Minipreps, Promega, Madison, Wis.), and used as a template for a PCR reaction conducted according to the method provided with a PCR reagent kit (Roche, Branchburg, N.J.). Oligonucleotide primers were developed based on the nucleotide sequence of the mgl1 gene (J. C. Mottram et al., Gene Bank, accession number AJ000486, NID g2330884, submitted Jul. 17, 1997).
The specific primers used were:
(sense) 5'-GGATTACATATGCATCATCATCATCATCACATGAGTGGCCACGCTATCGAC-3' (SEQ ID NO: 13), which includes a CATATG NdeI site; and (antisense)
5'-GGATTAGGATCCTTAGAGGACTAAGTCGAGAGCC-3' (SEQ ID NO:14), which includes a GGATCC BamHI site. Additional reagents used included restriction endonucleases, T4 DNA ligase, and BL21 (DE3) competent cells, all purchased from Stratagene (San Diego, Calif.). The GeneAmp PCR reagent kit was purchased from Roche (Branchburg, N.J.), and the DNA purification kit was purchased from Promega (Madison, Wis.). The oligonucleotide probes for PCR amplification were synthesized by IDT Inc. (Coralville, Iowa). All other reagents were purchased from Sigma (St. Louis, Mo.). Wild type Trichomonas vaginalis was purchased from the American Type Culture Collection (Rockville, Md.).
The PCR reaction conditions were as follows: 35 cycles of denaturation at 94.degree. C. for 1 minute; annealing at 50.degree. C. for 2 minutes; and extension at 72.degree. C. for 2 minutes. This was followed by a final extension step at 72.degree. C. for 10 minutes. The PCR-amplified product (which appeared as one band of 1.2K bp identified by Kb-ladder markers) was collected, digested with the NdeI and BamHI restriction enzymes, and then ligated into the pT7-7 vector at the NdeI and BamHI cloning sites thereof, using standard protocols (the pT7-7 vector was provided by Dr. Stan Tabor, Harvard Medical School, Boston, Mass., see Tabor, S. "Expression using the T7 RNA polymerase/promoter systemn," in Current Protocols in Molecular Biology, F. A. Ausubel, et al., eds., 1990, pp. 16.2.1-16.2.11, Greene Publishing and Wiley-Interscience, New York). The resulting plasmid was then transformed into E. coli BL21 (DE3) cells by electrotransformation.
After incubation at 37.degree. C. overnight, ampicillin-resistance clones were selected from ampicillin-containing plates. The cells from the selected colonies were grown in 5 ml LB medium (Fisher) at 37.degree. C. overnight. Suitable clones were selected based on enzyme activity of crude culture extracts in the .alpha.-ketobutyrate assay (using a modification of the method of K. Soda et al., Methods in Enzymology, 143, 459-465, 1981-based on reaction of methyl-2-benzothiazolinone hydrazone ), and/or a dethiomethylation assay in which H.sub.2 S is produced and quantified (see A. E. Braunstein et al., Biochimica et Biophysica Acta, 242, pp. 247-260, 1971), which are both recited directly below.
The .alpha.-Ketobutryate/Pyruvate Assay
In the first step of this assay, 1 ml volumes of 100 mM phosphate buffer pH 8.0, containing also 10 .mu.M pyridoxal phosphate, and different concentrations (25 .mu.M-25 mM) of DL-homocysteine, or L-methionine, or L-cysteine, respectively, were incubated, for 10 min at 37.degree. C., with a sufficient sample (typically 50 .mu.l) of crude cell extract (cells were sonicated, and the supernatant was recovered following centrifilgation) to provide about 1-100 units of homocysteinase ("HCYase") enzyme. The reactions were stopped by adding 0.1 ml of 50% TCA. The suspensions were then centrifuged using an Eppendorf centrifuge at 13k rpm for 2 minutes. 0.5 ml samples of the supernatants were then added to 0.5 ml of 0.05% 3-methyl-2-benzothiazolinone hydrazone ("MBTH") in 0.8 ml of 1M sodium acetate, pH 5.2 and incubated at 50.degree. C. for 30 min. The amount of reaction products was determined for each sample, by spectrophotometry at OD.sub.320. The amount of protein was determined with a Bio-Rad 500-0006 kit (Bio-Rad, Richmond, Calif.) with bovine serum albumin as a standard. The enzyme specific activity was calculated as units/mg protein, with one unit of enzyme defined as the amount that catalyzes the formation of 1 .mu.mol of .alpha.-ketobutyrate from homocysteine per minute. The assay procedure can, of course, also be used with purified homocysteinase samples that provide, for example, 1-100 units of enzyme per assay test.
The Dethiomethylation Screening Assay
As aforementioned, the assay used was a modification of the method of A. E. Braunstein et al. above. The standard reaction mnixture consisted of potassium phosphate buffer (pH 7.5, 100 mM), lead acetate (0.33 mM), and sufficient crude cell extract to provide 1-100 units of homocysteinase, to which mixture different concentrations (5 .mu.M-100 .mu.M) of substrate DL-homocysteine, or L-cysteine or L-methionine were added, such that the total reaction volume was 1.5 ml. After incubation at 37.degree. C. for 10 min, the determination of lead sulfide was obtained on a spectrophotometer at OD.sub.360. The assay procedure can also be used with purified homocysteinase samples, for example, those providing 1-100 units per assay test.
Purification of Product Homocysteinase
Following use of the above initial assay screens, homocysteinases ("HCYases") from promising clones were purified using protocols that included DEAE Sepharose Fast Flow chromatography (for resultant enzyme activity profiles from the pAC2-1 clone, see FIG. 3), or included nickel-NTA affinity chromatography (for resultant enzyme activity profiles from the pAC2-1 clone, see FIG. 4).
Cell Growth Conditions
10 .mu.l of frozen E. coli stock corresponding to a particular clone was seeded into 5 ml LB medium (Fisher) containing also 10 .mu.g/ml ampicillin, and cultured overnight at 30.degree. C. with moderate shaking (300 rpm). The culture was then divided into 2 fresh 100 ml volumes of LB medium in 500 ml flasks, and further cultured at 30.degree. C. for 6 hours, also at 300 rpm. The entire culture was then divided into 18 flasks (each of 6 liters) containing 800 ml of LB medium. Growth was continued, overnight, at 37.degree. C. at 300 rpm and an OD.sub.600 of approximately 10 was achieved. The bacteria were then spun down at 4000 g permitting replacement of the growth medium with fresh LB, and the incubation was continued for a further 6 hours, again at 37.degree. C. and 300 rpm. When the OD.sub.600 reached 20, the bacteria were harvested by centrifugation for 10 minutes at 4000 g, 4.degree. C.
Pre-treatment Prior to Chromatopraphy
The bacterial pellet was first suspended in extraction solution (20 mM potassium phosphate, 10 .mu.M pyridoxal phosphate and 0.01% .beta.-mercaptoethanol, pH 9.0), and the cells were then disrupted with a cavitator-type homogenizer (model HC 8000, Microfluidics Corporation, Newton, Mass.). The suspension was centrifuged with a refrigerated centrifuge (Sorvall, superspeed RC2-B) at 8000 g, 4.degree. C. for 30 minutes. The supernatant was then collected, and subject to ultrafiltration using a preparative scale device (model TFF PLHK 100 k, Millipore, Bedford, Mass.) using a 2.5 ft.sup.2 pressure cartridge containing lOmM potassium phosphate buffer, pH 8.3). The pH was adjusted to 7.2 during the ultrafiltration.
Chromatographic Conditions-First Column
The above-derived concentrate (at pH 7.2) was applied to a first column (100 mm diameter .times.30 cm) containing a 2400 ml packed volume of DEAE Sepharose.RTM. FF (Pharmacia, Uppsala, Sweden) in 40 mM KCI-PPM buffer (40 mM potassium chloride; and 10 mM potassium phosphate, 10 .mu.M pyridoxal phosphate, 0.01% .beta.-mercaptoethanol, pH 7.2). After loading the protein sample, the column was pre-washed with about 10 volumes of 40 mM KCl-PPM buffer until the OD.sub.280 dropped below 0.1. The protein was then eluted with a linear gradient of 40-300 mM KCl in PPM buffer, and 500 ml fractions were collected. The fractions containing homocysteinase were identified by their yellow color, and an activity assay.
Chromatographic Conditions-Second Column
Following a 24 hour dialysis period against a solution of 80 mM KCl, 10 mM potassium phosphate, pH 8.3, the recovered eluate (about 2-5 mg/ml representing a recovery of 5-10 total grams protein) was applied to a second column. After loading, the second column (Pharmacia XK 50/30 filled with DEAE Sepharose.RTM. FF - 500 ml volume, 50 mm diameter .times.25 cm) was pre-washed with 4 volumes of 80 mM KCl, 10 mM potassium phosphate, pH 8.3 (at a flow rate of about 6-8 ml/minute) until the OD.sub.280 dropped below 0.1. The homocysteinase was then eluted with a linear gradient of 80 to 300 mM potassium chloride in 10 mM potassium phosphate buffer (pH 8.3). Eluate was collected in 300 ml fractions, and active fractions were identifiable by yellow color and homocysteinase enzyme activity. Enzyme activity results (toward homocysteine, cysteine, and methionine) for homocysteinase purified in this manner are discussed in Example 8 below (see also FIG. 3).
Alternatively, an additional two stage strategy may be used. In the first stage, the partitioning material was DEAE Sepharose.RTM. FF, and loading and pre-washing were conducted with 20 mM sodium phosphate buffer, pH 7.2. Elution of the protein was accomplished using a linear gradient (8 ml/min) from 20 mM sodium phosphate buffer, pH 7.2 (solution A) to 20 mM sodium phosphate buffer, pH 7.2, 500 mM NaCl (solution B). In the second stage, the partitioning material was phenyl Sepharose.RTM. 6-FF, and loading and pre-washing were conducted with 0.6 M NH.sub.4 SO.sub.4 in 20 mM sodium phosphate buffer, pH 7.2. Elution of the protein was accomplished using a linear gradient (5 ml/min) from 0.6 M NH.sub.4 SO.sub.4, 20 mM sodium phosphate buffer, pH 7.2 (solution A) to 20 mM sodium phosphate buffer, pH 7.2, (solution B). The following purification results were obtained for this alternate procedure. The above-described cell-lysate contained 8400 units of homocysteinase at a specific activity (units/mg) of 5.2. Following completion of pre-column procedures, 6,300 units were recovered at a specific activity of 64 (about 75% yield). Upon completion of the DEAE Sepharose.RTM. -FF step (first column), 5,040 units were recovered at a specific activity of 172 (60% yield), while after the phenyl Sepharose.RTM. 6-FF step (second column), 4,200 units remained at a specific activity of 300 (50% yield).
Analysis of Resultant Homocysteinase
For EPLC analysis, an L-6200A Intelligent pump (Hitachi, Ltd., Tokyo, Japan) with a Supelco Progel.TM. TSK column (G3000 SW.sub.XL, 30 cm.times.7.8 mm, Supelco, Bellefonte, Pa.) was used. Typically samples of a 20 .mu.l size (containing about 0.1 to 0.5 mg/ml protein were loaded, and eluted with a solution of 0.12 M NaCl, 10 mM sodium phosphate buffer, pH 7.2, at a flow rate of about 1 ml/min. The protein containing fractions were identified with a spectrophotometer (Hitachi U2000) at a wavelength of 280 nm. Bovine serum albumin (MW 66,000) and .beta.-amylase from sweet potato (MW 200,000) (Sigma, St. Louis, Mo.) were used as MW standards. Resultant retetion times were: for BSA, 8.88 min; for .beta.-amylase, 7.82 min; and, for the product homocysteinase, 8.28 minutes.
Electrophoresis of resultant proteins was carried out on (non-reducing) 7.5% or 10% polyacrylamide-precasted plates in 0.2 M Tris-glycine buffer, pH 8.3, with and without 0.1% SDS. The molecular weight standards used were the Kaleidoscope Prestained Standards (Bio-Rad, Richmond, Calif.). The product homocysteinase resolved as a single band of about 43 kD in the presence of 0.1% SDS, and as a single band at about 172 kD absent 0.1% SDS.
DNA sequencing of suitable clones was then performed by ACGT Inc. (Northbrook, Ill.) using T7 DNA polymerase and the dideoxy nucleotide termination reaction. The primer walking method was used, and the sequences were analyzed on a DNA analyzer.
Purification of Homocosteinase as a 6.times.Histidine-Tagged Protein using Ni-NTA Methodology
An alternate method to purify recombinant homocysteinase from E. coil involves use of nickel-NTA affinity chromatography. This technology takes advantage of the affinity of protein histidine imidazoles for nickel cations immobilized in the NTA resin matrix. In order to take full advantage of this technology (Qiagen Company, Germany), a sequence of 6 additional histidine residues is added (preferably by modification of an encoding DNA which is then expressed) to the protein on the N-terminal side of the natural Met.sup.1 of the homocysteinase (see Example 7 above, and SEQ ID NOS 9 and 10).
According to this purification procedure (for additional information, see also "The QIAexpressionist, A handbook for high level expression and purification of 6.times.His-tagged proteins" March 1997, 3rd edition, available from Qiagen) 100 ml of densely grown culture of E. coli BL21 (DE3), clone pAC2-1 were harvested by centrifugation, and the resultant pellet was resuspended in 4 ml lysis buffer (300 mM NaCl, 10 mM imidazole, 50 mM NaH.sub.2 PO.sub.4, pH 8.0). The resultant cell suspension was then sonicated on ice for one minute.
Cellular debris was removed using a benchtop centrifuge set at maximum speed for 20 minutes. The clear supernatant was then mixed with 1 ml of Ni-NTA slurry (Qiagen), and gently shaken on ice for 60 minutes to allow adsorption. The mixture was then transfered to a disposable polypropylene column and the flowthrough fraction was discarded. The Ni-NTA resin beads were then washed with 8 ml of wash buffer (300 mM NaCl, 20 mM imidazole, 50 mM NaH.sub.2 PO.sub.4, pH 8.0), after which the recombinant protein was finally collected by elution using 2 ml of elution buffer (300 mM NaCl, 250 mM imidazole, 50 mM NaH.sub.2 PO.sub.4, pH 8.0). The purified protein was then characterized as above. Enzyme activity results (toward homocysteine, cysteine, and methionine) for homocysteinase purified in this fashion are described in Example 8 below (see also FIG. 4).
Example 8
Representative Catalytic Properties of the Homocysteinases of the Invention
FIGS. 2 through 4 evidence the significantly enhanced usefulness of the homocysteinases of the invention for single step assays. The results depicted in FIG. 2 reflect use of a crude lysate of the host E. coil cells containing the pAC2-1 clone, and show specific activity (u/mg) with respect to the 3 substrates (homocysteine, methionine, and cysteine) when each is present in a separate assay at 25 mM. The results depicted in FIGS. 3 and 4 (again for E. coli containing the pAC2-1 clone) reflect relative activity of purified enzyme preparations for homocysteine, methionine, and cysteine. For the assays shown in FIG. 3, the enzyme was purified using a DEAE Sepharose Fast Flowprocedure as described in Example 7; for FIG. 4, the purification procedure of Example 7 involving nickel-NTA agarose affinity reagent, was used (see above under the heading "The .alpha.-ketobutyrate assay/pyruvate assay" for methodology).
It is well recognized that numerous procedures are available to purify recombinant homocysteinases from host E. coli cells. As exemplified, the novel homocysteinases of the invention exhibit activities toward homocysteine (using the assays of the invention, see for example, Example 1) that are typically 100-fold, and even up to about 1000-fold, higher than their activities exhibited toward cysteine or methionine.
Example 9
Single Step Clinical Assays
It will be immediately recognized that procedures for multi-step assays of homocysteine in biological fluids are readily adapted for use in simplified single step assays in order to take advantage of the substrate specificity of novel species of homocysteinase. The concentrations of homocysteinase appropriate for such procedures are broadly equivalent those described above in Example 1, or elsewhere in the Specification, or are readily determined.
According to the practice of the invention, the concentration of homocysteine in a biological sample such as, for example, whole blood, blood plasma, or tissue fluid may be determined with sufficient accuracy to provide valuable diagnostic information to physicians, absent interference from contaminating concentrations of cysteine and/or methionine.
In a representative example, the concentration of cysteine in normal blood plasma may be about 30-120 .mu.M, and that of homocysteine only about 5-15 .mu.M. According to the practice of the invention, homocysteineases are provided wherein the relative activity of said enzymes toward homocysteine and cysteine are such that the apparent concentration of homocysteine measured in such a sample (which reflects also a contribution from cysteine) is less that about 125%, preferably less than about 110%, and most preferably less than about 105%, of the actual value thereof In a further prefered example of the invention, for example using the novel Trichomonas homocysteinase expressed from pAC2-1, the apparent concentration of homocysteine measured in a single step assay reflects no more than about a 1% contribution from cysteine.
Homocysteinase isolated from Trichomonas vaginalis (which may reflect expression from more than one gene) was reported (see Lockwood et al., 1991 above) to have a K.sub.m for homocysteine of about 0.5 mM, whereas K.sub.m values determined for the novel enzyme expressed from the pAC2-1 clone are (all at 37.degree. C., pH 8.0): 4.8 mM, 3.45 mM, and 3.1 mM for homocysteine, cysteine, and methionine, respectively. The K.sub.m calculations were determined from assays carried out in one ml volumes of 100 mM phosphate buffer, pH 8.0 containing 10 .mu.M pyridoxal phosphate at different concentrations (10 .mu.M to 1.6 mM) of, separately, DL-homocysteine, L-methionine, or L-cysteine, for 10 minutes at 37.degree. C., pH 8.0 using 50 .mu.l of enzyme (300 units/ml). The reaction was stopped by adding 0.1 ml of 50% TCA. The resultant suspension was then centrifuged with an Eppendorf centrifuge at 13 k rpm for 2 minutes. 0.5 ml samples of supernatant were then added to 0.5 ml volumes of 0.05% 3-methyl -2-benzothiazolinone hydrazone in 0.8 ml of 1 M sodium acetate, pH 5.2, and incubated at 50.degree. C. for 30 minutes. The amount of reaction product was then determined by spectrophotometry at OD.sub.320. The K.sub.cat (turnover number) values reported in FIG. 5, were determined from the calculation of V.sub.max values using standard kinetic expressions and plots.
It is apparent that the kinetics of the enzyme expressed from the pAC2-1 clone are quite different from those of the wild type enzyme. An additional aspect of the present invention involves recognition that although certain changes have been described in the amino acid sequence of the T. vaginalis enzyme in order to provide for enhanced kinetic properties, those skilled in the art will recognize other potential mechanisms to accomplish this. An example thereof is covalent modification of the enzyme, whether or not at the active site. Such other methods of modifying a homocysteinase are within the practice of the invention if they lead to production of an enzyme having kinetic properties such as those first disclosed herein.
In further support of the present disclosure, on Sep. 26, 1997, a deposit of biological material of confirmed viability was made with the American Type Culture Collection, Rockville, Md., USA under the Budapest Treaty. The material is identified as E. coli BL21 (DE3), clone pAC2-1, and has been assigned ATCC number 98549. Upon the granting of a patent herein, all restrictions on the availability of this material to the public will be irrevocably removed.
__________________________________________________________________________# SEQUENCE LISTING - - - - (1) GENERAL INFORMATION: - - (iii) NUMBER OF SEQUENCES: 14 - - - - (2) INFORMATION FOR SEQ ID NO:1: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 12 amino - #acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: - - Cys Ser Arg Ala Asp Ile Ile Ala Lys Val Ly - #s Ser 1 5 - # 10 - - - - (2) INFORMATION FOR SEQ ID NO:2: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 12 amino - #acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: - - Val Gly Ser Gln Ala Leu Val Asp Arg Ile Ar - #g Leu 1 5 - # 10 - - - - (2) INFORMATION FOR SEQ ID NO:3: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 3 amino - #acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: - - Asp Val Asp 1 - - - - (2) INFORMATION FOR SEQ ID NO:4: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 3 amino - #acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: - - Glu Leu Lys 1 - - - - (2) INFORMATION FOR SEQ ID NO:5: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 4 amino - #acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: - - Cys His Val Val 1 - - - - (2) INFORMATION FOR SEQ ID NO:6: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 4 amino - #acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: - - Ala Leu Gln Leu 1 - - - - (2) INFORMATION FOR SEQ ID NO:7: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 10 amino - #acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7: - - Cys Glu Asn Val Gln Asp Ile Ile Asp Asp 1 5 - # 10 - - - - (2) INFORMATION FOR SEQ ID NO:8: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 10 amino - #acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8: - - Gly Leu Glu Asp Ile Asp Asp Leu Leu Ala 1 5 - # 10 - - - - (2) INFORMATION FOR SEQ ID NO:9: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1240 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 18..1226 - - (ix) FEATURE: (A) NAME/KEY: mat.sub.-- - #peptide (B) LOCATION: 39 - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9: - - AAGAAGGAGA TATACAT ATG CAT CAT CAT CAT CAT CAC - #ATG TCT CAC GAG 50 - # Met His His His His His His Met Ser His - #Glu - # -7 -5 - # 1 - - AGA ATG ACC CCA GCA ACA GCA TGC ATC CAT GC - #T AAT CCA CAG AAG GAT 98 Arg Met Thr Pro Ala Thr Ala Cys Ile His Al - #a Asn Pro Gln Lys Asp 5 - # 10 - # 15 - # 20 - - CAG TTT GGA GCA GCC ATC CCA CCA ATC TAC CA - #A ACA TCA ACA TTC GTT 146 Gln Phe Gly Ala Ala Ile Pro Pro Ile Tyr Gl - #n Thr Ser Thr Phe Val 25 - # 30 - # 35 - - TTC GAT AAC TGC CAA CAG GGT GGA AAC AGA CT - #C GCT GGT CAG GAA TCC 194 Phe Asp Asn Cys Gln Gln Gly Gly Asn Arg Le - #u Ala Gly Gln Glu Ser 40 - # 45 - # 50 - - GGC TAC ATC TAC ACA CGT CTC GGC AAC CCA AC - #A GTT TCA AAC CTC GAA 242 Gly Tyr Ile Tyr Thr Arg Leu Gly Asn Pro Th - #r Val Ser Asn Leu Glu 55 - # 60 - # 65 - - GGC AAG ATC GCC TTC CTC GAG AAA ACA GAA GC - #A TGC GTT GCC ACA TCT 290 Gly Lys Ile Ala Phe Leu Glu Lys Thr Glu Al - #a Cys Val Ala Thr Ser 70 - # 75 - # 80 - - TCT GGC ATG GGT GCC ATT GCT GCT ACA GTT TT - #G ACA ATC CTC AAG GCC 338 Ser Gly Met Gly Ala Ile Ala Ala Thr Val Le - #u Thr Ile Leu Lys Ala 85 - # 90 - # 95 - #100 - - GGA GAT CAC TTA ATC TCC GAT GAG TGC CTT TA - #T GGC TGC ACA CAT GCT 386 Gly Asp His Leu Ile Ser Asp Glu Cys Leu Ty - #r Gly Cys Thr His Ala 105 - # 110 - # 115 - - CTC TTT GAG CAC GCA TTG ACA AAG TTC GGC AT - #C CAG GTC GAC TTC ATC 434 Leu Phe Glu His Ala Leu Thr Lys Phe Gly Il - #e Gln Val Asp Phe Ile 120 - # 125 - # 130 - - AAC ACA GCC ATC CCA GGC GAG GTC AAG AAG CA - #C ATG AAG CCA AAC ACA 482 Asn Thr Ala Ile Pro Gly Glu Val Lys Lys Hi - #s Met Lys Pro Asn Thr 135 - # 140 - # 145 - - AAG ATT GTC TAT TTC GAG ACA CCA GCC AAC CC - #A ACA CTC AAG ATC ATC 530 Lys Ile Val Tyr Phe Glu Thr Pro Ala Asn Pr - #o Thr Leu Lys Ile Ile 150 - # 155 - # 160 - - GAC ATG GAG CGC GTC TGC AAG GAA GCC CAC AG - #C CAG GAG GGC GTC TTA 578 Asp Met Glu Arg Val Cys Lys Glu Ala His Se - #r Gln Glu Gly Val Leu 165 1 - #70 1 - #75 1 -#80 - - GTT ATC GCC GAT AAC ACA TTC TGC TCA CCA AT - #G ATC ACA AAC CCAGTC 626 Val Ile Ala Asp Asn Thr Phe Cys Ser Pro Me - #t Ile Thr Asn Pro Val 185 - # 190 - # 195 - - GAC TTT GGC GTC GAT GTT GTT GTC CAC TCT GC - #A ACA AAG TAC ATC AAC 674 Asp Phe Gly Val Asp Val Val Val His Ser Al - #a Thr Lys Tyr Ile Asn 200 - # 205 - # 210 - - GGC CAC ACA GAT GTC GTC GCT GGC CTT ATC TG - #T GGC AAG GCT GAC CTC 722 Gly His Thr Asp Val Val Ala Gly Leu Ile Cy - #s Gly Lys Ala Asp Leu 215 - # 220 - # 225 - - CTT CAA CAG ATT CGT ATG GTT GGT ATC AAG GA - #T ATC ACA GGA TCT GTT 770 Leu Gln Gln Ile Arg Met Val Gly Ile Lys As - #p Ile Thr Gly Ser Val 230 - # 235 - # 240 - - ATC AGC CCA CAC GAC GCT TGG CTC ATC ACA CG - #T GGC CTC TCA ACA CTC 818 Ile Ser Pro His Asp Ala Trp Leu Ile Thr Ar - #g Gly Leu Ser Thr Leu 245 2 - #50 2 - #55 2 -#60 - - AAC ATC AGA ATG AAG GCT GAG AGC GAG AAC GC - #C ATG AAG GTC GCTGAG 866 Asn Ile Arg Met Lys Ala Glu Ser Glu Asn Al - #a Met Lys Val Ala Glu 265 - # 270 - # 275 - - TAC CTC AAA TCT CAC CCA GCC GTT GAG AAG GT - #T TAC TAC CCA GGC TTC 914 Tyr Leu Lys Ser His Pro Ala Val Glu Lys Va - #l Tyr Tyr Pro Gly Phe 280 - # 285 - # 290 - - GAG GAC CAC GAG GGC CAC GAT ATC GCT AAG AA - #G CAG ATG AGA ATG TAC 962 Glu Asp His Glu Gly His Asp Ile Ala Lys Ly - #s Gln Met Arg Met Tyr 295 - # 300 - # 305 - - GGT TCA ATG ATC ACA TTC ATC CTC AAG TCC GG - #C TTC GAA GGC GCT AAG 1010 Gly Ser Met Ile Thr Phe Ile Leu Lys Ser Gl - #y Phe Glu Gly Ala Lys 310 - # 315 - # 320 - - AAG CTC CTC GAC AAC CTC AAG CTT ATC ACA CT - #T GCA GTT TCC CTT GGT 1058 Lys Leu Leu Asp Asn Leu Lys Leu Ile Thr Le - #u Ala Val Ser Leu Gly 325 3 - #30 3 - #35 3 -#40 - - GGC TGC GAG TCC CTC ATC CAG CAC CCA GCT TC - #A ATG ACT CAC GCTGTC 1106 Gly Cys Glu Ser Leu Ile Gln His Pro Ala Se - #r Met Thr His Ala Val 345 - # 350 - # 355 - - GTT CCA AAG GAG GAG CGT GAG GCC GCT GGT AT - #T ACA GAT GGC ATG ATC 1154 Val Pro Lys Glu Glu Arg Glu Ala Ala Gly Il - #e Thr Asp Gly Met Ile 360 - # 365 - # 370 - - CGC CTT TCT GTC GGT ATT GAA GAT GCC GAC GA - #A CTC ATC GCT GAT TTC 1202 Arg Leu Ser Val Gly Ile Glu Asp Ala Asp Gl - #u Leu Ile Ala Asp Phe 375 - # 380 - # 385 - - AAA CAG GGC CTT GAC GCT CTT TTA TAAGGATCCT CT - #AG - # 1240 Lys Gln Gly Leu Asp Ala Leu Leu 390 - # 395 - - - - (2) INFORMATION FOR SEQ ID NO:10: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 403 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: protein - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10: - - Met His His His His His His Met Ser His Gl - #u Arg Met Thr Pro Ala -7 -5 - # 1 - # 5 - - Thr Ala Cys Ile His Ala Asn Pro Gln Lys As - #p Gln Phe Gly Ala Ala 10 - # 15 - # 20 - # 25 - - Ile Pro Pro Ile Tyr Gln Thr Ser Thr Phe Va - #l Phe Asp Asn Cys Gln 30 - # 35 - # 40 - - Gln Gly Gly Asn Arg Leu Ala Gly Gln Glu Se - #r Gly Tyr Ile Tyr Thr 45 - # 50 - # 55 - - Arg Leu Gly Asn Pro Thr Val Ser Asn Leu Gl - #u Gly Lys Ile Ala Phe 60 - # 65 - # 70 - - Leu Glu Lys Thr Glu Ala Cys Val Ala Thr Se - #r Ser Gly Met Gly Ala 75 - # 80 - # 85 - - Ile Ala Ala Thr Val Leu Thr Ile Leu Lys Al - #a Gly Asp His Leu Ile 90 - # 95 - #100 - #105 - - Ser Asp Glu Cys Leu Tyr Gly Cys Thr His Al - #a Leu Phe Glu His Ala 110 - # 115 - # 120 - - Leu Thr Lys Phe Gly Ile Gln Val Asp Phe Il - #e Asn Thr Ala Ile Pro 125 - # 130 - # 135 - - Gly Glu Val Lys Lys His Met Lys Pro Asn Th - #r Lys Ile Val Tyr Phe 140 - # 145 - # 150 - - Glu Thr Pro Ala Asn Pro Thr Leu Lys Ile Il - #e Asp Met Glu Arg Val 155 - # 160 - # 165 - - Cys Lys Glu Ala His Ser Gln Glu Gly Val Le - #u Val Ile Ala Asp Asn 170 1 - #75 1 - #80 1 -#85 - - Thr Phe Cys Ser Pro Met Ile Thr Asn Pro Va - #l Asp Phe Gly ValAsp 190 - # 195 - # 200 - - Val Val Val His Ser Ala Thr Lys Tyr Ile As - #n Gly His Thr Asp Val 205 - # 210 - # 215 - - Val Ala Gly Leu Ile Cys Gly Lys Ala Asp Le - #u Leu Gln Gln Ile Arg 220 - # 225 - # 230 - - Met Val Gly Ile Lys Asp Ile Thr Gly Ser Va - #l Ile Ser Pro His Asp 235 - # 240 - # 245 - - Ala Trp Leu Ile Thr Arg Gly Leu Ser Thr Le - #u Asn Ile Arg Met Lys 250 2 - #55 2 - #60 2 -#65 - - Ala Glu Ser Glu Asn Ala Met Lys Val Ala Gl - #u Tyr Leu Lys SerHis 270 - # 275 - # 280 - - Pro Ala Val Glu Lys Val Tyr Tyr Pro Gly Ph - #e Glu Asp His Glu Gly 285 - # 290 - # 295 - - His Asp Ile Ala Lys Lys Gln Met Arg Met Ty - #r Gly Ser Met Ile Thr 300 - # 305 - # 310 - - Phe Ile Leu Lys Ser Gly Phe Glu Gly Ala Ly - #s Lys Leu Leu Asp Asn 315 - # 320 - # 325 - - Leu Lys Leu Ile Thr Leu Ala Val Ser Leu Gl - #y Gly Cys Glu Ser Leu 330 3 - #35 3 - #40 3 -#45 - - Ile Gln His Pro Ala Ser Met Thr His Ala Va - #l Val Pro Lys GluGlu 350 - # 355 - # 360 - - Arg Glu Ala Ala Gly Ile Thr Asp Gly Met Il - #e Arg Leu Ser Val Gly 365 - # 370 - # 375 - - Ile Glu Asp Ala Asp Glu Leu Ile Ala Asp Ph - #e Lys Gln Gly Leu Asp 380 - # 385 - # 390 - - Ala Leu Leu 395 - - - - (2) INFORMATION FOR SEQ ID NO:11: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1191 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 1..1188 (D) OTHER INFORMATION: - #/codon.sub.-- start= 1 - - (ix) FEATURE: (A) NAME/KEY: mat.sub.-- - #peptide (B) LOCATION: 1 - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11: - - ATG TCT CAC GAG AGA ATG ACC CCA GCA ACA GC - #A TGC ATC CAT GCT AAT 48 Met Ser His Glu Arg Met Thr Pro Ala Thr Al - #a Cys Ile His Ala Asn 1 5 - # 10 - # 15 - - CCA CAG AAG GAT CAG TTT GGA GCA GCC ATC CC - #A CCA ATC TAC CAA ACA 96 Pro Gln Lys Asp Gln Phe Gly Ala Ala Ile Pr - #o Pro Ile Tyr Gln Thr 20 - # 25 - # 30 - - TCA ACA TTC GTT TTC GAT AAC TGC CAA CAG GG - #T GGA AAC AGA TTC GCT 144 Ser Thr Phe Val Phe Asp Asn Cys Gln Gln Gl - #y Gly Asn Arg Phe Ala 35 - # 40 - # 45 - - GGT CAG GAA TCC GGC TAC ATC TAC ACA CGT CT - #C GGC AAC CCA ACA GTT 192 Gly Gln Glu Ser Gly Tyr Ile Tyr Thr Arg Le - #u Gly Asn Pro Thr Val 50 - # 55 - # 60 - - TCA AAC CTC GAA GGC AAG ATC GCC TTC CTC GA - #G AAA ACA GAA GCA TGC 240 Ser Asn Leu Glu Gly Lys Ile Ala Phe Leu Gl - #u Lys Thr Glu Ala Cys 65 - # 70 - # 75 - # 80 - - GTT GCC ACA TCT TCT GGC ATG GGT GCC ATT GC - #T GCT ACA GTT TTG ACA 288 Val Ala Thr Ser Ser Gly Met Gly Ala Ile Al - #a Ala Thr Val Leu Thr 85 - # 90 - # 95 - - ATC CTC AAG GCC GGA GAT CAC TTA ATC TCC GA - #T GAG TGC CTT TAT GGC 336 Ile Leu Lys Ala Gly Asp His Leu Ile Ser As - #p Glu Cys Leu Tyr Gly 100 - # 105 - # 110 - - TGC ACA CAT GCT CTC TTT GAG CAC GCA TTG AC - #A AAG TTC GGC ATC CAG 384 Cys Thr His Ala Leu Phe Glu His Ala Leu Th - #r Lys Phe Gly Ile Gln 115 - # 120 - # 125 - - GTC GAC TTC ATC AAC ACA GCC ATC CCA GGC GA - #G GTC AAG AAG CAC ATG 432 Val Asp Phe Ile Asn Thr Ala Ile Pro Gly Gl - #u Val Lys Lys His Met 130 - # 135 - # 140 - - AAG CCA AAC ACA AAG ATT GTC TAT TTC GAG AC - #A CCA GCC AAC CCA ACA 480 Lys Pro Asn Thr Lys Ile Val Tyr Phe Glu Th - #r Pro Ala Asn Pro Thr 145 1 - #50 1 - #55 1 -#60 - - CTC AAG ATC ATC GAC ATG GAG CGC GTC TGC AA - #G GAC GCC CAC AGCCAG 528 Leu Lys Ile Ile Asp Met Glu Arg Val Cys Ly - #s Asp Ala His Ser Gln 165 - # 170 - # 175 - - GAG GGC GTC TTA GTT ATC GCC GAT AAC ACA TT - #C TGC TCA CCA ATG ATC 576 Glu Gly Val Leu Val Ile Ala Asp Asn Thr Ph - #e Cys Ser Pro Met Ile 180 - # 185 - # 190 - - ACA AAC CCA GTC GAC TTT GGC GTC GAT GTT GT - #T GTC CAC TCT GCA ACA 624 Thr Asn Pro Val Asp Phe Gly Val Asp Val Va - #l Val His Ser Ala Thr 195 - # 200 - # 205 - - AAG TAC ATC AAC GGC CAC ACA GAT GTC GTC GC - #T GGC CTT ATC TGT GGC 672 Lys Tyr Ile Asn Gly His Thr Asp Val Val Al - #a Gly Leu Ile Cys Gly 210 - # 215 - # 220 - - AAG GCT GAC CTC CTT CAA CAG ATT CGT ATG GT - #T GGT ATC AAG GAT ATC 720 Lys Ala Asp Leu Leu Gln Gln Ile Arg Met Va - #l Gly Ile Lys Asp Ile 225 2 - #30 2 - #35 2 -#40 - - ACA GGA TCT GTT ATC AGC CCA CAC GAC GCT TG - #G CTC ATC ACA CGTGGC 768 Thr Gly Ser Val Ile Ser Pro His Asp Ala Tr - #p Leu Ile Thr Arg Gly 245 - # 250 - # 255 - - CTC TCA ACA CTC AAC ATC AGA ATG AAG GCT GA - #G AGC GAG AAC GCC ATG 816 Leu Ser Thr Leu Asn Ile Arg Met Lys Ala Gl - #u Ser Glu Asn Ala Met 260 - # 265 - # 270 - - AAG GTC GCT GAG TAC CTC AAA TCT CAC CCA GC - #C GTT GAG AAG GTT TAC 864 Lys Val Ala Glu Tyr Leu Lys Ser His Pro Al - #a Val Glu Lys Val Tyr 275 - # 280 - # 285 - - TAC CCA GGC TTC GAG GAC CAC GAG GGC CAC GA - #T ATC GCT AAG AAG CAG 912 Tyr Pro Gly Phe Glu Asp His Glu Gly His As - #p Ile Ala Lys Lys Gln 290 - # 295 - # 300 - - ATG AGA ATG TCG GGT TCA ATG ATC ACA TTC AT - #C CTC AAG TCC GGC TTC 960 Met Arg Met Ser Gly Ser Met Ile Thr Phe Il - #e Leu Lys Ser Gly Phe 305 3 - #10 3 - #15 3 -#20 - - GAA GGC GCT AAG AAG CTC CTC GAC AAC CTC AA - #G CTT ATC ACA CTTGCA 1008 Glu Gly Ala Lys Lys Leu Leu Asp Asn Leu Ly - #s Leu Ile Thr Leu Ala 325 - # 330 - # 335 - - GTT TCC CTT GGT GGC TGC GAG TCC CTC ATC CA - #G CAC CCA GCT TCA ATG 1056 Val Ser Leu Gly Gly Cys Glu Ser Leu Ile Gl - #n His Pro Ala Ser Met 340 - # 345 - # 350 - - ACT CAC GCT GTC GTT CCA AAG GAG GAG CGT GA - #G GCC GCT GGT ATT ACA 1104 Thr His Ala Val Val Pro Lys Glu Glu Arg Gl - #u Ala Ala Gly Ile Thr 355 - # 360 - # 365 - - GAT GGC ATG ATC CGC CTT TCT GTC GGT ATT GA - #A GAT GCC GAC GAA CTC 1152 Asp Gly Met Ile Arg Leu Ser Val Gly Ile Gl - #u Asp Ala Asp Glu Leu 370 - # 375 - # 380 - - ATC GCT GAT TTC AAA CAG GGC CTT GAC GCT CT - #T TTA TAA - # 1191 Ile Ala Asp Phe Lys Gln Gly Leu Asp Ala Le - #u Leu 385 3 - #90 3 - #95 - - - - (2) INFORMATION FOR SEQ ID NO:12: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 396 amino - #acids (B) TYPE: amino acid (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: protein - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12: - - Met Ser His Glu Arg Met Thr Pro Ala Thr Al - #a Cys Ile His Ala Asn 1 5 - # 10 - # 15 - - Pro Gln Lys Asp Gln Phe Gly Ala Ala Ile Pr - #o Pro Ile Tyr Gln Thr 20 - # 25 - # 30 - - Ser Thr Phe Val Phe Asp Asn Cys Gln Gln Gl - #y Gly Asn Arg Phe Ala 35 - # 40 - # 45 - - Gly Gln Glu Ser Gly Tyr Ile Tyr Thr Arg Le - #u Gly Asn Pro Thr Val 50 - # 55 - # 60 - - Ser Asn Leu Glu Gly Lys Ile Ala Phe Leu Gl - #u Lys Thr Glu Ala Cys 65 - # 70 - # 75 - # 80 - - Val Ala Thr Ser Ser Gly Met Gly Ala Ile Al - #a Ala Thr Val Leu Thr 85 - # 90 - # 95 - - Ile Leu Lys Ala Gly Asp His Leu Ile Ser As - #p Glu Cys Leu Tyr Gly 100 - # 105 - # 110 - - Cys Thr His Ala Leu Phe Glu His Ala Leu Th - #r Lys Phe Gly Ile Gln 115 - # 120 - # 125 - - Val Asp Phe Ile Asn Thr Ala Ile Pro Gly Gl - #u Val Lys Lys His Met 130 - # 135 - # 140 - - Lys Pro Asn Thr Lys Ile Val Tyr Phe Glu Th - #r Pro Ala Asn Pro Thr 145 1 - #50 1 - #55 1 -#60 - - Leu Lys Ile Ile Asp Met Glu Arg Val Cys Ly - #s Asp Ala His SerGln 165 - # 170 - # 175 - - Glu Gly Val Leu Val Ile Ala Asp Asn Thr Ph - #e Cys Ser Pro Met Ile 180 - # 185 - # 190 - - Thr Asn Pro Val Asp Phe Gly Val Asp Val Va - #l Val His Ser Ala Thr 195 - # 200 - # 205 - - Lys Tyr Ile Asn Gly His Thr Asp Val Val Al - #a Gly Leu Ile Cys Gly 210 - # 215 - # 220 - - Lys Ala Asp Leu Leu Gln Gln Ile Arg Met Va - #l Gly Ile Lys Asp Ile 225 2 - #30 2 - #35 2 -#40 - - Thr Gly Ser Val Ile Ser Pro His Asp Ala Tr - #p Leu Ile Thr ArgGly 245 - # 250 - # 255 - - Leu Ser Thr Leu Asn Ile Arg Met Lys Ala Gl - #u Ser Glu Asn Ala Met 260 - # 265 - # 270 - - Lys Val Ala Glu Tyr Leu Lys Ser His Pro Al - #a Val Glu Lys Val Tyr 275 - # 280 - # 285 - - Tyr Pro Gly Phe Glu Asp His Glu Gly His As - #p Ile Ala Lys Lys Gln 290 - # 295 - # 300 - - Met Arg Met Ser Gly Ser Met Ile Thr Phe Il - #e Leu Lys Ser Gly Phe 305 3 - #10 3 - #15 3 -#20 - - Glu Gly Ala Lys Lys Leu Leu Asp Asn Leu Ly - #s Leu Ile Thr LeuAla 325 - # 330 - # 335 - - Val Ser Leu Gly Gly Cys Glu Ser Leu Ile Gl - #n His Pro Ala Ser Met 340 - # 345 - # 350 - - Thr His Ala Val Val Pro Lys Glu Glu Arg Gl - #u Ala Ala Gly Ile Thr 355 - # 360 - # 365 - - Asp Gly Met Ile Arg Leu Ser Val Gly Ile Gl - #u Asp Ala Asp Glu Leu 370 - # 375 - # 380 - - Ile Ala Asp Phe Lys Gln Gly Leu Asp Ala Le - #u Leu 385 3 - #90 3 - #95 - - - - (2) INFORMATION FOR SEQ ID NO:13: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 51 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13: - - GGATTACATA TGCATCATCA TCATCATCAC ATGAGTGGCC ACGCTATCGA C - # 51 - - - - (2) INFORMATION FOR SEQ ID NO:14: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 34 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: - - GGATTAGGAT CCTTAGAGGA CTAAGTCGAG AGCC - # -# 34__________________________________________________________________________

Number	Name	Date
4940658	Allen et al.	Jul 1990
5438017	Allen et al.	Aug 1995
5478729	Van Atta et al.	Dec 1995
5631127	Sundrehagen	May 1997
5827645	Sundrehagen et al.	Oct 1998

Number	Date	Country
WO 9315220	Aug 1993	WOX
WO 9807872	Feb 1998	WOX
WO 9814562	Apr 1998	WOX

	Number	Date
Parent	941921	Oct 1997
Parent	918214	Aug 1997
Parent	899776	Jul 1997

High specificity homocysteinases and genes therefor

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Abstract

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US Referenced Citations (5)

Foreign Referenced Citations (3)

Non-Patent Literature Citations (44)

Continuation in Parts (3)

Entry
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