# Patent

## Title
Metabolic engineering of viomycin biosynthesis

## Abstract

The invention provides a nucleic acid molecule comprising at least a functional fragment of the viomycin biosynthetic gene cluster, functional proteins encoded by the cluster, expression cassettes and recombinant host cells comprising a functional fragment of the viomycin cluster, and methods for generating biologically active agents using the nucleic acid molecules of the present invention.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application No. 60/496,760 filed Aug. 21, 2003, which is incorporated herein by reference to the extent not inconsistent herewith.


GOVERNMENT SUPPORT
This invention was made with United States government support USDA/CSREES 03-CRHF-0-6055. The United States government has certain rights in the invention.


FIELD OF INVENTION
The invention relates to antibiotic production and more specifically relates to the gene cluster responsible for viomycin antibiotic production and resistance. Materials of the invention have utility in transforming cells to produce various tuberactinomycins, derivatives thereof, and novel compounds useful in the preparation of biologically active compounds.
BACKGROUND OF THE INVENTION
It was recently estimated that between the years 1998 and 2030 there will be 225 million new cases of tuberculosis (TB) and 79 million TB-related deaths (Murray, C. J. L., and J. A. Salomon, 1998). These numbers are astonishing considering that treatments for this disease, in the forms of vaccines or chemotherapy, have been available for more than 50 years (Kramnik, I., et al., 2000). Mycobacterium tuberculosis, the causative agent of TB, is notoriously slow-growing and, during infection, can persist in a latent form in many individuals. These attributes contribute to the reasons why typical chemotherapy regimens for TB last 6-9 months (Bloom, B. R., and J. D. McKinney, 1999) and why TB is so persistent. This prolonged treatment presents significant hurdles in developing new antibiotics and in retaining the efficacy of currently used antibiotics. Side effects and toxicity from a particular compound can be magnified when a patient takes a drug for this length of time, and there are increased incidences of poor adherence to the chemotherapy regimen by unmonitored patients, resulting in the development of multidrug-resistant TB (MDR-TB) infections. These facts, together with alarming interactions between HIV and TB infections that can result in increased numbers of infected individuals and MDR-TB (Dye, C., et al., 2002; Gupta, R., et al., 2001; Lawn, S. D., et al., 2002; Barnes, P. F., et al., 1991; Bloom, B. R., and C. J. Murray, 1992), make it of paramount importance to develop new chemotherapy agents or introduce modifications to current agents to reduce toxicity and increase activity against MDR-TB.
One of the earliest antibiotics developed for the treatment of a bacterial infection was streptomycin, and its initial (and continued) use was for the treatment of tuberculosis (TB), the clinical manifestation of a M. tuberculosis infection. For over 50 years additional antibiotics and a vaccine have been developed to fight this infection. However, despite these developments this organism remains a significant human health concern.
Currently, the successful treatment of TB typically requires the simultaneous use of at least three drugs. These drugs are grouped into “first-line” and “second-line” antibiotics. The first-line drugs (e.g. streptomycin) are used first because they are less toxic and less expensive. It has been recommended that the second-line drugs (including viomycin, tuberactinomycins and capreomycins) be reserved specifically for the treatment of MDR-TB (Croft, J., et al., 1997). Use of the second-line drugs is increasing because resistance to many, if not all, of first-line drugs is increasing (Frieden, T. R., et al., 1993; Goble, M., et al., 1993), and it has been proposed that MDR-TB will soon be the norm (Davies, J. 1996). It has, however, been more than 25 years since a new drug to combat TB has been introduced (Duncan, K., and J. C. Sacchettini, 2000). Thus there is a continuing need in the art for the identification of antibiotics useful for the treatment of TB and particularly MDR-TB.
The tuberactinomycin family (TUBs) of antibiotics, including viomycin (VIO), tuberactinomycins (TUBs), capreomycins (CAPs) and tuberactinamines (FIG. 1) are a family of cyclic peptide natural products that are important second-line antibiotics for the treatment of MDR-TB. In fact, certain TUBs are included on the World Health Organization's “List of Essential Medicines” because of their anti-MDR-TB activity (WHO, 2002). Initial interest in the tuberactinomycins stemmed from the observation that VIO, the first tuberactinomycin to be isolated (Bartz, Q. R., et al., 1951; Ehrlich, J., et al., 1951; Finlay, A. C., et al., 1951), had the unusual property of having higher antimicrobial activity against mycobacterial species than against other bacteria (Ehrlich, J., et al., 1951; Finlay, A. C., et al., 1951; Marsh, W. S., et al., 1953 U.S. Pat No. 2,633,445; Mayer, R. L., et al., 1954). Importantly, VIO was active against strains of M. tuberculosis that were resistant to streptomycin (Hobby, G. L., et al., 1953). More recently, TUBs (Nagata, A., et al., 1968) and CAPs (Herr, E. B. J., et al., 1962 U.S. Pat. No. 3,143,168) were found to share a similar spectrum of antimicrobial activity with VIO. Currently, TUB N (FIG. 1) is used in Asia for the treatment of M. tuberculosis (Tsukamura, M., et al., 1989) and M. avium complex (Shigeto, E., et al., 2001) infections, while the CAPs are used in combination with other anti-TB drugs to treat MDR-TB (Goble, M. 1994).
New TUB derivatives are needed to combat the ever-expanding mycobacterial resistance to these drugs. A recent study analyzing 46 different strains of M. tuberculosis from TB patients found that 10% of these strains were resistant to CAP (Fattorini, L., et al., 1999). The continued spread of resistance without the development of new therapeutic alternatives will be devastating for patients who have limited options for treatment. It has recently been reported that 15 of 158 TB patients required treatment with CAP because the use of the standard aminoglycosides (amikacin, kanamycin, or streptomycin) was not appropriate (Tahaoglu, K., et al., 2001). Without the option of CAP, these patients would face an uncertain future.
In addition to their historical use in treating TB, the TUBs and analogs thereof have become lead compounds for use in treating other bacterial infections such as vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus (Dirlam, J. P., et al., 1997; Linde II, R. G., et al., 1997; Lyssikatos, J. P., et al., 1997), and in targeting catalytic RNAs to disrupt viral replication (Jenne, A., et al., 2001; Rogers, J., et al., 1996; Schroeder, R., et al., 2000; von Ahsen, U., et al., 1991; Wank, H., et al., 1994; Wank, H., and R. Schroeder, 1996). In these cases, the TUBs are also considered important as the starting compounds for the development of more potent drugs.
Tuberactinomycins are reported to inhibit group I intron RNA splicing at high concentrations (Wank, H., et al., 1994). At subinhibitory concentrations, they are reported to stimulate oligomerization of group I intron RNA and intermolecular reactions (Wank, H., and R. Schroeder, 1996). The former finding is of interest for targeting group I introns in pathogenic microorganisms, since this type of intron is not found in humans (Hermann, T., and E. Westhof, 1998). The latter finding is of interest for developing therapeutic ribozymes that can fix mutated RNAs involved in inherited diseases (James, H. A., and I. Gibson, 1998).
TUBs are also reported to inhibit the human hepatitis delta virus ribozyme (Rogers, J., et al., 1996), and recently it was reported that VIO binds to subdomains Ille/f of the hepatitis C virus (HCV) internal ribosome entry site, blocking HCV translation (Vos, S., et al., 2002). These studies indicate that derivatives of tuberactinomycins will be useful as antiviral agents.
Recent studies using TUB derivatives for the treatment of infections by the animal pathogen Pasteurella haemolytica and the human pathogens vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus (Dirlam, J. P., et al., 1997; Linde II, R. G., et al., 1997; Lyssikatos, J. P., et al., 1997) found that modifications to the cyclic pentapeptide core of TUBs could enhance their activity against these pathogens. This work extends earlier findings that chemical modifications of these antibiotics can extend their use to non-mycobacterial bacteria (Kitagawa, T., et al., 1979, 1976, 1975; Wakamiya et al., 1977). Thus, new TUB derivatives are likely candidate drugs for the treatment of other bacterial infections.
New antibiotics and variants or derivatives of known antibiotics can be obtained by screening of natural sources, by manipulation of biosynthetic pathways in antibiotic producing organisms or by a combination of biosynthesis and chemical synthesis.
Gene Clusters
The study of the biosynthesis of natural products has made significant advancements in recent years due to the understanding that bacteria cluster the genes encoding all the enzymes involved in the biosynthesis of a particular natural product into one region of its genome (Chater, K. F., and C. J. Bruton. 1985; Du, L., et al., 2000; van Wageningen, A. M. A., et al., 1998). Analysis of this sequence allows a researcher to develop testable models for how the necessary precursors are synthesized, condensed, and modified to generate the final metabolite. In addition to the basic understanding of how a compound is biosynthesized, this information has the ability to direct metabolic engineering of the pathway to generate previously unattainable structural diversity in the metabolite of interest. This approach can be used to transform the developmental process of new pharmaceutically and agriculturally important compounds.
Chater and Bruton (1985) recognized that genes conferring resistance to, as well as controlling regulation and production of, methylenomycin are clustered in S. violaceus-ruber and S. coelicolor. The close linkage between the gene conferring resistance to the antibiotic and the other genes involved in biosynthesis of the antibiotic provides the basis for isolating an antibiotic cluster if the gene conferring antibiotic resistance is known.
Subsequent studies have confirmed that genes that confer resistance to an antibiotic and genes involved in the biosynthesis of that antibiotic, including penicillin, cephalosporin and cephamycins, and associated secondary metabolites, are organized in clusters. (Martin, 1992; See review by Martin and Liras, 1989). These biosynthetic clusters typically contain at least one pathway-specific regulatory gene and at least one resistance gene. U.S. Pat. No. 4,935,340 (Baltz et al., Method of Isolating Antibiotic Biosynthetic Genes, 1990) reports a method for identifying and isolating an antibiotic biosynthetic gene via hybridization with a labeled antibiotic resistance-conferring gene. This method relies on the fact that the majority of antibiotic biosynthetic genes from antibiotic-producing organisms are linked to antibiotic resistance-conferring genes. In particular, Baltz et al. used the erythromycin resistance-conferring gene to identify erythromycin biosynthetic genes via their hybridization method. In addition, they identified a recombinant vector that encoded erythromycin biosynthesis to drive erythromycin expression in a host (Streptomyces lividans TK23) that when untransformed produced no measurable amount of erythromycin.
A biosynthetic gene cluster for vancomycin group antibiotics was identified from Amycolatopsis orientalis (van Wageningen et al. 1997). In particular, 39 putative genes spanning 72 kb of contiguous DNA, including genes encoding for chloroeremomycin biosynthesis, were identified. Other antibiotic gene clusters that have been identified include those for rifamycin (August et al., 1998. Chem Biol. 5:69-70), tetracenomycin (Guilfoile & Hutchinson, 1992, Journal of Bacteriology, 174: 3651 & 3659) and actinorhodin (Caballero et al, 1991, Mol Gen Genet., 228: 372-80).
The mitomycin biosynthetic gene cluster was recently isolated and characterized from S. iavendulae (Sherman et al., U.S. Pat No. 6,495,348). The mitomycin gene cluster contains 47 mitomycin biosynthetic genes spanning 55 kb of contiguous DNA. These genes include those which encode for polypeptides which function to generate precursor molecules, such as those for mitosane ring system assembly, and those to functionalize sites on the core mitosane ring system. U.S. Pat. No. 6,495,348 and others (see e.g. Chater; U.S. Pat. No. 4,935,340), report that genes that encode enzymes for natural product assembly, including antibiotic production, are clustered on the Streptomyces genome. Furthermore, genes associated with antibiotic resistance (mrt and mrd) were located within the mitomycin gene cluster. This is consistent with previous studies that indicated antibiotic biosynthetic gene clusters typically contain one or more genes that confer antibiotic protection (Seno and Baltz, 1989).
By disrupting a repressor gene, mitomycin production in S. Iavendulae is reported to increase several-fold (U.S. Pat No. 6,495,348). E. coli were transformed to co-express MRD and MCT, the mitomycin-resistance conferring proteins, so that transformed cells had a high level of resistance to mitomycin. This resistance was mediated by increased mitomycin export out of the cell. Thus, as in Baltz et al., the use of antibiotic biosynthetic clusters in expression cassettes can be used to drive expression of antibiotics in host cells that normally do not produce measurable quantities of the antibiotic, and to increase the production and yield for cells that normally produce the antibiotic.
Organisms that do not naturally produce a particular biological product can be transformed with biosynthetic genes to produce that biological product. This is exemplified in U.S. Pat. No. 6,391,583 (Hutchinson et al., Method of Producing Antihypercholesterolemic Agents, 2002), where increased production of a cholesterol lowering compound, lovastatin, in both lovastatin-producing and non-lovastatin-producing producing organisms, was disclosed using a cluster of 17 genes from a native-lovastatin-producing strain of bacteria (A. terreus). By inactivating certain genes contained within the lovastatin cluster, different HMG-CoA reductase inhibitors were generated in the host organism. By mutating certain genes it was possible to prevent lovastatin production. By introducing extra copies of other genes into A. terreus, it was possible to increase lovastatin production up to 7-fold. Introducing the entire lovastatin-cluster into a normally non-lovastatin producing cell can result in lovastatin production in the cell.
These studies show that it is well known in the art to use gene clusters to affect production of a biologically active product, including increasing production in a native producer, abolishing production of the biologically active product, and forcing production of the biologically active product in a host cell that normally does not produce the biologically active product. It is also known that by selectively inactivating certain genes by mutation, or transforming a host cell with only certain genes, it is possible to selectively generate particular precursors of the biologically active product, which themselves can be biologically active, and to generate novel derivatives of these precursors. In addition, directed biosynthesis wherein an alternative precursor is applied to these transformed cells can be utilized to manufacture novel antibiotics.
Thus, there is a continuing need in the art for identification and isolation of antibiotic biosynthetic genes, including genes that result in enhanced production of antibiotics and confer resistance to antibiotics. Understanding the antibiotic's biosynthetic pathway also allows novel antibiotics to be manufactured biosynthetically.
Chemical Variants
It is also known in the art that individual precursors of antibiotics can be isolated and purified from a transformed cell culture, and chemically modified to generate novel derivatives thereof. This is a semi-synthetic method of synthesis. In addition, it is well known in the art that altering fermentation conditions can alter antibiotic production and provide useful starting points for the production of new semi-synthetic antibiotics. Gastaldo L, and Marinelli F. Microbiology. 2003 June; 149(Pt 6):1523-32.
Such techniques involve a combination of biosynthetic and chemical techniques. For instance, it can be difficult to manufacture antibiotics solely by chemical means. However, isolating a precursor molecule produced biosynthetically in an organism permits the generation of novel analogs by chemical means. For example, Dirlam et al. (1997) modified a synthetic reaction reported by Momoto and Shiba (1977) that used ureido exchange reactions on tuberactinomycin N. 6a-(3′,4′-dichlorophenylamino)capreomycin was prepared by treating capreomycin sulfate with a 40-fold excess of 3,4-dichloroaniline in 2 N HCl/dioxane at 65° C. for 4 hours. Phenyl urea analogs could be generated in a similar manner. Other analogs were generated by reduction of the C-6-C-6a double bond by use of triethylsilane in trifluoroacetic acid. The activity of these derivatives was measured by assaying for antibacterial activity in different bacteria.
In addition to C-6a aryl urea modification, C-19 modification to viomycin and β-lysine substitutions and modification by chemical means have been reported. Lyssikatos et al., 1997; Linde et al., 1997. Such chemical modification studies were conducted in the hope of identifying antibiotic derivatives with improved potency. The free amino groups of the β-lysine residue in viomycin have also been chemically modified (Kitagawa et al., 1976) in an effort to determine the importance of the β-lysine residue in VIO's antimicrobial activity. Wakamiya et al. (1977) disclosed the antimicrobial activity for various TUB analogs where different amino acids were attached to the free α-amino group of the α,β-diaminopropionic acid residue in TUB N.
The ability to chemically generate antibiotic derivatives is limited by the amount, variety and purity of the starting material. Thus, need in the art remains for the generation of novel, chemically-pure antibiotic derivatives to serve as templates for chemical modification to generate improved antibiotics.
SUMMARY OF THE INVENTION
The present invention provides isolated and purified nucleic acid molecules, e.g., DNA, comprising a viomycin biosynthetic gene cluster, a functional variant or a functional fragment thereof. More specifically, the invention provides isolated and purified nucleic acid molecules comprising the viomycin gene cluster including one or more genes which confer resistance to viomycin.
Another embodiment is an isolated and purified nucleic acid molecule comprising at least a functional fragment of viomycin gene cluster whose nucleic acid sequence encodes at least one gene product of a vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT gene. Isolated and purified nucleic acid molecules of this invention include those which encode at least two gene products selected from the group consisting of a vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT gene product. Isolated and purified nucleic acid molecules of this invention include those which encode at least three gene products selected from the group consisting of a vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT gene product. Isolated and purified nucleic acid molecules of this invention include those which encode at least four gene products selected from the group consisting of a vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT gene product. Isolated and purified nucleic acid molecules of this invention include those which encode at least five gene products selected from the group consisting of a vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT gene product. Isolated and purified nucleic acid molecules of this invention include those which encode at least the vioC and vioD gene products. Isolated and purified nucleic acid molecules of this invention include those which encode at least the vioC and vioD gene products and further encode one or more gene products selected from the group consisting of a vioA, vioB, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT gene product. Isolated and purified nucleic acid molecules of this invention include those which encode at least the vioM, vioN, vioO and vioP gene products. Isolated and purified nucleic acid molecules of this invention include those which encode at least the vioM, vioN, vioO and vioP gene products.and further encode one or more gene products selected from the group consisting of a vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioQ, vioR, vioS or vioT gene product. Any isolated and purified nucleic acid molecules of this invention can in addition encode one or more genes which function for resistance to an antibiotic, particularly one or more genes which function for resistance to viomycin.
The isolated and purified nucleic acid molecule can also encode the gene products of vioB, vioC, vioD, vioG and one or more of the gene products of a vioA, vioE, vioF, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT gene.
The isolated and purified nucleic acid molecules of the invention can also comprise a nucleic acid sequence that encodes one or more of the proteins of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, or SEQ ID NO:22. The isolated and purified nucleic acid molecules of the invention can also comprise a nucleic acid sequence that encodes two or more of the proteins of SEQ ID NO:2-Seq ID NO:22. The isolated and purified nucleic acid molecules of the invention can also comprise a nucleic acid sequence that encodes three or more of the proteins of SEQ ID NO:2-Seq ID NO:22. The isolated and purified nucleic acid molecules of the invention can also comprise a nucleic acid sequence that encodes four or more of the proteins of SEQ ID NO:2-Seq ID NO:22. The isolated and purified nucleic acid molecules of the invention can also comprise a nucleic acid sequence that encodes five or more of the proteins of SEQ ID NO:2-Seq ID NO:22. In general the isolated and purified nucleic acid molecules of the invention can comprise a nucleic acid sequence that encodes any combination of the proteins VioA, VioB, VioC, VioD, VioE, VioF, VioG, VioH, Viol, VioJ, VioK, VioL, vVoM, VioN, VioO, VioP, VioQ, VioR, VioS or VioT. In general the isolated and purified nucleic acid molecules of the invention can comprise a nucleic acid sequence that encodes any combination of the proteins of SEQ ID NO:2-SEQ ID NO:22.
One embodiment of the present invention is an isolated and purified nucleic acid molecule comprising a functional fragment of a viomycin gene cluster whose nucleic acid sequence has at least 80% sequence identity with one or more of vioA (SEQ ID NO:1, from 415 to 6786), vioB (SEQ ID NO:1, from 6981 to 8021), vioC (SEQ ID NO:1, from 8018 to 9094), vioD (SEQ ID NO:1, from 9091 to 10260), vioE (SEQ ID NO:1, from 10257 to 11600), vioF (SEQ ID NO:1, from 11597 to 14818), vioG (SEQ ID NO:1, from 14908 to 18174), vioH (SEQ ID NO:1, from 18171 to 18959), vioI (SEQ ID NO:1, from 18956 to 20608), vioJ (SEQ ID NO:1, from 20605 to 21777), vioK (SEQ ID NO:1, from 21827 to 22909), vioL (SEQ ID NO:1, from 22906 to 23832), vioM (SEQ ID NO:1, from 23829 to 25202), vioN (SEQ ID NO:1, from 25199 to 25390), vioO (SEQ ID NO:1, from 25396 to 27228), vioP (SEQ ID NO:1, from 27303 to 28640), vioQ (SEQ ID NO:1, from 29590 to 30621), vioR (SEQ ID NO:1, from 31370 to 30660), vioS (SEQ ID NO:1, from 31752 to 33110), or vioT(SEQ ID NO:1, from 36299 to 33717).
Another embodiment is an isolated and purified nucleic acid molecule comprising a functional fragment of a viomycin gene cluster whose nucleic acid sequence has at least 80% sequence identity withone or more of vioA (SEQ ID NO:1, from 415 to 6786), vioE (SEQ ID NO:1, from 10257 to 11600), vioF (SEQ ID NO:1, from 11597 to 14818), vioH (SEQ ID NO:1, from 18171 to 18959), vioI (SEQ ID NO:1, from 18956 to 20608), vioJ (SEQ ID NO:1, from 20605 to 21777), vioK (SEQ ID NO:1, from 21827 to 22909), vioL (SEQ ID NO:1, from 22906 to 23832), vioM (SEQ ID NO:1, from 23829 to 25202), vioN (SEQ ID NO:1, from 25199 to 25390), vioO (SEQ ID NO:1, from 25396 to 27228), vioP (SEQ ID NO:1, from 27303 to 28640), vioQ (SEQ ID NO:1, from 29590 to 30621), vioR (SEQ ID NO:1, from 31370 to 30660), vioS (SEQ ID NO:1, from 31752 to 33110), or vioT(SEQ ID NO:1, from 36299 to 33717).
The isolated and purified nucleic acid molecules of the invention can also comprise SEQ ID NO:1 from 415 to 28640 and from 29590 to 36299, or a degenerate variant thereof.
Another embodiment of the isolated and purified nucleic acid molecules of the invention comprises SEQ ID NO:1 from 415 to 36299, or a degenerate variant thereof.
Isolated and purified nucleic acid molecules comprising functional gene combinations of individual genes within the viomycin gene cluster are included in the invention. One embodiment is an isolated and purified nucleic acid molecule which encodes the gene products of VioM, VioN, VioO and VioP genes. Another embodiment is an isolated and purified nucleic acid molecule which encodes the gene products of VioC and VioD genes.
The isolated and purified nucleic acid molecules of the invention can be obtained from any source that contains any one or more genes of the viomycin gene cluster. In particular, one or more genes of the viomycin gene cluster may be obtained from a strain of Streptomyces. It is preferred that the isolated and purified nucleic acid molecule of the invention is nucleic acid from Streptomyces sp. ATCC11861 (which is equivalently classified as Streptomyces vinaecus), Streptomyces californicus, or Streptomyces olivoreticuli subsp. olivoreticuli, although isolated and purified nucleic acid molecules from other organisms which produce viomycin, or biological or functional equivalents thereof, are also within the scope of the invention. More preferably the isolated and purified nucleic acid molecule of the invention is nucleic acid from Streptomyces sp. ATCC11861. The nucleic acid molecules of the invention are double-stranded or single-stranded.
The invention also relates to nucleic acid molecules which comprise the nucleic acid sequence complementary to the sequence of one or more genes of the viomycin biosynthetic gene cluster.
The nucleic acid molecules of the invention also comprise the viomycin gene cluster wherein genes within the cluster, alone or in combination with other genes within the cluster, are absent or disrupted. One embodiment is a nucleic acid molecule comprising at least a functional fragment of a viomycin gene cluster wherein one or more of the vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT genes is absent or disrupted. Another embodiment is a nucleic acid molecule comprising at least a functional fragment of a viomycin gene cluster wherein one or more of the vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT genes has been mutated such that the gene product of the mutated gene is not functional. Another embodiment is a nucleic acid molecule comprising at least a functional fragment of a viomycin gene cluster wherein the entire coding sequence or a portion thereof of one or more of the vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioO, vioP, vioQ, vioR, vioS or vioT genes is absent. Another embodiment is a nucleic acid molecule comprising at least a functional fragment of a viomycin biosynthetic gene cluster wherein the gene encoding VioB, VioC, VioD, VioK, VioL, VioM, VioN, VioO, VioP, VioQ or any combination thereof are absent or disrupted. The absent or disrupted gene combinations in the nucleic acid molecule can be, among others, those encoding: VioC and VioD; VioM, VioN, VioO and VioP; VioQ; VioL; VioM, VioN, VioO, VioP and VioQ; VioM, VioN, VioO, VioP and VioL; VioM, VioN, VioO, VioP, VioQ and VioL; VioQ and VioL.
The isolated and purified nucleic acid molecule of the invention can comprise a sequence encoding the gene product of the vioO gene. The nucleic acid sequence can also encode each of the twenty gene product genes (vioA through vioN, vioP through vioT, and vph) in addition to encoding the gene product of the VioO gene.
The adenylation domain (A domain) in any one or more of the genes in the viomycin gene cluster encoding nonribosomal peptide synthetase (NRPS) that generate the cyclic pentapeptide core of viomycin (or a derivate or precursor thereof can be replaced by A domains from noncognate systems, resulting in a nucleic acid that encodes one or more gene products (altered from those of the native gene cluster) that activate and add alternative amino acids to the cyclic pentapeptide core of viomycin (or a derivative or precursor thereof). Thus, in one embodiment, the invention comprises nucleic acid molecules in which the VioO adenylation domain is replaced with an adenylation domain from a noncognate system. The VioO adenylation domain replacement can encode an A domain for activation and attachment of L-Leucine, L-Phenylalanine, L-Tyrosine or L-Histidine. Replacing the VioO A domain by the A domain of pItF or redM are other embodiments. Other adenylation domains that can be replaced are vioG (capreomycidine-specific A domain) are vioF (2,3-diaminopropionate-specific A domain.)
The invention comprises methods for preparing biologically active agents or pharmaceutically acceptable salts thereof. These methods comprise transforming a host cell with one or more nucleic acid molecules of this invention, culturing the transformed host cell in a culture medium containing assimilable sources of carbon, nitrogen and inorganic salts under aerobic fermentation conditions so as to yield an increase in a biologically active agent relative to the level of the biologically active agent produced by a corresponding untransformed host cell.
Each isolated and purified nucleic acid molecule of the invention which comprises at least a functional fragment of a viomycin biosynthetic gene cluster can be introduced into a host cell for the expression of one or more gene products. One or more of the coding sequences (those sequences encoding the gene products) of the viomycin biosynthetic gene cluster can be operably linked to and under the regulatory control of one or more heterologous regulatory sequences (i.e., regulatory sequences which are not those operably linked to the coding sequence in the viomycin biosynthetic gene cluster.) In an embodiment, the invention provides isolated and purified nucleic acid sequences which comprise one or more of such heterologous regulatory sequences operably linked to one or more of the coding sequences of a gene of the viomycin biosynthetic gene cluster. The nucleic acid molecules of the invention can, in addition to one or more sequences which encode a gene product (i.e., coding sequences), contain one or more regulatory sequences operationally linked to the coding sequences. The invention also includes isolated and purified nucleic acid sequences comprising one or more of the regulatory sequences of the viomycin biosynthetic gene cluster. The invention further includes isolated and purified nucleic acid sequences comprising one or more of the regulatory sequences of the viomycin biosynthetic gene cluster in combination with one or more heterologous coding sequences (coding sequences which are not operably linked to the regulatory sequences in the viomycin biosynthetic gene cluster) operably linked to the one or more regulatory sequences of the viomycin biosynthetic gene cluster.
An embodiment of the invention is a method for preparing a biologically active agent or pharmaceutically acceptable salt thereof comprising transforming a host cell with nucleic acid molecule encoding at least a functional fragment of a viomycin gene cluster, and culturing the transformed host cell in a culture medium containing assimilable sources of carbon, nitrogen and inorganic salts under aerobic fermentation conditions so as to yield an increase in a biologically active agent relative to the level of the biologically active agent produced by a corresponding untransformed host cell.
In another embodiment, a biologically active agent is prepared by transforming a host cell with a functional fragment of the viomycin gene cluster that encodes the gene products of vioM, vioN, vioO and vioP genes, and culturing the transformed host cell in a culture medium containing assimilable sources of carbon, nitrogen and inorganic salts under aerobic fermentation conditions so as to yield an increase in a biologically active agent relative to the level of the biologically active agent produced by a corresponding untransformed host cell.
Another method of the invention is preparing a biologically active agent by transfroming a host cell with a functional fragment of the viomycin gene cluster that encodes the gene products of vioC and vioD genes, and culturing the transformed host cell in a culture medium containing assimilable sources of carbon, nitrogen and inorganic salts under aerobic fermentation conditions so as to yield an increase in a biologically active agent relative to the level of the biologically active agent produced by a corresponding untransformed host cell.
An embodiment of the invention is a method for preparing a biologically active agent by transforming a host cell with the viomycin gene cluster wherein the gene encoding the gene products of vioB, vioC, vioD, vioK, vioL, vioM, vioN, vioO and vioP, or vioQ genes, or any combination thereof, are absent or disrupted, and culturing the transformed host cell in a culture medium containing assimilable sources of carbon, nitrogen, inorganic salts and supplemented with one or more alternative amino acids under aerobic fermentation conditions so as to yield an increase in a biologically active agent relative to the level of the biologically active agent produced by a corresponding untransformed host cell.
In another embodiment, a biologically active agent is prepared by transforming a host cell with a functional fragment of the viomycin gene cluster that encodes the gene product of a vioO gene whose A domain has been replaced with an A domain from a noncognate system and culturing the transformed host cell in a culture medium containing assimilable sources of carbon, nitrogen and inorganic salts under aerobic fermentation conditions so as to yield an increase in a biologically active agent relative to the level of the biologically active agent produced by a corresponding untransformed host cell.
The host cell can also be transformed with a functional fragment of the viomycin gene cluster that encodes the gene product of a vioO gene whose A domain has been replaced with an A domain from a noncognate system and one or more gene product of a vioA, vioB, vioC, vioD, vioE, vioF, vioG, vioH, vioI, vioJ, vioK, vioL, vioM, vioN, vioP, vioQ, vioR, vioS, vioT or vph gene, or any combination thereof. The transformed host cell is cultured in a culture medium containing assimilable sources of carbon, nitrogen and inorganic salts under aerobic fermentation conditions so as to yield an increase in a biologically active agent relative to the level of the biologically active agent produced by a corresponding untransformed host cell.
The host cell for these methods is any cell that can be transformed with the isolated and purified nucleic acid molecules of the invention. The host cell can be a VIO-producing organism or a non-VIO-producing organism. Preferably, the host cell is E. coli, Saccharothrix mutabilis subsp. capreolus, or Streptomyces sp. ATCC11861. Host cells most generally include any eukaryotic or prokaryotic cells.
The invention also provides functional isolated and purified gene products, polypeptides or proteins encoded by a viomycin biosynthetic gene cluster. In one embodiment the isolated and purified polypeptide, or functional fragment thereof, has an amino acid sequence selected from the group consisting of VioA (SEQ ID NO:2), VioB (SEQ ID NO:3), VioC (SEQ ID NO:4), VioD (SEQ ID NO:5), VioE (SEQ ID NO:6), VioF (SEQ ID NO:7), VioG (SEQ ID NO:8), VioH (SEQ ID NO:9), VioI (SEQ ID NO:10), VioJ (SEQ ID NO:11), VioK (SEQ ID NO:12), VioL (SEQ ID NO:13), VioM (SEQ ID NO:14), VioN (SEQ ID NO:15), VioO (SEQ ID NO:16), VioP (SEQ ID NO:17), VioQ (SEQ ID NO:19), VioR (SEQ ID NO:20), VioS (SEQ ID NO:21) and VioT (SEQ ID NO:22).
In another embodiment the isolated and purified polypeptide, or functional fragment thereof, has an amino acid sequence selected from the group consisting of VioA (SEQ ID NO:2), VioE (SEQ ID NO:6), VioF (SEQ ID NO:7), VioH (SEQ ID NO:9), VioI (SEQ ID NO:10), VioJ (SEQ ID NO:11), VioK (SEQ ID NO:12), VioL (SEQ ID NO:13), VioM (SEQ ID NO:14), VioN (SEQ ID NO:15), VioO (SEQ ID NO:16), VioP (SEQ ID NO:17), VioQ (SEQ ID NO:19), VioR (SEQ ID NO:20), VioS (SEQ ID NO:21) and VioT (SEQ ID NO:22).
Another embodiment of the present invention is an expression cassette comprising a nucleic acid molecule of the invention that is operably linked to a promoter functional in a host cell. In one embodiment the nucleic acid molecule in the expression cassette is at least a functional fragment of a viomycin biosynthetic gene cluster. The expression cassette is also pBAC-VIO-Conj.
The invention includes recombinant host cells comprising any one or more of the nucleic acid molecules of the invention. The host cell is preferably a bacterial cell. The invention is also biologically active agents or pharmaceutically acceptable salts thereof produced by recombinant host cells of the invention that are not produced by a corresponding nonrecombinant host cell. These biologically active agents are preferably an antibiotic, an antibiotic precursor, or a molecule involved in the chemical or biosynthetic production of an antibiotic. The biologically active agent can be a TUB family derivative. The biologically active agent can also not be a TUB family derivative.
A recombinant host cell of the invention is one in which viomycin production by the recombinant cell is increased relative to viomycin production in a corresponding nonrecombinant host cell. An additional embodiment is a recombinant host cell of the invention wherein viomycin production is less than the corresponding production in a corresponding nonrecombinant host cell.
A recombinant host cell of the invention is also a host cell that contains the nucleic acid molecule that encodes for the gene products of VioM, VioN, VioO and VioP genes. The host cell can be Saccharothrix mutabilis subsp. capreolus. 
Another embodiment is a recombinant host cell wherein the nucleic acid molecule of the invention contained in the host cell encodes for the gene product of VioC and VioD genes. The host cell can be E. Coli. 
The recombinant host cell of the invention is also a host cell that contains the nucleic acid molecule encoding the viomycin gene cluster wherein the gene encoding VioB, VioC, VioD, VioK, VioL, VioM, VioN, VioO, VioP, VioQ or any combination thereof are absent or disrupted.
Another embodiment is a recombinant host cell containing a gene encoding a VioO gene product whose A domain has been replaced with an adenylation domain from a noncognate cell. The recombinant host cell encoding this altered VioO gene product can also encode one or more of the other gene products: VioA - VioN, VioP -VioT, or any combination thereof.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Exemplary chemical structures of the TUB family of antibiotics including viomycin, tuberactinomycins, tuberactinamines and capreomycins. Numbering within the cyclic pentapeptide core is illustrated and identifies residue number as noted in the text. The various R1, R2, R3 and R4 groups are defined. Figure is as in Wank et al., 1994, with modifications.
FIG. 2. Is a schematic representation of the viomycin biosynthetic gene cluster. The center line denotes 37 kb encoding all ORFs involved in viomycin biosynthesis with the bars above and below the center line representing DNA present on cosmids pVIO-P8C8RH and pVIO-P2C3RG, respectively. Arrows above and below the center line identify the direction of transcription of ORFs. Coding of ORF biosynthetic function is as follows: NRPS, gray; L-2,3-diaminopropionate, black; L-2,3-diaminopropionate→β-ureidodehydroalanine, white; (2S,3R)-capreomycidine, vertical bars; (2S,3R)-capreomycidine hydroxylation, horizontal bars; β-lysine, right-slant bars; resistance and activation, left-slant bars; regulation, cross-hatched bars; export, waves.
FIG. 3. Is a scheme illustrating the biosynthetic pathways for the four nonproteinogenic amino acids in VIO (reactions A-D). Abbreviations are as in the text. In reaction B, the end product labelled 3 is (2S,3R)-capreomycidine. In reaction D: R=(-H, or -tripeptide) and the last step in β-ureidodehydroalanine biosynthesis occurs after cyclic pentapeptide synthesis.
FIG. 4. Schematic representations of the viomycin NRPS. The domains of each subunit are shown as circles. The bars below the NRPS subunits denote specific modules, which are annotated M1 through M5. The arrow between VioF and VioI represents the in trans aminoacylation of VioI by the A1 domain of VioF. The gray arrows indicate the direction of peptide synthesis. The abbreviations for NRPS domains are the same as those used in Table I.
FIG. 5. Is a reaction scheme illustrating the VioO and VioM-catalyzed N-acylation of des-β-lysine-viomycin with β-lysine. VioP converts L-Lysine to β-Lysine and VioN plays a yet undefined role in β-Lysine biosynthesis and attachment.
FIG. 6. A) Schematic representation of the insertion of pOJ260-vioA into the chromosomal copy of vioA by single homologous recombination. The grey boxes indicate regions of identity between the cloned vioA fragment and vioA on the chromosome. Arrowheads represent the location of primers used to confirm the vioA::pOJ260-vioA mutations. The black box and associated AprR represent the apramycin resistance gene on pOJ260-vioA. Resistance to this antibiotic was used for selection of the single cross-over insertional inactivation of vioA. B) Representative HPLC traces comparing viomycin production from a wild-type and one of the vioA− strains (MGT1001) of Streptomyces sp. ATCC11861 to authentic viomycin (10 μg). Viomycin was not detected in vioA− strains MGT1002 or MGT1003 (data not shown).
FIG. 7. Is a scheme illustrating the relationship among the chemical structures of exemplary antibiotics that incorporate (2S, 3R)-capreomycidine. Highlighted in gray are the portions of the antibiotics derived from (2S, 3R)-capreomycidine. For compounds 1a-e and 2a-d, the shaded amino acids are residue 5 of the pentapeptide cores of the antibiotics. The shaded portion of 6 identifies the streptolidine lactam moiety.
FIG. 8. Is a scheme providing examples of tuberactinomycin derivatives that can be generated by gene deletions in the viomycin biosynthetic gene cluster.
FIG. 9. (A) Exemplary chemical structures of capreomycin derivatives when VioO and VioM are incubated with the purified capreomycin antibiotics or, alternatively, when these two enzymes are produced in Saccharothrix mutabilis subsp. capreolus. (B) Exemplary chemical structures of tuberactinomycin derivatives generated when the chimeric enzyme containing the PlfF or RedM A domain fused to the VioO PCP domain reacts with VioM and the accepting substrates tuberactinamine A (TUA), capreomycin IA (CAPIA), capreomycin IB (CAPIB), capreomycin IIA (CAPIIA), and capreomycin IIB (CAPIIB).



DETAILED DESCRIPTION OF THE INVENTION
Definitions
Through cloning and sequencing of the viomycin gene cluster, nucleic acid molecules, as well as nucleic acid molecules in expression cassettes and recombinant host cells, useful in the production of antibiotics, antibiotic precursors and novel antibiotics and antibiotic derivatives are obtained. In addition, useful molecules encoded by the viomycin biosynthetic gene cluster are obtained.
As used herein, “antibiotic” is a substance produced by a microorganism which, either naturally or with chemical modification, will inhibit the growth of or kill another microorganism or eukaryotic cell. Viomycin and other members of the TUB family are of particular interest. As used herein, the “TUB family” includes tuberactinomycins (TUB), viomycin (VIO), tuberactinamines and capreomycins (CAPs) (see FIG. 1).
“Derivative” as used herein means that a particular compound is modified chemically or biochemically so that it comprises other chemical moieties, e.g. TUB family derivatives are generated by manipulating the viomycin gene cluster such that different moieties attach to the cyclic pentapeptide core. Derivative can also include compounds with variant cyclic pentapeptide cores. FIG. 8 illustrates some examples of derivatives.
As used herein “TUB family derivative” includes “viomycin derivative,” “tuberactinamine derivative,” “tuberactinomycin derivative” and “capreomycin derivative.” Derivatives of particular interest are biologically active molecules, particularly having antibiotic activity, or useful starting molecules, precursors for the semisynthetic generation of antibiotics. Derivatives include molecules that have different moieties attached to the viomycin cyclic pentapeptide core. Derivatives also include compounds having one or more different amino acids in the cyclic pentapeptide cores.
An “antibiotic biosynthetic gene” is a nucleic acid, e.g. DNA, segment or sequence that encodes a step in the process of converting primary metabolites into antibiotics. Encodes refers to a polypeptide or protein amino acid sequnece being defined by a DNA sequence. A gene is a portion of DNA that is involved in producing a polypeptide chain or protein; it can include regions preceeding and following the coding DNA a well as introns between exons. A gene encodes a corresponding gene product.
An “antibiotic resistance-conferring gene” is a nucleic acid segment that encodes an enzymatic or other activity which alone or in combination with other gene products, confers resistance to an antibiotic.
“Antibiotic gene cluster” includes the entire set of antibiotic biosynthetic genes necessary for the process of converting primary metabolites into antibiotics and any antibiotic resistance conferring genes needed to protect the host organism from the detrimental effects of the antibiotic being produced, as well as regulatory, export and activation genes. “Antibiotic biosynthetic gene cluster” includes the entire set of biosynthetic genes necessary for the process of converting primary metabolites into antibiotics, including sequences encoding enzymes necessary for antibiotic synthesis, including sequences that encode enzymes for precursor formation, as well as regulatory, export, activation, but excludes sequences encoding resistance to viomycin
As used herein, the “viomycin gene cluster” includes sequences encoding enzymes necessary for viomycin synthesis, including sequences that encode enzymes for precursor formation, assembly of the cyclic pentapeptide core, modifications to the cyclic pentapeptide, as well as regulatory, export, activation and resistance to viomycin. As used herein, the “viomycin biosynthetic gene cluster” includes sequences encoding enzymes necessary for viomycin synthesis, including sequences that encode enzymes for precursor formation, assembly of the cyclic pentapeptide core, modifications to the cyclic pentapeptide, as well as regulatory, export, activation, but excludes sequences encoding resistance to viomycin.
“Antibiotic-producing organisms” include any organism including, but not limited to, Streptomyces sp, which produces an antibiotic. This definition encompasses organisms that naturally produce viomycin. “VIO-producing organisms” include cells that naturally produce viomycin or cells that are genetically manipulated to produce viomycin.
“Non-VIO-producing organisms” include organisms that naturally in the absence of genetic manipulation do not produce significantly measurable quantities of viomycin. This can include cells that may produce useful compounds related to VIO, such as the capreomycin producer Saccharothrix mutabilis subsp. capreolus, or a normally VIO-producing cell such as Streptomyces sp. that is genetically manipulated to not produce VIO, or a strain such as a Streptomyces that contains the VIO cluster but does not produce the viomycin because the necessary gene products are not expressed.
A “host cell” is any cell into which the nucleic acid molecules of this invention can be introduced and expressed to produce gene products and/or biologically active agents, or the naturally occurring genes have been altered to produce altered gene products or biologically active agents. The host cell may naturally contain one or more of the viomycin genes of this invention. In this case the introduction of the isolated and purified nucleic acid molecules of this invention into the host causes a measurable change in the gene products and/or biologically active agents compared to the wild-type host cell. A “recombinant” host cell of the invention has a genome that has been artificially manipulated in vitro to add, delete, mutate, excise, one or more genes or parts thereof. A “nonrecombinant host cell” is a wild-type cell whose genome is unaltered. A recombinant host cell of the invention is particularly useful in generating one or more biologically active agents.
Using one or more of the nucleotide sequences of the invention, viomycin production in a wide range of host cells can be manipulated. For example, viomycin production can be either increased or prevented in cells. Alternatively, by inactivating particular genes in the viomycin gene cluster, a host cell can also be manipulated to produce an antibiotic precursor, a particular member of the TUB family or novel derivatives thereof. Host cells that have been modified genetically (recombinant host cells), include host cells comprising an expression cassette of the invention, or host cells in which the genome has been genetically manipulated, e.g., by deletion of a portion of, replacement of a portion of, or by disruption of, the host chromosome, so as to reduce, eliminate or modify the expression of a particular viomycin biosynthetic gene of the invention.
One embodiment of the invention is a recombinant host cell, e.g. a bacterial cell and particularly a Streptomyces cell, in which a portion of a nucleic acid sequence comprising the viomycin gene cluster, i.e., the endogenous or native genomic sequence, is absent, disrupted or replaced, for example, by an insertion with heterologous sequences or substituted with a variant nucleic acid sequence of the invention, preferably so as to result in altered viomycin synthesis, such as an increase in viomycin production, and/or production of a novel compound. Absent and disrupted are used broadly herein to encompass any technique that results in decreased or absent gene product or gene activity. It can include gene mutation at one or more sites within a gene, and/or excising one or more genes or parts thereof. FIG. 8 provides examples of various disruptions to genes within the VIO cluster to produce non-VIO compounds in host cells that normally produce VIO. A given nucleic acid sequence may contain one or more of such disruptions or replacements in a gene or genes of the viomycin cluster.
Host cells useful to prepare the recombinant host cells of the invention include cells which do not express or do not comprise nucleic acid corresponding to the nucleic acid molecules of the invention, e.g., viomycin biosynthetic genes, including the CAP-producing strain Saccharothrix mutabilis subsp. capreolus (ATCC23892), Streptomyces lividans, E. coli, as well as cells that naturally produce viomycin including Streptomyces sp. (ATCC11861), Streptomyces californicus. (ATCC3312), and Streptomyces olivoreticulis subsp. olivoreticuli (ATCC 23943) (also called Streptomyces abikoensis).
For example, the genes that encode VioM, VioN, VioO and VioP can be moved into, and expressed in, Saccharothrix mutabilis subsp. capreolus to add a β-lysine moiety onto residue 1 of the CAP antibiotics to produce capreomycin derivatives.
The term “biologically active agent” is used broadly herein to encompass any functional gene product or expression product generated directly or indirectly from the nucleic acid molecules of this invention. It can be among others an end-product antibiotic, an antibiotic precursor or an enzyme useful in the production of antibiotics. An antibiotic precursor is a substrate or intermediate involved in the biosynthesis of downstream end-product antibiotics.
The biologically active agent can be generated as cationic or anionic species. The invention encompasses pharmaceutically acceptable salts of such cationic and anionic species.
Suitable pharmaceutically acceptable salts include salts of pharmaceutically acceptable inorganic acids such as hydrochloric, sulphuric, phosphoric, nitric, carbonic, boric, sulfamic, and hydrobromic acids, or salts of pharmaceutically acceptable organic acids such as acetic, propionic, butyric, tartaric, maleic, hydroxymaleic, fumaric, maleic, citric, lactic, mucic, gluconic, benzoic, succinic, oxalic, phenylacetic, methanesulphonic, toluenesulphonic, benezenesulphonic, salicylic, sulphanilic, aspartic, glutamic, edetic, stearic, palmitic, oleic, lauric, pantothenic, tannic, ascorbic and valeric acids.
Base salts include, but are not limited to, those formed with pharmaceutically acceptable cations, such as sodium, potassium, lithium, calcium, magnesium, ammonium and alkylammonium. Also, basic nitrogen-containing groups may be quaternised with such agents as lower alkyl halides, such as methyl, ethyl, propyl, and butyl chlorides, bromides and iodides; dialkyl sulfates like dimethyl and diethyl sulfate; and others.
“Genetic manipulation” or “genetic engineering” are used very broadly to encompass any means of altering the expression of one or more genes in the gene cluster so as to produce a measurable, phenotypic change. The term includes augmenting a non-VIO-producing host genome with one or more of the VIO genes or a VIO-producing host genome to overexpress one or more genes of the VIO cluster. The VIO cluster can be introduced into a host cell in whole or in part. Genes within the cluster can be inactivated, specifically by any kind of mutation, including in-frame deletions, insertion, or random mutagenesis. Genetic material can be introduced into the host cell by any known means in the art as described hereinbelow.
As used herein, the terms “isolated and/or purified” refer to in vitro isolation of a RNA, DNA or polypeptide molecule from its natural cellular environment, and from association with other components of the cell, such as nucleic acid or polypeptide, so that it can be sequenced, replicated and/or expressed.
An “isolated and purified nucleic acid molecule” is a nucleic acid the structure of which is not identical to that of any naturally occurring nucleic acid. This term covers, for example, DNA which has part of the sequence of a naturally occurring genomic DNA, but does not have the flanking portions of DNA found in the naturally occurring genome. The term also includes, for example, a nucleic acid incorporated in a vector or into the genome of a cell such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA.
Some protein and nucleic acid sequence variation is tolerated without loss of function. In fact, some nucleic acid and protein sequence variation is expected and understood in the art, without substantially affecting protein function.
A variant nucleic acid sequence of the invention has at least about 80%, more preferably at least about 90%, and even more preferably at least about 95%, but less than 100%, contiguous nucleic acid sequence identity to a nucleic acid sequence comprising SEQ ID NO:1, the individual genes of SEQ ID NO:1 (see Table 1), or a fragment thereof. However, these nucleic acid sequences still encode a functional gene product. The amino acid and/or nucleic acid similarity (or homology) of two sequences can be determined manually or using computer algorithms well known to the art.
The present invention further includes isolated and purified DNA sequences which hybridize under standard or stringent conditions to the nucleic acid molecules of the invention. Hybridization procedures are useful for identifying polynucleotides with sufficient homology to the subject sequences to be useful as taught herein. The particular hybridization techniques are not essential to the subject invention. As improvements are made in hybridization techniques, they can be readily applied by one of ordinary skill in the art.
Preferably, the isolated nucleic acid molecule comprising the gene cluster includes a nucleic acid sequence comprising the sequence given in SEQ ID NO:1, a variant or a fragment thereof, e.g., a nucleic acid molecule that hybridizes under moderate, or more preferably stringent, hybridization conditions to the sequence given in SEQ ID NO:1 or a fragment thereof. Isolated nucleic acid molecules which hybridize under moderate or more preferably stringent conditions to the sequence of SEQ ID NO:1 or a functional fragment thereof can include nucleic acid of a Streptomyces strain or particularly a VIO-producing Streptomyces strain. In addition, the particular order of the genes contained in the Vio gene cluster can vary.
A probe and sample are combined in a hybridization buffer solution and held at an appropriate temperature until annealing occurs. Thereafter, the membrane is washed free of extraneous materials, leaving the sample and bound probe molecules typically detected and quantified by autoradiography and/or liquid scintillation counting. As is well known in the art, if the probe molecule and nucleic acid sample hybridize by forming a strong non-covalent bond between the two molecules, it can be reasonably assumed that the probe and sample are essentially identical, or completely complementary if the annealing and washing steps are carried out under conditions of high stringency. The probe's detectable label provides a means for determining whether hybridization has occurred.
In the use of the oligonucleotides or polynucleotides as probes, the particular probe is labeled with any suitable label known to those skilled in the art, including radioactive and non-radioactive labels. Typical radioactive labels include 32p, 35S, or the like. Non-radioactive labels include, for example, ligands such as biotin or thyroxine, as well as enzymes such as hydrolases or peroxidases, or a chemiluminescer such as luciferin, or fluorescent compounds like fluorescein and its derivatives. Alternatively, the probes can be made inherently fluorescent as described in International Application No. WO 93/16094.
Various degrees of stringency of hybridization can be employed. The more stringent the conditions, the greater the complementarity that is required for duplex formation. Stringency can be controlled by temperature, probe concentration, probe length, ionic strength, time, and the like. Preferably, hybridization is conducted under moderate to high stringency conditions by techniques well known in the art, as described, for example in Keller, G. H., M. M. Manak (1987) DNA Probes, Stockton Press, New York, N.Y., pp. 169-170, hereby incorporated by reference. For example, stringent conditions are those that (1) employ low ionic strength and high temperature for washing, for example, 0.015 M NaCl/0.0015 M sodium citrate (SSC); 0.1% sodium lauryl sulfate (SDS) at 50° C., or (2) employ a denaturing agent such as formamide during hybridization, e.g., 50% formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM NaCl, 75 mM sodium citrate at 42° C. Another example is use of 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 times Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% sodium dodecylsulfate (SDS), and 10% dextran sulfate at 4° C., with washes at 42° C. in 0.2×SSC and 0.1% SDS.
An example of high stringency conditions is hybridizing at 68° C. in 5× SSC/5× Denhardt's solution/0.1% SDS, and washing in 0.2× SSC/0.1% SDS at room temperature. An example of conditions of moderate stringency is hybridizing at 68° C. in 5× SSC/5× Denhardt's solution/0.1% SDS and washing at 42° C. in 3× SSC. The parameters of temperature and salt concentration can be varied to achieve the desired level of sequence identity between probe and target nucleic acid. See, e.g., Sambrook et al. (1989) supra or Ausubel et al. (1995) Current Protocols in Molecular Biology, John Wiley & Sons, NY, N.Y., for further guidance on hybridization conditions.
In general, salt and/or temperature can be altered to change stringency. With a labeled DNA fragment >70 or so bases in length, the following conditions can be used: Low, 1 or 2× SSPE, room temperature; Low, 1 or 2× SSPE, 42° C.; Moderate, 0.2× or 1× SSPE, 65° C.; and High, 0.1× SSPE, 65° C.
“Complement” or “complementary sequence” means a sequence of nucleotides which forms a hydrogen-bonded duplex with another sequence of nucleotides according to Watson-Crick base-pairing rules. For example, the complementary base sequence for 5′-AAGGCT-3′ is 3′-TTCCGA-5′. This invention encompasses complementary sequences to any of the nucleotide sequences claimed in this invention.
A “fragment of a nucleic acid” is a partial sequence of the nucleic acid molecule such that the resultant polypeptide encoded by the fragment remains functional as determined by, for instance, a measurable amount of enzymatic activity. A fragment can also be useful as a probe or a primer for diagnosis, sequencing or cloning of the viomycin cluster. A “functional fragment” of a nucleic acid molecule encodes and can express a functional gene product. A functional gene product from such a fragment retains a measurable level of activity of the gene product encoded by the full nucleic acid from which the fragment is derived. For example, a functional fragment of a VioA gene encodes a gene product (protein) which retains any measurable function and activity of the VioA gene product (protein). Functional gene products of this invention include one or more of the gene products VioA through VioT, or functional variants or fragments thereof. These functional gene products include functional enzymes, functional transporters, functional transcriptional regulators and polypeptides and proteins that function in antibiotic resistance. Thus, a vio gene encodes a Vio gene product. A fragment of nucleic acid of a vio gene encodes a fragment of a Vio gene product. A functional fragment of nucleic acid of a vio gene encodes a functional Vio gene product.
The term “sequence homology” or “sequence identity” means the proportion of base matches between two nucleic acid sequences or the proportion of amino acid matches between two amino acid sequences. When sequence homology is expressed as a percentage, e.g., 50%, the percentage denotes the fraction of matches over the length of sequence that is compared to some other sequence. Gaps (in either of the two sequences) are permitted to maximize matching; gap lengths of 15 bases or less are usually used, 6 bases or less are preferred with 2 bases or less more preferred. When using oligonucleotides as probes, the sequence homology between the target nucleic acid and the oligonucleotide sequence is generally not less than 17 target base matches out of 20 possible oligonucleotide base pair matches (85%); preferably not less than 9 matches out of 10 possible base pair matches (90%), and more preferably not less than 19 matches out of 20 possible base pair matches (95%).
“Similarity,” when comparing two amino acid sequences, encompasses amino acids that are “identical” and amino acids whose side groups have similar properties (eg. basic, polar, etc). “Identical” or “identity” only encompasses amino acids that are identical.
Two amino acid sequences are homologous if there is a partial or complete identity between their sequences. For example, 85% homology means that 85% of the amino acids are identical when the two sequences are aligned for maximum matching. Gaps (in either of the two sequences being matched) are allowed in maximizing matching; gap lengths of 6 or less are preferred with 2 or less being more preferred. Alternatively and preferably, two protein sequences (or polypeptide sequences derived from them of at least 30 amino acids in length) are homologous, as this term is used herein, if they have an alignment score of more than 5 (in standard deviation units) using the program ALIGN with the mutation data matrix and a gap penalty of 6 or greater. See Dayhoff, M. O., in Atlas of Protein Sequence and Structure, 1972, volume 5, National Biomedical Research Foundation, pp. 101-110, and Supplement 2 this volume, pp. 1-10. The two sequences or parts thereof are more preferably homologous if their amino acids are greater than or equal to 50% identical when optimally aligned using the ALIGN program.
The following terms are used to describe the sequence relationships between two or more polynucleotides: “reference sequence”, “comparison window”, “sequence identity”, “percentage of sequence identity”, and “substantial identity”. A “reference sequence” is a defined sequence used as a basis for a sequence comparison; a reference sequence can be a subset of a larger sequence, for example, as a segment of a full-length cDNA or gene sequence given in a sequence listing, or can comprise a complete cDNA or gene sequence. Generally, a reference sequence is at least 20 nucleotides in length, frequently at least 25 nucleotides in length, and often at least 50 nucleotides in length. Since two polynucleotides can each (1) comprise a sequence (i.e., a portion of the complete polynucleotide sequence) that is similar between the two polynucleotides, and (2) can further comprise a sequence that is divergent between the two polynucleotides, sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a “comparison window” to identify and compare local regions of sequence similarity.
A “comparison window”, as used herein, refers to a conceptual segment of at least 20 contiguous nucleotides and wherein the portion of the polynucleotide sequence in the comparison window can comprise additions or deletions (i.e., gaps) of 20 percent or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Optimal alignment of sequences for aligning a comparison window can be conducted by the local homology algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2: 482, by the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48: 443, by the search for similarity method of Pearson and Lipman (1988) Proc; Natl. Acad. Sci. (U.S.A.) 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by inspection, and the best alignment (i.e., resulting in the highest percentage of homology over the comparison window) generated by the various methods is selected.
The term “sequence identity” means that two polynucleotide sequences are identical (i.e., on a nucleotide-by-nucleotide basis) over the window of comparison. The term “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C., G, U, or I) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. The terms “substantial identity” as used herein denote a characteristic of a polynucleotide sequence, wherein the polynucleotide when optimally aligned, such as by the programs GAP or BESTFIT using default gap weights, comprises a sequence that has at least 80 percent sequence identity, preferably at least 90 to 95 percent sequence identity, more usually at least 99 percent sequence identity as compared to a reference sequence over a comparison window of at least 20 nucleotide positions, frequently over a window of at least 20-50 nucleotides. The percentage of sequence identity is calculated by comparing the reference sequence to the polynucleotide sequence which can include deletions or additions which total 20 percent or less of the reference sequence over the window of comparison.
Nucleotide Sequence Variation
The present invention contemplates nucleic acid sequences which hybridize under low, moderate or high stringency hybridization conditions to the exemplified nucleic acid sequences set forth herein. Thus, nucleic acid sequences encoding variant polypeptides, i.e., those having at least one amino acid substitution, insertion, addition or deletion, or nucleic acid sequences having conservative (e.g., silent) nucleotide substitutions, are within the scope of the invention. Preferably, variant polypeptides encoded by the nucleic acid sequences of the invention are biologically active. The present invention also contemplates naturally occurring allelic variations and mutations of the nucleic acid sequences described herein.
Duplex formation and stability depend on substantial complementarity between the two strands of a hybrid, and, as noted above, a certain degree of mismatch can be tolerated. Therefore, the sequences of the subject invention include mutations (both single and multiple), deletions, insertions of the described sequences, and combinations thereof, wherein said mutations, insertions and deletions permit formation of stable hybrids with the target polynucleotide of interest. Mutations, insertions, and deletions can be produced in a given polynucleotide sequence in many ways, and those methods are known to an ordinarily skilled artisan. Other methods may become known in the future.
These variants can be used in the same manner as the exemplified sequences so long as the variants have substantial sequence homology with the original sequence. As used herein, substantial sequence homology refers to homology sufficient to enable the variant polynucleotide to function in the same capacity as the polynucleotide from which the variant was derived. The degree of homology or identity needed for the variant to function in its intended capacity depends upon the intended use of the sequence. It is well within the skill of a person trained in this art to make mutational, insertional, and deletional mutations which are equivalent in function or are designed to improve the function of the sequence or otherwise provide a methodological advantage.
As is well known in the art, because of the degeneracy of the genetic code, there are numerous other DNA and RNA molecules that can code for the same polypeptides as those encoded by the exemplified biosynthetic genes and fragments thereof. DNA and RNA molecules that have different genetic codes, but encode identical polypeptides, are called “degenerate variants.” The present invention, therefore, contemplates those other DNA and RNA molecules which, on expression, encode the polypeptides of, for example, portions of SEQ. ID NOs:2-22. Having identified the amino acid residue sequence encoded by a viomycin biosynthetic gene, and with knowledge of all triplet codons for each particular amino acid residue, it is possible to describe all such encoding RNA and DNA sequences. DNA and RNA molecules other than those specifically disclosed herein and, which molecules are characterized simply by a change in a codon for a particular amino acid, are within the scope of this invention.
The 20 common amino acids and their representative abbreviations, symbols and codons are well known in the art (see, for example, Molecular Biology of the Cell, Second Edition, B. Alberts et al., Garland Publishing Inc., New York and London, 1989). As is also well known in the art, codons constitute triplet sequences of nucleotides in mRNA molecules and as such, are characterized by the base uracil (U) in place of base thymidine (T) which is present in DNA molecules. A simple change in a codon for the same amino acid residue within a polynucleotide will not change the structure of the encoded polypeptide. By way of example, it can be seen from SEQ. ID NO:1 that a GAA codon for glutamic acid exists at nucleotide positions 418-420. However, glutamic acid can be encoded by a GAG codon. Substitution of the GAG codon with a GM codon, or vice versa, does not alter the fact that glutamic acid is placed at that location; nor does that substitution substantially alter the DNA sequence of SEQ ID NO:1. Such a substitution results in production of the same polypeptide. In a similar manner, substitutions of the recited codons with other equivalent codons can be made in a like manner without departing from the scope of the present invention.
A nucleic acid molecule, segment or sequence of the present invention can also be an RNA molecule, segment or sequence. An RNA molecule contemplated by the present invention corresponds to, is complementary to or hybridizes under low, moderate or high stringency conditions to, any of the DNA sequences set forth herein. Exemplary and preferred RNA molecules are mRNA molecules that comprise at least one viomycin biosynthetic gene of this invention.
Mutations can be made to the native nucleic acid sequences of the invention and such mutants used in place of the native sequence, so long as the mutants are able to function with other sequences to collectively catalyze the synthesis of an identifiable TUB. Such mutations can be made to the native sequences using conventional techniques such as by preparing synthetic oligonucleotides including the mutations and inserting the mutated sequence into the gene using restriction endonuclease digestion. (See, e.g., Kunkel, T. A. Proc, Natl. Acad. Sci. USA (1985) 82:448; Geisselsoder et al. BioTechniques (1987) 5:786). Alternatively, the mutations can be effected using a mismatched primer (generally 10-30 nucleotides in length) which hybridizes to the native nucleotide sequence (generally cDNA corresponding to the RNA sequence), at a temperature below the melting temperature of the mismatched duplex. The primer can be made specific by keeping primer length and base composition within relatively narrow limits and by keeping the mutant base centrally located. Zoller and Smith, Methods Enzymol. (1983) 100:468. Primer extension is effected using DNA polymerase, the product cloned and clones containing the mutated DNA, derived by segregation of the primer extended strand, selected. Selection can be accomplished using the mutant primer as a hybridization probe. The technique is also applicable for generating multiple point mutations. See, e.g., Dalbie-McFarland et al., Proc. Natl. Acad. Sci. USA (1982) 79:6409. PCR mutagenesis will also find use for effecting the desired mutations. Alternatively, in frame deletions can be used (Kieser et al., 2000ab).
Random mutagenesis of the nucleotide sequence can be accomplished by several different techniques known in the art, such as by altering sequences within restriction endonuclease sites, inserting an oligonucleotide linker randomly into a plasmid, by irradiation with X-rays or ultravioLet light, by incorporating incorrect nucleotides during in vitro DNA synthesis, by error-prone PCR mutagenesis, by preparing synthetic mutants or by damaging plasmid DNA in vitro with chemicals. Chemical mutagens include, for example, sodium bisulfite, nitrous acid, hydroxylamine, agents which damage or remove bases thereby preventing normal base-pairing such as hydrazine or formic acid, analogues of nucleotide precursors such as nitrosoguanidine, 5-bromouracil, 2-aminopurine, or acridine intercalating agents such as proflavine, acriflavine, quinacrine, and the like. Generally, plasmid DNA or DNA fragments are treated with chemicals, transformed into E. coli and propagated as a pool or library of mutant plasmids.
Protein Sequence Variation
Variation in the protein sequence of SEQ ID NOs:2-22 is expected. Proteins can also retain function even after deletion of one or both ends of the protein. Tolerance is also permitted in the precise start and stop locations of the genes encoding functionally equivalent polypeptides. Some adjacent genes can overlap, while others do not. In addition, one or more conservative amino acid substitutions will not substantially affect protein function. Non-conservative amino acid substitutions in regions of the protein that are not functional will not substantially affect protein function.
A preferred functional variant polypeptide includes a variant polypeptide or functional fragment thereof having at least about 1%, more preferably at least about 10%, and even more preferably at least about 50% of the activity of the polypeptide having the amino acid sequence comprising one of the encoded polypeptides of SEQ ID NOs:2-22. For example, the activity of a polypeptide of SEQ ID NO:17 (vioP) can be compared to a variant polypeptide of SEQ ID NO:17 having at least one amino acid substitution, insertion, or deletion relative to SEQ ID NO:17. Variant polypeptides are “substantially functionally equivalent” to the polypeptides in this invention (SEQ ID NOs:2-22), if the variant has at least about 1% the biological activity of the corresponding non-variant polypeptide of this invention. More preferably, the variant polypeptide is “functionally equivalent” and has at least about 50% the biological activity of the corresponding non-variant polypeptide of this invention, more preferably 80% and greater and all subcombinations between.
Similar to nucleotide sequences, the homology between two polypeptide sequences can be determined. Two proteins are substantially identical if they share 80% sequence identity, more preferably 90%, and more preferably at least about 95% or 99% sequence identity. Substantial identity also encompasses two sequences that have conservative amino acid substitutions, as described below. This invention comprises amino acid sequences that are functionally and substantially functionally equivalent to the amino acid sequences of this invention (SEQ ID NOs:2-22).
One or more of the residues of the polypeptides of the invention (SEQ ID NOs:2-22) can be altered, so long as the polypeptide variant is biologically active. Conservative amino acid substitutions are preferred—that is, for example, aspartic-glutamic as acidic amino acids; lysine/arginine/histidine as basic amino acids; leucine/isoleucine, methionine/valine, alanine/valine as hydrophobic amino acids; serine/glycine/alanine/threonine as hydrophilic amino acids. Conservative amino acid substitution also includes groupings based on side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. For example, it is reasonable to expect that replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar replacement of an amino acid with a structurally related amino acid will not have a major affect on the properties of the resulting variant polypeptide. Whether an amino acid change results in a functional polypeptide can readily be determined by assaying the specific activity of the polypeptide variant.
Amino acid substitutions falling within the scope of the invention, are, in general, accomplished by selecting substitutions that do not differ significantly in their affect on maintaining (a) the structure of the peptide backbone in the area of the substitution, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
The invention also encompasses polypeptide variants with non-conservative substitutions wherein the variant is functionally equivalent or substantially functionally equivalent to the native protein. Non-conservative substitutions entail exchanging a member of one of the classes described above for another.
Acid addition salts of the polypeptide or variant polypeptide or of amino residues of the polypeptide or variant polypeptide can be prepared by contacting the polypeptide or amine with one or more equivalents of the desired inorganic or organic acid, such as, for example, hydrochloric acid. Esters of carboxyl groups of the polypeptides can also be prepared by any of the usual methods known in the art.
In accordance with the present invention, there is provided a purified and isolated nucleic acid molecule which encodes the entire pathway for the biosynthesis of viomycin. Desirably, the nucleic acid molecule is a DNA isolated from Streptomyces sp. However, the cluster sequence can be isolated from other organisms. Alternatively the nucleic acids can be in whole or in part chemically synthesized by methods known in the art. Further nucleic acids isolated from natural sources can be ligated together using chemical means known in the art. As outlined hereinbelow (see Example 1), viomycin clusters from other organisms are obtained by isolating the organism's genomic DNA, partially digesting the DNA and packaging it into lambda phage to infect E. coli to generate a cosmid library. This library is screened for the presence of the viomycin resistance gene, vph, using, for example, Vph/FEco and VphREco primers. To ensure the entire cluster is located, a second screen using a primer for a different gene (e.g. VioG) in the cluster is performed. This second screen locates cosmids that contain the different gene but do not contain vph. Sequencing the plasmids identified by each of the screens permits a viomycin cluster to be identified. In such a manner viomycin clusters can be obtained from any organism, including organisms that contain silent viomycin biosynthetic genes and do not normally produce viomycin.
Further encompassed are nucleotide sequences for probes and primers to various portions of the gene cluster. Given a particular sequence, the generation of primers to that sequence is well known in the art. For example, because Streptomyces contain approximately 75% GC bases, cloning primers are generally 30 base pairs in length, with a 6 base pair restriction enzyme recognition site and 2 to 3 AT bases added on the end. Thus, for cloning primers, only 21 to 24 bases will be 100% identical to the sequence of interest. Sequencing and diagnostic primers are typically 20 to 28 base pairs, more preferably 24 base pairs in length, and generally match the sequence of interest between approximately 90% to 100%, most preferably approximately 100%. Primers are typically approximately 20 to 34 base pairs in length, more preferably 24 to 30 base pairs in length, with annealing temperatures in the 65 to 70° C. range. Gene probes are preferably approximately 1 kb in length comprising the gene of interest to be probed.
Vio biosynthetic clusters obtained from other strains of Streptomyces are not expected to have 100% identity with the cluster obtained from the ATCC11861 strain. For instance, functionally equivalent genes may not align in the genome in the same way. This is demonstrated in the glycopeptide antibiotics, where enzymes with equivalent functions have approximately 70% identity and 80% similarity between the various species. Pootoolal et al. (2002); van Wageningen et al. (1998); Pelzer et al., Antimicrob. Agents Chemother. 43(7), 1565-1573 (1999); Sosio et al., Chemistry & Biology 10(6), 541-9 (2003); Chiu et al., Proc. Natl. Acad. Sci 98(15), 8548-53 (2001). In addition, cph, the capreomycin resistance gene in Saccharothrix mutabilis subsp. capreolus, is functionally equivalent to vph, the viomycin resistance gene in Streptomyces sp., but these proteins only have 53% identity and 66% similarity. Another example is for the closest homologs to VioC and VioD, SttL and SttN from Streptomyces rochei, which have approximately 40% identity and 55% similarity to VioC and VioD. Thus, variation in the nucleotide sequence for Vio clusters obtained from other species is expected.
The stop/start points for each of the genes within the VIO cluster (SEQ ID NO:1) is given in Table 1. There is some tolerance in the exact start point of a given orf within the viomycin cluster. Many of the Streptomyces secondary metabolite gene clusters are proposed to be translationally coupled. The particular method by which the start location is determined is as follows. First, all ATG and GTG codons are assigned as possible start codons. Starting from the first ATG or GTG, the open reading frame is blastp, PSI-Blast, and RPS-Blast searched against the NCBI databank of proteins. Each of the homologs is analyzed for how closely the start codon aligns with the putative start of the Viomycin homolog. There may be conflicting results. For example, the start codons of VioS and VioR were revised and moved upstream based on the PSI-BLAST results finding many homologs with earlier potential start codons (VioR changed from 31397 to 31370; VioS changed from 31896 to 31752). However, there is still the possibility that the downstream codon is correct. Those of skill in the art understand and can take into account such uncertainty when practicing the methods of this invention. Without wishing to be bound to any particular theory, the predicted function of each gene contained within the isolated Vio cluster is given in Table 1.







TABLE 1







Summary of Genes and Predicted Encoded Functions:











SEQ




Gene
ID NO:
Start-Stop
Predicted Encoded Function













vioA
2
 415-6786
NRPS (A-PCP-C-A-PCP-C)a


vioB
3
6981-8021
2,3-diaminopropionate synthase


vioC
4
8018-9094
L-Arg hydroxylase


vioD
5
 9091-10260
Capreomycidine synthase


vioE
6
10257-11600
Permease


vioF
7
11597-14818
NRPS (A-PCP-C)


vioG
8
14908-18174
NRPS (A-PCP-C/-?)


vioH
9
18171-18959
Type II thioesterase


vioI
10
18956-20608
NRPS (PCP-C)


vioJ
11
20605-21777
2,3-diaminopropionyl α,β.-desaturase


vioK
12
21827-22909
Ornithine cyclodeaminase


vioL
13
22906-23832
Carbamoyltransferase


vioM
14
23829-25202
NRPS (C) - β-lysine transferase


vioN
15
25199-25390
MbtH homolog


vioO
16
25396-27228
NRPS (A-PCP) - β-lysine activation


vioP
17
27303-28640
Lysine 2,3-aminomutase


vph
18
29557-28676
Viomycin phosphotransferase


vioQ
19
29590-30621
Capreomycidine hydroxylase


vioR
20
31370-30660
Transcriptional regulator


vioS
21
31752-33110
Viomycin-phosphate phosphatase


vioT
22
36299-33717
Transcriptional Regulator





aAbbreviations for NRPS domains: A, adenylation; PCP, peptidylcarrier protein; C, condensation; C/, truncated condensation; ?, domain of unknown function.






The compounds produced by the recombinant host cells of the invention are preferably biologically active agents such as end-product antibiotics, antibiotics or compounds useful in synthesis of other antibiotics, enzymes involved in antibiotic synthesis, inhibitors or alterers of catalytic RNA function, antiviral or crop protection agents. Alternatively, they can be useful starting points in further chemical synthesis procedures. Methods employing these compounds, e.g. to treat humans for MDR-TB, are also encompassed.
The invention described herein is useful for the production of TUB family antibiotics including, viomycin, analogs or derivatives thereof, or novel compounds. See, e.g. Thomas et al. 2003; Ju et al. 2004. Commercial chemical syntheses of viomycin is difficult. The gene cluster described herein contains all the genes required for the production of the TUB family of antibiotics. Thus, the isolated and purified nucleic acids of this invention are useful for the selective production of specific TUB antibiotics, the overproduction or underproduction of particular compounds, e.g., overproduction of certain TUB antibiotics, and the production of novel compounds, e.g., viomycin-derived compounds as well as the production of novel non-viomycin related compounds. For example, combinational biosynthetic-based modification of viomycin antibiotics can be accomplished by selective activation or disruption of specific genes within the cluster, or incorporation of the genes into biased biosynthetic libraries which are assayed for a wide range of biological activities, to derive greater chemical diversity in the viomycin. A further example includes the introduction of a viomycin biosynthetic gene(s) into a particular host cell so as to result in the production of a novel non-viomycin related compound due to the activity of the viomycin biosynthetic gene(s) on other metabolites, intermediates or components of the host cells. The in vitro expression of polypeptides from this gene cluster also provides an enzymatic route for the production of known TUB compounds that are produced in low quantities by untransformed cells, or conversion of currently available TUBs to other known or novel TUBs through semisynthetic procedures.
A novel TUB can be generated by manipulation of VioO (see FIG. 5), a protein consisting of two domains, for example. The N-terminal domain (consisting of amino acids 1-527) contains the adenylation (A) domain of VioO. This domain binds a specific amino acid (β-Lysine), activates β-Lysine to a β-Lysyl-AMP intermediate, and subsequently tethers the β-Lysyl moiety to the 4′-phosphopantetheinyl prosthetic group of the C-terminal peptidylcarrier protein (PCP) domain (amino acids 528-610). The A domain of VioO can be removed and replaced with an A domain from a noncognate system that activates alternative amino acids because of the didomain nature of the protein. As used herein “noncognate system” means a non-VioO protein that has a domain functionally equivalent to the A domain of VioO but that activates a different amino acid than that activated by VioO. An “alternative amino acid” is any amino acid that is not the one originally activated by the original A domain. Once constructed, these protein “chimeras” can function to add the alternative amino acid to the α-carbon of residue 1 of the cyclic pentapeptide core of viomycin (see FIG. 9).
For example, the plasmid pVioO-PCP2 is constructed to contain the portion of vioO encoding amino acids 528-610 (DNA sequence 26976-27228). To this sequence, an in-frame HindIII restriction site is added to the 5′ end to allow for in-frame fusions of the PCP-encoding region of vioO with DNA encoding noncognate A domains. Thus, chimeric proteins can be produced that activate other amino acids besides β-Lysine for covalent attachment to the fused PCP domain of VioO. VioM can catalytically attach this alternative amino acid to residue 1 of the cyclic pentapeptide core of viomycin, generating a new TUB derivative.
As examples, the pItF and redM genes from the pyoluteorin (Nowak-Thompson et al., 1999) and prodiginine (Cerdeno et al., 2001; Thomas et al., 2002) pathways, have been fused to the PCP portion of vioO, generating plasmids pPItF/VioOPCP2 and pRedM/VioOPCP2, respectively. PlfF and redM each recognize and activate L-Proline (Thomas et al., 2002) and the resulting fusion proteins can catalyze the formation of L-Proline tethered to the PCP domain of the fusion protein. The tethered L-Prolyl moiety is subsequently transferred to the cyclic pentapeptide core of viomycin by VioM to form L-Prolyl-tuberactinamine A, a TUB derivative that has not been isolated or synthesized. FIG. 9 shows exemplary chemical structures of the types of antibiotics that can be generated when VioO is altered to have the PltF A domain replace the VioO A domain. The exemplary chemical structures of FIG. 9 can be generated by incubating the chimeric enzyme with the purified CAPs and tuberactinamine A, or when the chimeric enzyme along with VioM is produced in Saccharothrix mutabilis subsp capreolus. 
As an extension of this, any A domain is a candidate for fusion to the PCP domain of VioO. For example, the first A domain of CepA activates L-Leucine (van Wageningen et al., 1998; Trauger et al., 2000) and can be introduced onto the PCP domain of VioO to generate L-Leucyl-tuberactinamine A. Other examples include the A domain from GrsA (Stachelhaus et al., 1995) or NovH (Steffensky et al., 2000; Chen and Walsh, 2001) that recognize and activate L-Phenylalanine or L-Tyrosine, respectively. The A domain of NikP1 (Bormann et al., 1996; Chen et al., 2002) can introduce L-Histidine to tuberactinamine A. The A domains used are not limited to bacterial A domains. For example, the gene encoding the A domain of Lys2 from Saccharomyces cervisiae (Ehmann et al., 1999) can be fused to the PCP domain of VioO, or another such Vio protein, to alter the amino acid added. Such fusion with the PCP domain of VioO results in the formation of alpha-aminoadipate-tuberactinamine A.
In addition to generating tuberactinamine A derivatives with alternative amino acids replacing the β-Lysine moiety, these same chimeric genes can be introduced into Saccharothrix mutabilis subsp. capreolus to generate new derivatives of the CAP antibiotics.
Genetic engineering of the viomycin cluster in various host cells is particularly useful in directed biosynthesis experiments to generate particular antibiotics, including TUB family antibiotics and TUB family derivatives. Directed biosynthesis is well known to those skilled in the art. See e.g. Hojati et al. (2002). Directed biosynthesis is the process of feeding an alternative precursor(s) to a strain for incorporation into the molecule of interest by displacing the natural precursor.
Using targeted gene disruption, the ability of Streptomyces sp. ATCC11861 to generate the three nonproteinogenic amino acid precursors (2,3-diaminopropionate, capreomycidine, and beta-lysine) can be abolished. Alternative amino acid analogs can then be fed to the mutant strain(s) for incorporation into the natural product.
Disruption of vioP (ΔvioP), the lysine 2,3-aminomutase, will eliminate beta-lysine production by Streptomyces sp. ATCC11861. To this strain, alternative beta amino acids (e.g. beta-alanine, beta-histidine, beta-homolysine, 3-aminobutyric acid, and other structural analogs) can be fed and the product analyzed for incorporation into the viomycin structure. In these cases, the beta-lysine moiety will be replaced by the alternative amino acid. The culture medium for such directed biosynthesis can be a viomycin production medium (Tam and Jordan, 1972) wherein the culture is grown under conditions established for viomycin production (Thomas et al., 2002) that has been supplemented with the alternative beta amino acid of interest. The supplement can be added either at the start of culture growth or when viomycin production typically begins (after approximately 5 days of growth) or any time between start of growth and start of viomycin production. Under optimized growth conditions, the Streptomyces sp. strain ATCC11861 ΔvioP culture with added beta-histidine, for example, produces beta-histidine-tuberactinamine A. Using the same protocol beta histidine can be replaced by a variety of beta amino acids to increase the diversity of antibiotics generated.
Disruption of vioB or vioK will abolish the production of 2,3-diaminopropionate. To these mutant strains, alternative diamino acids can be fed (e.g. 2,4-diaminobutyric acid, 2,3-diaminobutanoic acid, ornithine, and other structural analogs) and the product analyzed for incorporation into the viomycin peptide backbone. The deleted VioB strain of Steptomyces sp ATCC11861 grown under conditions for viomycin production, supplemented with 2,4-diaminobutryate (DAB) resulted in the production of a new metabolite, possibly a novel tuberactinomycin antibiotic.
Disruption of vioC or vioD abolishes production of capreomycidine. To these mutant strains alternative aromatic amino acids can be fed (phenylglycine, 4-hydroxyphenylglycine, 4-fluorophenylglycine, 4-bromophenylglycine, 3,5-dihydroxyphenylglycine, and other structural analogs) and the product analyzed for incorporation into the viomycin peptide backbone. With VioC and VioD inactivated, competition between endogenous (2S,3R)-capreomycidine and the alternative precursor is eliminated thereby increasing the probability of incorporation of the alternative precursor into the molecule of interest.
These gene disruptions can be combined in concert with directed biosynthesis on multiple positions of the viomycin hexapeptide to generate novel antibiotics, TUB family antibiotics, derivatives thereof and precursor molecules.
The purified and isolated viomycin biosynthetic genes are useful to elucidate the molecular basis for the biosynthesis of viomycin, as well as to engineer the biosynthesis of novel natural products. For instance, host cells can be genetically manipulated to produce one or more specific members of the TUB family by using gene disruption techniques to disrupt particular genes within the viomycin biosynthetic cluster. Gene disruption techniques are well known in the art, see for example, Kieser et al., 2000ab, for one technique, in-frame deletions using a delivery vector. In addition, genetic engineering or overexpression of the transport, resistance and regulatory proteins can lead to higher titers of viomycin compounds and derivatives thereof from production cultures. The invention encompasses the isolation of any of these compounds from the production culture as a starting compound to chemically generate new antibiotics.
The polypeptides SEQ. ID NOs:2-17, 19-22 encoded by the viomycin gene cluster are useful as enzymes in producing novel derivatives of the TUB family as well as specific members of the TUB family. For instance, VioC (SEQ. ID NO:4) and VioD (SEQ ID NO:5) can be moved into a host cell, e.g. E. coli. The VioC and VioD can then be isolated and purified and used to produce (2S,3R)-capreomycidine in large scale amounts (Ju et al., 2004).
In addition, the antibiotics derived from the present invention are useful as starting material in semisynthetic processes to generate libraries of novel antibiotics. In a semisynthetic process host cells are transformed to produce a specific TUB family antibiotic. These specific antibiotics can then be chemically modified by methods well known in the art and screened to determine their efficacy against bacterial diseases, including drug resistant strains of TB.
The present isolated, biologically active purified polypeptides, variants or fragments thereof, can be further purified by well known techniques in the art, including fractionation on immunoaffinity or ion-exchange columns; ethanol precipitation; reverse phase HPLC; chromatography on silica or on an anion-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; or ligand affinity chromatography. These isolated polypeptides are useful as starting compounds or enzymes to generate particular antibiotics of the TUB family, and novel derivatives thereof.
Chimeric Expression Cassettes, Vectors and Host Cells of the Invention
As used herein, “chimeric” means that a vector comprises DNA from at least two different species, or comprises DNA from the same species, which is linked or associated in a manner which does not occur in the “native” or wild type of the species. The recombinant DNA sequence or segment, used for transformation herein, can be circular or linear, double-stranded or single-stranded. Generally, the DNA sequence or segment is in the form of chimeric DNA, such as plasmid DNA, that can also contain coding regions flanked by control sequences which promote the expression of the DNA present in the resultant transformed (recombinant) host cell. Aside from DNA sequences that serve as transcription units for the nucleic acid molecules of the invention or portions thereof, a portion of the DNA can be untranscribed, serving a regulatory or a structural function. For example, the preselected DNA can itself comprise a promoter that is active in a particular host cell.
Other elements functional in the host cells, such as introns, enhancers, polyadenylation sequences and the like, can also be a part of the DNA. Such elements may or may not be necessary for the function of the DNA, but may provide improved expression of the DNA by affecting transcription, stability of the mRNA, or the like. Such elements can be included in the DNA as desired to obtain the optimal performance of the transforming DNA in the cell.
“Control sequences” is defined to mean DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotic cells, for example, include a promoter, and optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers. Other regulatory sequences may also be desirable which allow for regulation of expression of the genes relative to the growth of the host cell. Regulatory sequences are known to those of skill in the art, and examples include those which cause the expression of a gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. Other types of regulatory elements can also be present in the vector, for example, enhancer sequences.
“Operably linked” means that the nucleic acids are placed in a functional relationship with another nucleic acid sequence. For example, a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, operably linked means that the DNA sequences being linked are contiguous and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accord with conventional practice.
The DNA to be introduced into the cells further will generally contain either a selectable marker gene or a reporter gene or both to facilitate identification and selection of transformed cells from the population of cells sought to be transformed. Alternatively, the selectable marker can be carried on a separate piece of DNA and used in a co-transformation procedure. Both selectable markers and reporter genes can be flanked with appropriate regulatory sequences to enable expression in the host cells. Useful selectable markers are well known in the art and include, for example, antibiotic and herbicide-resistance genes, such as neo, hpt, dhfr, bar, aroA, dapA and the like. See also, the genes listed on Table 1 of Lundquist et al. (U.S. Pat. No. 5,848,956).
Reporter genes are used for identifying potentially transformed cells and for evaluating the functionality of regulatory sequences. Reporter genes which encode for easily assayable proteins are well known in the art. In general, a reporter gene is a gene which is not present in or expressed by the recipient organism or tissue and which encodes a protein whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells.
Prokaryotic expression systems are preferred, and in particular, systems compatible with Streptomyces sp. are of particular interest. Control elements for use in such systems include promoters, optionally containing operator sequences, and ribosome binding sites. Particularly useful promoters include control sequences derived from the gene clusters of the invention. Preferred promoters are Streptomyces promoters, including but not limited to the ermE, pika, and tipA promoters. Additional examples include promoter sequences derived from biosynthetic enzymes such as tryptophan (trp), the β-lactamase promoter system, bacteriophage lambda PL, and T5. In addition, synthetic promoters, such as the tac promoter (U.S. Pat. No. 4,551,433), which do not occur in nature, also function in bacterial host cells.
The various nucleic acid molecules of interest can be cloned into one or more recombinant vectors as individual cassettes, with separate control elements, or under the control of, e.g., a single promoter. The nucleic acid molecules can include flanking restriction sites to allow for the easy deletion and insertion of other sequences. The design of such unique restriction sites is known to those of skill in the art and can be accomplished using the techniques, such as site-directed mutagenesis and PCR.
For sequences generated by random mutagenesis, the choice of vector depends on the pool of mutant sequences, i.e., donor or recipient, with which they are to be employed. Furthermore, the choice of vector determines the host cell to be employed in subsequent steps of the claimed method. Any transducible cloning vector can be used as a cloning vector for the donor pool of mutants. It is preferred, however, that phagemids, cosmids, or similar cloning vectors be used for cloning the donor pool of mutant encoding nucleotide sequences into the host cell. Phagemids and cosmids, for example, are advantageous vectors due to the ability to insert and stably propagate therein larger fragments of DNA than in M13 phage and lambda phage, respectively. Phagemids which will find use in this method generally include hybrids between plasmids and filamentous phage cloning vehicles. Cosmids which will find use in this method generally include lambda phage-based vectors into which cos sites have been inserted. Recipient pool cloning vectors can be any suitable plasmid. The cloning vectors into which pools of mutants are inserted can be identical or can be constructed to harbor and express different genetic markers (see, e.g., Sambrook et al., supra). Vectors containing marker genes are useful to determine whether or not transfection is successful.
Thus, for example, the cloning vector employed can be an E. coli/Streptomyces shuttle vector (see, for example, U.S. Pat. Nos. 4,416,994, 4,343,906, 4,477,571, 4,362,816, and 4,340,674), a cosmid, a plasmid, a bacterial artificial chromosome (BAC) (see, e.g., Zhang and Wing, Plant Mol. Biol., 35, 115 (1997); Schalkwyk et al., Curr, Op. Biotech., 6, 37 (1995); and Monaco and Lavin, Trends in Biotech., 12, 280 (1994)), or a phagemid. The host cell can be a bacterial cell such as E. coli, Penicillium patulum, Saccharothrix mutabilis subsp. capreolus and Streptomyces spp. such as S. lividans, S. venezuelae, or S. Iavendulae, or a eukaryotic cell such as fungi, yeast or a plant cell, e.g., monocot and dicot cells, preferably cells that are regenerable.
One example of such a vector is the pBAC-VIO-Conj vector. The DraI to HindIII fragment of pVIO-P8C8RH (containing the viomycin biosynthetic cluster from vioA to the internal HindlIl site of vioG) can be inserted between the HindlIl and Sfol sites of pBeloBAC11 (Shizuya, H. et al. 1992 PNAS 89:8794-8797), generating plasmid pBeloBAC11-vioA-G. Such an insert includes not only vioA-vioG but also  ̃20 kb of Streptomyces sp. ATCC11861 upstream of vioA.
The HindIII to HindIII fragment of pVIO-P2C3RG (containing the viomycin biosynthetic pathway from vioT to the internal HindIII fragment of vioG) is then inserted into the HindIII site of pBeloBAC11-vioA-G. Orientation can be determined by PCR amplification. The plasmid generated is pBAC-VIO. This clone also contains a small portion of SuperCos-1 (from Stratagene—Evans et al. 1989. Gene 79:9-20) in addition to  ̃20 kb of Streptomyces sp. ATCC11861 sequence upstream of vioT.
The pBAC-VIO vector is digested with Xbal (site lies between the repE and ori sites of pBAC-VIO) and blunt ended using Klenow. The DraI fragment from pOJ436 (Bierman et al. 1992 Gene 116:43-49) that contains the RK2 oriT, aac(3)IV apramycin resistance gene, attP ΦC31 integration site, and int ΦC31 integrase is inserted into this site. This results in the vector pBAC-VIO-conj.
This plasmid contains the entire viomycin biosynthetic gene cluster along with the ability to conjugate between Escherichia coli and Streptomyces species. Additionally the ΦC31 integration site and integrase enable the vector to integrate into the chromosome of various Streptomyces species including Streptomyces lividans and Streptomyces coelicolor. 
The viomycin biosynthetic gene cluster-containing plasmid pBAC-VIO-Conj can be mobilized into a heterologous host (i.e. Streptomyces coelicolor M145, Streptomyces coelicolor CH999, Streptomyces lividans 1326) using standard conjugation procedures (Kieser, T., et al., 2000b). Exconjugants are selected for using apramycin. These strains contain the pBAC-VIO-Conj vector integrated into the attB site of the chromosome.
These strains can be grown in viomycin production medium (Tam and Jordan, 1972) or alternative media (i.e. Yeast extract malt extract medium) for heterologous expression of the viomycin biosynthetic pathway. Increased production of viomycin in the heterologous host may involve supplementing or changing the concentration of the medium with various amino acids at various times during culture, manipulating the salts contained in the medium or altering the media's pH. For example, supplementing the medium with precursors (i.e. L-serine, (2S)-arginine, L-lysine), increasing the expression of the transcriptional regulator VioR (i.e. vioR expression by the snpA promoter in pANT851 (Dickens M L, Strohl W R (1996) J. Bacteriol. 178:3389-3395; Dickens M L, Ye J, Strohl W R (1996) J. Bacteriol. 178:3384-3388; Dickens M L, Priestley N D, Strohl W R (1997) J. Bacteriol. 179:2642-2650)), or increasing the expression of the vph resistance gene (i.e. addition of plasmid plJ364 which contains the vph resistance gene (Kieser T, Hopwood D A, Wright H M, Thompson C J (1982) Mol. Gen. Genet. 185:223-238) can result in increased viomycin production. Increased viomycin production may involve one or more of these processes. In addition, the flanking regions of the BAC that contain the 20 kb upstream of VioT and 20 kb upstream of VioA can be reduced or deleted so as to maximize viomycin production.
The general methods for constructing recombinant DNA which can transform target cells are well known to those skilled in the art, and the same compositions and methods of construction can be utilized to produce the DNA useful herein. For example, J. Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press (2d ed., 1989), provides suitable methods of construction.
The recombinant DNA can be readily introduced into the host cells by any procedure useful for the introduction into a particular cell, e.g., calcium phosphate precipitation, protoplast fusion, conjugation, lipofection, electroporation, gene gun and the like.
As used herein, the term “cell line” or “host cell” is intended to refer to well-characterized homogenous, biologically pure populations of cells. These cells can be eukaryotic cells that are neoplastic or which have been “immortalized” in vitro by methods known in the art, as well as primary cells, or prokaryotic cells. In particular, the cell line or host cell can be of mammalian, plant, insect, yeast, fungal or bacterial origin.
“Transfected” or “transformed” is used herein to include any host cell or cell line, the genome of which has been altered or augmented by the presence of at least one DNA sequence, which DNA is also referred to in the art of genetic engineering as “heterologous DNA,” “recombinant DNA,” “exogenous DNA,” “genetically engineered,” “non-native,” or “foreign DNA,” wherein said DNA was isolated and introduced into the genome of the host cell or cell line by the process of genetic engineering. The transfected DNA can be maintained as an extrachromosomal element or as an element which is stably integrated into the host chromosome of the host cell. Host cells with transfected DNA maintained as an extrachromosomal element or as an element stable integrated into the host chromosome are referred to as a “recombinant host cell.”
Moreover, recombinant polypeptides having a particular activity can be prepared via “gene-shuffling”. See, for example, Crameri et al., Nature, 391, 288 (1998); Patten et al., Curr. Op. Biotech., 8, 724 (1997), U.S. Pat. Nos. 5,837,458, 5,834,252, 5,830,727, 5,811,238, 5,605,793).
For phagemids, upon infection of the host cell which contains a phagemid, single-stranded phagemid DNA is produced, packaged and extruded from the cell in the form of a transducing phage in a manner similar to other phage vectors. Thus, clonal amplification of mutant encoding nucleotide sequences carried by phagemids is accomplished by propagating the phagemids in a suitable host cell.
Following clonal amplification, the cloned donor pool of mutants is infected with a helper phage to obtain a mixture of phage particles containing either the helper phage genome or phagemids mutant alleles of the wild-type encoding nucleotide sequence.
Infection, or transfection, of host cells with helper phage is generally accomplished by methods well known in the art (see., e.g., Sambrook et al., supra; and Russell et al. (1986) Gene 45:333-338).
The helper phage can be any phage which can be used in combination with the cloning phage to produce an infective transducing phage. For example, if the cloning vector is a cosmid, the helper phage will necessarily be a lambda phage. Preferably, the cloning vector is a phagemid and the helper phage is a filamentous phage, and preferably phage M13.
If desired after infecting the phagemid with helper phage and obtaining a mixture of phage particles, the transducing phage can be separated from helper phage based on size difference (Barnes et al. (1983) Methods Enzymol. 101:98-122), or other similarly effective techniques.
The entire spectrum of cloned donor mutations can now be transduced into clonally amplified recipient cells into which have been transduced or transformed a pool of mutant encoding nucleotide sequences. Recipient cells which can be employed in the method disclosed and claimed herein can be, for example, E. coli, or other bacterial expression systems which are not recombination deficient. A recombination deficient cell is a cell in which recombinatorial events are greatly reduced, such as rec.sup.-mutants of E. coli (see, Clark et al. (1965) Proc. Natl. Acad. Sci. USA 53:451-459).
These transductants can now be selected for the desired expressed protein property or characteristic and, if necessary or desirable, amplified. Optionally, if the phagemids into which each pool of mutants is cloned are constructed to express different genetic markers, as described above, transductants can be selected by way of their expression of both donor and recipient plasmid markers.
The recombinants generated by the above-described methods can then be subjected to selection or screening by any appropriate method, for example, enzymatic or other biological activity.
The above cycle of amplification, infection, transduction, and recombination can be repeated any number of times using additional donor pools cloned on phagemids. As above, the phagemids into which each pool of mutants is cloned can be constructed to express a different marker gene. Each cycle could increase the number of distinct mutants by up to a factor of 106. Thus, if the probability of occurrence of an inter-allelic recombination event in any individual cell is f (a parameter that is actually a function of the distance between the recombining mutations), the transduced culture from two pools of 106 allelic mutants will express up to 1012 distinct mutants in a population of 1012/f cells.
EXAMPLE 1
Sequence and Characterization of the Viomycin Biosynthetic Gene Cluster Materials and Methods
Bacterial strains and growth media. Streptomyces sp. ATCC11861 (which is equivalently named Streptomyces vinaceus) was obtained from the American Type Culture Collection and grown on ISP Medium 2 (Difco 0770). The strain was grown in BactoTm Tryptic Soy Broth (TSB) when obtaining mycelia for chromosomal DNA isolation. For the production and purification of viomycin, TSB-grown mycelia were used to inoculate 100 ml of viomycin production medium (Quadri, L. E., et al., 1998). For conjugations, mannitol soya flour agar was used (Kieser, T., et al., 2000).
Escherichia coli strains were grown in LB medium or on LB agar supplemented with the appropriate antibiotic as indicated. When grown in microtiter plates, cosmid-containing strains were grown in freezing medium (Whitman, W. B., et al., 1998) supplemented with kanamycin (Kan) (50 μg/ml). The E. coli strains used were DH5a, XL-1 Blue MR (Stratagene), HB101/pRK2013 (Figureski, D. H., and D. R. Helinski, 1979) (from M. Rondon, UW-Madison) and ET12567 (MacNeil, D. J., et al., 1992) (from C. Khosla, Stanford Univ.).
Genomic DNA isolation and cosmid library construction. 3.0 g (wet weight) of Streptomyces sp. ATCC11861 mycelia were used for genomic DNA isolation following a previously described protocol (Pootoolal, J., et al., 2002). Genomic DNA was partially digested with Sau3AI to give 30-50 kb fragments that were subsequently ligated into the BamHl site of SuperCos1 (Stratagene), prepared following the manufacturer's instructions. The DNA was then packaged into lambda phage using the Gigapack III XL Packaging Extract Kit (Stratagene) and used to infect E. coli XL-1 Blue MR, following the manufacturer's instructions. 1248 cosmid-containing clones were isolated and were frozen at −80° C. individually in microtiter dish wells as well as in pools of 8 clones consisting of 25 μl from each member of a microtiter dish column. Thus, 1248 individual cosmids were also represented in 156 cosmid pools.
Screening the cosmid library. The cosmid library was first screened by PCR amplification for those cosmids that contained vph, the viomycin resistance gene (Bibb, M. J., 1985). Primers used were the following: Vph/FEco (5′ AGMGTGGAGAATTCGCCCACCATGAG 3′) and Vph/REco (5′ CCTTCAGAATTCCTGTCACGCTGCCCG 3′). Boiled cells of each cosmid pool were used as a source of template DNA for PCR amplification. Individual members of each vph-positive cosmid pool were subsequently screened by PCR amplification to identify the specific cosmid containing vph. Cosmid pVIO-P2C3RG was identified in this manner.
From the pVIO-P2C3RG sequence, two primers based on the putative viomycin biosynthetic gene vioG were designed (vio-P2-5p (5′ GGGGAGACGTACTTCTTCCA 3′) and vio-P2-3p (5′ GGCGAGTTCACGGGAGATA 3′)). These primers were used to screen the library a second time, by PCR amplification, to identify cosmids containing vioG. The vioG-positive cosmids were then screened by PCR amplification for the absence of vph. A vioG-positive but vph-negative cosmid pVIO-P8C8RH was thus isolated.
Sequencing and annotating the viomycin biosynthetic gene cluster. 2-3 kb fragments from cosmids pVIO-P2C3RG and pVIO-P8C8RH were subcloned into PSMARTTMLCKan by Lucigen Corp. (Middleton, Wis.). Subclones were submitted to the Genome Center Sequencing Facility at UW-Madison where they were sequenced (seven-fold coverage, two-fold minimum). Contigs were assembled using SeqMan (Lasergene, Madison, Wis.). Annotation of ORFs and putative gene functions were assigned using a combination of MapDraw (Lasergene, Madison, Wis.), blastp, PSI-BLAST, and RPS-BLAST (NCBI) (Altschul, S. F., et al., 1997) (using default parameters). The completed viomycin biosynthetic gene cluster has been deposited in GenBank (accession no. AY263398, as of Aug. 25, 2003) and is given in SEQ ID NO:1. The gene product for each of the genes contained in this cluster is also available (see AAP924291 through AAP92511) and is given in SEQ ID NOs:2-22. In case of a discrepancy between the sequence listing and the GenBank listing, the GenBank listing controls.
Insertional inactivation of vioA. An internal fragment of vioA was introduced into the suicide vector pOJ260 (Bierman, M., et al., 1992) using PCR-based cloning. The primers for vioA PCR amplification were the following: VioA/Pst 5′ TCACGCCGGTCGAGCAGGA 3′ and VioA/Eco 5′ ACGCCGTACTCGCGCAGG 3′. The PCR-amplified product was digested with Pstl and EcoRI and cloned into the corresponding restriction sites of pOJ260, yielding pOJ260-vioA. This plasmid was transformed into ET12567, and the resulting strain was used for conjugation of pOJ260-vioA into Streptomyces sp. ATCC11861 using a triparental mating protocol (Kieser, T., et al., 2000). The triparental mating involved ET12567/pOJ260-vioA, HB101/pRK2013, and Streptomyces sp. ATCC11861s.
To confirm pOJ260-vioA insertion into the chromosomal copy of vioA, chromosomal DNA was purified from the mutant strains and analyzed by PCR amplification and subsequent restriction enzyme analysis of the amplified products. Primers used for this analysis were VioA/Pst and VioA/Eco, which are outside the region cloned into pOJ260, and the FOR (5′ CGCCAGGGTTTTCCCAGTCACGAC 3′) and REV (5′ TCACACAGGAAACAGCTATGA 3′) primers that anneal to regions just outside the multiple cloning site of pOJ260. During this analysis it was determined that the 5′ end of vioA in one mutant strain (MGT1001) had undergone a deletion of approximately 400 bp between a BgIII and an NcoI restriction site within vioA (data not shown). This was not characterized further because vioA was inactivated regardless of the nature of this deletion. The two other isolated vioA mutants (MGT1002 and MGT1003) did not contain this deletion (data not shown).
Production and isolation of viomycin. 100 ml cultures of the wild-type or mutant strains of Streptomyces sp. ATCC11861 were grown in viomycin production medium at 28° C. for five days. Mycelia were removed by centrifugation, and the resulting supernatant was used for viomycin purification following the previously published protocol (Tam, A. H. -K., and D. C. Jordan, 1972).
High-Performance Liquid Chromatography (HPLC) of purified viomycin. Purified viomycin samples were analyzed by HPLC (Beckman System Gold) using a Macrosphere SCX 300A 7U column (Alltech) at a flow rate of 1 ml/min. The following buffers were used: A −20 mM Tris-HCl pH 6.4; B −20 mM Tris-HCl, 1M sodium acetate pH 6.4. The separation profile was 5 min isocratic development at 100%A/O%B, 15 min linear gradient from 100%A/O%B to 0%A/100%B, 5 min isocratic development at 0%A/100%B. Elution of viomycin was monitored at the characteristic absorbance of 268 nm. Purified viomycin had the same UV/vis spectrum and HPLC retention time as authentic viomycin, and also co-eluted from the HPLC with authentic antibiotic regardless of elution profile.
Results
Cloning and sequencing of the viomycin biosynthetic gene cluster. We constructed a cosmid library of the Streptomyces sp. ATCC11861 genome, and used PCR amplification to screen the library for cosmids containing vph, the known viomycin resistance gene (Bibb, M. J., et al., 1985). The resistance gene was targeted because the resistance gene for a particular antibiotic is typically encoded in the same region of the chromosome as the biosynthetic gene cluster for that antibiotic (Martin, M. F., and P. Liras, 1989). Sequencing out of the resistance gene from one of the vph-positive cosmids, pVIO-P2C3RG, identified an ORF that encoded a putative lysine 2,3-aminomutase. Since viomycin contains a β-lysine moiety, and lysine 2,3-aminomutases catalyze the formation of β-lysine, we hypothesized that pVIO-P2C3RG contained a portion of the viomycin biosynthetic gene cluster.
Preliminary analysis of the DNA sequence from pVIO-P2C3RG suggested only a portion of the viomycin biosynthetic gene cluster was contained on the cosmid. We then screened the library a second time using PCR primers based on a putative viomycin biosynthetic gene, vioG, that was present on pVIO-P2C3RG. The vioG-positive cosmids were then screened for the absence of vph, identifying cosmids containing DNA that overlapped but was not redundant with the insert in pVIO-P2C3RG. From this analysis pVIO-P8C8RH was isolated, and both cosmids were completely sequenced.
Analysis of the viomycin biosynthetic gene cluster. The viomycin biosynthetic gene cluster includes approximately 36.3 kb of contiguous DNA encoding 20 ORFs involved in the biosynthesis, export, regulation, and activation of the antibiotic, in addition to the previously isolated resistance gene vph (FIG. 2 and Table 1). An additional  ̃20 kb on either side of the predicted gene cluster were sequenced and analysis of this DNA did not identify any genes predicted to be involved in viomycin production. Thus, vioA, vioT, and the genes between them, constitute the viomycin biosynthetic gene cluster.
Biosynthesis of the nonproteinogenic amino acids. Viomycin is a six amino acid peptide consisting of two L-serine residues and one residue of each of the following nonproteinogenic amino acids: L-2,3-diaminopropionate, β-ureidodehydroalanine, β-lysine, and L-tuberactidine. Based on the common observation that secondary metabolite biosynthetic gene clusters typically encode all the enzymes needed for the production of any precursors specific for that particular metabolite (Chater, K. F., and C. J. Bruton, 1985; Du, L., et al., 2000; van Wageningen, A. M. A., et al., 1998), the viomycin gene cluster should encode the enzymes needed to generate L-2,3-diaminopropionate, (2S,3R)-capreomycidine, and β-lysine. The conversion of L-2,3-diaminopropionate to β-ureidodehydroalanine and (2S,3R)-capreomycidine to L-tuberactidine occurs after precursor incorporation into the growing peptide chain as will be discussed below.
i. Biosynthesis of L-2,3-diaminopropionate. Precursor labeling studies on viomycin (Carter, J. H., et al., 1974) and the capreomycins (Wang, M., and S. J. Gould, 1993) have determined that L-serine is the precursor for L-2,3-diaminopropionate. Bioinformatic analysis of the viomycin biosynthetic gene cluster suggests that the conversion of L-serine to L-2,3-diaminopropionate is catalyzed by the concerted actions of VioB and VioK (FIG. 3A).
VioB is a homolog of cysteine synthases and serine dehydratases (38% identity, 52% similarity to Reut3764 from Ralstonia metallidurans; 35% identity, 52% similarity to SAVOL 16 from Staphylococcus aureus Mu50), enzymes that catalyze the pyridoxal phosphate (PLP)-dependent replacement or elimination, respectively, of the β-substituent of their substrate (Alexander, F. W., et al., 1994). During catalysis, both of these enzymes form a PLP bound a-aminoacrylate intermediate. VioB uses a similar mechanism to form a Schiff base linkage between PLP and an α-aminoacrylate intermediate (FIG. 3A). VioB then catalyzes a β-replacement reaction analogous to that seen for cysteine synthases. However, while cysteine synthases use sulfur from sulfide as the nucleophile, VioB uses the nitrogen of ammonia as the nucleophile (FIG. 3A). The source of this nucleophile for viomycin biosynthesis is the ammonia liberated from L-ornithine by VioK (FIG. 3A). VioK is a homolog of ornithine cyclodeaminases (31% identity, 47% similarity to Reut3765 from Ralstonia metallidurans; 28% identity, 47% similarity to SAVOL 17 from Staphylococcus aureus Mu50), enzymes that convert L-ornithine to L-proline with the release of ammonia (Costilow, R. N., and L. Laycock, 1971; Muth, W. L., and R. N. Costilow, 1974ab). Thus, VioK functions as an amidotransferase during viomycin biosynthesis since ammonia is the relevant product of the reaction, not L-Pro.
The role of VioB was verified by construction of an in frame deletion of VioB (ΔVioB). The ΔVioB strain no longer produces viomycin. When DAP was added to the growth medium, viomycin production was restored, confirming our prediction that vioB is involved specifically in DAP biosynthesis.
ii. Biosynthesis of (2S,3R)-capreomycidine. Precursor labeling studies have determined that L-tuberactidine of viomycin (Carter, J. H., et al., 1974) and (2S,3R)-capreomycidine of the capreomycins (Gould, S. J., and D. A. Minott, 1992) are derived from (2S)-arginine. As discussed below, (2S,3R)-capreomycidine is incorporated into the growing peptide chain and is subsequently converted to L-tuberactidine after peptide synthesis is completed (FIG. 7). VioC and VioD convert (2S)-arginine to (2S,3R)-capreomycidine (FIG. 3B) (Ju et al., 2004).
VioC is a homolog of clavaminic acid synthases (45% identity, 60% similarity to SttL from Streptomyces rochel), which are non-heme iron dioxygenases involved in clavulanic acid biosynthesis (Townsend, C. A., 2002). The first reaction catalyzed by one of the clavaminic acid synthases, CS2, is the hydroxylation of the β-carbon of the arginine moiety of 5-guanidino-2-(2-oxo-azetidin-1-yl)-pentanoic acid (Salowe, S. P., et al., 1990). VioC catalyzes a similar reaction to generate β-hydroxyarginine (FIG. 3B). This product is then a substrate for VioD, a homolog of PLP-dependent aromatic amino acid aminotransferases (40% identity, 51% similarity to SttN from Streptomyces rochei). VioD catalyzes a β-elimination reaction to generate a PLP-linked α,β-dehydroarginine that would allow for intramolecular addition of the δ-guanido moiety to the carbon, thus generating (2S,3R)-capreomycidine.
Gould and Minott predicted the presence of the α,β-dehydroarginine intermediate in the pathway based on their results from feeding experiments with [2,3,3,5,5-2H5]-arginine during capreomycin biosynthesis (Gould, S. J., and D. A. Minott, 1992). Their prediction was based on the loss of the deuterium from C2 and the loss of one deuterium from C3, which would be consistent with such an intermediate. They also predicted that the (2S)-arginine-to-(2S,3R)-capreomycidine conversion would occur after peptide synthesis so that the α,β-dehydroarginine intermediate could be stabilized by an amide bond. Our studies indicate (2S,3R)-capreomycidine is produced before peptide synthesis (FIG. 3B), with the PLP cofactor stabilizing the α,β-dehydroarginine intermediate.
The two putative enzymes showing the highest amino acid identity with VioC and VioD are SttL (45% identity, 60% similarity) and SttN, respectively (40% identity, 52% similarity). The genes encoding SttL and SttN are within the proposed biosynthetic gene cluster for the broad-spectrum antibiotic streptothricin (Fernandez-Moreno, M. A., et al., 1997), and (2S,3R)-capreomycidine is predicted to be an intermediate in the biosynthesis of this antibiotic (Gould, S. J., and K. J. Martinkus, 1981a,b; Jackson, M. D., et al., 2002; Martinkus, K. J., et al., 1983). Thus, the (2S,3R)-capreomycidine intermediate in streptothricin biosynthesis is generated by an analogous mechanism to that proposed for viomycin. The function of VioC and VioD was verified by heterologously overexpressing these enzymes in E. coli as outlined below in Example 3.
iii. Biosynthesis of β-lysine. Viomycin and streptothricin also contain β-lysine moieties (FIG. 7). Both biosynthetic clusters encode homologs to lysine-2,3-aminomutases (VioP in viomycin; SttO in streptothricin) (32% identity, 47% similarity to SttO from Costridium subterminale). Frey and colleagues have extensively studied lysine-2,3-aminomutases and have shown these enzymes catalyze the migration of the a-amino group of L-lysine to the β-carbon (Frey, P. A., 1993). We predict both VioP and SttO catalyze the same reaction to generate a source of β-lysine for viomycin and streptothricin, respectively (FIG. 3C).
Assembly of the cyclic pentapeptide core. Although viomycin is a peptide consisting of six amino acids, the cyclic pentapeptide core of the antibiotic is biosynthesized first, followed by acylation of residue 1 with β-lysine. This pathway is based on TUBs being isolated with or without a β-lysine moiety (FIG. 1), suggesting β-lysine addition is separate from cyclic pentapeptide synthesis. We predict that a five-module NRPS synthesizes and cyclizes the pentapeptide core of viomycin.
During NRPS-catalyzed peptide synthesis, the domains, modules, and subunits of these enzymes are typically aligned in a sequence that is co-linear with the resulting peptide. Additionally, the organization of the NRPS subunits usually follows the order in which the corresponding genes are found on the genome (Cane, D. E., and C. T. Walsh, 1999). Neither of these rules appear to be followed by the viomycin NRPS. First, there are five modules for cyclic pentapeptide biosynthesis, but one of these modules lacks an adenylation (A) domain (FIG. 4). Therefore, one of the other A domains must function twice (FIG. 4). Secondly, it is not anticipated that the NRPS subunits function in the order their corresponding genes are arrayed on the chromosome (FIG. 2, and 4).
To determine the order in which the NRPS subunits function, we analyzed A domain specificity codes (Challis, G. L., et al., 2000; Stachelhaus, T., et al., 1999), conserved domain sequences (Konz, D., and M. A. Marahiel, 1999), and domain organizations. As shown in FIG. 4, VioF activates and tethers L-2,3-diaminopropionate (residue 1) to its peptidyl carrier protein (PCP) domain. Thus, the first two domains (A-PCP) of VioF form the initiating module of the NRPS. The condensation (C) domain of VioF then catalyzes peptide bond formation between residue 1 bound to VioF, and the L-serine (residue 2) bound to the first PCP domain of VioA. Thus module 2 of the NRPS spans both VioF and VioA. The first C domain of VioA catalyzes peptide bond formation between the dipeptide (residues 1-2) bound to the first VioA PCP domain and L-serine (residue 3) bound to the second PCP domain of VioA. Consistent with this, both A domains of VioA have specificity codes for L-serine recognition (DVYHFSLVDK and DVRHMSMVMK) (Challis, G. L., et al., 2000; Stachelhaus, T., et al., 1999). The second C domain of VioA then catalyzes peptide bond formation between the tripeptide (residues 1-2-3) on VioA and L-2,3,-diaminopropionate (residue 4) bound to the PCP domain of VioI.
There are two unusual aspects of the viomycin NRPS to highlight at this point in cyclic pentapeptide synthesis. First, VioI lacks the necessary A domain to aminoacylate itself with L-2,3-diaminopropionate. Thus, the A domain of VioF aminoacylates VioI in trans (FIG. 4). Second, VioJ catalyzes the next step in peptide synthesis by desaturating the α,β-bond of residue 4 to generate a tetrapeptide that includes the desaturated 2,3-diaminopropionate (FIG. 4). This is based on VioJ being a homolog of acyl-CoA dehydrogenases (38% identity, 54% similarity from Pseudomonas fluorescens pfO-1-Pflu 1686) (Thorpe, C., and J. J. Kim, 1995), but it lacks the conserved aspartate residue in acyl-CoA dehydrogenases needed for the recognition of the adenine base of coenzyme A (Battaile, K. P., et al., 2002; Tiffany, K. A., et al., 1997). We have recently shown that acyl-CoA dehydrogenase homologs in the undecylprodigiosin and pyoluteorin pathways, that also lack this residue, catalyze α,β-desaturations of PCP-bound substrates, not their CoA derivatives (Thomas, M. G., et al., 2002). Thus, VioJ functions in an analogous manner, and would be the first α,β-desaturase to be an integral part of a peptide synthesizing NRPS.
VioG is the best candidate for the terminal subunit since the C-terminus of VioG contains a truncated condensation (C) domain (immediately after the C3 core motif, suggesting it is inactive. This is consistent with VioG containing the terminal module since peptide bond formation with a downstream PCP-bound substrate is not required. This truncated C domain precedes a terminal domain of unknown function. Typically, the terminal domain of an NRPS is a thioesterase that catalyzes hydrolysis or cyclization and release from the final PCP domain (Marahiel, M. A., et al., 1997). While a weak thioesterase motif (GSAG) could be found in this terminal domain, it is not clear whether it plays any role in peptide cyclization and release, therefore, the mechanism of pentapeptide macrocyclization remains an open question.
Modifications of the cyclic pentapeptide. Following the formation of the cyclic pentapeptide shown in FIG. 4, there are three modifications that must occur: 1) carbamoylation of the α-amino group of residue 4 to form β-ureidodehydroalanine, 2) hydroxylation of the C6 of residue 5 to form tuberactidine, and 3) acylation of the α-amino group of residue 1 with β-lysine.
VioL is predicted to catalyze the carbamoylation of residue 4 based on the amino acid similarity between VioL and ornithine carbamoyltransferases (55% identity, 67% similarity from Streptomyces avennitilis (SAV3641)) (Legrain, C., and V. Stalon, 1976). The biosynthetic pathway for L-2,3-diaminopropionate conversion to β-ureidodehydroalanine is predicted to occur as shown in FIG. 3D. However, we cannot eliminate the possibility that carbamoylation occurs immediately after the desaturation of residue 4 while it is bound to the Viol. Further analysis is needed to discriminate between these possibilities.
The hydroxylation of the C6 of residue 5, which generates tuberactidine from (2S,3R)-capreomycidine, is catalyzed by VioQ based on its similarity to phenylpentanoic acid dioxygenase and related ring-hydroxylating dioxygenases (30% identity, 48% similarity with 3-chlorobenzoate 3,4-dioxygenase from Comamonas testosteroni) (Mason, J. R., and R. Cammack, 1992). Hydroxylation of residue 5 to generate the L-tuberactidine moiety occurs after peptide synthesis based on the isolation of tuberactinomycin derivatives with and without this hydroxylation (FIG. 1), suggesting that the hydroxylation is not a prerequisite for peptide synthesis. However, as with the carbamoylation discussed above, we cannot eliminate the possibility that the hydroxylation precedes the completion of peptide synthesis.
The sixth amino acid present in viomycin is β-lysine. This attachment of β-lysine to the α-amino group of residue 1 occurs by the actions of VioO (A-PCP) and VioM (C) (FIG. 5). Since these two proteins contain the three core domains of an NRPS module, this can be considered a monomodular NRPS. VioO will activate and tether β-lysine to its C-terminal PCP domain. Consistent with this, the A domain of VioO has the specificity code for β-lysine (DTEDVGTMVK, (Grammel, N., et al., 2002)) and preliminary results with partially purified VioO suggests it activates β-lysine (Y. Chan and M. Thomas, unpublished) (35% identity, 49% similarity to SanO of Streptomyces ansochromogenes).
VioM, a homolog of C domains (39% identity, 54% similarity between VioM (aa 14-434) and Nostoc punctiforme (Npun 5654) (aa 1160-1584)) then catalyzes amide bond formation between β-lysine bound to VioO and the soluble substrate des-β-lysine-viomycin (FIG. 5). This monomodular NRPS, therefore, does not function as a peptide synthetase per se, but rather as an N-acyltransferase. This mechanism is analogous to the terminal portion of the vibriobactin biosynthesis, whereby the acceptor site of the VibH C domain binds a soluble substrate instead of an amino acid tethered to a PCP (Keating, T. A., et al., 2000).
It is not clear what role VioN plays in viomycin biosynthesis. It is a homolog of a family of small proteins found in many NRPS systems (61% identity, 75% similarity to Agr_L—2317p from Agrobacterium tumefaciens C58), the standard of which is MbtH, a protein of unknown function in mycobactin biosynthesis (Quadri, L. E., et al., 1998). The location of vioN between vioM and vioO, suggests VioN plays some role in β-lysine addition.
Regulation, Export, Resistance, and Activation. Two putative transcriptional regulators are encoded in the viomycin biosynthetic gene cluster. VioR belongs to the OxyR family of transcriptional regulators (37% identity, 59% similarity with Streptomyces avermitilis SAV5624), while VioT is a homolog of NysRI (61% identity, 71% similarity with putative transcriptional regulator from Streptomyces avermitilis), a putative transcriptional regulator in the nystatin biosynthetic pathway (Brautaset, T., et al. 2000). The involvement of both transcriptional regulators in viomycin biosynthesis remains to be determined.
The export of the antibiotic is catalyzed by VioE, which is a permease homolog (29% identity, 43% similarity to a putative multidrug-resistance protein from Streptomyces avernitilis SAV3640; 29% identity, 45% similarity to a putative export protein from Streptomyces spectabilis SpcT). Our hypothesis is viomycin is exported in its phosphorylated form. This is based on VioS being a homolog of StrK (66% identity, 75% similarity with StrK from Streptomyces griseus), the streptomycin-phosphate phosphatase that removes the phosphate and activates streptomycin outside the cell (Mansouri, K., and W. Piepersberg, 1991). Thus, Vph, the previously identified viomycin phosphotransferase, catalyzes the phosphorylation of viomycin, which is then exported by VioE. VioS will reactivate the antibiotic once it is outside the cell. This mechanism of resistance and export will need to be considered when metabolically engineering the viomycin biosynthetic pathway.
Genetic evidence that the sequenced gene cluster encodes for the viomycin biosynthetic enzymes. To confirm the gene cluster we identified is involved in viomycin biosynthesis, vioA was inactivated as shown in FIG. 6A. We chose to inactivate vioA because it encodes an essential component of the viomycin NRPS (FIG. 4), and the absence of VioA should abolish viomycin production. This result would strongly support our hypothesis that the biosynthetic gene cluster we identified assembles viomycin. Three independently isolated vioA::pOJ260-vioA strains (MGT1001, MGT1002, and MGT1003) were grown under conditions optimized for viomycin production, and the antibiotic was purified from the supernatants. The purified components of the supernatant were then analyzed for the presence of viomycin using HPLC. Viomycin was not produced by any of the vioA::pOJ260-vioA strains (FIG. 6B). Therefore, we can conclude that the gene cluster sequenced and analyzed is the viomycin biosynthetic gene cluster.
Conclusions. We have isolated, sequenced, and annotated the biosynthetic gene cluster for the antibiotic viomycin from Streptomyces sp. ATCC11861. This pathway involves novel precursor biosynthetic mechanisms and atypical NRPS components to generate the hexapeptide antibiotic. It is anticipated that all TUB antibiotics are biosynthesized in a similar manner to viomycin, with subtle changes to generate the structural diversity shown in FIG. 1.
We hypothesize that Saccharothrix mutabilis subsp. capreolus, the producing strain of the capreomycins, does not encode a VioQ homolog since the capreomycins contain (2S,3R)-capreomycidine, not L-tuberactidine (FIG. 1). We also predict that the tuberactinomycin producers encode an additional enzyme that catalyzes γ-hydroxylation of the β-lysine residue to generate tuberactinomycin A and N (FIG. 1).
The central pentapeptide core of the TUBs varies in two respects besides the (2S,3R)-capreomycidine hydroxylation discussed above. First, for viomycin and the tuberactinomycins, residue 3 of the pentapeptide core is L-serine not L-2,3-diaminopropionate as seen in the capreomycins (FIG. 1). This difference is one of the reasons why residue 3 of viomycin and the tuberactinomycins cannot be N-acylated with β-lysine, as seen in the capreomycins. It is anticipated the A domain specificity code for module 3 in the capreomycin producer is altered to activate L-2,3-diaminopropionate instead of L-serine. Secondly, residue 2 in the capreomycins can be either L-serine or L-alanine (FIG. 1), suggesting the A domain of module 2 of the NRPS has relaxed substrate specificity.
Finally, the capreomycins, while containing L-2,3-diaminopropionate at residue 1 of the pentapeptide core, are only N-acylated at residue 3 (FIG. 1). It is anticipated that the VioM homolog in Sac. mutabilis subsp. capreolus has an altered acceptor site leading to β-lysine addition at the opposing side of the cyclic pentapeptide core compared to viomycin and the tuberactinomycins. This selectivity is due, in part, to the N-acylation of the β-amino group of residue 3, not the α-amino group of residue 1 as seen in viomycin and the tuberactinomycins.
With the knowledge gained from the analysis of the viomycin biosynthetic gene cluster, a clear picture of how the TUB family of antibiotics is biosynthesized has been developed. This permits metabolic engineering and chemical modification of this family of antibiotics to combat resistant bacteria, remove unwanted side-effects for MDR-TB treatment, and develop derivatives of these antibiotics for use in the treatment of other bacterial and viral infections.
EXAMPLE 2
Metabolic Engineering to Generate Alternative Tuberactinomycin Antibiotics
Streptomyces sp. ATCC11861 can be metabolically engineered to produce alternative tuberactinomycin antibiotics through the use of genetic manipulation of the viomycin biosynthetic gene cluster. Outlined below are genetic techniques to generate previously isolated tuberactinomycins or new derivatives that have not been isolated in nature or generated chemically.
1. Production of Tuberactinamine A.
Tuberactinamine A differs from viomycin in the absence of the β-Lysine moiety tethered to the a-amino group of residue 1 FIG. 1). Tuberactinamine A has been produced by Streptomyces griseoverticillatus var. tuberacticus NRRL3482 (Morse, B. K., et al., 1997) but only when the organism was grown in the presence of (S)-2-aminoethyl-L-cysteine. Even with the addition of (S)-2-aminoethyl-L-cysteine, tuberactinamine A was still produced at a low level. The genetic inactivation of the genes involved in β-lysine biosynthesis and/or attachment results in Streptomyces sp. ATCC11861 producing only tuberactinamine A, with no contaminating viomycin.
The metabolic engineering of Streptomyces sp. ATCC11861 to produce tuberactinamine A involves the deletion of the viomycin biosynthetic genes vioM, vioN, vioO, and vioP. These four genes encode the necessary enzymes for β-Lysine biosynthesis and attachment to tuberactinamine A (FIG. 5). The deletion of these genes abolishes β-Lysine synthesis in addition to the attachment of any amino acids to the α-amino group of residue 1. Thus, the ΔvioMNOP strain of Streptomyces sp. ATCC11861 produces tuberactinamine A instead of viomycin.
To generate these deletions, we follow standard protocols (Kieser, T., et al., 2000a) for the generation of in-frame deletions of all four genes. Briefly, PCR-based cloning is used to fuse the first few codons of vioM to the final few codons of vioP. In addition to these codons, DNA containing approximately 3 kb upstream of vioM and approximately 3 kb 3′ to vioP is cloned into an appropriate Streptomyces suicide vector (i.e. the temperature-sensitive plasmid pKC1139). (Bierman, M., et al., 1992)). The resulting delivery vector contains approximately 3 kb upstream of vioM through 3 kb 3′ of vioP, with vioMNOP being deleted.
The resulting delivery vector is introduced into Streptomyces sp. ATCC11861 by conjugation following standard protocols (Kieser, T., et al., 2000b). Exconjugants are selected for by using the appropriate antibiotic (i.e. apramycin for pKC1139 delivery constructs). These strains contain the delivery vector replicating in Streptomyces sp ATCC11861. The plasmid-containing strains are then grown at non-permissive temperatures (37C) on antibiotic-containing medium (i.e. apramycin for pKC1139 derivatives) to select for those strains where pKC1139 has integrated into the chromosome. Those strains that grow under these conditions are then transfered to fresh medium lacking antibiotic (i.e. apramycin for pKC1139 derivatives) and grown at a permissive temperature (28C). These strains are then screened for those that have resolved the delivery vector (i.e. apramycin sensitive for pKC1139 delivery constructs). The wild-type and mutant colonies are then distinguished by PCR screening for the AvioMNOP mutation.
The resulting ΔvioMNOP mutants are grown under conditions optimized for viomycin production (Tam, A. H. -K., and D. C. Jordan, 1972). These mutants are analyzed for viomycin and tuberactinamine A production as described in Example 1 (FIG. 6B). The ΔvioMNOP mutant strain produces tuberactinamine A, not viomycin. The insertional inactivation of any of these genes with an antibiotic resistance gene cassette also results in the production of tuberactinamine A.
The analogous protocol can be followed to delete any one or more other genes from the viomycin biosynthetic cluster including vioB, vioC., vioD, vioK, vioL and vioQ alone or in combination.
2. Production of Tuberactinomycin O.
Tuberactinomycin O differs from viomycin in that it lacks the hydroxylation of the (2S,3R)-capreomycidine ring of residue 5 (FIG. 1). Streptomyces griseoverticillatus var. tuberacticus NRRL3482 is known to make low quantities of tuberactinomycin O, but the strain also generates tuberactinomycins A, B, and N. Using our molecular information of the viomycin biosynthetic gene cluster, Streptomyces sp. ATCC11861 can be engineered to produce solely tuberactinomycin O.
In a procedure analogous to that discussed for tuberactinamine A formation, we use genetic inactivation of a viomycin biosynthetic gene, vioQ, to convert Streptomyces sp. ATCC11861 from producing viomycin, to producing tuberactinomycin O. VioQ encodes the putative residue 5 hydroxylase (Thomas, M. G., et al., 2003). Briefly, the first few codons of vioQ are fused to the final few codons of vioQ using PCR-based cloning. An additional 2 kb on either side of the fusion site is also cloned. This ΔvioQ construct is generated in a delivery vector, and the subsequent introduction of the ΔvioQ onto the Streptomyces sp. ATCC11861 genome follows the protocol outlined above for ΔvioMNOP construction. The resulting strain is grown under conditions optimized for viomycin production (Tam, A. H. -K., and D. C. Jordan, 1972). The ΔvioQ stain generates tuberactinomycin O instead of viomycin.
3. Production of des-carbamoyl-viomycin.
VioL catalyzes the carbamoylation of the β-amino group of residue 4 (FIG. 1) (Thomas, M. G., et al., 2003). By genetically inactivating vioL, the resulting Streptomyces sp. ATCC11861 strain will generate a viomycin derivative lacking the carbamoylation of residue 4. This tuberactinomycin derivative has not been produced naturally, or by using chemical modifications or strain mutagenesis techniques.
In an analogous manner as discussed above, vioL is deleted from the chromosome of Streptomyces sp. ATCC11861 using standard techniques. The resulting strain produces des-carbamoyl-viomycin instead of viomycin.
4. Production of Tuberactinamine N.
Tuberactinamine N differs from viomycin by the absence of both the β-Lysine moiety and the hydroxylation of the capreomycidine ring of residue 5 (FIG. 1). Tuberactinamine N has only been generated by acid treatment of tuberactinomycin N (Wakamiya, T., et al., 1977). Through genetic manipulation of Streptomyces sp. ATCC11861, this strain is altered to generate tuberactinamine N instead of viomycin. This is accomplished by combining the ΔvioMNOP and ΔvioQ mutations that are discussed above. The resulting strain is grown under standard conditions for viomycin production, however the strain produces tuberactinamine N instead of viomycin.
5. Production of Alternative Tuberactinomycins by Constructing ΔvioMNOP, ΔvioQ, and ΔvioL Mutations in Various Combinations.
As discussed for the production of tuberactinamine N, the deletions discussed in sections 1-3 can be combined to generate new tuberactinomycins that have not been isolated or synthesized. These combinations are summarized in FIG. 8. Importantly, the genetic inactivation of these genes results in the production of only the desired tuberactinomycin instead of a mixture of compounds as previously seen with the random chemical mutagenesis of Streptomyces griseoverticillatus var. tuberacticus NRRL3482.
EXAMPLE 3
Overproduction and Purification of VioC and VioD
Introducing VioC and VioD into host cells, such as Streptomyces lividans or E. coli, causes the cells to produce large quantities of either (3S)-hydroxy-(2S)-Arginine or (2S,3R)-capreomycidine. Neither of these molecules are commercially available, but are useful as starting materials in chemical synthesis procedures. In particular, (2S,3R)-capreomycidine chemical synthesis is quite difficult. Total chemical synthesis of capreomycidine for synthetic purposes has resulted in protocols having either six (DeMong and Williams 2003 JACS 125:8561-8565) or seven (DeMong and Willams 2002 Tetrahedron Lett. 42:3529-3532) steps with, at best, a 28% yield. Our recent work has shown we can generate mg quantities of capreomycidine using purified VioC and VioD (approximately 15 mg of (2S,3R)-capreomycidine from 40 mg of (2S)-arginine). Ju et al. (2004). Thus, these enzymes can be used to generate larger quantities of enantiomerically pure (2S,3R)-capreomycidine for downstream use in synthesis procedures, including synthesis of new tuberactinomycins antibiotics. Additionally, since the substrates used in these reactions are present in Escherichia coli, these genes cab be introduced into E. coli for large scale production of (2S,3R)-capreomycidine.
The genes coding for VioC and VioD were independently PCR amplified from cosmid pVIO-P8C8RH, Thomas et al., 2003, cloned into the overexpression vector pET28b (Novagen), and the resulting plasmids were transformed into E. coli BL21(DE3) for overproduction of the proteins with N-terminal hexahistidine affinity tags. Overproduction strains were grown in LB supplemented with kanamycin (50 μg/mL) in 3×1 L batches. For overproduction, 1 L medium was inoculated with 10 mL of a fresh overnight culture of BL21 (DE3) carrying either plasmid. Cultures were grown for 24 hr at 25° C. after which cells were harvested by centrifugation.
Cells overproducing VioC were resuspended in buffer A (30 mL; Tris-HCl pH 8.0 (20 mM), NaCl (300 mM), glycerol (10% v/v)) with imidazole (5 mM). Cells were broken by sonication and cell debris removed by centrifugation. The supernatant was incubated with Ni-NTA Agarose (Qiagen) resin (1 mL) at 4° C. for 1 hr with gentle rocking. The resin was recovered and washed with buffer A containing imidazole (20 mM). VioC was eluted using a step gradient of buffer A plus varying concentrations of imidazole (40, 60, 100, or 250 mM). Fractions containing VioC., based on SDS-PAGE/Coomassie staining, were pooled and dialyzed against buffer B (Tris-HCl pH 8.0 (50 mM), NaCl (100 mM), glycerol (10% v/v)). The same protocol was followed for VioD purification with the exception that PLP (0.1 mM) was included in all buffers. The concentration of VioC was determined spectrophotometrically at 280 nm by use of the calculated molar extinction coefficient of VioC (47,630 M−1 cm−1). The concentration of VioD was determined by BCA assay (Pierce) using bovine serum albumin as a standard.
VioC and VioD Assays. Reactions monitoring VioC activity contained Na-phosphate pH 7.5 (0.1 M), NaCl (0.1 M), glycerol (10% v/v), Na-ascorbate (1 mM), Na-aKG (1 mM), dithiothreitol (1 mM), FeSO4 (50 μM), 4 (400 μM), and VioC (1 μM). After the desired time of reaction, a sample (25 mL) was removed and added to OPA (Pierce)(25 mL) to derivatize all free primary amines. (Benson, 1975). Derivatized reactants and products were separated by HPLC with a Vydac C18 small pore column at a flow rate of 1 mL min−1. The following solvents were used: solvent A—ddH2O and 0.1% trifluoroacetic acid (TFA); solvent B—acetonitrile and 0.1% TFA. The profile for separation was 5 min isocratic development at 91%A/9%B; 20 min linear gradient from 91%A/9%B to 70%A/30%B. The elution of OPA-derivatized product was monitored at A340.
Reactions for monitoring VioD activity contained Na-phosphate pH 7.5 (0.1 M), NaCl (50 mM), glycerol (5% v/v), PLP (0.1 mM), 5 (2 mM), and VioD (25 mg). Termination of the reaction by OPA-derivatization and analysis by HPLC were performed as described for VioC.
VioC was overproduced in Escherichia coli with an N-terminal hexahistidine affinity tag and purified to near homogeneity using nickel-chelate chromatography. To assay for VioC turnover, we developed an assay that utilized Ophthalaldehyde (OPA) derivatization of primary amines in the reaction mixture, followed by separation of derivatized products by high-performance liquid chromatography (HPLC). Using this assay, we detected a new product with an elution time distinct from (2S)-arginine. The appearance of this product peak correlated with the loss of the peak associated with (2S)-arginine, and formation of this product required VioC., (2S)-arginine, FeSO4, and aKG. Furthermore, repeating the reactions with [1-14C]-αKG and trapping [14C]-CO2 released during VioC turnover, using a protocol established for the analysis of CASs, (Salowe et al., 1990) we determined [14C]-CO2 was released from the reaction in a VioC-(2S)-arginine-, and FeSO4-dependent manner. These data are all consistent with the hypothesis that VioC is an αKG-dependent non-heme iron dioxygenase. Collection of the eluted product peak from the HPLC and subsequent analysis of the product by positive electrospray ionization mass spectrometry (ESIMS) gave results consistent with the product being the OPA-derivatized and hydroxylated (2S)-arginine ([M+H]+: observed, 307.6; calculated, 307.1 for C14H18N4O4).
The product was analyzed by MS and NMR and determined to be (3S)-hydroxy-(2S)-arginine. While the site of hydroxylation was as expected, the surprising finding was the stereochemistry of the C3 hydroxylation. VioC is a homolog of CASs, enzymes that catalyze the hydroxylation of the comparable C3 position of their substrates. However, the hydoxylation by CASs results in the (3R)-hydroxylation (Salowe et al., 1990) rather than the (3S)-hydroxylation catalyzed by VioC.
VioD is a homolog of PLP-dependent enzymes that catalyze β-replacement reactions. VioD catalyzes the replacement of the C3 hydroxyl of (3S)-hydroxy-(2S)-arginine with its own guanido group, thus catalyzing a novel intramolecular cyclization of the side chain of (3S)-hydroxy-(2S)-arginine (FIG. 3B). This proposed mechanism proceeds via a PLP-linked 2,3-dehydroarginine intermediate, consistent with prior precursor labeling studies. (Gould and Minott, 1992) Furthermore, the PLP stabilizes this intermediate, thereby eliminating the need for peptide synthesis to occur prior to desaturation and cyclization of the side chain of (2S)-arginine as previously proposed. (Gould and Minott, 1992)
VioD was overproduced in E. coli with an N-terminal hexahistidine affinity tag and purified to near homogeneity using nickel-chelate chromatography. Incubation of purified VioD with (3S)-hydroxy-(2S)-arginine, followed by OPA derivatization and HPLC separation, identified a new product that eluted 0.5 min later than (3S)-hydroxy-(2S)-arginine. The formation of this product peak required VioD and (3S)-hydroxy-(2S)-arginine, and its formation correlated to the loss of the peak associated with (3S)-hydroxy-(2S)-arginine. No change in the elution of (2S)-arginine was observed if (2S)-arginine and VioD were incubated together prior to OPA derivatization and HPLC separation. The product of the VioD reaction was identified by MS and NMR analysis as (2S,3R)-capreomycidine.
We have presented the complete in vitro reconstitution of the (2S,3R)-capreomycidine biosynthetic pathway. The first enzyme, VioC, is an unusual αKG-dependent non-heme iron dioxygenase that catalyzes the stereospecific hydroxylation of the C3 of (2S)-arginine to generate (3S)-hydroxy-(2S)-arginine (FIG. 3B). This product is subsequently recognized by a novel PLP-dependent enzyme, VioD, which catalyzes the C3-replacement of the C3 hydroxyl of (3S)-hydroxy-(2S)-arginine with the guanido group of (3S)-hydroxy-(2S)-arginine (FIG. 3B). This intramolecular cyclization of the side chain of an amino acid by a PLP-dependent enzyme is unprecedented in enzymology. This study establishes the enzymatic steps needed for the biosynthesis of (2S,3R)-capreomycidine, and this two-enzyme pathway is likely to be followed during Tuberactinomycin A, B, N, O and Capreomycin IA, IB, IIA, IIB biosynthesis. Furthermore, as we have previously noted, homologs of VioC and VioD are coded by the biosynthetic gene cluster for Streptothricin F (SttL and SttN, respectively). (Thomas et al., 2003).
Thus, the same mechanism of (2S,3R)-capreomycidine formation will be followed during formation of the streptolidine lactam moiety of the streptothricin antibiotics. This work provides the basis for using these enzymes for combinatorial biosynthesis as well as for the production of enantiomerically pure (2S,3R)-capreomycidine for semisynthetic purposes to introduce new structural diversity to natural products. VioC and VioD enzymes are useful because the availability of (2S,3R)-capreomycidine is one of the major limitations in chemically synthesizing reasonable quantities of tuberactinomycin derivatives and it is difficult to chemically synthesize enantiomerically pure (2S,3R)-capreomycidine.
As used herein, “comprising” is synonymous with “including,” “containing,” or “characterized by,” and is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. As used herein, “consisting of” excludes any element, step, or ingredient not specified in the claim element. As used herein, “consisting essentially of does not exclude materials or steps that do not materially affect the basic and novel characteristics of the claim. Any recitation herein of the term comprising”, particularly in a description of components of a composition or in a description of elements of a device, is understood to encompass those compositions and methods consisting essentially of and consisting of the recited components or elements. The invention illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein.
The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims.
In general the terms and phrases used herein have their art-recognized meaning, which can be found by reference to standard texts, journal references and contexts known to those skilled in the art. The definitions included herein are provided to clarify their specific use in the context of the invention.
All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the invention pertains.
One skilled in the art would readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The antibiotic compounds, enzymes and methods and accessory methods described herein as presently representative of preferred embodiments are exemplary and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art, which are encompassed within the spirit of the invention, are defined by the scope of the claims.
Although the description herein contains many specificities, these should not be construed as limiting the scope of the invention, but as merely providing illustrations of some of the embodiments of the invention. Thus, additional embodiments are within the scope of the invention and within the following claims. All references cited herein are hereby incorporated by reference to the extent that there is no inconsistency with the disclosure of this specification. Some references provided herein are incorporated by reference herein to provide details concerning additional starting materials, additional methods of synthesis, additional methods of analysis and additional uses of the invention.
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## Claims

1. An isolated and purified nucleic acid molecule comprising at least a functional fragment of a viomycin biosynthetic gene cluster that encodes a VioA gene product having at least 95% sequence identity to the amino acid sequence of SEQ ID NO:2, wherein the VioA gene product is a non-ribosomal peptide synthetase product capable of forming a peptide bond between a dipeptide that comprises L-2,3-diaminopropionate and L-serine and a second L-serine.

2. The nucleic acid of claim 1 comprising the nucleic acid sequence set forth in SEQ ID NO:1 from position 415 through position 36299.

3. The nucleic acid molecule of claim 1 wherein the functional fragment of a viomycin biosynthetic gene cluster encodes at least one additional gene product selected from the group consisting of
a VioB gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:3 and having 2,3-diaminopropionate synthase activity,
a VioC qene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:4 and havinq L-arqinine hydroxylase activity,
a VioD gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:5 and having capreomycidine synthase activity,
a VioE gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:6 and having permease activity,
a VioF gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:7 and having non-ribosomal peptide synthetase carrier protein activity conveying L-2,3-diaminopropionate to the VioA gene product,
a VioG gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:8 and having non-ribosomal peptide synthetase pentapeptide cyclization activity,
a VioH gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:9 and having Tyoe II thioestererase activity,
a Viol gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:10 and having non-ribosomal peptide synthetase carrier protein activity conveyinq a desaturated 2,3-diaminopropionate-comprising tetrapeptide to the VioG gene product,
a VioJ gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:11 and having 2,3-diaminopropionyl α,β-desaturase activity,
a VioK gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:12 and having ornithine cyclodeaminase activity,
a VioL gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:13 and having carbamoyltransferase activity,
a VioM gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:14 and having non-ribosomal peptide synthetase condensation β-lysine transferase activity,
a VioN gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:15 and having β-lysine addition activity,
a VioO gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:16 and having non-ribosomal peptide synthetase carrier protein β-lysine thioesterification activity,
a VioP gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:17 and having lysine 2,3-aminomutase activity,
a VioQ gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:19 and having capreomycidine hydroxylase activity,
a VioR gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:20 and having transcriptional regulatory activity,
a VioS gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:21 and having viomycin-phosphate phosphatase activity, and
a VioT gene product having the amino acid sequence set forth in SEQ ID NO:22 and having transcriptional regulatory activity.

4. The nucleic acid molecule of claim 1 which further encodes
a VioB gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:3 and having 2,3-diaminopropionate synthase activity,
a VioC gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:4 and having L-arginine hydroxylase activity,
a VioD gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:5 and having capreomycidine synthase activity, and
a VioG gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:8 and having non-ribosomal peptide synthetase pentapeptide cyclization activity, and additionally encodes at least one other gene product selected from the group of gene products consisting of
a VioE gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:6 and having permease activity,
a VioF gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:7 and having non-ribosomal peptide synthetase carrier protein activity conveying L-2,3-diaminopropionate to the VioA gene product,
a VioH gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:9 and having Type II thioestererase activity,
a Viol gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:10 and having non-ribosomal peptide synthetase carrier protein activity conveying a desaturated 2,3-diaminopropionate-comprising tetrapeptide to the VioG gene product,
a VioJ gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:11 and having 2,3-diaminopropionyl α,β-desaturase activity,
a VioK gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:12 and having ornithine cyclodeaminase activity,
a VioL gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:13 and having carbamoyltransferase activity,
a VioM gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:14 and having non-ribosomal peptide synthetase condensation β-lysine transferase activity,
a VioN gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:15 and having β-lysine addition activity,
a VioO gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:16 and having non-ribosomal peptide synthetase carrier protein β-lysine thioesterification activity,
a VioP gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:17 and having lysine 2,3-aminomutase activity,
a VioQ gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:19 and having capreomycidine hydroxylase activity,
a VioR gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:20 and having transcriptional regulatory activity,
a VioS gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:21 and having viomycin-phosphate phosphatase activity, and
a VioT gene product having the amino acid sequence set forth in SEQ ID NO:22 and having transcriptional regulatory activity.

5. The nucleic acid molecule of claim 1 which further encodes a VioM gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:14 and having non-ribosomal peptide synthetase condensation β-lysine transferase activity,
a VioN gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:15 and having β-lysine addition activity,
a VioO gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:16 and having non-ribosomal peptide synthetase carrier protein β-lysine thioesterification activity, and
a VioP gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:17 and having lysine 2,3-aminomutase activity.

6. The nucleic acid molecule of claim 1 which further encodes a VioC gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:4 and having L-arginine hydroxylase activity and a VioD gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:5 and having capreomycidine synthase activity.

7. The isolated and purified nucleic acid molecule of claim 1 further comprising genes that encode for a gene product selected from the group consisting of a VioF gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:7 and having non-ribosomal peptide synthetase carrier protein activity conveying L-2,3-diaminopropionate to the VioA gene product,
a VioG gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:8 and having non-ribosomal peptide synthetase pentapeptide cyclization activity,
a Viol gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:10 and having non-ribosomal peptide synthetase carrier protein activity conveying a desaturated 2,3-diaminopropionate-comprising tetrapeptide to the VioG gene product,
a VioM gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:14 and having non-ribosomal peptide synthetase condensation β-lysine transferase activity, and
a VioO gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:16 and having non-ribosomal peptide synthetase carrier protein β-lysine thioesterification activity.

8. The nucleic acid molecule of claim 1 comprising a nucleic acid sequence which further encodes one or more polypeptides having an amino acid sequence selected from the group consisting of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, and SEQ ID NO:22.

9. The nucleic acid molecule of claim 1 wherein the nucleic acid sequence has at least 80% nucleic acid sequence identity with the nucleic acid sequence set forth in SEQ ID NO:1 from position 415 through position 6786.

10. The nucleic acid molecule of claim 9, wherein the nucleic acid sequence identity is at least 90% with the nucleic acid sequence set forth in SEQ ID NO:1 from position 415 through position 6786.

11. The nucleic acid molecule of claim 9, wherein the nucleic acid sequence identity is at least 95% with the nucleic acid sequence set forth in SEQ ID NO:1 from position 415 through position 6786.

12. The nucleic acid molecule of claim 1 which is from a wild-type Streptomyces sp. ATCC11861, Streptomyces californicus, or Streptomyces olivoreticulis subsp. Olivoreticuli.

13. The nucleic acid molecule of claim 12 which is from wild-type Streptomyces sp. ATCC11861.

14. The nucleic acid molecule of claim 1 comprising a viomycin gene cluster.

15. An expression cassette comprising the nucleic acid molecule of claim 1 operably linked to a promoter functional in a host cell, wherein the expression of the cassette in a host transformed with the cassette permits the production of viomycin by the host cell.

16. The expression cassette of claim 15, wherein the nucleic acid molecule further encodes at least one additional gene product selected from the group consisting of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21 and SEQ ID NO:22, and wherein the expression of the cassette in a host cell comprising the nucleic acid permits the production of viomycin by the host cell.

17. The expression cassette of claim 16, wherein the nucleic acid molecule further encodes the gene products comprising SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21 and SEQ ID NO:22, and wherein the expression of the cassette in a host cell comprising the nucleic acid permits the production of viomycin by the host cell.

18. An isolated, recombinant, host cell transformed with at least the nucleic acid molecule of claim 1 and capable of expressing the encoded VioA gene product.

19. The recombinant host cell of claim 18 in which viomycin levels are increased relative to the levels in a corresponding nonrecombinant host cell.

20. The recombinant host cell of claim 18 wherein the recombinant host cell is a prokaryote or a eukaryote host cell.

21. The recombinant host cell of claim 18 wherein the recombinant host cell is a cell of the genus Streptomyces.

22. The recombinant host cell of claim 18 wherein the recombinant host cell is Streptomyces sp. ATCC11861.

23. The recombinant host cell of claim of claim 18 wherein the nucleic acid molecule further encodes a VioM gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:14 and having non-ribosomal peptide synthetase condensation β-lysine transferase activity,
a VioN gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:15 and having β-lysine addition activity,
a VioO gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:16 and having non-ribosomal peptide synthetase carrier protein β-lysine thioesterification activity, and
a VioP gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:17 and having lysine 2,3-aminomutase activity.

24. The recombinant host cell of claim 23 which is a Saccharothrix mutabolis subsp. capreolus host cell.

25. The recombinant host cell of claim 18 wherein the nucleic acid molecule further encodes a VioC gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:4 and having L-arginine hydroxylase activity and a VioD gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:5 and having capreomycidine synthase activity.

26. The recombinant host cell of claim 25 wherein the recombinant host cell is E. coil.

27. The recombinant host cell of claim 18, wherein the gene cluster further encodes and expresses at least one gene product selected from the group consisting of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21 and SEQ ID NO:22, and wherein the expression of the nucleic acid in a host cell comprising the nucleic acid permits the production of viomycin by the host cell.

28. The recombinant host cell of claim 27, wherein the gene cluster further encodes and expresses the gene products comprising SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21 and SEQ ID NO:22, and wherein the expression of the nucleic acid in a host cell comprising the nucleic acid permits the production of viomycin by the host cell.

29. A method for preparing viomycin or a pharmaceutically acceptable salt thereof comprising transforming a host cell with the expression cassette of claim 15, culturing the host cell in a culture medium containing assimilable sources of carbon, nitrogen and inorganic salts under aerobic fermentation conditions to yield an increase in the viomycin relative to the level of the viomycin produced by a corresponding untransformed host cell.

30. The method of claim 29 wherein the host cell is a prokaryote or a eukaryote host cell.

31. The method of claim 29 wherein the host cell is a cell of the genus Streptomyces.

32. The method of claim 29 wherein the host cell is Streptomyces sp. ATCC11861.

33. The method of claim 29 wherein the transforming expression cassette encodes a VioM gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:14 and having non-ribosomal peptide synthetase condensation β-lysine transferase activity,
a VioN qene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:15 and havinq β-lysine addition activity,
a VioO gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:16 and having non-ribosomal peptide synthetase carrier protein β-lysine thioesterification activity, and
a VioP gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:17 and having lysine 2,3-aminomutase activity.

34. The method of claim 33 wherein the host cell is a prokaryote or a eukaryote host cell.

35. The method of claim 33 wherein the host cell is a cell of the genus Streptomyces.

36. The method of claim 33 wherein the host cell is Streptomyces sp. ATCC11861.

37. The method of claim 33 wherein the host cell is Saccharothrix mutabolis subsp. capreolus.

38. The method of claim 29 wherein expression cassette encodes a VioC gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:4 and having L-arqinine hydroxylase activity and a VioD gene product having an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO:5 and having capreomycidine synthase activity.

39. The method of claim 38 wherein the host cell is a prokaryote or a eukaryote host cell.

40. The method of claim 38 wherein the host cell is a cell of the genus Streptomyces.

41. The method of claim 38 wherein the host cell is Streptomyces sp. ATCC11861.

42. The method of claim 38 wherein the host cell is E. coil.

43. The method of claim 29 wherein the expression cassette encodes the viomycin gene cluster.

44. The method of claim 43 wherein the host cell is a prokaryote or a eukaryote host cell.

45. The method of claim 43 wherein the host cell is a cell of the genus Streptomyces.

46. The method of claim 43 wherein the host cell is Streptomyces sp. ATCC11861.

47. An isolated and purified polypeptide having the amino acid sequence of the VioA gene product set forth in SEQ ID NO:2.