# Patent

## Title
Inactivation of genes of the MEP pathway

## Abstract

The invention relates to cells and organisms as well as to methods for producing said cells and organisms, according to which intermediates of the mevalonate-independent pathway for isoprenoid biosynthesis (MEP pathway) are enriched by deleting or inactivating genes. The derivatives can also be enriched by using enzyme inhibitors. The enriched intermediates may be used as substrates in enzyme activity tests. The inventive cells and organisms and the enriched intermediates can further be used in the production of medicaments.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application is the U.S. national stage application of International Patent Application No. PCT/EP02/04134, filed Apr. 13, 2002.
BACKGROUND OF THE INVENTION
This invention refers to cells and organisms for which intermediates of the mevalonate independent isoprenoid metabolism pathway (MEP pathway) are enriched through deletion or inactivation of genes. Furthermore, it refers to processes for producing intermediates and products derived from the MEP pathway from organisms, for which the genes according to the invention have been deleted or inactivated and genetic engineering and convention processes for producing these organisms. It also refers to the application of enzyme inhibitors for enriching MEP pathway intermediates. It also refers to the therapeutic application of cells and organisms for which the genes or enzymes according to the invention have been deleted or inhibited and the production of medication from these cells and organisms.
The biosynthesis of isoprenoids using the classic acetate/mevalonate pathway (Beytia E D, Porter J W, Annu Rev Biochem, 1976; 45: 113-42) and an alternative, mevalonate independent biosynthesis pathway, the 2-methyl-D-erythritol pathway (MEP pathway, synonymous with DOXP pathway) is known (Rohmer M. Nat Prod Rep, 1999 October; 16(5): 565-74). Both pathways lead to isopentenylpyrophosphate (IPP), the common precursor of all higher isoprenoids. While the acetate/mevalonate pathway has been known for some time and is fully understood, at present not all biosynthetic steps in the reaction of the MEP pathway are known.
In the past, various biotechnological processes have been derived, based on the application of knowledge regarding the MEP pathway:
1. Inhibitors of various enzymes through the MEP pathway are suitable as disinfectants and herbicides as the MEP pathway does not occur in humans.
2. Certain intermediates of the MEP pathway lead to a massive stimulation of human gamma/delta T cells. These intermediates are suitable as immunomodular medicines.
3. Through the over-expression of certain genes of the MEP pathway (e.g. DOXP synthase, LytB), the enriching of higher isoprenes can be achieved as subsequent products of the MEP pathway.
It was previously unknown that through the deletion of a gene of the MEP pathway or through inactivation of the corresponding enzyme, an intermediate of the MEP pathway can be achieved.
It is known that human gamma/delta T cells are activated through one or more intermediate of the MEP pathway. This means that with the incubation of peripheral blood lymphocytes with extracts from organisms which have an MEP pathway, there is a selective proliferation and cytokine secretion of the gamma/delta T cell population (Jomaa H, Feurle J, Luhs K, Kunzmann V, Tony H P, Herderich M, Wilhelm m, FEMS Immunol Med. Microbiol. 1999 September; 25(4): 371-8). The exact chemical composition of this activating substance of substances is still unknown. Published data suggest that 3-formyl-1-butylpyrophosphate plays a role as a hypothetical intermediate of the MEP pathway in activating gamma/delta T cells (Belmant C, Espinosa E, Poupot R, Peyrat M A, Guiraud M Poquet Y, Bonneville M Fournte J J, J. Biol. Chem. 1999 Nov. 5; 274(45): 32079-84).
Consequently, it was shown that bacteria, where various genes of the MEP pathway (e.g. DOXP reductoismerase, gepE) had been deleted, were no longer able to activate gamma/delta T cells (Altincicek B, Moll J, Campos N, Foerster G, Beck E, Hoeffler J F, Grosdemange-Billiard C, Rodriguez-Concepcion M, Rohmer M, Boronat A, Eberl M Jomaa H, J. Immunol. 2001 Mar. 15; 166(6):3655-8). In order to produce these deletion mutations it is necessary to introduce genes of the mevalonate pathway using genetic engineering into the bacteria. As a result, the bacteria can then survive in the medium in the presence of mevalonate if the MEP pathway is no longer functional (FIG. 1).
BRIEF SUMMARY OF THE INVENTION
The invention relates to cells and organisms as well as to methods for producing said cells and organisms, according to which intermediates of the mevalonate-independent pathway for isoprenoid biosynthesis (MEP pathway) are enriched by deleting or inactivating genes. The derivatives can also be enriched by using enzyme inhibitors. The enriched intermediates may be used as substrates in enzyme activity tests. The inventive cells and organisms and the enriched intermediates can further be used in the production of medicaments.



BRIEF DESCRIPTION OF THE DRAWINGS
The following explains the invention using the enclosed figures:
FIG. 1 shows the principle of enriching the intermediates of the MEP pathway through the deletion of genes of the MEP pathway. Substantial steps of the MEP pathway occurring naturally in E. coli are represented with the enzymes Dxs, Dxr, YgbP, YchB, YgbB, Gcpe, LytB. In order to be able to delete genes of the MEP pathway, genes of the mevalonate pathway (coding for Mvk, Pmk, Mpd) are introduced through genetic engineering. Through the deletion of lytB, the intermediates are enriched which activate the gamma/delta T cells.
FIG. 2 shows the activation of gamma/delta T cells from the blood of healthy donors, measured as an expression of CD25, through extracts from various bacteria sources (wild type, wtDeltagcpE, wtDeltalytB) in various dilution stages. IPP serves as a control with an end concentration of 10 uM (IPP activates gamma/delta T cells substantially weaker than the intermediate according to the invention, but is suitable as a control for the test system). The wtDeltagcpE mutants were produced analogously to the wtDeltagcpB mutants.



DETAILED DISCLOSURE OF THE INVENTION
Surprisingly, it was found that bacteria, whose lytB gene had been deleted (example 1) activated gamma/delta T cells significantly more strongly than typical bacteria (example 2, FIG. 2). An essential participation of the lytB gene in the MEP pathway was displayed (example 3). A blockage of the MEP pathway at the level of the lytB enzyme thus leads to the intermediate, which is responsible for the gamma/delta T cells, being enriched.
Therefore, a process is available, through which the enriching of intermediates of the MEP pathway is achieved through deletion, mutation or functional inactivation of the corresponding genes. The enriching of the intermediates of the MEP pathway can also be achieved through inhibiting the enzymatic function of the corresponding polypeptide.
DNA sequences, which code for a polypeptide with the amino acids represented in SEQ ID NO: 2 or for an analogue or derivative of the polypeptide according to SEQ ID NO: 2, are particularly suitable for carrying out the process according to the process, where one or more amino acids are deleted, added or substituted by other amino acids without the enzymatic effect of the polypeptide being substantially reduced.
Furthermore, the invention is defined by claims 1-17. Further images of the invention are defined in the subordinate claims.
The genes and their genetic products (polypeptide) are listed in the sequence protocol with their primary structures and are allocated as follows:
SEQ ID NO: 1 lytB-gene
SEQ ID NO:2 lytB-protein.
The sequences come from escherichia coli. 
Apart from the DNA sequences named in the sequence protocol, others are suitable which have another DNA code as a result of the degeneration of the genetic code but which code for the same polypeptide or for an analogue or derivative of the polypeptide. This also includes sequences which come from organisms other than E. coli, specifically, other bacteria, algae, plants and protozoa, and which are recognized, based on sequence comparisons or function analyses, as homologous to the sequences named in the sequence protocol.
The invention refers to cells and organisms and the production of cells and organisms, for which the genes according to the invention are functionally inactivated principally as a result of known methods. The genes do not have to be fully inactivated but instead can have their function reduced or modified. This can be achieved by the following:

    
    
        Complete or partial deletion of the genes
        Substitution of the gene through an artificial DNA sequence or a gene for a selection marker
        Insertion of a gene for a selection marker
        Deletion, insertion and substitution of one or several base pair
        Mutations in the 5′ and 3′ area of the coding sequences (influence of promoter, enhancer, terminator sequences, ribosome conjugates)
        Introduction of DNA constructs which code for antisense DNA
        Application of mutagen agents, ionising radiation, UV radiation
        Screening for spontaneous mutants.
    
    


The inactivation or modification of the sequences according to the invention can occur in bacteria, algae, plants and protozoa. In order to maintain stable mutants, it can be necessary to introduce the genes of the acetate/mevalonate pathway partially or in full and, if necessary, to add mevalonate or another intermediate of the MEP pathway to the medium. Alternatively or additionally, intermediates of the MEP pathway or derivatives or analogues to these intermediates (e.g. 3-methyl-3-buten-1-ol, 3-methyl-2-buten-1-ol) can be added to the medium.
Cells and organisms can also be used, which do not naturally have the MEP pathway, if genes of the MEP pathway have been introduced through genetic engineering and bio-engineering methods. It is also possible to achieve enriching of intermediates of the MEP pathway of their derivatives by only incompletely introducing the genes of the MEP pathway. Mammal and insect cells, lower and higher fungi, slime mold and various protozoa, among others, are suitable for this.
Apart from through genetic methods, inactivation or reduction of the enzymatic activity of the polypeptides according to the invention can also be achieved through enzyme inhibitors which are added to the culture medium of the organisms or cell extracts from the organisms. The enzyme inhibitors can have synthetic or natural conjugates which reversibly or irreversibly inhibit the function of the polypeptide through competitive or allosteric interactions.
The cells and organisms according to the invention, including complete plants and parts of plants, can be reproduced and cultivated through known processes. A co-culture with other cells or organisms, including those which do not have an MEP pathway, is also possible. The enriched intermediates of the MEP pathway or their derivatives can be obtained through breaking down the cells or from the culture. Various known methods are suitable for purifying the intermediates, including chromatography, electrophoreses and precipitation (e.g. as barium salts).
The enriched intermediates of the MEP pathway are suitable for various applications. It has been found that the intermediates contain the product of the GcpE enzyme and the substrate of the LytB enzyme. Thus, the intermediates can be used as substrates in the enzyme activity test for LytB and GcpE. In the activity test for GcpE, the reverse reaction is observed. This type of enzyme activity test is suitable for finding GcpE and LytB inhibitors.
The enriched intermediates of the MEP pathway are also suitable for producing medicines. The effectiveness of the substances is based on the activation of gamma/delta T cells. Depending on the area of application, the immunity can be strengthened (e.g. against tumors) or immunological tolerance against auto-antigens and allergens can be induced.
Areas of application are the treatment of immune, auto-immune diseases and allergies. For example: allergies, multiple sclerosis, rheumatoid arthritis, Hashimoto's thyroiditis, myasthenia gravis, lupus erythematosus, diabetes mellitus, primary biliary cirrhosis, active chronic hepatitis, adrenalitis/Addison's disease, polymyositis, dermatomyositis, auto-immune haemolytic anaemia, myocardial and cardiac infections, scleroderma, uveitis (phacouveitis, sympathetic ophthalmia), pemphigus vulgaris, pemphigoid, pernicious anaemia, auto-immune atrophic gastritis, inflammatory disease of the intestines such as Crohn's disease and colitis ulcerosa, inflammatory disease of the lungs such as asthmatic diseases and bronchitis.
The application is preferred for morbus Crohn, colitis ulcerosa, multiple sclerosis, asthma, chronic bronchitis, allergies.
Other applications are infections of the bone, especially osteoporosis.
The intermediates of the MEP pathway can be isolated from the organisms according to the invention or used as raw extracts for medical application. The complete organisms can also be used living or dead. The intermediates and organisms according to the invention can be used alone or in combination with other medications. Application as adjuvant for strengthening or for modulation of an immune response is also included. Preferred methods of application are oral, inhalative and rectal application, as well as application on the skin or mucous membranes.
The following are suitable as pharmaceutical compositions: tablets, drops, capsules, pills, granules, suppositories, solutions, suspensions and emulsions, pastes, ointments, gels, creams, lotions, powders and sprays.
Tablets, drops, capsules, pills and granules can contain the active ingredients alongside the usual carriers such as (a) fillers and mixers, e.g. starch, lactose, cane sugar, glucose, mannitol and silicic acid, (b) binders, e.g. carboxymethylcelulose, alginate, gelatine, polyvinylpyrrolidone, (c) moisturizers, e.g. glycerine, (d) explosive, e.g. agar-agar, calcium carbonate and sodium carbonate, (e) emulsifier, e.g. paraffin (f) re-absorption accelerator, e.g. quanternary ammonium conjugates, (g) nets, e.g. cetylalcohol, glycerine monostearate, (h) absorbers, e.g. kaolin and bentonite and (i) lubricant, e.g. talcum, calcium and magnesium stearate and solid polyethylglycol or mixtures of the substances listed in (a) to (i). Moreover, the conjugates according to the invention can be included in other carriers such as plastics (plastic chains for local treatment), collages or bone cement.
Tablets, drops, capsules, pills and granules can be produced with the usual, if necessary opaque, casings and cases and also combined such that the active ingredients are only released, or preferably with a delay, in a specific section of the intestinal tract where embedders can be used, e.g. polymer substances and waxes.
The active ingredients can also exist in micro-capsule form in one or more of the above carriers.
Suppositories can contain the usual water soluble or insoluble carriers along with the active ingredients, e.g. polyethylglycol, fats, e.g. cocoa fat and higher ester (e.g. C14 alcohol with C16 fatty acid) or mixtures of same.
Ointments, pastes, creams and gels can contain the usual carriers along with the active ingredients, e.g. animal and vegetable fats, waxes, paraffin, starch, tragant, cellulose derivatives, polyethylglycol, silicone, bentonite, silicic acid, talcum and zinc oxide or mixtures of same.
Powders and sprays can contain the usual carriers along with the active ingredients, e.g. lactose, talcum, silicic acid, aluminium hydroxide, calcium silicate and polyamide powder or mixtures of same. In addition, sprays can contain propellants such as CFCs.
Solutions and emulsions can contain the usual carriers along with the active ingredients, such as solvents, solubilisers and emulsifiers, e.g. water, ethylalcohol, isopropylalcohol, ethylcarbonate, ethylacetate, benzylalcohol, benzylbenzoate, propylenglycol, 1,3-butylenglycol, dimethylformamide, oils, especially cotton seed oil, peanut oil, maize oil, olive oil, ricinus oil and sesame oil, glycerine, glycerine formal, tetrahydrofurylalcohol, polyethylglycols and fatty acid ester of sorbitol or mixtures of same.
Particularly beneficial is the selection of a medical application which also contains a substance which can be recognized by the immune system as a foreign object or auto-antigen.
Example 1
Construction of lytB Deletion Mutant
Construction of the Gene Exchange Plasmid pKO3-ΔlytB
In order to produce a lytB deletion mutant from E. coli, the pKO3 vector was used (Link, A. J.; Philips, D.; Church, G. M.; J. Bacteriol 179, 6228-6237). In order to produce the deletion design, two sequences were amplified downstream and upstream of the lytB gene in two asymmetrical PCR stages. The primers were used in a 1:10 molar ratio (50 nM and 500 nM). Both PCR products were fused in a second PCR amplification to form one product. The product was cloned using the pCR-TA-TOPO cloning kit (Invitrogen) and recloned using the restriction interfaces Bam HI and Sal I in the pKO3 vector. The following primers were used:







(SEQ ID NO: 3)


lytB-N-out,


5′-TAGGATCCccggcctagatgactgcg-3′;


 


(SEQ ID NO: 4)


ltyB-N-in,


5′-CCCATCCACTAAACTTAAACAcaacaggatctgcatgttacg-3′;


 


(SEQ ID NO: 5)


ltyB-C-in,


5′-TGTTTAAGTTTAGTGGATGGGcgtgaagtcgattagtcat-3′;


 


(SEQ ID NO: 6)


ltyB-C-out,


5′-TAGTCGACagaaccacccatgatcacc-3′.






The restriction interfaces are underlined. Overlapping sequences, which define a 21 bp-“in frame” insertion, are printed in bold.
Construction of the Synthetic Mevalonate Operon pSC-MVA
In order to be able to produce mutants whose individual genes of the MEP pathway are deleted, first of all a genetically altered E. coli source was produced which was able to use mevalonate from the culture medium for the synthesis of IPP. To do this, a synthetic operon was constructed which contained the gene for the following enzyme of the mevalonate pathway from saccharomyces cerevisiae (yeast): mevalonate kinase (ERG12), phosphomevalonate kinase (ERG8) and diphosphomevalonate-decarboxylase (ERG19). The three genes were amplified in three asymmetrical PCR stages with genome yeast DNA as a matrix, with the primers being used in a 1:10 molar ratio (50 nM and 500 nM). Ribosome binders were included with the primers. The three PCR products were mixed so that they could hybridize with the overlapping areas and were amplified using the external primer as a fragment. The product was cloned in the pBAD vector using pBAD-TA-TOPO cloning kits (Invitrogen) and verified using restriction and sequence analysis. The following primer set was used:







(SEQ ID NO: 7)


Mev-kin-Sc-for:


5′-TAGGAGGAATTAACCATGTCATTACCGTTCTTAACT-3′ 


 


(SEQ ID NO: 8)


Mev-kin-Sc-rev:


5′-TTGATCTG ATGAAGTCCATGGTAAATT-3′ 


 


(SEQ ID NO: 9)


Pmev-kin-Sc-for:


5′-ACTTCAT CAGATCAAATGTCAGAGTTGAGAGCCTTC-3′


 


(SEQ ID NO: 10)


Pmev-kin-Sc-rev:


5′-GAGTATTAT ATTTATCAAGATAAGTTTC-3′;


 


(SEQ ID NO: 11)


Decarb-Sc-for:


5′-GATAAAT TAATACTCATGACCCGTTACACAGCATCC-3′


 


(SEQ ID NO: 12)


Decarb-Sc-rev:


5′-TTATTCCTTTGGTAGACCAGT-3′.






Overlapping sequences are printed in bold and sequences which define ribosome conjugates are in italics.
In order to check the functionality of the operon, the sensitivity to fosmidomycin from bacteria which have been transformed with the synthetic operon was tested in the presence of mevalonate. As expected, bacteria grew, which contained fosmidomycin at a reduced rate as long as the medium contained mevalonate. Without mevalonate, the bacteria died under fosmidomycin.
Construction of the Deletion Mutant wtΔlytB
The plasmid pKO3-DeltalytB was transformed in the E. coli K-12 source DSM No. 498 (ATCC 23716), which had previously been transformed with pSC-MVA. The medium was supplemented with 100 uM mevalonate. After 1 hour incubation at 30° C., bacteria with integrated plasmid were selected through a temperature shift to 43° C. As a result of the subsequent test for sucrose resistance and chloramphenicol sensitivity, the bacteria, which had lost the vector sequences, were selected and then analyzed through PCR for the desired gene type.
Example 2
Activation of Gamma/Delta T Cells Through Enriched Intermediates of the MEP Pathway
The enriching of intermediates of the MEP pathway was detected from the ability of these intermediates to activate gamma/delta T cells. Various bacteria sources (wild type, wtDeltagcpE, wtDeltalytB) were cultivated in liquid cultures up an optical thickness of approximately 0.8. Obtaining low molecular extracts (low molecular weight, LMW) with an exclusion limit of 3 kDa occurs as described (Jomaa H, Feurle J, Luhs K, Kunzmann V, Tony H P, Herderich M and Wilhelm M, FEMS Immunol Med Microbiol, 25:371). Lymphocytes are obtained from the peripheral blood of three healthy donors through the ficoll-density gradient centrifugation. For each test, 2 lots of 105 of the cells obtained are shown in a volume of 0.2 ml RPMI-1640-Medium (Life Technologies), which was enriched with 25 mM HEPES, 2 mM L-glutamine, 0.025 mg/ml gentamycin, 100 U/ml human interleukin-2 (IL-2) (all from Life Technologies), and 10% human AB serum (Bavarian Red Cross). LMW preparations were added to various solutions, IPP (sigma) was used in a final concentration of 10 uM as a positive control. The incubation was carried out at 37° C. and 5% CO2 in the incubator. After 72 hours, the cells were harvested and analyzed in a throughflow cytometer. The expression of the activation marker CD25 was measured on the surface of V gamma 9+ T cells using the monoclonal antibodies CD25-PE (B1.49.9), V gamma 9-FITC (Immu360) and CD3-PC5 (UCHT1) from the Beckman-Coulter Company. Extracts from the wild type bacteria source activated the gamma/delta T cells at a concentration of 1:500 (corresponds to approx. 2×107 bacteria/10. Extracts from the DeltagcpE-deletion mutants led to a significantly reduced activation. By contrast, the activation by extracts from the DeltalytB-deletion mutants was considerably stronger than through extracts from the wild type source. A significant gamma/delta T cell activation was also measured at a concentration of 1:12500 (corresponds to approx. 8×105 bacteria/ml) (FIG. 2).
Example 3
Participation of lytB in the MEP Pathway
All lytB deletion mutants obtained grew strictly mevalonate dependent. In order to investigate this observation more closely, the deletion mutants wtDeltalytB were complemented by a wild type lytB gene on a plasmid. The lytB gene was amplified with the primer eclytbfor (5′-GGATCCATGCAGATCCTGTTGGCCAAC-3′, SEQ ID NO: 13) and ecltybrev (5′-AAGCTTTTAATCGACTTCACGAATATCG-3′, SEQ ID NO: 14) from genomic E. coli DNA and cloned in the pCR2.1-TOPO vector. The insert was recloned through the restriction interfaces BamHI and HindIII and in the expression vector pQE30. Bacteria from the wtDeltalytB source, which were transformed with this construct, were able to grow without mevalonate. This result confirms that lytB is an essential participant in the MEP metabolism pathway. The enriched intermediates therefore come from the MEP pathway.

## Claims

1. A method of activating γδ (gamma delta) T-cells in a subject comprising administering a composition comprising an intermediate of the melavonate independent isoprenoid metabolism pathway (MEP) to a subject in an amount effective to activate γδ T-cells in said subject, wherein the intermediate of the MEP pathway is 3-formyl-1-butylpyrophosphate obtained by a process comprising: deleting lytB in selected cells or organisms to reduce the enzymatic activity of a gene product encoded by lytB within the MEP pathway and producing an accumulation of said intermediate of the MEP pathway within the selected cell or organism is from bacteria.

2. The method according to claim 1, wherein the process further comprises concentrating said intermediate of the MEP pathway.

3. The method according to claim 1 wherein the method additionally comprises administering an immunogen to the subject.