Patent Publication Number: US-2005119462-A1

Title: Expression vectors and promoters for heterologous gene expression

Description:
The present invention relates to novel vectors and nucleic acid sequences, which comprise promoters which are induced by nucleotides (with or without a phosphate group). The invention further relates to expression vectors utilising elements of the xanthosine operon and methods for the production of heterologous proteins.  
      Expression of cloned genes introduced into bacteria is still the most widely used mechanism for producing large amounts of a protein of interest for diagnostic and therapeutic purposes. In order to efficiently produce proteins in a prokaryotic host, a strong, regulated promoter is an essential element of the expression system. Promoters and expression systems already known in the art include the bacteriophage lambda pL and pR promoters, which can be regulated by a temperature-sensitive repressor which represses transcription from that promoter at low temperatures and allows expression of the heterologous protein by means of temperature induction EP-A41767), or alternatively by use of an inducible antirepressor system which can be induced using isopropyl-β-D-thiogalactopyranoside (IPTG) at lower temperatures, whilst still employing the strong pL/pR promoters (WO 98/48025). However, high temperatures routinely lead to the formation of the heterologous protein as insoluble aggregates, or inclusion bodies, which subsequently require costly refolding steps using toxic chemicals.  
      Other promoters include the lac operon and derivatives, such as the trp-lac promoter or tac promoter, (EP-A-67540) which has been used to produce high levels of proteins in  E. coli . This promoter is induced in the presence of IPTG. In order to subject the promoter to repression it must be used together with a plasmid overproducing the lac repressor, or in an  E. coli  strain which produces lac repressor protein. T7 promoter-based systems (U.S. Pat. No. 5,869,320) utilise the 17 RNA polymerase, inducibly expressed, are routinely used in research laboratories for the overproduction of proteins, again using IPTG. However, the strength of such promoters again can lead to the production of inclusion bodies, or aggregates, of the heterologous proteins.  
       Escherichia coli , a Gram-negative bacterium, is able to grow on xanthosine as the sole carbon source (Hammer-Jespersen et al., 1980). This occurs via the induction and utilisation of genes in the xanthosine operon, comprising of at least three genes, located at approximately 52′ on the  E. coli  chromosome ( FIG. 1 ) (Seeger et al., 1995). The genes in the operon are xapA, xapB and xapR. XapA encodes for xanthosine phosphorylase, which catalyses the breakdown of the N-glycosidic bond in nucleoside molecules, resulting in a free base and a pentose-1-phosphate. The free bases can then be subsequently used in the purine and pyrimidine salvage pathways and also as a nitrogen source (Nygaard, 1983), and the pentose molecule can subsequently be utilised as a carbon source, hence the ability of  E. coli  to grow on xanthosine minimal media. The function of the xapB protein has not been fully elucidated, but would appear by homology to other proteins and by its cellular location to be a membrane transport protein, almost certainly involved in transporting nucleosides across the cell membrane (Seeger, supra). XapR shows significant homology to the LysR family of transcriptional regulatory proteins, DNA-binding proteins involved in gene activation (Henikoff et al., 1988), and appears to be constitutively expressed. The xapA and B genes appear to be co-expressed, and xapA expression is found only in the presence of xanthosine, and the xapR protein (Seeger, supra). The xapR protein, if a true LysR family member, would bind to specific regions within the xapA promoter, enabling the subsequent binding of  E. coli  RNA Polymerase, and subsequent transcription of the xapA (and xapB) genes. Such DNA-binding proteins appear to recognise an inverted complimentary consensus sequence ATATTGTTT (Bohannon 1989), and there appears to be such a region within the xapA promoter region ( FIG. 2 ), at 120 bp upstream of the transcription start (CCAATACAGTTTT), and the corresponding sequence at 40 bp upstream, overlapping the −35 region (AAAACTGTATTGG) (Seeger, supra). Sequences of the genes comprising the xanthosine operon of  E. coli  have been deposited at several online public databases, e.g. the GenBank database, accessible through the home page of the National Center for Biotechnology Information (NCBI), Bethesda, Md., USA at www.ncbi.nlm.nih.gov, using the accession numbers AE000328, D90869, D90870 or X73828.  
      The current invention relates to the expression of heterologous proteins using a novel expression vector and system, which avoids the problems of insoluble inclusion bodies associated with temperature induction or very strong promoters, and which does not require the use of toxic inducers, such as IPTG, which would require costly validation procedures to verify its absence when producing therapeutic proteins.  
      Accordingly, a first aspect of the present invention provides a vector, comprising a promoter which can be operably linked to a gene encoding a heterologous protein, wherein the promoter induces expression of any operably linked heterologous protein, in the presence of nucleotides, which nucleotides may or may not have a phosphate group. The phosphate group may result in the molecule being a phosphate ester. There may be one or more phosphate groups attached.  
      The vector may be any, including a plasmid or a bacteriophage. Preferably, the vector is an inducible expression vector.  
      The induction of the promoter is by the presence of nucleotides in the media (usually culture media).  
      The term “nucleotides with or without a phosphate group” include both nucleotides and nucleosides.  
      In accordance with the present invention, nucleotides include any one or more nucleoside molecule containing one or more phosphate groups covalently linked to the sugar molecule, which can be of the oxy, deoxy or dideoxy form. Examples of such include: adenosine triphosphate (ATP), guanosine triphsophate (GTP), cytidine triphsophate (CTP), thymidine triphsophate (TTP), and uridine triphosphate (UTP). The deoxy forms of these (commonly written as dATP, dCTP, dGTP and dM and commonly known as bases) form the basic structure of DNA. The oxy forms of these (commonly written as ATP or rATP, CTP or RCTP, GTP or rGTP, UTP or rUTP and commonly known as RNA bases) form the basic structure of RNA.  
      In accordance with the present invention, nucleosides include any one or more compound comprising a purine or pyrimidine joined by an N-glycosidic link to a sugar, particularly an oxy- or deoxy- or dideoxy-ribose sugar molecule. Examples of such nucleosides include the oxy, deoxy and dideoxy-forms of adenosine, guanosine, inosine, cytidine, thymidine, uridine, xanthosine, and derivatives thereof.  
      Xanthosine is known under the USPTO classification is: 536/27.8. It is also known as xanthosine, or 9-beta-D-ribofuranosyl xanthine (Chemical Abstract Service number 5968-90-1), and includes the compound either as an anhydrous salt or a dihyrate salt. Synonymous names for xanthosine are: Xanthine riboside, 9-beta-D-ribofuranosyl-9H-purine-2,6-diol and 9-beta-D-ribofuranosyl-9H-purine-2,6-(1H,3H)-dione.  
      Preferred concentrations of nucleotides as an inducer are in the range of from 0.01 to 10 mg/ml, more preferably from 0.1 to 1 mg/ml.  
      Any promoter can be used which can be operably linked to a gene encoding a heterologous protein and wherein the promoter induces expression of any such operably linked heterologous protein, in the presence of nucleotides.  
      Steps to operably link nucleic acid sequences are well known in the art and are currently predominantly based on the use of restriction enzymes to cut nucleic and polymerases to join nucleic acid. Examples of such steps are shown in the example section.  
      The promoter may be directly or indirectly induced by the presence of nucleotides. Suitable promoters include those from a xapA gene. Any xapA gene is acceptable. The xapA promoter region from  E. coli  is set out in  FIG. 1   a . Modified xapA promoter regions, included within the present invention, are shown in  FIGS. 1   b  and  1   c . These modified regions have useful restriction enzymes site included.  
      In addition to this sequence, any modified sequence can be used which sequence induces expression of an operably linked nucleic acid sequence in the presence of nucleotides or nucleosides. For example, the modified sequence may be a substantially homologous sequence. A substantially homologous sequence preferably has at least 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 100% sequence identity with the defined sequence.  
      “% identity” is a measure of the relationship between two nucleic acid or polypeptide sequences, as determined by comparing their sequences. In general, the two sequences to be compared are aligned to give a maximum correlation between the sequences. The alignment of the two sequences is examined and the number of positions giving an exact amino acid or nucleotide correspondence is determined, and divided by the total length of the alignment, and the result is multiplied by 100 to give a % identity. The % identity may be determined over the whole length of the sequence to be compared, which is particularly suitable for sequences of the same or similar lengths or for sequences which are highly homologous, or over shorter defined lengths which is more suitable for sequences of unequal lengths and with a lower homology.  
      Methods for comparing the identity of two or more sequences are known in the art. For example, programs available in the Wisconsin Sequence Analysis Package version 9.1 (Devereux J et al.,  Nucl Acid Res  12 387-395 (1984), available from Genetics Computer Group, Madison, Wis., USA), such as BESTFIT and GAP may be used.  
      BESTFIT uses the “local homology” algorithm of Smith and Waterman (Advances in Applied Mathematics, 2:482-489, 1981) and finds the best single region of similarity between two sequences. BESTFIT is more suited to comparing two polynucleotide or two polypeptide sequences which are dissimilar in length, the program assuming that the shorter sequence represents a portion of the longer. In comparison, GAP aligns two sequences finding a “maximum similarity” according to the algorithm of Neddleman and Wunsch (J. Mol. Biol. 48:443-354, 1970).  
      GAP is more suited to comparing sequences which are approximately the same length and an alignment is expected over the entire length. Preferably, the parameters “Gap Weight” and “Length Weight” used in each program are 50 and 3 for polynucleotide sequences and 12 and 4 for polypeptide sequences, respectively. Preferably, % identities and similarities are determined when the two sequences being compared are optimally aligned.  
      Other programs for determining identity and/or similarity between sequences are also known in the art, for instance the BLAST family of programs (Altschul et al.,  J. Mol. Biol.,  215:403-410, (1990) and Altschul et al.,  Nuc Acids Res.,  25:289-3402 (1997), available from the National Center for Biotechnology Information (NCBI), Bethesda, Md., USA and accessible through the home page of the NCBI at www.ncbi.nlm.nih.gov) and FASTA (Pearson W. R. and Lipman D. J.,  Proc. Nat. Acac. Sci., USA,  85:2444-2448 (1988), available as part of the Wisconsin Sequence Analysis Package).  
      In relation to the present invention, “stringent conditions” refers to the washing conditions used in a hybridisation protocol. In general, the washing conditions should be a combination of temperature and salt concentration so that the denaturation temperature is approximately 5 to 20° C. below the calculated T m  of the nucleic acid under study. The T m  of a nucleic acid probe of 20 bases or less is calculated under standard conditions (1M NaCl) as [4° C.×(G+C)+2° C.×(A+T)], according to Wallace rules for short oligonucleotides. For longer DNA fragments, the nearest neighbour method, which combines solid thermodynamics and experimental data may be used, according to the principles set out in Breslauer et al.,  PNAS  83: 3746-3750 (1986). The optimum salt and temperature conditions for hybridisation may be readily determined in preliminary experiments in which DNA samples immobilised on filters are hybridised to the probe of interest and then washed under conditions of different stringencies. While the conditions for PCR may differ from the standard conditions, the T m  may be used as a guide for the expected relative stability of the primers. For short primers of approximately 14 nucleotides, low annealing temperatures of around 44° C. to 50° C. are used. The temperature may be higher depending upon the base composition of the primer sequence used. Suitably stringent conditions are those under which non-specific hybridisation are avoided. Suitable stringent conditions are 0.5×SSC/1% SDS/58° C./30 mins for a 21mer oligonucleotide probe.  
      The vector may further comprise a regulatory element which the nucleotides interact with in order to regulate promoter. The regulatory element is preferably a nucleic acid sequence. Where the regulatory element is a xapR gene, it may need to be expressed in order for the expressed protein to interact with the nucleotides and regulate the promoter, for increased expression of any heterologous protein.  
      Most preferably, in accordance with the invention, the regulatory element is from a xapR gene. Any xapR gene is acceptable. The xapR gene from  E. coli  is set out in  FIG. 2 .  
      In addition to this given xapR sequence, any modified xapR sequence can be used which acts in the same manner on the promoter. For example, the modified sequence may be a substantially homologous xapR sequence (as defined above). The xapR sequence may need to be expressed. Suitable modified xapR sequences are described in Jorgensen and Dandanell, 1999.  
      The expressed xapR protein is believed to bind to specific regions within the xapA promoter, enabling the subsequent binding of RNA Polymerase, and subsequent transcription of any operably linked heterologous gene.  
      In order for the xapR, or other regulatory element to be expressed, it may be necessary for the vector to comprise a further promoter which is operably linked to the regulatory element to control its expression. Preferably, such a promoter is a constitutive or inducible promoter, such that the regulatory element is constitutively expressed. The further promoter may be a xapR promoter or any other know constitutive or inducible promoter, such as the lac, trc, lambda pR, lambda pL or trp promoters.  
      In an alternative, the regulatory element, which regulates expression by the promoter may be present but not as part of the vector on which the inducible promoter is present. The regulatory element (preferably with constitutive or inducible promoter) may be present in a cell as part of another vector, or integrated into the cell&#39;s genome.  
      The vector of the first aspect of the invention may be with or without an operably linked gene encoding a heterologous protein. The form of the vector without such a gene can be termed an “empty cassette”, which enables the addition of any such gene, for use in expression of that gene. The addition is by steps known in the art (predominantly the use of cutting restriction enzymes and joining polymerases), examples of which are given in the examples.  
      Any gene encoding any heterologous protein can be inserted into the vector of the first aspect of the invention. Examples of such genes include those which encode cytokines, hormones, chemokines, enzymes, antigens etc (preferably human forms). Cytokines include interleukins, e.g. human interleukin-4. Hormones include human growth hormone. The heterologous protein produced can be a fusion protein, e.g. attached to a leader peptide, for secretion into the periplasmic space or extracellular media, using such leader peptides as ompA or pelB, or a secondary polypeptide, operably linked to the heterologous protein, the function of which can be to prevent proteolytic degradation of the heterologous protein, or to provide an affinity tag for purification, or to assist in solubilisation of the heterologous protein. Examples of such secondary polypeptides include thioredoxin, maltose binding protein, histidine tags, and such secondary polypeptides may or may not include cleavage sites, for removal of the secondary polypeptide by selective cleavage using chemical or enzymatic means. Examples of such include cyanogens bromide, trypsin, enterokinase and Factor Xa.  
      A second aspect of the invention provides an isolated nucleic acid, comprising a regulatory gene from xapR of the xanthosine operon together with a promoter from a xapA gene.  
      The xapA promoter may be as herein described in  FIG. 1   a  and includes any substantially homologous sequence, also as hereinbefore described.  
      The xapR gene may be as herein described in  FIG. 2  and includes any substantially homologous sequence, also as hereinbefore described.  
      The nucleic acid may also comprise a further promoter which is operably linked to the xapR gene. Such a promoter is as described for the first aspect of the invention. It may be from the xapR promoter or may be any inducible or constitutive promoter. The xapR promoter may be as herein described in  FIG. 2 .  
      The isolated nucleic acid of the second aspect of the invention may be part of an expression vector.  
      The vector or nucleic acid of the first or second aspect may, of course, comprise other elements, such as a phenotypic selection marker, such as antibiotic resistance, replication gene(s), etc.  
      A third aspect of the invention provides nucleic acid which comprises a ribosomal binding site having any one of the following sequences:  
                                      AGGAGG xxxxx                           AGGAGG xxxxxx                       AGGAGA xxxxx                       AGGAGA xxxxxx          
 
 wherein x is any base. 
 
      The optional bases (x) may be those as described in Example 2 (taccc or tatccc).  
      The nucleic acid sequences of the third aspect may comprise the 5′ sequences, also as shown in Example 2. The nucleic acid sequences of the third aspect may be part of a promoter sequence. The promoter sequence may be from a xapA promoter. The nucleic acid sequences of the third aspect of the inventor may be part of a vector, as described according to the first aspect of the invention.  
      A fourth aspect of the invention provides host cell, which comprises one or more vectors or nucleic acid sequences, according to any one of the first, second or third aspects of the invention. Such a host cell may be any, preferably those which can be used in culture to provide protein production on a commercial scale. Examples of such host cells include  E. coli, Bacillus  sp., and yeasts such as  Saccharomyces  and  Pichia.    
      The vector and/or nucleic acid is introduced to the host cell by any technique, such as transformation, electroporation etc.  
      A fifth aspect of the invention provides a method for the expression of a heterologous protein, the method comprising culture of host cells, according to the fourth aspect of the invention under conditions which induce the expression of the heterologous protein. Such methods are well known in the art (see for example “Manual of Industrial Microbiology and Biotechnology” “2nd Edition. Demain A, &amp; Davies J, 1999). Suitable conditions include culturing said transformed host cells in a culture medium containing nutrients that meet the requirements of said host cells, such as carbon and nitrogen sources, vitamins and trace elements, together with a compound suitable for selecting those cells containing the expression vector, which may contain a selective marker, such as an antibiotic resistance gene. Cells are cultivated under conditions to achieve optimal growth, with regard to pH, typically ranging from pH6-8, temperature, which typically ranges from 20-42C, and also with a provision of oxygen, ranging from 10-50%, with 30% being a typical optimal value. Cells are grown under such conditions until a suitable density is reached, at which point the inducer is added in sufficient quantity to achieve maximal induction of the expression vector within the cells, and consequently allowing the expression of the protein of interest. Induction is allowed to continue for the optimal, empirically-defined time, at which point the protein of interest can then be harvested.  
      The method may further comprise purification of the heterologous protein. Such purification steps are also known in the art (see for example “Protein Purification”, 2nd Edition, Janson, J-C &amp; Ryden, L, 1998). Basic steps for the extraction of intracellularly produced heterologous protein would typically involve a step of breaking open the cells, by a variety of means, e.g. homogenisation, or chemical lysis, or freeze-thawing, or ultrasonication. Intracellular protein which was present in the soluble extract could then be captured by a wide variety of chromatographic steps well known in the art, e.g. ion-exchange, hydrophobic interaction, affinity chromatography, reverse-phase chromatography, size exclusion or gel filtration and ultrafiltration. Typically, additional chromatographic steps are employed to further purify the heterologous protein away from contaminating host cell proteins and impurities, resulting in a highly purified protein. Intracellular protein which was present in the insoluble part of the extract, e.g. present as inclusion bodies, could be solubilised using a number of methods known in the art, using such compounds as guanidine, urea or sodium dodecyl sulphate for example, and subsequently purified using one or more chromatographic steps as mentioned above. Heterologous protein which was produced in the periplasmic space, using an expression vector which employed a leader peptide as described above, could be released from said space by employing an osmotic shock, to release the contents of the periplasmic space into the media, using such compounds as sucrose, or magnesium sulphate, or lysozyme/EDTA, following which, one or more chromatographic steps are employed to purify said protein.  
      A sixth aspect of the invention provides a protein, produced by the method of the fifth aspect of the invention.  
      A seventh aspect of the invention provides the use of one or more vectors or nucleic acid sequences, according to any one of the, second or third aspects of the invention in the production of a heterologous protein.  
      All preferred features of the various aspects of the invention apply to each other,  mutatis mutandis.    
      It is the object of this invention to provide expression vectors, comprising a promoter and regulatory repressor, which is derived from an operon for xanthosine metabolism in  E. coli , for the expression of heterologous proteins of commercial value. In one particular embodiment of the invention, the xapR regulatory protein, together with its promoter, are isolated and introduced into an expression vector, together with a heterologous gene operably linked to the promoter from the xapA gene. The resulting expression vector is transformed into a suitable host cell, which is subsequently grown under suitable conditions to achieve optimal growth. Expression of the heterologous protein does not occur until the addition of xanthosine, which subsequently activates the xapR protein, enabling it to bind to the xapA promoter region, allowing expression of the heterologous protein from the xapA promoter.  
      It is a further object of this invention to provide novel ribosmal binding site sequences for the xanthosine operon, which have increased levels of expression of heterologous proteins, whereby specific changes have been made to the natural ribosmal binding site of the xapA operon, as detailed in the first embodiment, and whereby a screening method has been utilised to identify those mutations resulting in increased expression levels.  
      It is a further object of this invention to provide a method for production of heterologous proteins using an expression system inducible with nucleotides, such as xanthosine. In the examples below, the construction of the xanthosine-inducible expression vectors is described, and the utility of the invention is illustrated using the production of human growth hormone (hGH) and human interleukin-4, in  E. coli.    
      It is apparent to a person skilled in the art that other genes can be expressed in the system described here. In addition, such a system could be integrated into the genome of  E. coli , or other organisms, or a similar expression system could be constructed utilising homologous genes from xanthosine operons from other organisms, including such genera as  Salmonella, Pseudomonas, Bacillus  or  Streptococcus , etc. 
    
    
      The present invention is described with reference to the accompanying figures, in which:  
       FIG. 1   a  shows the nucleotide sequence of the  E. coli  xapA promoter region.  
      (RBS—Ribosomal Binding Site)  
       FIG. 1   b  shows the nucleotide sequence of the  E. coli  xapA promoter region, together with new HindIII and NdeI restriction sites  
       FIG. 1   c  shows the nucleotide sequence of the  E. coli  xapA promoter region, together with new HindIII and NcoI restriction sites  
       FIG. 2  shows the nucleotide and amino acid sequence of the  E. coli  xapR gene (upper case) and the xapR promoter region (lower case italics), together with new restriction sites BamHI and KpnI.  
       FIG. 3  shows the vectors pUC19x, pXap1a and pXap1b  
       FIG. 4  shows the map of pXap1b-βgal  
       FIG. 5  shows the maps of Xap 1a-hGH and of pXap-IL4  
       FIG. 6  shows the protein analysis of pXap-hGH fractions:  
      (A)-SDS-PAGE; (B)-Western-blot.  
      Lanes: 
      1) hGH protein standard; 2) Molecular Weight Marker;    

      Lanes 3-7 LB Medium 
      3) Oh induction; 4) 2 h induction; 5) 3 h induction; 6) 4 h induction; 7) 6 h induction    

      Lanes 8-12 Defined medium 
      8) Oh induction; 9) 2 h induction; 10) 3 h induction; 11) 4 h induction;     12) 6 h induction.    

      In part A of the figure, the protein of interest is the one most cearly and abundantly present (indicated by the arrow) and which has rigrated with the protein standard in lane 1.  
      In part B, the Western Blot shows that the protein sought (by means of a specific antibody) is present.  
       FIG. 7  shows the protein analysis of pXap-IL4 fractions at 20° C. and 28° C.:  
      (A) SDS-PAGE; (B) Western Blot.  
      Lane M: Protein Markers.  
      Lanes 14: 20C, Oh, 2 b, 5 h and overnight induction.  
      Lanes 5-7: 28C, after 2 h, 5 h and overnight induction. Lane Std: IL4 standard.  
      In part A of the figure, the protein of interest is the one most clearly and abundantly present (indicated by an arrow) and which has migrated with the protein standard in the lane marked Std on the right hand side.  
      In part B, the Western Blot shows that the protein sought (by means of a specific antibody) is present.  
    
    
      The present invention is now described with reference to the following non-limiting examples:  
     EXAMPLES  
      The materials and methods used are described below, and the invention is illustrated in the examples. In support of most of the methods, reference is made to the following books: Sambrook et al., (1989) “Molecular Cloning: A Laboratory Manual”, 2 nd  Edition, and Miller, J. (1972) “Experiments in Molecular Genetics”, both from Cold Spring Harbor Press, Cold Spring Harbor, N.Y., USA, and Dieffenbach C. W &amp; Dveksler G. S. (1995);  PCR Primer: A Laboratory Manual . Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.  
     Example 1  
     Xanthosine-Inducible Expression Vector Construction  
      PCR Amplification of the XapR Gene (Regulatory Protein)  
      The XapR gene, together with its own promoter sequence, was amplified from  E. coli  genomic DNA from strain MG1655 (ATCC # 700926), using forward primer xap2 (SEQ_ID1) 5′-ACGGTACCTTTTGCTATCTGCGATTTGCG-3′ and reverse primer xap5 (SEQ_ID2) 5′-CTCATTAAAAGGATCCGCGGCTCTGCTCTTCAG-3′. The reaction mixture contained Pfu Buffer (20 mM Tris-HCl pH8.8 at 25° C.; 10 mM ammonium sulphate; 10 mM potassium chloride; 0.1% Triton X-100; 0.1 mg/ml bovine serum albumin and 2 mM magnesium sulphate), 0.25 mM of each dATP, dCTP, dGTP and DTTP, 500 ng of  E. coli  genomic DNA, 50 pmol of each primer, 1.25 units of PfA DNA polymerase (MBI Fermentas) and water to a final volume of 50 ul. The PCR amplification method used was as follows:  
                                       1 cycle of:           94° C.   5 minutes initial denaturation       72° C.   hold (polymerase addition)       14 cycles of:       65° C.   1 minute annealing (−1° C. decrease per cycle)       72° C.   5 minutes elongation       94° C.   1 minute denaturation       19 cycles of:       55° C.   1 minute annealing       72° C.   5 minutes elongation (+0.02 minutes increment per cycle)       94° C.   1 minute denaturation       55° C.   1 minute annealing       72° C.   7 minutes final elongation                  
 
      A 1.2 kb fragment corresponding to the xapR gene was amplified. The DNA fragment resulting from this PCR reaction was analysed on a 0.8% TAE/agarose gel stained with 0.1 ug/ml ethidium bromide. The fragment was subsequently purified from the gel.  
      PCR Amplification of the xapA Promoter  
      The xapA promoter region was PCR amplified from  E. coli  genomic DNA from strain MG1655 using forward primer xap1 (SEQ_ID3) 5′-CCAAGCTTAGCATAATTCCCTATGCCGATC-3′, and phosphorylated reverse primer xap4 (SEQ_ID4) 5′-GAACCTGAGACATATGTATCCTIG-3′, or phosphorylated xapNco R (SEQ_ID5) 5′-GTGGTCACCATGGGTATCCTTTTTCTG TAG G-3′, using the reaction mixture as described above. The amplification method used was as follows:  
                                                       1 cycle of:               94° C.     5 minutes initial denaturation           72° C.   Hold (polymerase addition)           35 cycles of:           65° C.     1 minute annealing           72° C.   0.5 minute elongation           94° C.     1 minute denaturation            1 cycle of:           65° C.     1 minute annealing           72° C.     3 minutes final elongation                      
 
      A 270 bp fragment corresponding to the xapA promoter was amplified. The DNA fragment resulting from these PCR reactions was analysed on a 1% TAE/agarose gel stained with 0.1 ug/ml ethidium bromide, and again purified from the gel.  
      Expression Vector Construction  
      The first vector to be constructed was pUC19X. To construct this vector, pUC19 was digested with Sacd and NdeI and the resulting overhangs were filled-in using T4 DNA polymerase (Promega), according to the manufacturer&#39;s instructions. The resulting 2.4 kb fragment was then self-ligated and transformed into XL1-Blue competent cells (Stratagene). The purified xapR gene and the xapA promoter PCR products, as described above, were inserted into pUC19X, using restriction endonucleases BamHI and KpnI from the xapR gene and HindIII and HincII for the xapA promoter. The resulting plasmids were called pXap1a, and pXap1b, differing only by the presence of either a unique NcoI site or NdeI site. Maps of the initial construct and the expression vector constructs are given in  FIG. 3 .  
      The construct is designed such that the xapR protein, under the control of its own promoter (incorporated into the PCR product as described above), is expressed constitutively. The xapA promoter is inserted into a suitable region of the vector, and allows for the cloning of heterologous genes into the NcoI site (pXap1a) or NdeI site (pXap1b). This ensures that any such heterologous gene is correctly positioned with respect to the promoter region of the xapA promoter, with respect to the transcriptional start site, the ribosomal binding site and the RNA Polymerase binding site of the promoter, allowing correct expression of the heterologous protein, upon induction with xanthosine, but not allowing non-induced expression in the absence of xanthosine.  
     Example 2  
     Creation of Ribosomal Binding Site Mutants and Activity Analysis  
      Expression Analysis of pXap1b Using β-Galactosidase  
      The  E. coli  β-galactosidase (β-Gal) gene was initially obtained by PCR amplification of the β-gal gene from  E. coli  genomic DNA from strain MG1655, using the amplification methods described above, with the following primers—β-Gal-1 (SEQ_ID6) 5′-ATATGGGCCCATGGATCCCGTCGTTTTAC-3′, and β-Gal-2 (SEQ_ID7) 5′-AGTGTGAAGCTTTATATTTTTGACACCAG-3′. The PCR fragment was then ligated into the expression vector pSE420 (Invitrogen), using NcoI/HindIII double digests, and used to transform chemically competent DH5 cells (Gibco-BRL). Positive clones were identified by restriction analysis.  
      Subsequently, the β-galactosidase gene was cloned into one of the pXap vectors, namely pXap1b, by digestion of pSE420-β-Gal with HindIII, followed by blunt-ending of the fragment using Klenow enzyme, and subsequent digestion with NcoI.  
      The purified fragment was then introduced into similarly digested pXap1b, so as to be in-frame with the xapA promoter. After ligation and transformation, the positive clones were identified by blue colour development when plated on LAXX plates (LB/Ampicillin Agar plates supplemented with 1 mg/ml Xanthosine, 80 ug/ml X-gal). The xanthosine induces the expression of the β-gal gene, which subsequently forms a blue coloured product on hydrolysis of the substrate X-gal. Positive blue colonies were screened for β-Gal activity by the assay of Miller (1972), and one such colony was designated plasmid pXap1b-β-Gal ( FIG. 4 ).  
      Mutagenesis of the Ribosomal Binding Site Region of pXap1b-β-Gal  
      In order to develop novel vectors with increased expression, mutagenic PCR was performed upon plasmid pXap1b-β-Gal, in order to change the natural ribosomal binding site (RBS) and analyse for increased expression. Two such mutants were constructed, RBS1 and RBS2. RBS1 was designed to replace the natural RBS of xapA, AGGA, with the stronger AGGAGG consensus RBS sequence. RBS2 was designed to introduce a similarly strong AGGAGA RBS sequence, plus an additional base between the RBS and the start codon, as it has been observed that altering the spacing between the RBS and start codon can affect the expression levels, either positively or negatively, in other expression systems (Marquis et al., 1986; Chen et al., 1994).  
      Plasmid pXap1b-β-Gal was PCR amplified using the following primers: 
      pXapRBS1A 5′-CCTACAGAAAAAGGAGGTACCCATGGATCCCGTCG-3′ (SEQ_ID12)     together with     pXapRBS1B 5′-CGGGATCCATGGGTACCTCCTTTTTCTGTAGGGTGG-3′, (SEQ_ID13), for     the RBS1 mutant, &amp;     pXapRBS2A 5′CCCTACAGAAAAAGGAGATATCCCATGGATCCCGTCGTTTTACAACG-3′ (SEQ_ID14) together with     pXapRBS2B 5′-CGACGGGATCCATGGGATATCTCCTTTTTCTGTAGGGTGGAATCTAACG -3′, (SEQ_ID15), for the RBS2 mutant, in separate reactions, using the following conditions.    

      The reaction mixture was as described in example 1, except that 1 ng of purified pXap1b-β-Gal was used as the template. The reaction conditions used were:  
                                                       1 cycle of:               94° C.    5 minutes initial denaturation           72° C.   hold (polymerase addition)           18 cycles of:           55° C.    1 minute annealing           72° C.   15 minutes elongation           94° C.    1 minute denaturation                      
 
      DpnI restriction endonuclease (Fermentas) was then added to the reaction mixture and incubated at 37 C for 2 hours. 5 ul of the reaction mixture was used to transform chemically competent D115  E. coli  cells, and the transformed cells were plated out on LAXX plates as described above. Several positive blue colonies were screened and identified by restriction digestion  
      Screening of the Expression Activity of pXap1b-β-Gal and RBS Mutants  
      Cultures of pXap1b-β-Gal and of positive RBS mutants, transformed into DH5 competent cells, were grown at 37° C. in defined medium supplemented with ampicillin and induced with 1 mg/ml xanthosine (final concentration) in order to determine their β-galactosidase activity, as measured by the ONPG assay (Miller, 1972) (Table 1).  
               TABLE 1                          Comparison of the β-galactosidase activity of pXap1b-β-Gal       and RBS mutants pXap1b-β-Gal-RBS1 and pXap1b-β-Gal-RBS2.                     Plasmid/Strain   β-Galactosidase Activity, in Miller Units               pXap1b-β-Gal/DH5   16,900       pXap1b-β-Gal-RBS1/DH5   21,500       pXap1b-β-Gal-RBS2/DH5   24,600                  
 
      It is thought (Chen et al., 1994) that a 5 nucleotide (nt) spacing between the RBS and the ATG start codon is the optimal spacing in  E. coli  promoters. This is the case in the naturally occurring xapA RBS. Altering the RBS of pXap1b-β-Gal to the consensus sequence AGGAGG resulted in higher levels of expression (RBS1), and surprisingly, increasing the spacing between the consensus sequence and the start codon (RBS2) increased expression levels further still.  
      RBS regions of the RBS1 and RBS2 plasmids, compared to plasmid pXap1b-β-Gal.  
                              CCACCCTACAGAAAAAGGAtacccATGGATC -   (5 nt spacing)                   pXap1b-β-Gal               CCACCCTACAGAAAAAGGAGGtacccATGGATC -   (5 nt spacing)               pXap1b-β-Gal-RBS1               CCACCCTACAGAAAAAGGAGAtatcccATGGATC -   (6 nt spacing)               pXap1b-β-Gal-RBS2          
 
     Example 3  
     Expression of Heterologous Genes  
      Expression of Human Growth Hormone  
      The human growth hormone gene (hGH) was PCR amplified from plasmid phgh107 (ATCC#40011) using primers hGH-Nde  
                                      hGH-Nde                           (SEQ_ID 8)                       5′ AAGAATCCCATATGTTCCCAACCATTCCCTTATCC 3′                       and                       hGH-Rev                       (SEQ_ID 9)                       5′ CGCGGATCCAAGCTTATTAGAAGCCACAGCTGCCCTCC 3′.          
 
      The amplification conditions and parameters were as described in example 1. The amplified fragment was cloned into pXap1a using the NdeI/BamHI restriction sites ( FIG. 5 ). The production of human growth hormone by this new clone was tested in  E. coli  strain TG1, at 30° C. in both complex (LB) and defined media (Miller 1992).  
      The expression of hGH was induced by addition of 1 mg/ml of xanthosine to the cultures. The presence and identity of human growth hormone produced was confirmed by SDS-PAGE, and by Western-blot analysis, using a monoclonal antibody and detected using goat anti-mouse IgG-AP from BIO-RAD according to the manufacturers instructions ( FIG. 6 ). Densitometry analysis showed that the recombinant hGH protein represented greater than 20% of the total cell protein, even after only 2 hours induction, in either media.  
      Expression of Human Interleukin-4  
      The Interleukin-4 gene (IL-4) was PCR amplified from a hIL-4 plasmid-pPlc299hIL4 (Dr. Nico Mertens, VIB, Belgium) using primers IL4-Nde (SEQ_ID10) 5′ AAGAATCCCATATGCACAAGTGCGATATCACC 3′ and IL4-Rev (SEQ_ID 1) 5′AAGGATCCCAAGCTTAGCTCGAACACTTTGAATATTTC 3′.  
      The amplification conditions and parameters were as described before (Section: PCR amplification of the XapR gene). The amplified fragment was cloned into pXap2a using the NdeI/BamHI restriction sites ( FIG. 5 ). The presence and identity of interleukin-4 was evaluated at 20° C. and 28° C. in LB medium. The expression of IL-4 was induced by addition of 1 mg/ml of xanthosine to the cultures, and confirmed by SDS-PAGE and by Western-blot analysis, using a monoclonal antibody and detected using goat anti-mouse IgG-AP from BIO-RAD according to the manufacturer&#39;s instructions ( FIG. 7 ). Densitometry analysis showed that the recombinant IL-4 constituted over 30% of the total cell protein, at both temperatures.  
     REFERENCES  
      Bohannon, D and Soneshein, A (1989); J Bact 171: 4718-27 
      Chen H, et al. (1994); Nuc Acid Res 22: 4953-7     Demain A, and Davies J (1999) “Manual of Industrial Microbiology and Biotechnology” “2nd Edition. ASM Press, Washington D.C., USA.     Hammer-Jespersen, K et al. (1980); Mol Gen Genet 179: 341-8     Henikoff, S et al. (1988); PNAS 85: 6602-6     Janson, J-C and Ryden, L (1998) “Protein Purification: Principles, High-Resolution Methods, and Applications”. John Wiley &amp; Sons, NY, USA.     Jorgensen, C. and Dandanell, G., (1999); J. Bact. 181: 14, 4397-4403     Marquis D, et al. (1986); Gene 42: 175-83     Miller J. H. (1972);  Experiments in Molecular Genetics . Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.     Miller J. H. (1992);  A Short Course in Bacterial Genetics . Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.     Nygaard, P (1983); pp 27-93 ; Metabolism of nucleotides, nucleosides and nucleobases in microorganisms . Academic Press, London.     Seeger, C. et al. (1995); J Bact 177:19 5506-16    

      Appendix 1-DNA Sequences  
                          SEQ_ID 1                   Primer Xap2               ACGGTACCTTTTGCTATCTGCGTTTGCG               SEQ_ID 2               Primer Xap5               CTCATTAAAAGGATCCGCGGCTCTGCTCTTCAG               SEQ_ID 3               Primer Xap1               CCAAGCTTAGCATAATTCCCTATGCCGATC               SEQ_ID 4               Primer Xap4               GAACCTGAGACATATGTATCCTTTTG               SEQ_ID 5               Primer xapNcoR               GTGGTCACCATGGGTATCCTTTTTCTGTAGG               SEQ_ID 6               Primer B-Gal-1               ATATGGGCCCATGGATCCCGTCGTTTTAC               SEQ_ID 7               Primer B-Gal-2               AGTGTGAAGCTTATTATTTTTGACACCAG               SEQ_ID 8               Primer hGH-Nde               AAGAATCCCATATGTTCCCAACCATTCCCTTATCC               SEQ_ID 9               Primer hGH-Rev               CGCGGATCCAAGCTTATTAGAAGCCACAGCTGCCCTCC               SEQ_ID 10               Primer IL4-Nde               AAGAATCCCATATGCACAAGTGCGATATCACC               SEQ_ID 11               Primer IL4-Rev               AAGGATCCCAAGCTTAGCTCGAACACTTTGAATATTTC               SEQ_ID 12               Primer pXapRBS1A               CCTACAGAAAAAGGAGGTACCCATGGATCCCGTCG               SEQ_ID 13               Primer pXapRBS1B               CGGGATCCATGGGTACCTCCTTTTTCTGTAGGGTGG               SEQ_ID 14               Primer pXapRBS2A               CCCTACAGAAAAAGGAGATATCCCATGGATCCCGTCGTTTTACAACG               SEQ_ID 15               Primer pXapRBS2B               CGACGGGATCCATGGGATATCTCCTTTTTCTGTAGGGTGGAATCTAACG