Improved riboflavin production

Abstract: The present invention is directed to a recombinant bacterium comprising a bacterium which has been transformed by three vectors, two of them each comprising a DNA sequence coding for the riboflavin synthesizing enzymatic activities of Bacillus subtilis or a DNA sequence which is substantially homologous and one or more transcription elements and a third vector comprising a DNA sequence coding for the ribA gene product of Bacillus subtilis or a DNA sequence which is substantially homologous and optionally further comprising a transcription element whereby one or a plurality of copies of each of these vectors has/have been integrated at three different sites within its chromosome; and a process for the production of riboflavin by such a recombinant bacterium.

Description: Production of riboflavin by recombinant bacteria is known in the state of the art, see e.g. European Patent Application Publication No. (EP) 405,370. However there is an ongoing need for an improved riboflavin production process. It is therefore an object of the present invention to provide a recombinant bacterium comprising a bacterium which has been transformed by three or four vectors, two of them each comprising a DNA sequence coding for the riboflavin synthesizing enzymatic activities of Bacillus subtilis or a DNA sequence which is substantially homologous and one or more transcription elements and a third and/or fourth vector comprising a DNA sequence coding for the ribA gene product of Bacillus subtilis or a DNA sequence which is substantially homologous and optionally further comprising transcription element whereby one or a plurality of copies of each of these vectors has/have been integrated at three or four different sites within its chromosome. More preferably it is an object of the present invention to provide a recombinant bacterium as described above whereby the two vectors which comprise the DNA sequence coding for the riboflavin synthesizing enzymatic activities of Bacillus subtilis or a DNA sequence which is substantially homologous further comprise two transcription elements for each vector, preferably promoters and the third and/or fourth vector comprise the DNA sequence coding for the ribA gene product of Bacillus subtilis or a DNA sequence which is substantially homologous and a transcription element, preferably a promotor. Furthermore it is an object of the present invention to provide a recombinant bacterium as described above whereby the two vectors which comprise the DNA sequence coding for the riboflavin synthesizing enzymatic activities of Bacillus subtilis or a DNA sequence which is substantially homologous have been integrated at two different sites of the chromosome in a plurality of copies and the third and/or fourth vector, has/have been integrated at the third and/or fourth site as a single copy. Furthermore it is an object of the present invention to provide a recombinant bacterium characterized therein that the additional DNA sequence coding for the ribA gene product of Bacillus substilis or a DNA sequence which is substantially homologous is not integrated at a third and/or fourth additional site in the chromosome but integrated at the same site as one of the two vectors with DNA sequences coding for the riboflavin synthesizing enzymatic activities and amplified together with this vector in this site. Such constructs can be made by the man skilled in the art based upon his general knowledge and detailed teachings as given e.g. in EP 405 370. Furthermore it is understood by a man skilled in the art that for transformation the DNA sequences used must not necessarily be in form of vectors but could also be used without additional vector DNA. Furthermore it is an object of the present invention to provide a recombinant bacterium as described above which is E.coli or Bacillus, preferably Bacillus subtilis, Cyanobacter or Corynebacteria. Furthermore it is an object of the present invention to provide a process for the production of riboflavin characterized therein that a recombinant bacterium as described above is grown under suitable growth conditions and the riboflavin secreted into the medium is isolated by methods known in the art. It is also an object of the present invention to provide a process for the preparation of a food or feed composition characterized therein that such a process has been effected and the riboflavin obtained thereby is converted into a food or feed composition by methods known in the art. The expression "a DNA sequence which is substantially homologeous" means in the context of the present invention a DNA sequence which encodes an amino acid sequence which shows more than 60%, preferably more than 70%, more preferably more than 80% and most preferably more than 90% identical amino acids when compared to the amino acid sequence encoded by the DNA sequence to which it refers and encodes the same enzyme or enzymes from the same or different organisms or is of partial or complete synthetic origin. DNA sequences which are useful for the purpose of the present invention comprise DNA sequences which code for proteins having the same type of enzymatic activity as the proteins encoded by the DNA sequences described above and which are selected from the following DNA sequences: (a) a DNA sequence which hybridizes under standard conditions with sequences defined above. (b) a DNA sequence which, because of the degeneracy of the genetic code, does not hybridize with sequence (a), but which codes for polypeptides having exactly the same amino acid sequences as the polypeptides encoded by these DNA sequences; and (c) a DNA sequence which is a fragment of the DNA sequences specified in (a) or (b). "Standard conditions" for hybridization in this context the conditions which are generally used by a man skilled in the art to detect specific hybridization signals and which are described, e.g. by Sambrook et al., "Molecular Cloning" second edition, Cold Spring Harbor Laboratory Press 1989, New York, or preferably so called stringent hybridization and non-stringent washing conditions or more preferably so called stringent hybridization and stringent washing conditions a man skilled in the art is familiar with and which are described, e.g. in Sambrook et al. (s.a.). "Fragment of the DNA sequences" means in this context a fragment which codes for a polypeptide still having the enzymatic activity as specified above. DNA sequences which can be used for the purpose of the present invention are disclosed, e.g. in the specification of EP 405,370. Sequence information for such sequences can also be obtained from any known sequence data bank, e.g. the European Bioinformatics Institute (Hinxton Hall, Cambridge, GB). The DNA sequences can then be prepared on the basis of such sequence information using, e:g. the PCR method known in the state of the art and described, e.g. in the examples or other methods of molecular cloning known in the art and described, e.g. in EP 405,370. Once such DNA sequences are available they can be integrated for further manipulation into suitable vectors known in the state of the art and described, e.g. in the examples of EP 405,370. Preferred are such vectors for integration into the chromosome of the host which is preferably Bacillus and more preferably a Bacillus subtilis and subsequent amplification, if desired. Such vectors are described, e.g. in the Examples or known in the state of the art, see e.g. EP 405,370. Such vectors can further carry so called transcription elements, like enhancers and/or promoters, like the veg-promoter and/or natural or synthetic ribosomal binding sites and/or terminators, like e.g. the cryT-terminator which are known in the state of the art, see e.g. EP 405,370. The desired host cells can then be transformed by such vectors by methods described e.g. in the examples or which are known in the state of the art, see e.g. EP 405,370 and grown in a suitable medium and the riboflavin secreted into such medium can be isolated as described in the examples or as known in the state of the art. After the invention has been described in general hereinbefore, the following figures and examples are intended to illustrate details of the invention, without thereby limiting it in any matter. Figure 1: The expression vector pDSNdeHis. A: construction of pDSNdeHis from the parent vector pDS/RBSII, 6xHis(-2). The existing NdeI site was eliminated by cutting, filling in of the sticky ends and religating. The resulting plasmid was cut with BamHI and HindIII and a synthetic polylinker containing the restriction sites Clal, NdeI, SalI, BamHI and HindIII was introduced. B: The sequence of pDSNdeHis from the Shine-Delgarno sequence (S/D box) to the multiple cloning sites and the peptide with the consecutive histidine residues for purification of recombinant proteins are shown. Figure 2: Plasmids pXI12 and pXI16. The plasmid pXI12 is represented by a circle. The recognition sites for some restriction enzymes are indicated by standard abbreviations. The important elements of the vector are labelled as follows: PvegI: medium strenght, constitutive promoter from B. subtilis ; RBS: synthetic ribosome binding site; cryT: transcriptional terminator from B. thuringiensis ; ermAM: constitutively expressed erythromycin resistance gene; sacB-3' and sacB-5': homology regions for integration via homologous recombination, derived from the levansucrase gene of B. subtilis ; amp: ampicillin resistance gene from pBR322; ori: origin of replication from pBR322; rop: rop gene from pBR322. The direction of some of the elements is indicated by arrows. Above the plasmid, the promoter with the -35 and -10 regions is shown. The arrow points to the T to C mutation which was introduced to create the ApaI site (box in middle line) in pXI16. The uppermost line shows the promoter interrupting sequence of pXI16 and the introduced restriction sites. Figure 3: Integration of the rib A gene into the sac B locus of B. subtilis. The sac B locus is schematically shown in the upper part. The sites for the restriction endonucleases EcoRI and EcoRV are indicated. The homology regions present in the pXI clones are represented as shaded boxes. The lower part shows the linearized pXI plasmid without the pBR322 derived section and the rib A gene cloned between the NdeI and BamHI sites. The integration of the pXI derived DNA via double cross-over is indicated. Figure 4: Effect of the introduction of a ribA, ribA-M or ribA-C gene into the sacB locus of RB50::(pRF69) n ::(pRF93) m on cell growth and riboflavin production. Fermentations were carried out with RB50::(pRF69) n ::(pRF93) m or its derivatives having the mutase encoding half of ribA ( ribA-M ), the cyclohydrolase II encoding half of ribA ( ribA-C ) or the entire ribA inserted in the sacB locus. The modified operons pRF69 and pRF93 of all strains were amplified. Panel A shows the OD 540 values of samples taken during the fermentations and the corresponding riboflavin titers are plotted in panel B. Examples Example 1 Construction of B. subtilis strain RB50::[pFR69]::[pRF93] The riboflavin producing strain RB50::[pRF69] is a genetically modified strain of B. subtilis . RB50 refers to the host strain of B. subtilis , which contains several mutations introduced to improve production of nucleotides and riboflavin. pRF69 refers to a rib operon modified by the introduction of strong phage promoters which was introduced at the rib locus of pRF50. The modified operon pRF69 can be amplified to high copy numbers. A detailed description of the strain RB50::[pRF69] is presented in EP 0405370. To further increase the number of rib operons, a second plasmid with a modified rib operon and a tetracycline resistance gene was introduced at the bpr locus (essentially as described in EP 0405370, example 8, second site integration). This second plasmid, pRF93, was constructed from pRF89 (EP 0405370, fig. 14) by replacing the chloramphenicol resistance gene by a tetracyclin resistance gene (EP 0405370, example 8, second site integration). The resulting strain is RB50::[pRF69] n ::[pRF93] m (n and m refer to the copy numbers of the modified operons). Example 2 Cloning vectors pDSNdeHis, pXI12 and pXI16 NdeI is a restriction enzyme with a 6 bp recognition site ending with ATG. It is therefore the enzyme of choice for the cloning of open reading frames (ORFs) which generally begin with the translation start codon ATG. The vectors pDSNdeHis, pXI12 and pXI16 all contain an NdeI cloning site. In the pXI vectors, the ATG of the NdeI site was positioned such that it corresponds to the translational start codon, whereas in pDSNdeHis, a histidine-tag is added at the amino-terminus of the expressed protein (see below). Construction of pDSNdeHis The expression vector pDS/RBSII, 6xHis(-2) (Stüber, D., Matile, H. and Garotta, G., 1990. System for high-level production in Escherichia coli and rapid purification of recombinant proteins: application to epitope mapping, preparation of antibodies and structure-function analysis. Immunol. Meth. vol. IV, p. 121-152) was used as parent plasmid for the construction of pDSNdeHis. pDS/RBSII, 6xHis(-2) is identical to pDS/RBSII, 6 His (Stüber et al. 1990; see also Accession No. DSM 5298) except for an additional G nucleotide in front of the BamHI site. An existing NdeI site in a non-essential region of the plasmid was eliminated by cutting, filling-in of the sticky ends and religating. The resulting plasmid was cut with BamHI and HindIII and a polylinker carrying sites for the restriction endonucleases ClaI, NdeI, SalI, BamHI and HindIII was introduced (Fig. 1). The proteins expressed from this vector possess an N-terminal extension containing six consecutive histidine residues which permit a one step purification (Stüber et al., 1990). Construction of pXI12 (Fig. 2) The backbone of the vector is the EagI-AatII fragment of pBR322 containing the ampicillin resistance gene, the origin of replication and the rop gene (Bolivar, F., Rodriguez, R. L., Greene, P. J., Betlach, M. C., Heynecker, H. L., Boyer, H. W., Crosa, J. H. and Falkow, S., 1977. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2, 95-113). The pBR322 sequence is flanked by two sequences derived from the levansucrase gene ( sacB ) of B. subtilis which were obtained by polymerase chain reaction (PCR). The recognition sites for the restriction endonucleases AatII, EagI and NheI (Fig. 4) were introduced through the PCR primers. The sacB-5' sequence starts at position 729 of the levansucrase sequence (database accession number X02730 of the Genebank database or the database of the European Bioinformatics Institute, Hinxton Hall, Cambridge, GB) and ends at position 1266. The sacB-3' fragment includes the sequence between positions 1336 and 1794. As a selectable marker the erythromycine resistance gene ermAM from the plasmid pAMβ1 (accession number Y00116 of the Genebank database or the database of the European Bioinformatics Institute, Hinxton Hall, Cambridge, GB) was introduced. The sequence, also obtained by PCR, starts at position 107 of the sequence with the accession number Y00116 and ends at position 1091. The flanking AatII and Pmel sites originate from the PCR primers. The promoter driving the transcription of the cloned gene is the medium strength, constitutive vegI promoter from B. subtilis and corresponds to positions 30 to 101 of the published sequence (accession number J01552 of the Genebank database or the database of the European Bioinformatics Institute, Hinxton Hall, Cambridge, GB). The restriction sites EagI and XhoI which flank the promoter originate from the PCR primers. The cryT transcriptional terminator is from B. thuringiensis and corresponds to positions 268 to 380 of the sequence in accession number M13201 of the Genebank database or the database of the European Bioinformatics Institute, Hinxton Hall, Cambridge, GB. Again, the flanking Pmel and SmaI sites are primer derived. The ribosome binding site (underlined) and the polylinker stretch including the translational start site within the NdeI site (bold) was introduced as synthetic DNA with the sequence CTCGAGAA TTAAAGGAGG GTTTCAT ATG AATTCGGATCCCGGG. The sequences at the joints of the various elements are shown in table 1. Construction of pXI16 The expression of the genes cloned in pXI12 might not be tolerated in E. coli. To avoid potential problems, a variant of pXI12 was created in which the veg promoter is interrupted by a short sequence. To construct this modified vector, named pXI16, a point mutation was introduced between the -35 and the -10 regions of the veg promoter to create an ApaI site and a 30 bp polylinker was then introduced (Fig. 2). Example 3 Cloning of the ribA gene The ribA gene was isolated from plasmid pRF2 (EP 0405370, fig. 6) with polymerase chain reaction (PCR) using the primers ribA5 and ribA3. This approach allowed the introduction of an NdeI restriction endonuclease site site at the start codon of the gene and a BamHI site after the stop codon. The primers had the following sequence: The underlined sequences correspond to the restriction endonuclease sites NdeI (CATATG) and BamHI (GGATCC), small caps indicate changed nucleotides as compared to the sequence of the B. subtilis rib operon and bold sequences mark the translational start codon (ATG) and the reverse complement of the stop codon (TTA). The GeneAmp DNA amplification reagent kit from Perkin Elmer Cetus was used for PCR reactions following the instructions of the manufacturer. Reaction conditions were: 1 min 94°C, 1 min 45°C and 2 min 72°C for 25 cycles. The concentration of each primer was 1 µM and the template DNA was added at a concentration of about 1 pM. The PCR reaction product was separated from the primers by agarose gel electrophoresis and the PCR fragment containing ribA was isolated (Heery, D. M., Gannon, F. and Powell, R., 1990. A simple method for subcloning DNA fragments from gel slices. Trends in Genetics 6 , 173; Vaux, D. L., 1992. Rapid recovery of DNA from agarose gels. Trends in Genetics 8 , 81), cut with Ndel and BamHI and cloned into the vector pDSNdeHis, resulting in the plasmid pDSribA. Example 4 Construction of the strain VB2XL1 The ribA gene was excised from pDSribA with Ndel and BamHI and subcloned into the NdeI-BamHI cleaved pXI16. After isolation of the plasmid from E. coli the DNA was cut with Apal, the 30 bp insert was deleted and the veg promoter was reconstituted by ligation. The plasmid was then linearised by cutting with FspI which cleaves only in the pBR322 derived sequence (Fig. 2) and the cloned gene was introduced into transformation-competent B. subtilis cells following the described two-step procedure (Cutting, S. M. and Vander Horn, P. B., 1990. In: Molecular biological methods for Bacillus (Harwood and Cutting, eds.), p. 67-71, John Wiley & Sons Ltd., Chichester, England). Since the production strain RB50::[pRF69]::[pRF93] cannot be made competent for transformation B. subtilis strain 1012 (Saito, H., Shibata, T. and Ando, T., 1979. Mapping of genes determining nonpermissiveness and host-specific restriction to bacteriophages in Bacillus subtilis Marburg. Mol. Gen. Genet. 170, 117-122) was chosen as an intermediate host. Erythromycin resistant clones had the ribA gene and the erythromycin-resistance gene ermAM inserted in the sacB locus by double cross-over in the homology regions sacB -3' and sacB-5' (Fig. 3). The modified sacB locus was then introduced into RB50::[pRF69]::[pRF93] by transduction with the phage PBS1 according to the liquid culture method as described (Cutting and Vander Horn, 1990). Example 5 Construction of RB50::[pFR69]::[pRF93] strains with ribA-M or ribA-C in the sacB locus RibA encodes two enzymatic activities, the GTP cyclohydrolase II and the mutase (3,4-dihydroxy-2-butanone 4-phosphate synthase), which are encoded by two separate genes in E. coli (Richter, G., Ritz, H., Katzenmeier, G., Volk, R., Kohnle, A., Lottspeich, F., Allendorf, D. and Bacher, A., 1993. Biosynthesis of riboflavin: cloning, sequencing, mapping and expression of the gene coding for GTP cyclohydrolase II of Escherichia coli . J. Bact. 175 , 4045-4051). The mutase activity is located in the aminoterminal half of the B. subtilis ribA and the GTP cyclohydrolase II activity resides in the carboxyterminal half. The mutase encoding portion of ribA , named ribA-M , was excised from pDSribA with NdeI and HincII and cloned into the NdeI and SmaI cleaved pXI16 vector. The single HincII site is conveniently located in the middle of ribA and cleavage occurs between two codons separating the two activities encoding halfs of the gene. The introduction of ribA-M into the sacB locus of RB50::[pRF69]::[pRF93] was done as described above. The GTP cyclohydrolase encoding portion of ribA , named ribA-C , was excised from pDSribA with HincII and BamHI and introduced into the HincII-BamHI cleaved pDSNdeHis. Note that the single HincII recognition site in pDSNdeHis is the same as the SalI site (GTCGAC, Fig. 1) and HincII cleavage results in a blunt end cut through the middle of the recognition site. The resulting plasmid was then cut with NdeI and BamHI and ribA-C was cloned into the NdeI BamHI cut pXI12. The introduction of ribA-C into the sacB locus of RB50::[pRF69]::[pRF93] was done as described above except that the ApaI cleavage and religation step was omitted, since pXI12 with an uninterrupted veg promoter was used (Fig. 2). Example 6 Amplification of the modified operons pRF69 and pRF93 Amplification of the modified operons is important for high riboflavin titers (EP 0405370). The following amplification scheme was used: 30 µl of an overnight culture grown in VY (25 g/L veal infusion broth (Difco), 5 g/L yeast extract, 15 g/L glucose) with 20 µg/ml tetracycline and 10 µg/ml chloramphenicol were used to inoculate three tubes containing 3 ml VY and 30, 60 or 75 µg/ml tetracycline. After 8-9 hours at 37°C and 200 rpm, 30-50 µl of the culture with the highest tetracycline concentration still resulting in good growth was used to inoculate tubes containing 3 ml VY and 30, 45 or 60 µg/ml chloramphenicol. After overnight incubation at 37°C and 200 rpm, 30-50 µl of the culture with the highest chloramphenicol concentration still resulting in good growth was used to inoculate tubes containing 3 ml VY and 60, 75, 90 or 120 µg/ml tetracycline. In the same manner growth continued in VY with 45, 60 or 80 µg/ml chloramphenicol, VY with 75, 90, 120 or 140 µg/ml tetracycline and VY with 60 or 80 µg/ml chloramphenicol. The last transfer was with 200 µl into two tubes containing 15 ml VY and 120 or 140 µg/ml tetracycline. The cells were grown to an OD 600 of about 0.8 and then distributed into 1 ml aliquots. Glycerol was added to a final concentration of 15% and the cells were stored at -70°C. The strain VB2XL1 reached the maximal antibiotic concentrations of 140 µg/ml tetracycline and 80 µg/ml chloramphenicol. Fermentative production of riboflavin Fermentative production of riboflavin was done by using the transformed B.subtilis strains as described above in glucose limited feedbatch as described in EP 405 370. Example 7 Fourth site integration The strain VB2XL3 is generically identical to VB2XL1 except that an additional ribA gene was introduced in the amyE locus to further increase the ribA level. VB2XL3 was constructed basically as described above for VB2XL1. In brief, the erythromycin marker in pXI6 (Fig. 2) was replaced by a neomycin resistance gene and the sacB homology regions were replaced by amyE homology sequences resulting in the vector pXI191. The neomycin resistance gene was obtained from the plasmid pBEST501 (M. Itaya et al., Nucl. Acids Res., 1989, p. 4410) and the inherent ApaI site was eliminated by a silent point mutation. The amyE homology regions were amplified with PCR from the B. subtilis genome with primers which were designed according to the known sequence (Accession number X02150). The ribA gene was then cloned in pXI191 and the resulting plasmid was used as a vehicle to introduce the ribA gene into the amyE locus of VB2XL1 essentially as described above. The new strain was named VB2XL3.

Claims: A recombinant bacterium which has been transformed by three vectors or DNA sequences, two of them each comprising a DNA sequence coding for the riboflavin synthesizing enzymatic activities of Bacillus subtilis or a DNA sequence which encodes an amino acid sequence which shows more than 60 % identical amino acids when compared to the amino acid sequence encoded by the DNA sequence to which it refers and encodes the same enzyme or enzymes from the same or different organism, and one or more transcription elements, and a third vector or DNA sequence consisting of a DNA sequence coding for the ribA gene product of Bacillus subtilis showing GTP cyclohydrolase II and 3,4-di-hydroxy-2-butanone 4-phosphate synthase activity, or a DNA sequence encoding an enzyme showing GTP cyclohydrolase II and 3,4-dihydroxy-2-butanone 4-phosphate synthase activity with an amino acid sequence which shows more than 60 % identical amino acids when compared to the amino acid sequence of the enzyme encoded by ribA, and optionally further comprising transcription elements whereby one or a plurality of copies of each of these vectors has/have been integrated at three different sites within its chromosome. A recombinant bacterium according to claim 1 whereby the two vectors or DNA sequences which comprise the DNA sequence coding for the riboflavin synthesizing enzymatic activities of Bacillus subtilis or a DNA sequence which encodes an amino acid sequence which shows more than 60 % identical amino acids when compared to the amino acid sequence encoded by the DNA sequence to which it refers and encodes the same enzyme or enzymes from the same or different organism, further comprise two transcription elements for each vector, preferably promotors, and the third vector or DNA sequence consists of a DNA sequence coding for the ribA gene product of Bacillus subtilis showing GTP cyclohydrolase II and 3,4-dihydroxy-2-butanone 4-phosphate synthase activity, or a DNA sequence encoding an enzyme showing GTP cyclohydrolase II and 3,4-dihydroxy-2-butan-one 4-phosphate synthase activity with an amino acid sequence which shows more than 60 % identical amino acids when compared to the amino acid sequence of the enzyme encoded by ribA, and a transcription element, preferably a promotor. A recombinant bacterium according to claim 1 or 2 whereby the two vectors or DNA sequences which comprise the DNA sequence coding for the riboflavin synthesizing enzymatic activities of Bacillus subtilis or a DNA sequence which encodes an amino acid sequence which shows more than 60 % identical amino acids when compared to the amino acid sequence encoded by the DNA sequence to which it refers and encodes the same enzyme or enzymes from the same or different organism, have been integrated at two different sites of the chromosome in a plurality of copies and the third vector or DNA sequence has been integrated at the third site as a single copy. A recombinant bacterium according to any one of claims 1 to 3 which is E. coli or Bacillus, preferably Bacillus subtilis. A process for the production of riboflavin characterized therein that a recombinant bacterium according to any one of claims 1 to 4 is grown under suitable growth conditions and the riboflavin secreted into the medium is isolated by methods known in the art. A process for the preparation of a food or feed composition characterized therein that a process according to claim 5 has been effected and the riboflavin obtained thereby is converted into a food or feed composition by methods known in the art.

Inventors: HOHMANN HANS-PETER, HUEMBELIN MARKUS, SCHURTER WALTER, VAN LOON ADOLPHUS, HOHMANN, HANS-PETER, HUEMBELIN, MARKUS, SCHURTER, WALTER, VAN LOON, ADOLPHUS, Hümbelin, Markus
Applicants: HOFFMANN LA ROCHE, F. HOFFMANN-LA ROCHE AG
Application year: 1997
Main classification: C12N15
IPC codes: C12N1, C12P25, C12N15