WO2006084724A1 - Nouveau gene rcs 28 - Google Patents

Nouveau gene rcs 28 Download PDF

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Publication number
WO2006084724A1
WO2006084724A1 PCT/EP2006/001219 EP2006001219W WO2006084724A1 WO 2006084724 A1 WO2006084724 A1 WO 2006084724A1 EP 2006001219 W EP2006001219 W EP 2006001219W WO 2006084724 A1 WO2006084724 A1 WO 2006084724A1
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microorganism
vitamin
production
polynucleotide
rcs
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PCT/EP2006/001219
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English (en)
Inventor
Bastien Chevreux
Anne Françoise MAYER
Anja Meury
Nigel John Mouncey
Masako Shinjoh
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Dsm Ip Assets B.V.
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Publication of WO2006084724A1 publication Critical patent/WO2006084724A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P17/00—Preparation of heterocyclic carbon compounds with only O, N, S, Se or Te as ring hetero atoms
    • C12P17/02—Oxygen as only ring hetero atoms
    • C12P17/04—Oxygen as only ring hetero atoms containing a five-membered hetero ring, e.g. griseofulvin, vitamin C
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria

Definitions

  • the present invention relates to newly identified genes that encode proteins that are involved in the synthesis of L-ascorbic acid (hereinafter also referred to as Vitamin C).
  • the invention also features polynucleotides comprising the full-length polynucleotide sequences of the novel genes and fragments thereof, the novel polypeptides encoded by the polynucleotides and fragments thereof, as well as their functional equivalents.
  • the present invention also relates to the use of said polynucleotides and polypeptides as biotechnological tools in the production of Vitamin C from microorganisms, whereby a modification of said polynucleotides and/or encoded polypeptides has a direct or indirect impact on yield, production, and/or efficiency of production of the fermentation product in said microorganism. Also included are methods/processes of using the polynucleotides and modified polynucleotide sequences to transform host microorganisms. The invention also relates to genetically engineered microorganisms and their use for the direct production of Vitamin C.
  • Vitamin C is one of very important and indispensable nutrient factors for human beings. Vitamin C is also used in animal feed even though some farm animals can synthesize it in their own body.
  • Vitamin C has been produced industrially from D-glucose by the well-known Reichstein method. All steps in this process are chemical except for one (the conversion of D-sorbitol to L-sorbose), which is carried out by microbial conversion. Since its initial implementation for industrial production of Vitamin C, several chemical and technical modifications have been used to improve the efficiency of the Reichstein method. Recent developments of Vitamin C production are summarized in Ullmann's Encyclopedia of Industrial Chemistry, 5 th Edition, Vol. A27 (1996), pp. 547ff.
  • 2-keto-L-gulonic acid (2 -KGA)
  • 2 -KGA 2-keto-L-gulonic acid
  • -KGA an intermediate compound that can be chemically converted into Vitamin C by means of an alkaline rearrangement reaction
  • L-sorbose or D-sorbitol may be produced by a fermentation process starting from L-sorbose or D-sorbitol, by means of strains belonging e.g. to the Ketogulonicigenium or Gluconobacter genera, or by an alternative fermentation process
  • Vitamin C Current chemical production methods for Vitamin C have some undesirable characteristics such as high-energy consumption and use of large quantities of organic and inorganic solvents. Therefore, over the past decades, other approaches to manufacture Vitamin C using microbial conversions, which would be more economical as well as ecological, have been investigated.
  • Direct Vitamin C production from a number of substrates including D-sorbitol, L-sorbose and L-sorbosone has been reported in several microorganisms, such as algae, yeast and acetic acid bacteria, using different cultivation methods.
  • bacteria able to directly produce Vitamin C include, for instance, strains from the genera of Gluconobacter, Gluconacetobacter, Acetobacter, Ketogulonicigenium, Pantoea, Pseudomonas ox Escherichia.
  • yeast or algae include, e.g., Candida, Saccharomyces, Zygosaccharomyces, Schizosaccharomyces, Kluyveromyces or Chlorella.
  • Microorganisms able to assimilate D-sorbitol for growth usually possess enzymes able to oxidize this compound into a universal assimilation substrate such as D-fructose. Also microorganisms able to grow on L-sorbose possess an enzyme, NAD(P)H-dependent L- sorbose reductase, which is able to reduce this compound to D-sorbitol, which is then further oxidized into D-fructose.
  • D-fructose is an excellent substrate for the growth of many microorganisms, after it has been phosphorylated by means of a D-fructose kinase.
  • acetic acid bacteria which are obligate aerobe, gram-negative microorganisms belonging to the genus Acetobacter, Gluconobacter, and Gluconacetobacter
  • these microorganisms are able to transport D-sorbitol into the cytosol and convert it into D-fructose by means of a cytosolic NAD-dependent D-sorbitol dehydrogenase.
  • Some individual strains such as Gluconobacter oxydans IFO 3292, and IFO 3293, are able as well to transport L-sorbose into the cytosol and reduce it to D- sorbitol by means of a cytosolic NAD(P)H-dependent L-sorbose reductase, which then is further oxidized into D-fructose.
  • the Embden-Meyerhof-Parnas pathway, as well as the tricarboxyclic acid cycle are not fully active, and the main pathway channeling sugars into the central metabolism is the pentose phosphate pathway.
  • D- fructose-6-phosphate obtained from D-fructose by a phosphorylation reaction enters the pentose phosphate pathway, being further metabolized and producing reducing power in the form OfNAD(P)H and tricarboxylic compounds necessary for growth and maintenance.
  • OfNAD(P)H and tricarboxylic compounds necessary for growth and maintenance.
  • Acetic acid bacteria are well known for their ability to incompletely oxidize different substrates such as alcohols, sugars, sugar alcohols and aldehydes. These processes are generally known as oxidative fermentations or incomplete oxidations, and they have been well established for a long time in the food and chemical industry, especially in vinegar and in L-sorbose production.
  • a useful product known to be obtained from incomplete oxidations of D-sorbitol or L-sorbose using strains belonging to the Gluconobacter genus is 2-KGA.
  • Acetic acid bacteria accomplish these incomplete oxidation reactions by means of different dehydrogenases located either in the periplasmic space, on the periplasmic membrane as well as in the cytoplasm.
  • Different co-factors are employed by the different dehydrogenases, the most common being PQQ and FAD for membrane-bound or periplasmic enzymes, andNAD/NADP for cytoplasmic enzymes.
  • Proteins in particular enzymes and transporters, that are active in transport of electrons are herein referred to as being involved in the Respiratory Chain System. Such proteins are abbreviated herein as RCS proteins and function in the well-known respiratory chain of an organism, also known as the electron transport system.
  • RCS proteins are known to be important in the mechanism through which electrons generated by any oxidoreduction reaction in the cell are further transported, in general by means of a series of oxidoreduction reactions involving co-factors and oxidases, and a final electron acceptor.
  • the main mechanism that living organisms use for producing energy necessary for vital activities is respiration.
  • carbohydrates, proteins, aliphatic acids are metabolised into acetyl-CoA by means of the glycolysis catabolic pathway and oxidation in cytoplasm.
  • Acetyl-CoA is further metabolised through a series of reactions known as the citric acid cycle, which happens at the mitochondria.
  • Energy resulting from these reactions is used for the production of reducing power, saved in the form of compounds such as FADH 2 and NADH.
  • These compounds are then used in the so-called electron transport chain, a series of oxido-reduction chain reactions involving different components localized in the mitochondrial inner membranes.
  • the final electron acceptor is oxygen, - 4 - 24654 which then reacts with the protons resulting from the reaction chain and forms water.
  • the proton concentration gradient resulting from this process is the driving force of the ATP synthesis.
  • acetic acid bacteria which are obligate aerobe, gram-negative microorganisms belonging to the genus Acetobacter, Gluconobacter, and
  • Gluconacetobacter present peculiar characteristics in terms of energy generating processes. These bacteria are well known for their ability to incompletely oxidize different substrates such as alcohols, sugars, sugar alcohols and aldehydes. These processes are generally known as oxidative fermentations, and they have been well established for a long time in the food and chemical industry, especially in vinegar and in L-sorbose production.
  • Useful products known to be obtained from incomplete oxidations using strains belonging to the Gluconobacter genus are 2-keto-L-gulonic acid (2-KGA) starting from D-sorbitol and L-sorbose, and 5-keto-D-gluconic acid, a precursor for the biosynthesis of D-tartaric acid, starting from D-glucose.
  • Incomplete oxidations are the main mechanism of generation of energy for acetic acid bacteria. They accomplish these reactions by means of different dehydrogenases located either in the periplasmic space, on the periplasmic membrane as well as in the cytoplasm. Different co-factors are employed by the different dehydrogenases, the most common being PQQ and FAD for membrane-bound or periplasmic enzymes, and NAD/NADP for cytoplasmic enzymes.
  • the electron transport chain of Gluconobacter/Gluconacetobacter and Acetobacter strains is known to include co-enzyme QlO (CoQlO) and CoQ9 , respectively, as universal electron transport compound for all processes, as well as in some cases several kinds of cytochrome c elements. Gluconobacter strains are reported not to contain cytochrome c oxidase, but have other kinds of terminal oxidases, such as the bo type.
  • An object of the present invention is to improve the yields and or productivity of Vitamin C production.
  • RCS proteins of the present invention are selected from oxidoreductases [EC 1], preferably from oxidoreductases acting on diphenols and related substances as donors [EC 1.10], more preferably from oxidoreductases with oxygen as acceptor [EC 1.10.3] and oxidoreductases with other acceptors [EC 1.1.99], most preferably alcohol dehydrogenases (acceptor) [EC 1.1.99.8].
  • the RCS proteins of the present invention may be selected from respiratory chain proteins, more preferably from carrier proteins or proteins functioning in the biosynthesis of co factors and/or prosthetic groups, in particular proteins involved in the biosynthesis or maturation of cofactors and/or their precursors such as FAD, NAD, NADP, PQQ, ubiquinones including CoQ8, 9 or CoQlO, cytochromes a, b, c, d, and heme, cyanide-insensitive bd-type terminal oxidase subunits I and EL, cyanide-sensitive bo-type terminal oxidase subunits in particular subunit I, ⁇ , DI and IV, cytochrome c oxidase subunits in particular membrane-bound alcohol dehydrogenase g3-ADH cytochrome c subunit. Most preferably, they are selected from PQQ biosynthetic proteins such as PQQ biosynthetic proteins A, B, C, D, E or from heme exporters such as
  • RCS proteins encoded by polynucleotides having a nucleotide sequence that hybridizes preferably under highly stringent conditions to a sequence shown in SEQ ID NO:1 play an important role in the biotechnological production of Vitamin C. It has also been found, that by genetically altering the expression level of nucleotides according to the invention in a microorganism capable of directly producing Vitamin C 5 such as for example Gluconobacter, the direct fermentation of Vitamin C by said microorganism can be even greatly improved.
  • the invention relates to a polynucleotide selected from the group consisting of:
  • polynucleotides comprising a nucleotide sequence obtainable by nucleic acid amplification such as polymerase chain reaction, using genomic DNA from a microorganism as a template and a primer set according to SEQ ID NO: 3 and SEQ ID NO:4;
  • polynucleotides comprising a nucleotide sequence encoding a fragment or derivative of a polypeptide encoded by a polynucleotide of any of (a) to (c) wherein in said derivative - 6 - 24654 one or more amino acid residues are conservatively substituted compared to said polypeptide, and said fragment or derivative has the activity of carrier protein, preferably a heme exporter (RCS 28);
  • polynucleotides the complementary strand of which hybridizes under stringent conditions to a polynucleotide as defined in any one of (a) to (d) and which encode a carrier protein, preferably a heme exporter (RCS 28); and
  • polynucleotides which are at least 70%, such as 85, 90 or 95% identical to a polynucleotide as defined in any one of (a) to (d) and which encode a carrier protein, preferably a heme exporter (RCS 28);
  • the RCS protein as isolated from Gluconobacter oxydans DSM 17078 shown in SEQ E) NO:2 and described herein was found to be a particularly useful RCS protein, since it appeared that it performs a crucial function in the direct Vitamin C production in microorganisms, in particular in bacteria, such as acetic acid bacteria, such as .
  • the invention relates to a polynucleotide encoding a polypeptide according to SEQ ID NO:2.
  • This protein may be encoded by a nucleotide sequence as shown in SEQ ID NO: 1.
  • the invention therefore also relates to polynucleotides comprising the nucleotide sequence according to SEQ ID NO:1.
  • the nucleotide and amino acid sequences determined above were used as a "query sequence" to perform a search with Blast2 program (version 2 or BLAST from National Center for Biotechnology [NCBI] against the database PRO SW-SwissProt (full release plus incremental updates). From the searches, the RCS 28 polynucleotide according to SEQ ID NO: 1 was annotated as heme exporter protein (CcroA) involved in cytochrome c biosynthesis.
  • Blast2 program version 2 or BLAST from National Center for Biotechnology [NCBI] against the database PRO SW-SwissProt (full release plus incremental updates).
  • the RCS 28 polynucleotide according to SEQ ID NO: 1 was annotated as heme exporter protein (CcroA) involved in cytochrome c biosynthesis.
  • a nucleic acid according to the invention may be obtained by nucleic acid amplification using cDNA, mRNA or alternatively, genomic DNA, as a template and appropriate oligonucleotide primers such as the nucleotide primers according to SEQ ID NO: 3 and SEQ TD NO:4 according to standard PCR amplification techniques.
  • the nucleic acid thus amplified may be cloned into an appropriate vector and characterized by DNA sequence analysis. - 7 - 24654
  • the template for the reaction may be cDNA obtained by reverse transcription of mRNA prepared from strains known or suspected to comprise a polynucleotide according to the invention.
  • the PCR product may be subcloned and sequenced to ensure that the amplified sequences represent the sequences of a new nucleic acid sequence as described herein, or a functional equivalent thereof.
  • the PCR fragment may then be used to isolate a full length cDNA clone by a variety of known methods.
  • the amplified fragment may be labeled and used to screen a bacteriophage or cosmid cDNA library.
  • the labeled fragment may be used to screen a genomic library.
  • the invention relates to polynucleotides comprising a nucleotide sequence obtainable by nucleic acid amplification such as polymerase chain reaction, using DNA such as genomic DNA from a microorganism as a template and a primer set according to SEQ ID NO:3 and SEQ ID NO:4.
  • the invention also relates to polynucleotides comprising a nucleotide sequence encoding a fragment or derivative of a polypeptide encoded by a polynucleotide as described herein wherein in said derivative one or more amino acid residues are conservatively substituted compared to said polypeptide, and said fragment or derivative has the activity of a RCS polypeptide, preferably a RCS 28 polypeptide.
  • the invention also relates to polynucleotides the complementary strand of which hybridizes under stringent conditions to a polynucleotide as defined herein and which encode a RCS polypeptide, preferably a RCS 28 polypeptide.
  • the invention also relates to polynucleotides which are at least 70% identical to a polynucleotide as defined herein and which encode a RCS polypeptide; and the invention also relates to polynucleotides being the complementary strand of a polynucleotide as defined herein above.
  • the invention also relates to microorganisms wherein the activity of a RCS polypeptide, preferably a RCS 28 polypeptide, is reduced or abolished so that the yield of Vitamin C which is directly produced from D-sorbitol or L-sorbose is increased.
  • RCS protein preferably a RCS 28 protein
  • Such may be for instance accomplished by either genetically modifying the host organism in such a way that it produces less or no copies of the RCS protein, preferably the RCS 28 protein, than the wild type organism or by decreasing or abolishing the specific activity of the RCS protein, preferably the RCS 28 protein.
  • Modifications in order to have the organism produce less or no copies of the RCS 28 gene and/or protein may include the use of a weak promoter, or the mutation ⁇ e.g. insertion, deletion or point mutation) of (parts of) the RCS 28 gene or its regulatory elements. Decreasing or abolishing the specific activity of a RCS 28 protein may also be accomplished by methods known in the art. Such methods may include the mutation ⁇ e.g. insertion, deletion or point mutation) of (parts of) the RCS 28 gene.
  • RCS 28 protein may be expressed and tested for activity in the presence of compounds suspected to inhibit the activity of the RCS 28 protein.
  • Potential inhibiting compounds may for instance be monoclonal or polyclonal antibodies against the RCS 28 protein. Such antibodies may be obtained by routine immunization protocols of suitable laboratory animals.
  • the invention may be performed in any microorganism carrying a RCS 28 gene or homologue thereof.
  • Suitable microorganisms may be selected from the group consisting of yeast, algae and bacteria, either as wild type strains, mutant strains derived by classic mutagenesis and selection methods or as recombinant strains.
  • yeast may be, e.g., Candida, Saccharomyces, Zygosaccharomyces, Schizosaccharomyces, or Kluyveromyces.
  • An example of such algae maybe, e.g., Chlorella.
  • Examples of such bacteria may be, e.g., Gluconobacter, Acetobacter, Gluconacetobacter,
  • Gluconobacter oxydans DSM 17078 (formerly known as Gluconobacter oxydans N44-1) has been deposited at Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ), Mascheroder Weg IB, D-38124 Braunschweig, Germany according to the Budapest Treaty on 26. January 2005.
  • DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen
  • Microorganisms which can be used for the present invention may be publicly available from different sources, e.g. , Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ), Mascheroder Weg IB, D-38124 Braunschweig, Germany, American Type - 9 - 24654
  • DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen
  • Mascheroder Weg IB Mascheroder Weg IB
  • D-38124 Braunschweig Germany
  • American Type - 9 - 24654 American Type - 9 - 24654
  • JFO 3244 Gluconobacter frateurii (formerly known as G. industrius) J-FO 3260, Gluconobacter cerinus JJPO 3266, Gluconobacter oxydans JFO 3287, and Acetobacter aceti subsp. orleanus JJFO 3259, which were all deposited on April 05, 1954; Acetobacter aceti subsp. xylinum IFO 13693 deposited on October 22, 1975, and Acetobacter aceti subsp. xylinum JFO 13773 deposited on December 08, 1977. Strain Acetobacter sp.
  • ATCC 15164 which is also an example of a preferred bacterium, was deposited with ATCC.
  • Strain Gluconobacter oxydans (formerly known as G. melanogenus) N 44-1 as another example of a preferred bacterium is a derivative of the strain JJ 7 O 3293 and is described in Sugisawa et al., Agric. Biol. Chem. 54: 1201-1209, 1990.
  • a microorganism as of the present invention may carry further modifications either on the DNA or protein level (see above), as long as such modification has a direct impact on the yield, production and/or efficiency of the direct production of Vitamin C from substrates like e.g. D-sorbitol or L-sorbose.
  • Such further modifications may for instance affect other genes encoding RCS proteins as described above, in particular genes encoding membrane- bound L-sorbosone dehydrogenases, such as L-sorbosone dehydrogenase SNDHai, or membrane-bound PQQ bound D-sorbitol dehydrogenases.
  • Methods of performing such modifications are known in the art, with some examples further described herein.
  • SNDHai for direct production of vitamin C as well as the nucleotide and amino acid sequence thereof we refer to WO 2005/017159 which is incorporated herein by reference.
  • Jn accordance with a further object of the present invention there is provided the use of a polynucleotide as defined above or a microorganism which is genetically engineered using such polynucleotides in the production of Vitamin C.
  • the invention also relates to processes for the expression of endogenous genes in a microorganism, to processes for the production of polypeptides as defined above in a microorganism and to processes for the production of microorganisms capable of producing Vitamin C. All these processes may comprise the step of altering a microorganism, wherein "altering” as used herein encompasses the process for "genetically altering” or “altering the composition of the cell culture media and/or methods used for culturing” in such a way that the yield and/or productivity of the fermentation product can be improved compared to the wild-type organism. As used herein, "improved yield of - 10 - 24654
  • Vitamin C means an increase of at least 5%, 10%, 25%, 30%, 40%, 50%, 75%, 100%, 200% or even more than 500%, compared to a wild-type microorganism, i.e. a microorganism which is not genetically altered.
  • genetically engineered or “genetically altered” means the scientific alteration of the structure of genetic material in a living organism. It involves the production and use of recombinant DNA. More in particular it is used to delineate the genetically engineered or modified organism from the naturally occurring organism. Genetic engineering may be done by a number of techniques known in the art, such as e.g. gene replacement, gene amplification, gene disruption, transfection, transformation using plasmids, viruses, or other vectors.
  • a genetically modified organism e.g. genetically modified microorganism, is also often referred to as a recombinant organism, e.g. recombinant microorganism.
  • the present invention provides a process for the direct production of Vitamin C comprising converting a substrate into Vitamin C. This may for instance be done in a medium comprising a microorganism, which may be a resting or a growing microorganism, preferably a resting microorganism.
  • substrates may be used as a carbon source in a process of the present invention, i.e. a process for direct conversion of a given substrate into Vitamin C such as e.g. mentioned above.
  • Particularly suited carbon sources are those that are easily obtainable from the D- glucose or D-sorbitol metabolization pathway such as, for example, D-glucose, D-sorbitol, L-sorbose, L-sorbosone, 2-keto-L-gulonate, D-gluconate, 2-keto-D-gluconate or 2,5- diketo-gluconate.
  • the substrate is selected from for instance D-glucose, D- sorbitol, L-sorbose or L-sorbosone, more preferably from D-glucose, D-sorbitol or L- sorbose, and most preferably from D-sorbitol, L-sorbose or L-sorbosone.
  • substrate and "production substrate” in connection with the above process using a microorganism is used interchangeably herein.
  • a medium as used herein for the above process using a microorganism may be any suitable medium for the production of Vitamin C.
  • the medium is an aqueous medium comprising for instance salts, substrate(s), and a certain pH.
  • the medium in which the substrate is converted into Vitamin C is also referred to as the production medium.
  • “Fermentation” or “production” or “fermentation process” as used herein may be the use of growing cells using media, conditions and procedures known to the skilled person, or the use of non-growing so-called resting cells, after they have been cultivated by using media, - 11 - 24654 conditions and procedures known to the skilled person, under appropriate conditions for the conversion of suitable substrates into desired products such as Vitamin C.
  • resting cells are used for the production of Vitamin C.
  • direct fermentation is intended to mean that a microorganism is capable of the conversion of a certain substrate into the specified product by means of one or more biological conversion steps, without the need of any additional chemical conversion step.
  • direct conversion of D-sorbitol into Vitamin C is intended to describe a process wherein a microorganism is producing Vitamin C and wherein D-sorbitol is offered as a carbon source without the need of an intermediate chemical conversion step.
  • a single microorganism capable of directly fermenting Vitamin C is preferred. Said microorganism is cultured under conditions which allow such conversion from the substrate as defined above.
  • microorganisms also include synonyms or basonyms of such species having the same physiological properties, as defined by the International Code of Nomenclature of Prokaryotes.
  • the nomenclature of the microorganisms as used herein is the one officially accepted (at the filing date of the priority application) by the International Committee on Systematics of Prokaryotes and the Bacteriology and Applied Microbiology Division of the International Union of Microbiological Societies, and published by its official publication vehicle International Journal of Systematic and Evolutionary Microbiology (IJSEM).
  • resting cells refer to cells of a microorganism which are for instance viable but not actively growing, or which are growing at low specific growth rates, for instance, growth rates that are lower than 0.02 h "1 , preferably lower than 0.01 h "1 . Cells which show the above growth rates are said to be in a "resting cell mode”.
  • step (a) or growth phase a first step
  • step (b) the growth rate of the microorganism
  • step (b) the production of Vitamin C from the substrate using the (b)
  • Growth and production phase as performed in the above process using a microorganism may be performed in the same vessel, i.e., only one vessel, or in two or more different vessels, with an optional cell separation step between the two phases.
  • the produced Vitamin C can be recovered from the cells by any suitable means. Recovering means for instance that the produced Vitamin C may be separated from the production medium.
  • the thus produced Vitamin C may be further processed.
  • growth phase For the purpose of the present invention relating to the above process using a microorganism, the terms “growth phase”, “growing step”, “growth step” and “growth period” are used interchangeably herein. The same applies for the terms “production phase”, “production step”, “production period”.
  • One way of performing the above process using a microorganism as of the present invention may be a process wherein the microorganism is grown in a first vessel, the so- called growth vessel, as a source for the resting cells, and at least part of the cells are transferred to a second vessel, the so-called production vessel.
  • the conditions in the production vessel may be such that the cells transferred from the growth vessel become resting cells as defined above. Vitamin C is produced in the second vessel and recovered therefrom.
  • the growing step can be performed in an aqueous medium, i.e. the growth medium, supplemented with appropriate nutrients for growth under aerobic conditions.
  • the cultivation may be conducted, for instance, in batch, fed-batch, semi-continuous or continuous mode.
  • the cultivation period may vary depending on for instance the host, pH, temperature and nutrient medium to be used, and maybe for instance about 10 h to about 10 days, preferably about 1 to about 10 days, more preferably about 1 to about 5 days when run in batch or fed-batch mode, depending on the microorganism.
  • the residence time may be for instance from about 2 to about 100 h, preferably from about 2 to about 50 h, depending on the microorganism.
  • the cultivation may be conducted for instance at a pH of about 3.0 to about 9.0, preferably about 4.0 to about 9.0, more preferably about 4.0 to about 8.0, even more preferably about 5.0 to about 8.0.
  • algae or yeast are used, the cultivation may be conducted, for instance, at a pH below about 7.0, preferably below about 6.0, more preferably below about 5.5, and most preferably below about 5.0.
  • a suitable temperature range for carrying out the cultivation using bacteria may be for instance from about 13 0 C to about 40°C, preferably from about 18 0 C to about 37°C, more preferably from about 13 0 C to about 36°C, and most preferably from about 18°C to about 33°C. If algae or yeast are used, a suitable temperature range for carrying out the cultivation may be for instance from about 15 0 C to about 4O 0 C, preferably from about - 13 - 24654
  • the culture medium for growth usually may contain such nutrients as assimilable carbon sources, e.g., glycerol, D-mannitol, D-sorbitol, L-sorbose, erythritol, ribitol, xylitol, arabitol, inositol, dulcitol, D-ribose, D-fractose, D-glucose, sucrose, and ethanol, preferably L-sorbose, D-glucose, D-sorbitol, D-mannitol, glycerol and ethanol; and digestible nitrogen sources such as organic substances, e.g., peptone, yeast extract and amino acids.
  • assimilable carbon sources e.g., glycerol, D-mannitol, D-sorbitol, L-sorbose, erythritol, ribitol, xylitol, arabitol, inos
  • the media may be with or without urea and/or corn steep liquor and/or baker's yeast.
  • Various inorganic substances may also be used as nitrogen sources, e.g., nitrates and ammonium salts.
  • the growth medium usually may contain inorganic salts, e.g., magnesium sulfate, manganese sulfate, potassium phosphate, and calcium carbonate.
  • inorganic salts e.g., magnesium sulfate, manganese sulfate, potassium phosphate, and calcium carbonate.
  • Cells obtained using the procedures described above can then be further incubated at essentially the same modes, temperature and pH conditions as described above, in the presence of substrates such as D-sorbitol, L-sorbose, or D-glucose, in such a way that they convert these substrates directly into Vitamin C.
  • Incubation can be done in a nitrogen-rich medium, containing, for example, organic nitrogen sources, e.g., peptone, yeast extract, baker's yeast, urea, amino acids, and corn steep liquor, or inorganic nitrogen sources, e.g., nitrates and ammonium salts, in which case cells will be able to further grow while producing Vitamin C.
  • organic nitrogen sources e.g., peptone, yeast extract, baker's yeast, urea, amino acids, and corn steep liquor
  • inorganic nitrogen sources e.g., nitrates and ammonium salts
  • incubation can be done in a nitrogen-poor medium, in which case cells will not grow substantially, and will be in a resting cell mode, or biotransformation mode.
  • the incubation medium may also contain inorganic salts, e.g., magnesium sulfate, manganese sulfate, potassium phosphate, and calcium chloride.
  • the specific growth rates are for instance at least 0.02 h "1 .
  • the growth rate depends on for instance the composition of the growth medium, pH, temperature, and the like.
  • the growth rates may be for instance in a range from about 0.05 to about 0.2 h "1 , preferably from about 0.06 to about 0.15 h "1 , and most preferably from about 0.07 to about 0.13 h "1 .
  • resting cells may be provided by cultivation of the respective microorganism on agar plates thus serving as growth vessel, using essentially the same conditions, e.g., cultivation period, pH, temperature, nutrient medium as described above, with the addition of agar agar.
  • the cells from the growth phase may be harvested or concentrated and transferred to a second vessel, the so-called production vessel.
  • This vessel may contain an aqueous medium supplemented with any applicable - 14 - 24654 production substrate that can be converted to Vitamin C by the cells.
  • Cells from the growth vessel can be harvested or concentrated by any suitable operation, such as for instance centrifugation, membrane crossflow ultrafiltration or microfiltration, filtration, decantation, flocculation.
  • the cells thus obtained may also be transferred to the production vessel in the form of the original broth from the growth vessel, without being harvested, concentrated or washed, i.e. in the form of a cell suspension.
  • the cells are transferred from the growth vessel to the production vessel in the form of a cell suspension without any washing or isolating step in-between.
  • cells may be grown under appropriate conditions to the desired cell density followed by a replacement of the growth medium with the production medium containing the production substrate.
  • Such replacement may be, for instance, the feeding of production medium to the vessel at the same time and rate as the withdrawal or harvesting of supernatant from the vessel.
  • operations for cell recycling or retention may be used, such as for instance cell recycling steps.
  • recycling steps include but are not limited to methods using centrifuges, filters, membrane crossflow microfiltration of ultrafiltration steps, membrane reactors, flocculation, or cell immobilization in appropriate porous, non-porous or polymeric matrixes.
  • the aqueous medium in the production vessel as used for the production step in connection with the above process using a microorganism, hereinafter called production medium may contain only the production substrate(s) to be converted into Vitamin C, or may contain for instance additional inorganic salts, e.g., sodium chloride, calcium chloride, magnesium sulfate, manganese sulfate, potassium phosphate, calcium phosphate, and calcium carbonate.
  • the production medium may also contain digestible nitrogen sources such as for instance organic substances, e.g., peptone, yeast extract, urea, amino acids, and corn steep liquor, and inorganic substances, e.g.
  • the medium may be with or without urea and/or corn steep liquor and/or baker's yeast.
  • the production step may be conducted for instance in batch, fed-batch, semi-continuous or continuous mode. In case of fed-batch, semi-continuous or continuous mode, both cells from the growth vessel and production medium can be fed continuously - 15 - 24654 or intermittently to the production vessel at appropriate feed rates. Alternatively, only production medium may be fed continuously or intermittently to the production vessel, while the cells coming from the growth vessel are transferred at once to the production vessel.
  • the cells coming from the growth vessel may be used as a cell suspension within the production vessel or may be used as for instance flocculated or immobilized cells in any solid phase such as porous or polymeric matrixes.
  • the production period defined as the period elapsed between the entrance of the substrate into the production vessel and the harvest of the supernatant containing Vitamin C, the so-called harvest stream, can vary depending for instance on the kind and concentration of cells, pH, temperature and nutrient medium to be used, and is preferably about 2 to about 100 h.
  • the pH and temperature can be different from the pH and temperature of the growth step, but is essentially the same as for the growth step.
  • the production step is conducted in continuous mode, meaning that a first feed stream containing the cells from the growth vessel and a second feed stream containing the substrate is fed continuously or intermittently to the production vessel.
  • the first stream may either contain only the cells isolated/separated from the growth medium or a cell suspension, coming directly from the growth step, i.e. cells suspended in growth medium, without any intermediate step of cell separation, washing and/or isolating.
  • the second feed stream as herein defined may include all other feed streams necessary for the operation of the production step, e.g. the production medium comprising the substrate in the form of one or several different streams, water for dilution, and base for pH control.
  • the ratio of the feed rate of the first stream to feed rate of the second stream may vary between about 0.01 and about 10, preferably between about 0.01 and about 5, most preferably between about 0.02 and about 2. This ratio is dependent on the concentration of cells and substrate in the first and second stream, respectively.
  • Another way of performing the process as above using a microorganism of the present invention may be a process using a certain cell density of resting cells in the production vessel.
  • the cell density is measured as absorbance units (optical density) at 600 nm by methods known to the skilled person.
  • the cell density in the production step is at least about 10, more preferably between about 10 and about 200, even more preferably between about 15 and about 200, even more preferably between about 15 to about 120, and most preferably between about 20 and about 120.
  • any means known in the art may be used, such as for instance cell recycling by centrifugation, filtration, membrane crossflow ultrafiltration of microfiltration, decantation, flocculation, cell retention in the vessel by membrane devices or cell immobilization.
  • the cell density in the production vessel may be kept at a constant level by, for instance, harvesting an amount of cells from the production vessel corresponding to the amount of cells being fed from the growth vessel.
  • the produced Vitamin C contained in the so-called harvest stream is recovered/harvested from the production vessel.
  • the harvest stream may include, for instance, cell-free or cell-containing aqueous solution coming from the production vessel, which contains Vitamin C as a result of the conversion of production substrate by the resting cells in the production vessel.
  • Cells still present in the harvest stream may be separated from the Vitamin C by any operations known in the art, such as for instance filtration, centrifugation, decantation, membrane crossflow ultrafiltration or microfiltration, tangential flow ultrafiltration or microfiltration or dead end filtration. After this cell separation operation, the harvest stream is essentially free of cells.
  • the process of the present invention may be combined with further steps of separation and/or purification of the produced Vitamin C from other components contained in the harvest stream, i.e., so-called downstream processing steps.
  • steps may include any means known to a skilled person, such as, for instance, concentration, crystallization, precipitation, adsorption, ion exchange, electrodialysis, bipolar membrane electrodialysis and/or reverse osmosis.
  • Vitamin C may be further purified as the free acid form or any of its known salt forms by means of operations such as for instance treatment with activated carbon, ion exchange, adsorption and elution, concentration, crystallization, filtration and drying.
  • a first separation of Vitamin C from other components in the harvest stream might be performed by any suitable combination or repetition of, for instance, the following methods: two- or three-compartment electrodialysis, bipolar membrane electrodialysis, reverse osmosis or adsorption on, for instance, ion exchange resins or non-ionic resins. If the resulting form of Vitamin C is a salt of L-ascorbic acid, conversion of the salt form into the free acid form maybe performed by for instance bipolar membrane electrodialysis, ion exchange, simulated moving bed chromatographic techniques, and the like.
  • Combination of the mentioned steps, e.g., electrodialysis and bipolar membrane electrodialysis into one step might be also used as well as combination of the mentioned steps e.g. several steps of ion exchange by using simulated moving bed chromatographic methods. Any of these procedures alone or in combination constitute a - 17 - 24654 convenient means for isolating and purifying the product, i.e. Vitamin C.
  • the product thus obtained may further be isolated in a manner such as, e.g. by concentration, crystallization, precipitation, washing and drying of the crystals and/or further purified by, for instance, treatment with activated carbon, ion exchange and/or re-crystallization.
  • Vitamin C is purified from the harvest stream by a series of downstream processing steps as described above without having to be transferred to a nonaqueous solution at any time of this processing, i.e. all steps are performed in an aqueous environment.
  • Such preferred downstream processing procedure may include for instance the concentration of the harvest stream coming from the production vessel by means of two- or three-compartment electrodialysis, conversion of Vitamin C in its salt form present in the concentrated solution into its acid form by means of bipolar membrane electrodialysis and/or ion exchange, purification by methods such as for instance treatment with activated carbon, ion exchange or non-ionic resins, followed by a further concentration step and crystallization. These crystals can be separated, washed and dried. If necessary, the crystals may be again re-solubilized in water, treated with activated carbon and/or ion exchange resins and recrystallized. These crystals can then be separated, washed and dried.
  • sequence of the gene comprising a nucleotide sequence according to SEQ ID NO.l encoding a RCS 28 protein was determined by sequencing a genomic clone obtained from Gluconobacter oxydans DSM 17078.
  • the invention also relates to a polynucleotide encoding at least a biologically active fragment or derivative of a RCS 28 polypeptide as shown in SEQ ID NO.2.
  • biologically active fragment or derivative means a polypeptide which retains essentially the same biological function or activity as the polypeptide shown in SEQ ID NO:2.
  • biological activity may for instance be enzymatic activity, signaling activity or antibody reactivity.
  • standard biological function or “functional equivalent” as used herein means that the protein has essentially the same biological activity, e.g. enzymatic, signaling or antibody reactivity, as a polypeptide shown in SEQ ID NO:2.
  • polypeptides and polynucleotides of the present invention are preferably provided in an isolated form, and preferably are purified to homogeneity. - 18 - 24654
  • isolated means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring).
  • a naturally-occurring polynucleotide or polypeptide present in a living microorganism is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated.
  • Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition and still be isolated in that such vector or composition is not part of its natural environment.
  • An isolated polynucleotide or nucleic acid as used herein may be a DNA or RNA that is not immediately contiguous with both of the coding sequences with which it is immediately contiguous (one on the 5'-end and one on the 3'-end) in the naturally occurring genome of the organism from which it is derived.
  • a nucleic acid includes some or all of the 5'-non-coding (e.g., promoter) sequences that are immediately contiguous to the coding sequence.
  • isolated polynucleotide therefore includes, for example, a recombinant DNA that is incorporated into a vector, into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA or a genomic DNA fragment produced by PCR or restriction endonuclease treatment) independent of other sequences. It also includes a recombinant DNA that is part of a hybrid gene encoding an additional polypeptide that is substantially free of cellular material, viral material, or culture medium (when produced by recombinant DNA techniques), or chemical precursors or other chemicals (when chemically synthesized). Moreover, an "isolated nucleic acid fragment” is a nucleic acid fragment that is not naturally occurring as a fragment and would not be found in the natural state.
  • polynucleotide As used herein, the terms “polynucleotide”, “gene” and “recombinant gene” refer to nucleic acid molecules which may be isolated from chromosomal DNA, which include an open reading frame encoding a protein, e.g. G. oxydans DSM 17078 RCS proteins.
  • a polynucleotide may include a polynucleotide sequence as shown in SEQ ID NO:1 or fragments thereof and regions upstream and downstream of the gene sequences which may include, for example, promoter regions, regulator regions and terminator regions important for the appropriate expression and stabilization of the polypeptide derived thereof.
  • a gene may include coding sequences, non-coding sequences such as for instance untranslated sequences located at the 3'- and 5 '-ends of the coding region of a gene, and regulatory sequences. Moreover, a gene refers to an isolated nucleic acid molecule as defined herein. It is furthermore appreciated by the skilled person that DNA sequence polymorphisms that lead to changes in the amino acid sequences of RCS proteins may exist within a population, e.g., the Gluconobacter oxydans population. Such genetic polymorphism in the RCS 28 gene may exist among individuals within a population due to - 19 - 24654 natural variation or in cells from different populations.
  • Such natural variations can typically result in 1-5% variance in the nucleotide sequence of the RCS 28 gene. Any and all such nucleotide variations and the resulting amino acid polymorphism in RCS 28 are the result of natural variation and that do not alter the functional activity of RCS proteins are intended to be within the scope of the invention.
  • nucleic acid molecule As used herein, the terms “polynucleotide” or “nucleic acid molecule” are intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs.
  • the nucleic acid molecule may be single-stranded or double-stranded, but preferably is double-stranded DNA.
  • the nucleic acid may be synthesized using oligonucleotide analogs or derivatives (e.g., inosine or phosphorothioate nucleotides). Such oligonucleotides may be used, for example, to prepare nucleic acids that have altered base-pairing abilities or increased resistance to nucleases.
  • sequence information as provided herein should not be so narrowly construed as to require inclusion of erroneously identified bases.
  • the specific sequences disclosed herein may be readily used to isolate the complete gene from a recombinant or non-recombinant microorganism capable of converting a given carbon source directly into Vitamin C, in particular Gluconobacter oxydans, preferably Gluconobacter oxydans DSM 17078 which in turn may easily be subjected to further sequence analyses thereby identifying sequencing errors.
  • nucleotide sequences determined by sequencing a DNA molecule herein were determined using an automated DNA sequencer and all amino acid sequences of polypeptides encoded by DNA molecules determined herein were predicted by translation of a DNA sequence determined as above. Therefore, as is known in the art for any DNA sequence determined by this automated approach, any nucleotide sequence determined herein may contain some errors. Nucleotide sequences determined by automation are typically at least about 90% identical, more typically at least about 95% to at least about 99.9% identical to the actual nucleotide sequence of the sequenced DNA molecule. The actual sequence may be more precisely determined by other approaches including manual DNA sequencing methods well known in the art.
  • a single insertion or deletion in a determined nucleotide sequence compared to the actual sequence will cause a frame shift in translation of the nucleotide sequence such that the predicted amino acid sequence encoded by a determined nucleotide sequence will be completely different from the amino acid sequence actually encoded by the sequenced DNA molecule, beginning at the point of such an insertion or deletion.
  • a nucleic acid molecule according to the invention may comprise only a portion or a fragment of the nucleic acid sequence provided by the present invention, such as for instance the sequence shown in SEQ ID NO: 1 , for example a fragment which may be used as a probe or primer such as for instance SEQ ID NO:3 or SEQ ID NO.4 or a fragment encoding a portion of a protein according to the invention.
  • the nucleotide sequence determined from the cloning of the RCS 28 gene allows for the generation of probes and primers designed for use in identifying and/or cloning other RCS 28 family members, as well as RCS 28 homologues from other species.
  • the probe/primer typically comprises substantially purified oligonucleotides which typically comprises a region of nucleotide sequence that hybridizes preferably under highly stringent conditions to at least about 12 or 15, preferably about 18 or 20, more preferably about 22 or 25, even more preferably about 30, 35, 40, 45, 50, 55, 60, 65, or 75 or more consecutive nucleotides of a nucleotide sequence shown in SEQ ID NO: 1 or a fragment or derivative thereof.
  • a nucleic acid molecule encompassing all or a portion of the nucleic acid sequence of SEQ ID NO:1 may be also isolated by the polymerase chain reaction (PCR) using synthetic oligonucleotide primers designed based upon the sequence information contained herein.
  • PCR polymerase chain reaction
  • a nucleic acid of the invention may be amplified using cDNA, niRNA or alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques.
  • the nucleic acid thus amplified may be cloned into an appropriate vector and characterized by DNA sequence analysis.
  • Fragments of a polynucleotide according to the invention may also comprise polynucleotides not encoding functional polypeptides. Such polynucleotides may function as probes or primers for a PCR reaction.
  • Nucleic acids according to the invention may be used as hybridization probes or polymerase chain reaction (PCR) primers.
  • Uses of the nucleic acid molecules of the present invention that do not encode a polypeptide having a RCS 28 activity include, inter alia, (1) isolating the gene encoding the protein of the present invention, or allelic variants thereof from a cDNA library, e.g., from other organisms than Gluconobacter oxydans and (2) Northern blot analysis for detecting expression of niRNA of said protein in specific cells or (3) use in enhancing and/or improving the function or activity of homologous RCS 28 genes in said other organisms.
  • PCR polymerase chain reaction
  • Probes based on the nucleotide sequences provided herein may be used to detect transcripts or genomic sequences encoding the same or homologous proteins for instance in other organisms.
  • Nucleic acid molecules corresponding to natural variants and non-G. oxydans homologues of the G. oxydans RCS 28 DNA of the invention which are also embraced by the present invention may be isolated based on their homology to the G. oxydans RCS 28 nucleic acid disclosed herein using the G. oxydans DNA, or a portion thereof, as a hybridization probe according to standard hybridization techniques, preferably under highly stringent hybridization conditions.
  • the probe further comprises a label group attached thereto, e.g., the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme cofactor.
  • the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme cofactor.
  • Homologous gene sequences may be isolated, for example, by performing PCR using two degenerate oligonucleotide primer pools designed on the basis of nucleotide sequences as taught herein.
  • the template for the reaction may be cDNA obtained by reverse transcription of mRNA prepared from strains known or suspected to express a polynucleotide according to the invention.
  • the PCR product may be subcloned and sequenced to ensure that the amplified sequences represent the sequences of a new nucleic acid sequence as described herein, or a functional equivalent thereof.
  • the PCR fragment may then be used to isolate a full length cDNA clone by a variety of known methods.
  • the amplified fragment may be labeled and used to screen a bacteriophage or cosmid cDNA library.
  • the labeled fragment may be used to screen a genomic library.
  • RNA may be isolated, following standard procedures, from an appropriate cellular or tissue source.
  • a reverse transcription reaction may be performed on the RNA using an oligonucleotide primer specific for the most 5'-end of the amplified fragment for the priming of first strand synthesis.
  • RNA/DNA hybrid may then be "tailed" (e.g., with guanines) using a standard terminal transferase reaction, the hybrid may be digested with RNaseH, and second strand synthesis may then be primed (e.g., with a poly-C primer).
  • second strand synthesis may then be primed (e.g., with a poly-C primer).
  • cDNA sequences upstream of the amplified fragment may easily be isolated.
  • nucleic acids encoding other RCS 28 family members which thus have a nucleotide sequence that differs from a nucleotide sequence according to SEQ ID NO:1 are within the scope of the invention.
  • nucleic acids encoding RCS 28 proteins from different species which thus may have a nucleotide sequence which differs from a nucleotide sequence shown in SEQ ID NO: 1 are within the scope of the invention.
  • the invention also relates to an isolated polynucleotide hybridisable under stringent conditions, preferably under highly stringent conditions, to a polynucleotide as of the present invention, such as for instance a polynucleotide shown in SEQ ID NO: 1.
  • a polynucleotide as of the present invention such as for instance a polynucleotide shown in SEQ ID NO: 1.
  • such polynucleotide may be obtained from a microorganism capable of converting a given carbon source directly into Vitamin C, in particular Gluconobacter oxydans, preferably Gluconobacter oxydans DSM 17078.
  • hybridizing is intended to describe conditions for hybridization and washing under which nucleotide sequences at least about 50%, at least about 60%, at least about 70%, more preferably at least about 80%, even more preferably at least about 85% to 90%, most preferably at least 95% homologous to each other typically remain hybridized to each other.
  • a nucleic acid of the invention is at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more homologous to a nucleic acid sequence shown in SEQ ID NO:1 or the complement thereof.
  • a preferred, non-limiting example of stringent hybridization conditions are hybridization in 6x sodium chloride/sodium citrate (SSC) at about 45 0 C, followed by one or more washes in Ix SSC, 0.1% SDS at 50°C, preferably at 55°C, more preferably at 60 0 C and even more preferably at 65 0 C.
  • SSC sodium chloride/sodium citrate
  • Highly stringent conditions include incubations at 42°C for a period of several days, such as 2-4 days, using a labeled DNA probe, such as a digoxigenin (DIG)-labeled DNA probe, followed by one or more washes in 2x SSC, 0.1% SDS at room temperature and one or more washes in 0.5x SSC, 0.1% SDS or O.lx SSC, 0.1% SDS at 65-68 0 C.
  • highly stringent conditions include, for example, 2 h to 4 days incubation at 42 0 C using a DIG-labeled DNA probe (prepared by e.g.
  • an isolated nucleic acid molecule of the invention that hybridizes under preferably highly stringent conditions to a nucleotide sequence of the invention corresponds to a naturally-occurring nucleic acid molecule.
  • a "naturally- occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).
  • the nucleic acid encodes a natural G. oxydans RCS 28 protein.
  • a polynucleotide which hybridizes only to a poly (A) sequence such as the 3 '-terminal poly (A) tract of mRNAs), or to a complementary stretch of T (or U) residues, would not be included in a polynucleotide of the invention used to specifically hybridize to a portion of a nucleic acid of the invention, since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly (A) stretch or the complement thereof (e.g., practically any double-stranded cDNA clone).
  • genomic DNA or cDNA libraries constructed from other organisms e.g. microorganisms capable of converting a given carbon source directly into Vitamin C, in particular other Gluconobacter species may be screened.
  • Gluconobacter strains may be screened for homologous polynucleotides by Southern and/or Northern blot analysis.
  • DNA libraries may be constructed from RNA isolated from the appropriate strain, utilizing standard techniques well known to those of skill in the art.
  • a total genomic DNA library may be screened using a probe hybridisable to a polynucleotide according to the invention.
  • a nucleic acid molecule of the present invention such as for instance a nucleic acid molecule shown in SEQ ID NO: 1 or a fragment or derivative thereof, may be isolated using standard molecular biology techniques and the sequence information provided herein.
  • nucleic acid molecules according to the invention maybe isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook, J., Fritsh, E. F. , and Maniatis, T. Molecular Cloning : A Laboratory Manual. - 24 - 24654
  • oligonucleotides corresponding to or hybridisable to nucleotide sequences according to the invention may be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
  • the terms “homology” or “percent identity” are used interchangeably herein. For the purpose of this invention, it is defined here that in order to determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps may be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position.
  • the two sequences are the same length.
  • the skilled person will be aware of the fact that several different computer programs are available to determine the homology between two sequences. For instance, a comparison of sequences and determination of percent identity between two sequences may be accomplished using a mathematical algorithm. In a preferred embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (J. MoI. Biol. (48): 444-453 (1970) ) algorithm which has been incorporated into the GAP program in the GCG software package (available at http://www.accelrys.com), using either a Blossom 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6 or 4 and a length weight of 1, 2, 3, 4, 5 or 6. The skilled person will appreciate that all these different parameters will yield slightly different results but that the overall percentage identity of two sequences is not significantly altered when using different algorithms.
  • the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at http://www.accelrys.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70 or 80 and a length weight of 1, 2, 3, 4, 5 or 6.
  • the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Meyers and W.
  • the nucleic acid and protein sequences of the present invention may further be used as a "query sequence" to perform a search against public databases to, for example, identify other family members or related sequences.
  • Such searches may be performed using the BLASTN and BLASTX programs (version 2.0) of Altschul, et al. (1990) J. MoI. Biol. 215:403-10.
  • Gapped BLAST may be utilized as described in Altschul et al., (1997) Nucleic Acids Res. 25 (17): 3389-3402.
  • the default parameters of the respective programs e.g., BLASTX and BLASTN
  • BLASTX and BLASTN the default parameters of the respective programs
  • an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is the complement of a nucleotide sequence as of the present invention, such as for instance the sequence shown in SEQ ID NO:1.
  • a nucleic acid molecule, which is complementary to a nucleotide sequence disclosed herein, is one that is sufficiently complementary to a nucleotide sequence shown in SEQ ID NO: 1 such that it may hybridize to said nucleotide sequence thereby forming a stable duplex.
  • a nucleic acid of the invention as shown in SEQ ID NO:1 or the complement thereof contains at least one mutation leading to a gene product with modified function/activity.
  • the at least one mutation may be introduced by methods described herein.
  • the at least one mutation leads to a RCS 28 protein whose function compared to the wild type counterpart is completely or partially destroyed. Methods for introducing such mutations are well known in the art.
  • reduction of activity encompasses decreasing activity of one or more polypeptides in the producing organism, which in turn are encoded by the corresponding polynucleotides described herein.
  • RCS 28 protein There are a number of methods available in the art to accomplish reduction of activity of a given protein, in this case the RCS 28 protein. In general, the specific activity of a protein may be decreased or the copy number of the protein maybe decreased.
  • the copy number of the genes corresponding to the polynucleotides described herein may be decreased, such as for instance by - 26 - 24654 underexpression or disruption of a gene.
  • a gene is said to be "underexpressed” if the level of transcription of said gene is reduced in comparison to the wild type gene. This may be measured by for instance Northern blot analysis quantifying the amount of mRNA as an indication for gene expression.
  • a gene is underexpressed if the amount of generated mRNA is decreased by at least 1%, 2%, 5% 10%, 25%, 50%, 75%, 100%, 200% or even more than 500%, compared to the amount of mRNA generated from a wild-type gene.
  • a weak promoter may be used to direct the expression of the polynucleotide
  • the promoter, regulatory region and/or the ribosome binding site upstream of the gene can be altered to achieve the down-expression.
  • the expression may also be reduced by decreasing the relative half-life of the messenger RNA.
  • the activity of the polypeptide itself may be decreased by employing one or more mutations in the polypeptide amino acid sequence, which decrease the activity. For example, altering the affinity of the polypeptide for its corresponding substrate may result in reduced activity.
  • the relative half-life of the polypeptide may be decreased.
  • the reduction may be achieved by altering the composition of the cell culture media and/or methods used for culturing.
  • “Reduced expression” or “reduced activity” as used herein means a decrease of at least 5%, 10%, 25%, 50%, 75%, 100%, 200% or even more than 500%, compared to a wild-type protein, polynucleotide, gene; or the activity and/or the concentration of the protein present before the polynucleotides or polypeptides are reduced.
  • the activity of the RCS 28 protein may also be reduced by contacting the protein with a specific or general inhibitor of its activity.
  • the terms “reduced activity”, “decreased or abolished activity” are used interchangeably herein.
  • vectors containing a nucleic acid encoding a protein according to the invention or a functional equivalent or portion thereof.
  • vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • plasmid refers to a circular double stranded DNA loop into which additional DNA segments may be ligated.
  • viral vector Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication). Other vectors are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome.
  • the recombinant vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vector includes one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic - 27 - 24654 acid sequence to be expressed.
  • "operatively linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).
  • regulatory sequence is intended to include promoters, enhancers and other expression control elements (e.g., attenuator). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Regulatory sequences include those which direct constitutive or inducible expression of a nucleotide sequence in many types of host cells and those which direct expression of the nucleotide sequence only in a certain host cell (e.g. tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc.
  • the expression vectors of the invention may be introduced into host cells to thereby produce proteins or peptides, encoded by nucleic acids as described herein, including, but not limited to, mutant proteins, fragments thereof, variants or functional equivalents thereof, and fusion proteins, encoded by a nucleic acid as described herein, e.g., RCS 28 proteins, mutant forms of RCS 28 proteins, fusion proteins and the like.
  • the recombinant expression vectors of the invention may be designed for expression of RCS 28 proteins in a suitable microorganism.
  • a protein according to the invention may be expressed in bacterial cells such as strains belonging to the genera Gluconobacter, Gluconacetobacter or Acetobacter.
  • Expression vectors useful in the present invention include chromosomal-, episomal- and virus-derived vectors e.g., vectors derived from bacterial plasmids, bacteriophage, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids.
  • the DNA insert may be operatively linked to an appropriate promoter, which may be either a constitutive or inducible promoter.
  • an appropriate promoter which may be either a constitutive or inducible promoter.
  • the skilled person will know how to select suitable promoters.
  • the expression constructs may contain sites for transcription initiation, termination, and, in the transcribed region, a ribosome binding site for translation.
  • the coding portion of the mature transcripts expressed by the constructs may preferably include an initiation codon at the beginning and a termination codon appropriately positioned at the end of the polypeptide to be translated.
  • Vector DNA may be introduced into suitable host cells via conventional transformation or transfection techniques.
  • transformation transformation
  • transconjugation and “transfection” are intended to refer to a variety of art-recognized techniques for - 28 - 24654 introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, transduction, infection, lipofection, cationic lipidmediated transfection or electroporation.
  • Suitable methods for transforming or transfecting host cells may be found in Sambrook, et al. (supra), Davis et al., Basic Methods in Molecular Biology (1986) and other laboratory manuals.
  • a gene that encodes a selectable marker is generally introduced into the host cells along with the gene of interest.
  • selectable markers include those that confer resistance to drugs, such as kanamycin, tetracycline, ampicillin and streptomycin.
  • a nucleic acid encoding a selectable marker is preferably introduced into a host cell on the same vector as that encoding a protein according to the invention or can be introduced on a separate vector such as, for example, a suicide vector, which cannot replicate in the host cells. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g. , cells that have incorporated the selectable marker gene will survive, while the other cells die).
  • the invention provides also an isolated polypeptide having the amino acid sequence shown in SEQ ID NO:2 or an amino acid sequence obtainable by expressing a polynucleotide of the present invention, such as for instance a polynucleotide sequence shown in SEQ ID NO: 1 in an appropriate host.
  • Polypeptides according to the invention may contain only conservative substitutions of one or more amino acids in the amino acid sequence represented by SEQ ID NO:2 or substitutions, insertions or deletions of non-essential amino acids.
  • a nonessential amino acid is a residue that may be altered in the amino acid sequences shown in SEQ ID NO:2 without substantially altering the biological function.
  • amino acid residues that are conserved among the proteins of the present invention are predicted to be particularly unamenable to alteration.
  • amino acids conserved among the proteins according to the present invention and other RCS 28 proteins are not likely to be amenable to alteration.
  • substitution is intended to mean that a substitution in which the amino acid residue is replaced with an amino acid residue having a similar side chain.
  • These families are known in the art and include amino acids with basic side chains (e.g., lysine, arginine and histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), non-polar side chains (e.g., alanine, valine, leucine, isoleucine, proline, - 29 - 24654 phenylalanine, methionine, tryptophan), beta-branched side chains ⁇ e.g., threonine, valine, isoleucine) and aromatic side chains ⁇ e.g., tyrosine, phenylalanine, tryptophan, histidine).
  • basic side chains
  • the polynucleotides of the invention may be utilized in the genetic engineering of a suitable host cell to make it better and more efficient in the fermentation, for example in a direct fermentation process for Vitamin C.
  • a genetically engineered/recombinantly produced host cell (also referred to as recombinant cell or transformed cell) carrying such a modified polynucleotide wherein the function of the linked protein is significantly modified in comparison to a wild-type cell such that the yield, production and/or efficiency of production of one or more fermentation products such as Vitamin C is improved.
  • the host cell may be selected from a microorganism capable of directly producing one or more fermentation products such as for instance Vitamin C from a given carbon source, in particular Gluconobacter oxydans, preferably G. oxydans DSM 17078.
  • a “transformed cell” or “recombinant cell” is a cell into which (or into an ancestor of which) has been introduced, by means of recombinant DNA techniques, a nucleic acid according to the invention, or wherein the activity of the RCS 28 protein has been decreased or abolished.
  • Suitable host cells include cells of microorganisms capable of producing a given fermentation product, e.g., converting a given carbon source directly into Vitamin C.
  • strains from the genera Pseudomonas, Pantoea, Escherichia, Corynebacterium, Ketogulonicigenium and acetic acid bacteria like e.g., Gluconobacter, Acetobacter or Gluconacetobacter, preferably Acetobacter sp., Acetobacter aceti, Gluconobacter frateurii, Gluconobacter cerinus, Gluconobacter thailandicus, Gluconobacter oxydans, more preferably G. oxydans, most preferably G. oxydans DSM 17078.
  • RCS 28 gene expression may be inhibited in that organism for instance by targeting nucleotide sequences complementary to the regulatory region of a RCS 28 nucleotide sequence ⁇ e.g., a RCS 28 promoter and/or enhancers) to form triple helical structures that prevent transcription of a RCS 28 gene in target cells.
  • nucleotide sequences complementary to the regulatory region of a RCS 28 nucleotide sequence ⁇ e.g., a RCS 28 promoter and/or enhancers
  • Inhibition or prevention of gene expression may also be achieved by modifying the RCS 28 gene, e.g., by introducing one or more mutations into the RCS 28gene wherein said modification leads to a RCS 28 protein with a function which is significantly decreased in comparison to the wild-type protein.
  • modifying the RCS 28 gene e.g., by introducing one or more mutations into the RCS 28gene wherein said modification leads to a RCS 28 protein with a function which is significantly decreased in comparison to the wild-type protein.
  • the polynucleotide carrying the at least one mutation is derived from a polynucleotide as represented by SEQ ID NO:1 or equivalents thereof.
  • a mutation as used herein may be any mutation leading to a less functional or unstable polypeptide, e.g. less functional or unstable RCS 28 gene products. This may include for instance an alteration in the genome of a microorganism, which interferes with the synthesis of RCS 28 or leads to the expression of a RCS 28 protein with an altered amino acid sequence whose function compared with the wild type counterpart having a non- altered amino acid sequence is completely or partially destroyed. The interference may occur at the transcriptional, translational or post-translational level.
  • the alteration in the genome of the microorganism may be obtained e.g. by replacing through a single or double crossover recombination a wild type DNA sequence by a DNA sequence containing the alteration.
  • the alteration may, e.g. be a DNA sequence encoding an antibiotic resistance marker or a gene complementing a possible auxotrophy of the microorganism.
  • Mutations include, but are not limited to, deletion- insertion mutations.
  • An example of such an alteration includes a gene disruption, i.e. a perturbation of a gene such that the product that is normally produced from this gene is not produced in a functional form.
  • the entire rnRNA for the gene is absent, in others the amount of mRNA produced varies.
  • the polypeptide encoded by said gene is not produced in a functional form, either absent or in a mutated form, such as e.g. a protein having reduced activity as defined herein.
  • An alteration in the genome of the microorganism leading to a less or non-functional polypeptide may also be obtained by randomly mutagenizing the genome of the microorganism using e.g. chemical mutagens, radiation or transposons and selecting or screening for mutants which are better or more efficient producers of one or more fermentation products. Standard methods for screening and selection are known to the skilled person.
  • the RCS 28 gene of the present invention i.e., wherein its gene expression is artificially suppressed in order to improve the yield, productivity, and/or efficiency of production of the fermentation product when introduced into a suitable host cell.
  • Methods of providing knockouts as well as microorganisms carrying such suppressed genes are well known in the art.
  • the suppression of the endogenous RCS 28 gene may be induced by deleting at least a part of - 31 - 24654 the gene or the regulatory region thereof.
  • "suppression of the gene expression” includes complete and partial suppression, as well as suppression under specific conditions and also suppression of the expression of either one of the two alleles.
  • the RCS 28 gene may be cloned and then a vector for homologous recombination may be constructed by using the gene to inactivate the endogenous RCS 28 gene in the target microorganism.
  • the vector for homologous recombination then contains a nucleic acid sequence designed to inactivate the endogenous RCS 28 gene in the target microorganism.
  • Such a nucleic acid may be for instance a nucleic acid sequence of the RCS 28 gene or the regulatory region thereof, such as the existing flanking region of the gene to be inactivated (in cis), or existing separately (in trans), containing at least a partial deletion, or alternatively it may be a nucleic acid sequence of the RCS 28 gene or the regulatory region thereof containing other genes.
  • a gene which can also function as a marker is preferably selected as the gene to be inserted into the RCS 28 gene or the regulatory region thereof.
  • the insert genes to be used include for instance drug-resistance genes as defined above.
  • in-frame silent deletions can be introduced by using, for example, the sacB system or long-flanking homology PCR. These techniques are well known to the person skilled in the art.
  • the aforementioned mutagenesis strategies for RCS 28 proteins may result in increased yields of a desired compound in particular Vitamin C.
  • This list is not meant to be limiting; variations on these mutagenesis strategies will be readily apparent to one of ordinary skill in the art.
  • the nucleic acid and protein molecules of the invention may be utilized to generate microorganisms such as Gluconobacter oxydans or related strains of bacteria expressing mutated RCS 28 nucleic acid and protein molecules such that the yield, productivity, and/or efficiency of production of a desired compound such as Vitamin C is improved.
  • the process of the present invention leads to yields of Vitamin C which are at least about more than 5.7 g/1, such as 10 g/1, 20 g/1, 50 g/1, 100 g/1, 200 g/1, 300 g/1, 400 g/1 or more than 600 g/1.
  • the yield of Vitamin C produced by the process of the present invention is in the range of from about more than 5.7 to about 600 g/1.
  • the yield of Vitamin C refers to the concentration of Vitamin C in the harvest stream coming directly out of the production vessel, i.e. the cell-free supernatant comprising the Vitamin C. - 32 - 24654
  • microorganisms in particular from the genera of Gluconobacter, Gluconacetobacter and Acetobacter are provided that are able to directly produce Vitamin C from a suitable carbon source like D-sorbitol and/or L-sorbose. When measured for instance in a resting cell method after an incubation period of 20 hours, these organisms were found to be able to produce Vitamin C directly from D-sorbitol or L- sorbose, even up to a level of 280 mg/1 and 670 mg/1 respectively.
  • a microorganism capable of directly producing Vitamin C in quantities of 300 mg/1 when starting from D-sorbitol or more or 800 mg/1 or more when starting from L-sorbose, respectively when for instance measured in a resting cell method after an incubation period of 20 hours. Such may be achieved by decreasing or abolishing the activity of a RCS polypeptide, preferably a RCS 28 polypeptide.
  • the yield of Vitamin C produced from D-sorbitol may even be as high as 400, 600, 1000 mg/1 or even exceed 1.5, 2, 4, 10, 20, 50 g/1.
  • the yield of Vitamin C produced from L-sorbose may even be as high as 1000 mg/1 or even exceed 1.5, 2, 4, 10, 20, 50 g/1.
  • these amounts of Vitamin C can be achieved when measured by resting cell method after an incubation period of 20 hours.
  • measurement in a "resting cell method” comprises (i) growing the cells by means of any method well know to the person skilled in the art, (ii) harvesting the cells from the growth broth, and (iii) incubating the harvested cells in a medium containing the substrate which is to be converted into the desired product, e.g. Vitamin C, under conditions where the cells do not grow any longer, i.e. there is no increase in the amount of biomass during this so-called conversion step.
  • a medium containing the substrate which is to be converted into the desired product e.g. Vitamin C
  • the recombinant microorganism carrying e.g. a modified RCS 28 gene and which is able to produce the fermentation product in significantly higher yield, productivity, and/or efficiency may be cultured in an aqueous medium supplemented with appropriate nutrients under aerobic conditions as described above.
  • nucleic acid molecules, polypeptides, vectors, primers, and recombinant microorganisms described herein may be used in one or more of the following methods: identification of Gluconobacter oxydans and related organisms; mapping of genomes of organisms related to Gluconobacter oxydans; identification and localization of
  • Gluconobacter oxydans sequences of interest sequences of interest; evolutionary studies; determination of RCS 28 protein regions required for function; modulation of a RCS 28 protein activity or function; modulation of the activity of a RCS pathway; and modulation of cellular production of a desired compound, such as Vitamin C.
  • the invention provides methods for screening molecules which modulate the activity of a RCS 28 protein, either by interacting with the protein itself or a substrate or binding - 33 - 24654 partner of the RCS 28 protein, or by modulating the transcription or translation of a RCS 28 nucleic acid molecule of the invention.
  • a microorganism expressing one or more RCS 28 proteins of the invention is contacted with one or more test compounds, and the effect of each test compound on the activity or level of expression of the RCS 28 protein is assessed.
  • the biological, enzymatic or other activity of RCS proteins can be measured by methods well known to a skilled person, such as, for example, by incubating a membrane fraction or cell-free extract containing the RCS protein in the presence of coenzyme Q2 (CoQ2), an artificial electron acceptor, and by measuring the consumption of oxygen by methods such as the Clark-type oxygen electrode (Rank Brothers, Cambridge, United Kingdom).
  • CoQ2 coenzyme Q2
  • the activity of ubiquinol oxidase bd can be measured in an assay where membrane fractions or cell-free extracts containing this enzyme are incubated in the presence of 50 mM phosphate buffer at pH 6.5, 0.02% of the detergent Tween20 and 100 ⁇ M cyanide in order to inactivate other cyanide-sensitive oxidases.
  • the enzyme reaction can then be started by addition of 30 mM of the reduced artificial electron acceptor, CoQ 2red , and followed by measuring the increase in absorbance at 275 run.
  • the rate of consumption of oxygen can be measured with help of the Clark- type electrode, and is directly proportional to the ubiquinol oxidase bd activity present in the membrane fraction or in the cell-free extract.
  • the fermentation product of the methods according to the invention may not be limited to Vitamin C alone.
  • the "desired compound” or “fermentation product” as used herein may be any natural product of Gluconobacter oxydans, which includes the final products and intermediates of biosynthesis pathways, such as for example L-sorbose, L-sorbosone, D-gluconate, 2-keto- D-gluconate, 5-keto-D-gluconate, 2,5-diketo-D-gluconate and 2-keto-L-gulonate (2- KGA), in particular the biosynthetic generation of Vitamin C.
  • the present invention is directed to the use of a polynucleotide, polypeptide, vector, primer and recombinant microorganism as described herein in the production of Vitamin C, i.e., the direct conversion of a carbon source into Vitamin C.
  • a modified polynucleotide, polypeptide, vector and recombinant microorganism as described herein is used for improving the yield, productivity, and/or efficiency of the production of Vitamin C.
  • production or “productivity” are art-recognized and include the concentration of the fermentation product (for example, Vitamin C) formed within a given time and a given fermentation volume (e.g., kg product per hour per liter).
  • efficiency of production includes the time required for a particular level of production to be achieved - 34 - 24654
  • yield is art-recognized and includes the efficiency of the conversion of the carbon source into the product (i.e., Vitamin C). This is generally ⁇ written as, for example, kg product per kg carbon source.
  • increasing the yield and/or production/productivity of the compound it is meant that the quantity of recovered molecules, or of useful recovered molecules of that compound in a given amount of culture over a given amount of time is increased.
  • biosynthesis or a “biosynthetic pathway” are art-recognized and include the synthesis of a compound, preferably an organic compound, by a cell from intermediate compounds in what may be a multistep and highly regulated process.
  • the language “metabolism” is art-recognized and includes the totality of the biochemical reactions that take place in an organism. The metabolism of a particular compound, then, (e.g., the metabolism of an amino acid such as glycine) comprises the overall biosynthetic, modification, and degradation pathways in the cell related to this compound.
  • transport or “import” is art-recognized and includes the facilitated movement of one or more molecules across a cellular membrane through which the molecule would otherwise either be unable to pass or be passed inefficiently.
  • Vitamin C as used herein maybe any chemical form of L-ascorbic acid found in aqueous solutions, such as for instance undissociated, in its free acid form or dissociated as an anion.
  • the solubilized salt form of L-ascorbic acid may be characterized as the anion in the presence of any kind of cations usually found in fermentation supernatants, such as for instance potassium, sodium, ammonium, or calcium.
  • isolated crystals of the free acid form of L-ascorbic acid are called by their corresponding salt name, i.e. sodium ascorbate, potassium ascorbate, calcium ascorbate and the like.
  • the present invention is related to a process for the production of Vitamin C wherein a nucleotide according to the invention or a modified polynucleotide sequence as described above is introduced into a suitable microorganism, the recombinant microorganism is cultured under conditions that allow the production of Vitamin C in high productivity, yield, and/or efficiency, the produced fermentation product is isolated from the culture medium and optionally further purified.
  • Example 1 Preparation of chromosomal DNA and amplification of DNA fragment by PCR
  • Chromosomal DNA of Gluconobacter oxydans DSM 17078 was prepared from the cells cultivated at 30 0 C for 1 day in mannitol broth (MB) liquid medium consisting of 25 g/1 mannitol, 5 g/1 of yeast extract (Difco), and 3 g/1 of Bactopeptone (Difco) by the method described by Sambrook et al (1989) "Molecular Cloning: A Laboratory Manual/Second Edition", Cold Spring Harbor Laboratory Press).
  • a DNA fragment was prepared by PCR with the chromosomal DNA prepared above and a set of primers, Pf(SEQ ID NO:3) and Pr (SEQ ID NO:4).
  • the Expand High Fidelity PCR kit (Roche Diagnostics) and 10 ng of the chromosomal DNA was used in total volume of 100 ⁇ according to the supplier's instruction to have the PCR product containing RCS 28 DNA sequence (SEQ ID NO: 1).
  • the PCR product was recovered from the reaction and its correct sequence confirmed.
  • Example 2 Disruption of the RCS 28 gene in G. oxydans DSM 17078
  • LCS 28LFH Long-Flanking Homology
  • oxydans DSM 17078 genomic DNA is used as a template and the reaction conditions consist of 35 cycles of denaturation at 94 0 C for 30 sec, annealing at 5O 0 C for 30 sec and extension at 72°C for 1 min. In both cases, the GC-rich PCR kit (Roche Molecular Biochemicals) is used to minimize PCR-generated errors.
  • the kanamycin-resistance cassette is amplified using plasmid pUC4K (Amersham Bioscience, accession No. X06404) as a template and primer pair Km+1 (SEQ ID NO:9) / Km-I (SEQ ID NO:10) to generate a 1.3-kb fragment.
  • the reaction conditions are as above.
  • the three products are gel-purified, mixed and used in the second round PCR reaction with the flanking primers RCS 28LFH+1 / RCS 28LFH-1 to generate a product of 2.4-kb.
  • the reaction conditions for the second round reaction consist of 94°C, 2 min, then 10 cycles of [94°C, 30 sec, 63°C, 30 sec, 68°C, 6 min], followed by 20 cycles of [94°C, 30 sec, 63°C, 30 sec, 68°C, 6 min with an additional 20 sec per cycle] and a final extension at 68°C for 10 min.
  • the PCR product is cloned into the pGEM-TEasy vector (Promega Corp.) to give plasmid pGEM-RCS 28.
  • This plasmid is transformed into competent G. oxydans DSM 17078 cells - 36 - 24654 selecting transformants on MB agar medium containing kanamycin to a final concentration of 50 ⁇ g ml "1 .
  • Several putative transformants are observed of which two are analyzed by PCR using the flanking primers RCS 28LFH+1 / RCS 28LFH-1 to verify that the RCS 28::Km mutation has integrated via a double crossover. Both strains carrying the mutation are named G. oxydans DSM 17078-RCS 28::Kml and G. oxydans DSM 17078-RCS 28::Km2.
  • G. oxydans DSM 17078, G. oxydans DSM 17078-RCS 28::Kml and G. oxydans DSM 17078-RCS 28::Km2 are grown at 27 0 C for 3 days on No. 3BD agar medium containing 70 g/1 D-sorbitol, 0.5 g/1 glycerol, 7.5 g/1 yeast extract (Difco), 2.5 g/1 MgSO 4 -7H 2 O, 10 g/1 CaCO 3 and 18 g/1 agar (Difco).
  • the identification of the L-ascorbic acid is done using an amino-column (YMC-Pack Polyamine-II, YMC, Inc., Kyoto, Japan) with UV detection at 254 nm.
  • the mobile phase is 50 mM NH 4 H 2 PO 4 and acetonitrile (40:60).
  • MS HPLC-mass spectrometry
  • the G. oxydans DSM 17078-RCS 28::Kml and G. oxydans DSM 17078-RCS 28::Km2 mutant strains are able to produce approximately at least 20 % increased levels of Vitamin C compared to strain G. oxydans DSM 17078.
  • SEQ ID N0:l and/or equivalents showing similarity/identity to SEQ ID NO:1 in other organisms than the ones disclosed herein before, e.g. organisms as mentioned in Table 1, may be determined by a simple DNA hybridization experiment.
  • Acetobacter aceti subsp. xylinum IFO 13693 and IFO 13773 are grown at 27°C for 3 days on No. 350 medium containing 5 g/1 Bactopeptone (Difco), 5 g/1 yeast extract (Difco), 5 g/1 glucose, 5 g/1 mannitol, 1 g/1 MgSO 4 -7H 2 O, 5 ml/1 ethanol, and 15 g/1 agar.
  • Gluconacetobacter and all Gluconobacter strains are grown at 27°C for 3 days on mannitol broth (MB) agar medium containing 25 g/1 mannitol, 5 g/1 yeast extract (Difco), 3 g/1 Bactopeptone (Difco), and 18 g/1 agar (Difco).
  • E. coli K-12 is grown on Luria Broth agar medium. The other strains/cells are grown on medium recommended by the suppliers or according to methods known in the art. Genomic DNA is extracted as described by e.g. Sambrook et ah, 1989, "Molecular Cloning: A Laboratory Manual/Second Edition", Cold Spring Harbor Laboratory Press) from a suitable organism as e.g. mentioned in Table 1.
  • Genomic DNA preparations are digested with restriction enzymes such as EcoRI or EcoRI.
  • HindHL, and 1 /xg of the DNA fragments are separated by agarose gel electrophoresis (1% agarose).
  • the gel is treated with 0.25 N HCl for 15 min and then 0.5 N NaOH for 30 min, and then blotted onto nitrocellulose or a nylon membrane with Vacuum Blotter Model 785 (BIO-RAD Laboratories AG, Switzerland) according to the instruction of the supplier.
  • the resulting blot is then brought into contact/hybridized with a solution wherein the probe, such as e.g. a DNA fragment with SEQ ID NO:1 sequence or a DNA fragment containing the part or whole of the SEQ ID NO:1 sequence to detect positive DNA fragment(s) from a test organism.
  • a DIG-labeled probe e.g. SEQ ID NO: 1
  • SEQ ID NO:1 may be prepared according to Example 1 by using the PCR-DIG labeling kit (Roche Diagnostics) and a set of primers, SEQ ID NO:3 and SEQ ID NO:4.
  • SEQ ID NO:3 a set of primers
  • SEQ ID NO:4 a set of primers
  • the hybridization may be performed under stringent or highly stringent conditions.
  • a preferred, non-limiting example of such conditions are hybridization in 6x sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in Ix SSC 5 0.1 % SDS at 50°C, preferably at 55°C, more preferably at 6O 0 C and even more preferably at 65 0 C.
  • SSC 6x sodium chloride/sodium citrate
  • Highly stringent conditions include, for example, 2 h to 4 days incubation at 42°C in a solution such as DigEasyHyb solution (Roche Diagnostics GmbH) with or without 100 ⁇ g/ml salmon sperm DNA, or a solution comprising 50% formamide, 5x SSC (150 mM NaCl, 15 niM trisodium citrate), 0.02% sodium dodecyl sulfate, 0.1% N- lauroylsarcosine, and 2% blocking reagent (Roche Diagnostics GmbH), followed by washing the filters twice for 5 to 15 min in 2x SSC and 0.1% SDS at room temperature and then washing twice for 15-30 min in 0.5x SSC and 0.1% SDS or O.lx SSC and 0.1% - 38 - 24654
  • the genes corresponding to the positive signals within the respective organisms shown in Table 1 can be cloned by a PCR method well known in the art using genomic DNA of such an organism together with a suitable primer set, such as e.g. SEQ ID NO:3 and SEQ ID NO:4 under conditions as described in Example 1 or as follows: 5 to 100 ng of genomic DNA is used per reaction (total volume 50 ⁇ ).
  • a suitable primer set such as e.g. SEQ ID NO:3 and SEQ ID NO:4 under conditions as described in Example 1 or as follows: 5 to 100 ng of genomic DNA is used per reaction (total volume 50 ⁇ ).
  • Expand High Fidelity PCR system (Roche Diagnostics) can be used with reaction conditions consisting of 94 0 C for 2 min; 30 cycles of (i) denaturation step at 94 0 C for 15 sec, (ii) annealing step at 6O 0 C for 30 sec, (iii) synthesis step at 72°C for 0.5 to 5 min depending to the target DNA length (1 min /1 kb); extension at 72°C for 7 min.
  • PCR with degenerate primers, which can be synthesized based on SEQ ID NO:2 or amino acid sequences as consensus sequences selected by aligning several amino acid sequences obtained by a sequence search program such as BLASTP (or BLASTX when nucleotide sequence is used as a "query sequence") to find proteins having a similarity to the protein of SEQ ID NO:2.
  • a sequence search program such as BLASTP (or BLASTX when nucleotide sequence is used as a "query sequence”
  • temperature of the second annealing step can be lowered to 55°C, or even to 50-45 0 C. A result of such an experiment is shown in Table 1.
  • Consensus sequences mentioned above might be amino acid sequences belonging to certain categories of several protein domain/family databases such as PROSITE (database of protein families and domains), COGs (Cluster of Ortholog Groups), CDD (Conserved Domain Databases), pfam (large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families).
  • PROSITE database of protein families and domains
  • COGs Cluster of Ortholog Groups
  • corresponding DNA encoding the protein can be amplified by PCR using the protein sequence or its nucleotide sequence when it is available in public databases.
  • the RCS 27 gene and equivalents as - 39 - 24654 e.g. a PCR product obtained in Example 4, referred to hereafter as gene X
  • gene X can be disrupted in accordance to the RCS 27 gene in G. oxydans DSM 17078 (see Example 2) to generate a knockout mutant carrying RCS 27 equivalent gene::Km.
  • Suitable host strains for generation of such knockout mutants may be selected from e.g. Gluconobacter strains listed in Table 1, in particular e.g. G. oxydans WO 3293, G. oxydans WO 3292, G.
  • the knockout mutant such as, e.g. a knockout mutant G. oxydans WO 3293-RCS 27 equivalent gene::Km can be generated as follows: the PCR product obtained in Example 4 is cloned in an E. coli vector pCR2.1-TOPO and used to transform E. coli TGl to have a Apr transformant carrying ⁇ CR2.1-gene X. Then, Rmr cassette isolated from pUC-4K (Amersham Bioscience, accession No. X06404) is inserted into one of the restriction site of the target gene with ligase and the resulting ligation product is used to transform E. coli TGl to have Apr Kmr transformant carrying pCR2.1-gene X::Km.
  • the pCR2.1-gene X::Km plasmid prepared from the transformant is digested by two restriction enzymes selected from the multi-cloning site of the vector part to isolate a DNA fragment containing gene X: :Km.
  • the resulting DNA fragment is used to transform the host strain carrying the RCS 27 equivalent gene by electroporation to have the gene disraptant carrying RCS 27 equivalent gene::Rm.
  • Vitamin C using the cells of the knockout mutant, e.g. G. oxydans WO 3293-RCS 27 equivalent gene::Km, and the corresponding wild-type strain, e.g. G. oxydans WO 3293, are performed according to Example 3.
  • the mutant strain can produce at least more than 20% Vitamin C compared to the wild-type strain.
  • Signal 1 Detection of DNA on a blot with genomic DNA of different strains and SEQ ID NO:1 as labeled probe.
  • Signal 2 Detection of DNA of different strains in a PCR reaction using primer pair - 41 - 24654
  • Signal 3 Detection of DNA of different strains in a PCR reaction using degenerate primers. For more explanation refer to the text.
  • the microorganism identified under 1. above was accompanied by:
  • the mieroorganism identified under I above was received by this International Depositary Authority on (date of original deposit) and a request to convert the original deposit to a deposit under the Budapest Treaty was received by it on (date of receipt of request for conversion).

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Abstract

La présente invention a trait à des gènes nouvellement identifiés codant pour des protéines qui sont impliquées dans la synthèse de l'acide L-ascorbique (désigné ci-après Vitamine C). L'invention a également trait à des polynucléotides comportant des séquences polynucléotidiques pleine longueur des nouveaux gènes et des fragments de ceux-ci, aux nouveaux polypeptides codés par les polynucléotides et des fragments de ceux-ci, ainsi qu'à leurs équivalents fonctionnels. La présente invention a trait en outre à l'utilisation desdits polynucléotides et polypeptides comme outils biotechnologiques dans la production de la Vitamine C à partir de micro-organismes, selon lequel une modification desdits polynucléotides et/ou polypeptides codés ont un impact direct ou indirect sur le rendement, la production et/ou l'efficacité de production du produit de fermentation dans ledit micro-organisme. L'invention a trait en outre à des procédés/processus d'utilisation des polynucléotides et de séquences polynucléotidiques modifiées pour la transformation de micro-organismes hôtes. Enfin, l'invention a trait à des micro-organismes génétiquement modifiés et à leur utilisation pour la production directe de la Vitamine C.
PCT/EP2006/001219 2005-02-11 2006-02-10 Nouveau gene rcs 28 WO2006084724A1 (fr)

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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2004029268A1 (fr) * 2002-09-27 2004-04-08 Dsm Ip Assets B.V. Production microbienne de vitamine c
WO2004029269A1 (fr) * 2002-09-27 2004-04-08 Dsm Ip Assets B.V. Procede pour produire de la vitamine c
WO2005017159A2 (fr) * 2003-08-14 2005-02-24 Dsm Ip Assets B.V. Production microbienne d'acide l-ascorbique

Patent Citations (3)

* Cited by examiner, † Cited by third party
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