# Patent

## Title
Mutant GTP cyclohydrolase II enzymes

## Abstract

The present invention relates to modified GTP cyclohydrolase II enzymes that display increased specific activity, and to polynucleotides encoding them. The invention further pertains to vectors comprising these polynucleotides and host cells containing such vectors. The invention provides a method for producing the modified enzyme and a method for producing riboflavin, a riboflavin precursor, FMN, FAD, or a derivative thereof.

## Background
This application is the National Stage of International Application No. PCT/EP2005/007320, filed Jul. 7, 2005.
The present invention provides modified enzymes with higher GTP cyclohydrolase II activity than the respective wild-type enzymes. The modified enzymes and polynucleotides encoding the same can be used for the production of riboflavin, riboflavin precursors, flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), and derivatives thereof.
Riboflavin (vitamin B2) is synthesized by all plants and many microorganisms but is not produced by higher animals. Because it is a precursor to coenzymes such as flavin adenine dinucleotide and flavin mononucleotide that are required in the enzymatic oxidation of carbohydrates, riboflavin is essential to basic metabolism. In higher animals, insufficient riboflavin can cause loss of hair, inflammation of the skin, vision deterioration, and growth failure.
Engineering of riboflavin production strains with increased rates and yields of riboflavin has been achieved in the past in a number of different ways. For instance, (1) classical mutagenesis was used to create variants with random mutations in the genome of the organism of choice, followed by selection for higher resistance to purine analogs and/or by screening for increased production of riboflavin. (2) Alternatively, the terminal enzymes of riboflavin biosynthesis, i.e., the enzymes catalyzing the conversion of guanosine triphosphate (GTP) and ribulose-5-phosphate to riboflavin, were overexpressed, resulting also in a higher flux towards the target product. However, in this latter approach, strong overexpression of the riboflavin biosynthesis proteins imposes an additional metabolic burden on the host cells which may, in turn, induce stress response reactions and other undesirable negative effects on the cells' physiology.
The enzymes required catalyzing the biosynthesis of riboflavin from guanosine triphosphate (GTP) and ribulose-5-phosphate are encoded by four genes (ribG, ribB, ribA, and ribH) in B. subtilis. These genes are located in an operon, the gene order of which differs from the order of the enzymatic reactions catalyzed by the enzymes. For example, GTP cyclohydrolase II, which catalyzes the first step in riboflavin biosynthesis, is encoded by the third gene in the operon, ribA. The ribA gene also encodes a second enzymatic activity, i.e., 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBPS), which catalyzes the conversion of ribulose-5-phosphate to the four-carbon unit 3,4-dihydroxy-2-butanone 4-phosphate (DHBP). Deaminase and reductase are encoded by the first gene of the operon, ribG. The penultimate step in riboflavin biosynthesis is catalyzed by lumazine synthase, the product of the last rib gene, ribH. Riboflavin synthase, which controls the last step of the pathway, is encoded by the second gene of the operon, ribB. The function of the gene located at the 3′ end of the rib operon is, at present, unclear; however, its gene product is not required for riboflavin synthesis.
Transcription of the riboflavin operon from the ribP1 promoter is controlled by an attenuation mechanism involving a regulatory leader region located between ribP1 and ribG. The ribO mutations within this leader region result in deregulated expression of the riboflavin operon. Deregulated expression is also observed in strains containing missense mutations in the ribC gene. The ribC gene has been shown to encode the flavin kinase/FAD synthase of B. subtilis (Mack, M., et al., J. Bacteriol., 180:950-955, 1998). Deregulating mutations reduce the flavokinase activity of the ribC gene product resulting in reduced intracellular concentrations of flavin mononucleotide (FMN), the effector molecule of the riboflavin regulatory system.
Recently, Bacillus subtilis was genetically engineered to produce high yields of riboflavin during a short fermentation cycle (U.S. Pat. No. 5,837,528). This approach combined classical genetic mutant selection and fermentation improvement with genetic engineering of the riboflavin biosynthetic genes by deregulating and increasing the level of gene expression. In this system, the expression of the rib genes was increased by mutating the flavokinase encoding ribC gene, by linking the rib genes to strong, constitutive promoters, and by increasing the copy number of the rib genes.
As already discussed above, overexpression of the rib genes poses an additional burden on the production strains which may, potentially, have a negative impact on the production of riboflavin precursors, riboflavin, FMN, FAD, or their derivatives. In order to circumvent this shortcoming, it is a subject of the present invention to describe GTP cyclohydrolase II mutants with increased specific activity. Use of such mutant enzymes in production strains, either alone or combined with improved mutants of the other Rib proteins, will allow higher flux rates with less or no additional burden on the cells' metabolism.
As used herein, the term “GTP cyclohydrolase II” may include any enzyme that is capable of catalyzing the conversion of GTP to 2,5-diamino-6-ribosylamino-4 (3H)-pyrimidinone-5′-phosphate (DRAPP). It is irrelevant whether this enzyme is capable of catalyzing further reactions, as for example the conversion of ribulose-5-phosphate to DHBP. A “GTP cyclohydrolase II” may be homologous to one or more of the enzymes the amino acid sequences of which are shown in Table 4. “Homologous” refers to a GTP cyclohydrolase II that is at least about 50% identical, preferably at least about 60% identical, more preferably at least about 70% identical, even more preferably at least about 80% identical, even more preferably at least about 85% identical, even more preferably at least about 90% or 95% identical, and most preferably at least about 98% identical to one or more of the amino acid sequences as shown in Table 4.
The term “% identity”, as known in the art, means the degree of relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” can be readily determined by known methods, e.g., with the program BESTFIT (GCG Wisconsin Package, version 10.2, Accelrys Inc., 9685 Scranton Road, San Diego, Calif. 92121-3752, USA) using the following parameters: gap creation penalty 8, gap extension penalty 2 (default parameters).
“Wild-type enzyme” or “wild-type GTP cyclohydrolase II” may include any GTP cyclohydrolase II homologous to any one of the enzymes shown in Table 4 that is used as starting point for designing mutants with increased activity according to the present invention. “Wild-type” in the context of the present invention may include both GTP cyclohydrolase II sequences derivable from nature as well as variants of synthetic GTP cyclohydrolase II enzymes (as long as they are homologous to any one of the sequences shown in Table 4), if they can be made more active by any of the teachings of the present invention. The terms “wild-type GTP cyclohydrolase II” and “non-modified GTP cyclohydrolase II” are used interchangeably herein.
A “mutant”, “mutant enzyme”, or “mutant GTP cyclohydrolase II” may include any variant derivable from a given wild-type enzyme/GTP cyclohydrolase II (according to the above definition) according to the teachings of the present invention and being more active than the respective wild-type enzyme. For the scope of the present invention, it is not relevant how the mutant(s) are obtained; such mutants may be obtained, e.g., by site-directed mutagenesis, saturation mutagenesis, random mutagenesis/directed evolution, chemical or UV mutagenesis of entire cells/organisms, and other methods which are known in the art. These mutants may also be generated, e.g., by designing synthetic genes, and/or produced by in vitro (cell-free) translation. For testing of specific activity, mutants may be (over-) expressed by methods known to those skilled in the art. The terms “mutant GTP cyclohydrolase II” and “modified GTP cyclohydrolase II” are used interchangeably herein. This also applies to the terms “mutant enzyme” and “modified enzyme”.
“Riboflavin precursor” and “derivatives of riboflavin, FMN or FAD” in the context of this patent application may include any and all metabolite(s) requiring GTP cyclohydrolase II as an intermediate enzyme in their (bio-) synthesis. In the context of this patent application, it is irrelevant whether such (bio-) synthesis pathways are natural or non-natural (i.e., pathways not occurring in nature, but engineered biotechnologically). Preferably, the synthesis pathways are biochemical in nature. Riboflavin precursors and derivatives of riboflavin, FMN or FAD include but are not limited to: DRAPP; 5-amino-6-ribosylamino-2,4 (1H,3H)-pyrimidinedione-5′-phosphate; 2,5-diamino-6-ribitylamino-4 (3H)-pyrimidinone-5′-phosphate; 5-amnino-6-ribitylamino-2,4 (1H,3H)-pyrimidinedione-5′-phosphate; 5-amino-6-ribitylamino-2,4 (1H,3H)-pyrimidinedione; 6,7-dimethyl-8-ribityllumazine (DMRL); and flavoproteins. The term “riboflavin” also includes derivatives of riboflavin, such as e.g. riboflavin-5-phosphate and salts thereof, such as e.g. sodium riboflavin-5-phosphate.
It is in general an object of the present invention to provide an enzyme having GTP cyclohydrolase II activity, said enzyme being modified in a way that its catalytic properties are more favorable (i.e., showing higher specific activity) than those of the non-modified GTP cyclohydrolase II enzymes.
The invention relates to a modified GTP cyclohydrolase II which exhibits higher (specific) activity in comparison to the corresponding non-modified GTP cyclohydrolase II wherein
(i) the amino acid sequence of the modified GTP cyclohydrolase II contains at least one mutation when compared with the amino acid sequence of the corresponding non-modified GTP cyclohydrolase II, and
(ii) the at least one mutation is at one or more amino acid positions selected from the group consisting of amino acid positions corresponding to positions 261, 270, 276, 279, 308 and 347 of the amino acid sequence of Bacillus subtilis GTP cyclohydrolase II as shown in SEQ ID NO:2.
Thus, it is an object of the present invention to provide a modified GTP cyclohydrolase II, wherein
(i) the specific activity of the modified enzyme is increased in comparison to the corresponding non-modified enzyme, and
(ii) the amino acid sequence of the modified enzyme comprises one or more mutation(s) including 1, 2, 3, 4, 5, or 6 mutation(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308 and/or 347 of SEQ ID NO:2.
The term “at least one mutation” means one or more mutation on a position as defined above leading to a modified GTP cyclohydrolase II having an increased specific activity compared to the non-modified enzyme. A modified enzyme as described above may consists of only 1, 2, 3, 4, 5 or 6 mutation(s) on a position as defined above leading to an increased specific activity compared to the non-modified enzyme, but may also include further amino acid mutations on other positions, as long as the resulting modified enzyme has an increased specific activity. Thus, the modified enzyme comprises one or more mutation(s) including 1, 2, 3, 4, 5, or 6 mutation(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308 and/or 347 of the amino acid sequence of Bacillus subtilis GTP cyclohydrolase II as shown in SEQ ID NO:2. Examples of such mutations on positions other than the ones defined above are amino acid mutation(s) on a position corresponding to amino acid position 196, 282, and/or 325 of SEQ ID NO:2.
As used herein, the term “specific activity” denotes the reaction rate of the wild-type and mutant GTP cyclohydrolase II enzymes under properly defined reaction conditions as described e.g. in Ritz et al. (J. Biol. Chem. 276, 22273-22277, 2001), Koh et al. (Mol. Gen. Genet. 251, 591-598, 1996), or Schramek et al. (J. Biol. Chem. 276, 44157-44162, 2001) or as described in detail in Example 2. The “specific activity” defines the amount of substrate consumed and/or product produced in a given time period and per defined amount of protein at a defined temperature. Typically, “specific activity” is expressed in μmol substrate consumed or product formed per min per mg of protein. Typically, μmol/min is abbreviated by U (=unit). Therefore, the unit definitions for specific activity of μmol/min/(mg of protein) or U/(mg of protein) are used interchangeably throughout this document. It is understood that in the context of the present invention, specific activity must be compared on the basis of a similar, or preferably identical, length of the polypeptide chain. The invention shall not be circumvented by increasing the size of a given wild-type enzyme through, e.g., formation of a fusion protein, thereby reducing the apparent specific activity of the overall enzyme.
According to the present invention the modified GTP cyclohydrolase II exhibits a specific activity that is higher than that of the corresponding non-modified enzyme. Preferably, the specific activity of the modified GTP cyclohydrolase II of the invention is increased by at least about 5, 10, 25, 40, 60, 70, 80, 85, 90%, more preferably at least about 70% in comparison to the corresponding non-modified GTP cyclohydrolase II (for measurement of specific activity, see below). Preferably, increases in specific activity refer to the experimental conditions described in Example 1 of this application. Approx. 0.004-0.02 U/ml (corresponding to approx. 40 μg/ml of Bacillus subtilis GTP cyclohydrolase II or 20 μg/ml for the best mutants described here), preferably approx. 0.004 U/ml of GTP cyclohydrolase II activity, were present in the assay mixture, and the reaction was carried out at 37° C.
The amino acid sequence of the modified GTP cyclohydrolase II of the invention contains at least one mutation as defined above when compared with the amino acid sequence of the corresponding non-modified GTP cyclohydrolase II. Said mutation may be one or more addition, deletion and/or substitution, preferably one or more amino acid substitution wherein a given amino acid present in the amino acid sequence of the non-modified GTP cyclohydrolase II is replaced with a different amino acid in the amino acid sequence of the modified GTP cyclohydrolase II of the invention. The amino acid sequence of the modified GTP cyclohydrolase II may contain at least one amino acid substitution when compared with the amino acid sequence of the corresponding non-modified GTP cyclohydrolase II, i.e. may comprise one or more mutation(s) including 1, 2, 3, 4, 5, or 6 amino acid substitution(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308 and/or 347 of SEQ ID NO:2, preferably 2, 3, 4 or 5 amino acid substitutions. Thus, the modified enzyme preferably contains at least 2, at least 3, at least 4 or at least 5 substitutions when compared with the amino acid sequence of the corresponding non-modified GTP cyclohydrolase II.
In one embodiment, a modified GTP cyclohydrolase II obtainable from Bacillus, preferably Bacillus subtilis, is provided, wherein
(i) the specific activity of the modified enzyme is increased in comparison to the corresponding non-modified enzyme, and
(ii) the amino acid sequence of the modified enzyme comprises one or more mutation(s) including 1, 2, 3, 4, 5, or 6 mutation(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308 and/or 347 of SEQ ID NO:2.
In one embodiment the non-modified enzyme corresponds to Bacillus subtilis GTP cyclohydrolase II as shown in SEQ ID NO:2. Thus, the modified enzyme having an increased specific activity in comparison to the wild type enzyme comprises one or more mutation(s) including 1, 2, 3, 4, 5, or 6 mutation(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308 and/or 347 of SEQ ID NO:2. In a further embodiment the modified enzyme having increased specific activity as defined above contains amino acid mutation(s) beside the amino acid positions as above, said further mutation(s) being on a position selected from the group consisting of position 196, 282, 235, and any combination thereof, preferably amino acid substitutions, more preferably the substitutions are Y196C (replacement of tyrosine by cysteine), A282T (replacement of alanine by threonine) or F325Y (replacement of phenylalanine by tyrosine).
A non-modified GTP cyclohydrolase II may be any GTP cyclohydrolase II for which increasing the specific activity is desirable. Non-modified GTP cyclohydrolase II enzymes include but are not limited to GTP cyclohydrolase II enzymes derivable from nature, such as enzymes of eukaryotic or prokaryotic origin, preferably fugal or bacterial origin. More preferably the non-modified enzyme is selected from the ones shown in Table 4 or which is homologous to any of the amino acid sequences as shown in Table 4, in particular selected from the group consisting of Ashbya, Saccharomyces, Eremothecium, Candida, Neurospora, Schizosaccharomyces, Archeoglobus, Streptomyces, Helicobacter, Escherichia, Corynebacterium, Thermotoga, Arabidopsis, Lycopersicum, Oryza, Alcaligenes, Pseudomonas, Dinococcus, Lactobacillus, Photobacterium and Bacillus and preferably selected from the group consisting of Candida guilliermondii, Ashbya gossypii (Eremothecium ashbyii) (SEQ ID NO:33), Saccharomyces cerevisiae, Neurospora crassa, Schizosaccharomyces pombe, Archeoglobus fulgidus, Streptomyces coelicolor, Helicobacter pylori J99, Escherichia coli (SEQ ID NO:35), Corynebacterium glutamicum (SEQ ID NO:37), Bacillus amyloliquefaciens (SEQ ID NO:39), Bacillus cereus (SEQ ID NO:41), Bacillus halodurans (SEQ ID NO:43), Thermotoga maritima, Arabidopsis thaliana, Lycopersicum exculentum, Oryza sativum, Alcaligenes eutrophus, Pseudomonas putida strain KT2440, Corynebacterium efficiens, Deinococcus radiodurans, Lactobacillus plantarum, Photobacterium phosphoreum, Pseudomonas putida strain KT2440 (second gene) and Bacillus subtilis (SEQ ID NO:2). Most preferably the non-modified enzyme is obtainable from Bacillus subtilis. 
The modified GTP cyclohydrolase II of the invention may be obtained by mutating the corresponding non-modified GTP cyclohydrolase II. In one embodiment, the non-modified enzyme corresponds to the B. subtilis GTP cyclohydrolase II shown in SEQ ID NO:2 and the modified enzyme comprises one or more amino acid mutation(s) including 1, 2, 3, 4, 5, or 6 mutation(s) on amino acid position(s) 261, 270, 276, 279, 308 and/or 347 of SEQ ID NO:2, wherein the specific activity of said modified enzyme is increased compared to the non-modified enzyme.
Preferably, the at least one mutation is at one or more amino acid positions selected from the group consisting of amino acid positions corresponding to positions 261, 279, 308 and 347 of the amino acid sequence of Bacillus subtilis GTP cyclohydrolase II as shown in SEQ ID NO: 2. Thus, in one embodiment the modified GTP cyclohydrolase II comprises one or more mutation(s) including 1, 2, 3 or 4 mutation(s) on amino acid position(s) corresponding to positions 261, 279, 308, and/or 347 of SEQ ID NO:2. In a preferred embodiment, the modified enzyme is obtainable from B. subtilis and comprises mutated amino acid positions 261, 279, 308, and/or 347 as shown in SEQ ID NO:2, corresponding to amino acids V261, Q279, K308, and M374, respectively.
In another preferred embodiment the at least one mutation is at one or more amino acid positions selected from the group consisting of amino acid positions corresponding to positions 270, 279, 308 and 347 of the amino acid sequence of Bacillus subtilis GTP cyclohydrolase II as shown in SEQ ID NO: 2. Thus, in one embodiment the modified GTP cyclohydrolase II comprises one or more mutation(s) including 1, 2, 3 or 4 mutation(s) on amino acid position(s) corresponding to positions 270, 279, 308, and/or 347 of SEQ ID NO:2. Preferably, the modified enzyme is obtainable from B. subtilis and comprises mutated amino acid positions 270, 279, 308, and/or 347 as shown in SEQ ID NO:2, corresponding to amino acids G270, Q279, K308, and M374, respectively.
In a further preferred embodiment the at least one mutation is at one ore more amino acid positions selected from the group consisting of amino acid positions corresponding to positions 276, 279, 308 and 347 of the amino acid sequence of Bacillus subtilis GTP cyclohydrolase II as shown in SEQ ID NO: 2. Thus, in a further embodiment the modified GTP cyclohydrolase II comprises one or more mutation(s) including 1, 2, 3 or 4 mutation(s) on amino acid position(s) corresponding to positions 276, 279, 308, and/or 347 of the amino acid sequence of Bacillus subtilis GTP cyclohydrolase II as shown in SEQ ID NO:2. Preferably, the modified enzyme is obtainable from B. subtilis and comprises mutated amino acid positions 276, 279, 308, and/or 347 as shown in SEQ ID NO:2, corresponding to amino acids A276, Q279, K308, and M374, respectively.
Preferably, the one or more amino acid mutation(s) of the modified GTP cyclohydrolase II is one or more amino acid substitution(s).
A modified GTP cyclohydrolase II may comprise one or more mutation(s) including only one mutation on an amino acid position as defined above, such mutation, particularly an amino acid substitution, may include one mutation on an amino acid position corresponding to position 261, 270, 276, 279, 308, or 347 of the amino acid sequence of Bacillus subtilis GTP cyclohydrolase II as shown in SEQ ID NO:2. The amino acid present in the non-modified GTP cyclohydrolase II corresponding to position 261 may be valine, the amino acid present in the non-modified GTP cyclohydrolase II corresponding to position 270 may be glycine, the amino acid present in the non-modified GTP cyclohydrolase II corresponding to position 276 may be alanine, the amino acid present in the non-modified GTP cyclohydrolase II corresponding to position 279 may be glutamine, the amino acid present in the non-modified GTP cyclohydrolase II corresponding to position 308 may be lysine, and the amino acid present in the non-modified GTP cyclohydrolase II corresponding to position 347 may be methionine.
The amino acid in the sequence of the non-modified GTP cyclohydrolase II maybe changed such that the amino acid corresponding to position 261 may be changed to alanine (e.g. V261A), the amino acid corresponding to position 270 may be changed to alanine or arginine (e.g. G270A and G270R), the amino acid corresponding to position 276 may be changed to threonine (e.g. A276T), the amino acid corresponding to position 279 may be changed to arginine (e.g. Q279A), the amino acid corresponding to position 308 may be changed to arginine (e.g. K308R), and the amino acid corresponding to position 347 may be changed to isoleucine (e.g. M374I). In one embodiment, the modified enzyme is obtainable from B. subtilis comprising an amino acid substitution in a position of SEQ ID NO:2 which is selected from the group consisting of position 261, 270, 276, 279, 308, and 347. Preferably, the substitution is V261A, G270A, G270R, A276T, Q279R, K308R or M347I.
A modified GTP cyclohydrolase II may comprise one or more mutation(s) including two mutations on amino acid positions as defined above, such mutations, particularly amino acid substitutions, may include mutations on amino acid positions corresponding to two of the positions as defined above, e.g. combinations of positions corresponding to positions 261/270, 261/276, 261/279, 261/308, 261/347, 270/276, 270/279, 270/308, 270/347, 276/279, 276/308, 276/347, 279/308, 279/347, or 308/347 as shown in SEQ ID NO:2. Preferred are amino acid substitutions such as V261A/A276T, V261A/Q279R, V261A/K308R, V261A/M347I, G270A/Q279R, G270A/K308R, G270A/M347I, A276T/Q279R, A276T/K308R, or A276T/M347I, wherein the positions correspond to the amino acid positions of SEQ ID NO:2. In one embodiment, such preferred substitutions are comprised in a modified GTP cyclohydrolase II obtainable from B. subtilis wherein the non-modified enzyme corresponds to SEQ ID NO:2. Preferably, the modified B. subtilis GTP cyclohydrolase II as of SEQ ID NO:2 comprises substitutions V261A/A276T or A276T/M347I.
A modified GTP cyclohydrolase II may comprise one or more mutation(s) including three mutations on amino acid positions as defined above, such mutations, particularly amino acid substitutions, may include mutations on amino acid positions corresponding to three of the positions as defined above, in particular combinations of positions corresponding to positions 261/279/308, 261/279/347, 261/308/347, 270/279/308, 270/279/347, 270/308/347, 276/279/308, 276/308/347, or 276/279/347 as shown in SEQ ID NO:2. Preferred are amino acid substitutions such as V261A/Q279R/K308R, V261A/K308R/M347I, V261A/Q279R/M347I, G270A/Q279R/K308R, G270A/K308R/M347I, G270A/Q279R/M347I, A276T/Q279R/K308R, A276T/K308R/M347I, or A276T/Q279R/M347I, wherein the positions correspond to the amino acid positions of SEQ ID NO:2. In one embodiment, such preferred substitutions are comprised in a modified GTP cyclohydrolase II obtainable from B. subtilis wherein the non-modified enzyme corresponds to SEQ ID NO:2. Preferably, the modified B. subtilis GTP cyclohydrolase II as of SEQ ID NO:2 comprises substitutions A276T/Q279R/M347I.
A modified GTP cyclohydrolase II may comprise one or more mutation(s) including four mutations on amino acid positions as defined above, such mutations, particularly amino acid substitutions, may include mutations in amino acid positions corresponding to four of the positions as defined above, in particular combinations of positions corresponding to positions 261/279/308/347, 270/279/308/347, or 276/279/308/347 as shown in SEQ ID NO:2. Preferred are amino acid substitutions such as V261A/Q279R/K308R/M347I, G270A/Q279R/K308R/M347I or A276T/Q279R/K308R/M347I, wherein the positions correspond to the amino acid positions of SEQ ID NO:2. In one embodiment, such preferred substitutions are comprised in a modified GTP cyclohydrolase II obtainable from B. subtilis wherein the non-modified enzyme corresponds to SEQ ID NO:2. Preferably, the modified B. subtilis GTP cyclohydrolase II as of SEQ ID NO:2 comprises substitutions A276T/Q279R/K308R/M347I.
Most preferred are the combinations of mutations disclosed in Table 1 or 2 (see infra). The amino acid positions identified in these examples may be transferred to GTP cyclohydrolase II enzymes of different origin, as e.g. shown in Table 4.
The modified GTP cyclohydrolase II of the invention may comprise foreign amino acids, preferably at its N- or C-terminus. “Foreign amino acids” mean amino acids which are not present in a native (occurring in nature) GTP cyclohydrolase II, preferably a stretch of at least about 3, at least about 5 or at least about 7 contiguous amino acids which are not present in a native GTP cyclohydrolase II. Preferred stretches of foreign amino acids include but are not limited to “tags” that facilitate purification of the recombinantly produced modified GTP cyclohydrolase II. Examples of such tags include but are not limited to a “His6” tag, a FLAG tag, a myc tag, and the like. For calculation of specific activity, the values need to be corrected for these additional amino acids (see also above).
In another embodiment the modified GTP cyclohydrolase II may contain one or more, e.g. two, deletions when compared with the amino acid sequence of the corresponding non-modified GTP cyclohydrolase II. Preferably, the deletions affect N- or C-terminal amino acids of the corresponding non-modified GTP cyclohydrolase II and do not significantly reduce the functional properties, e.g., the specific activity, of the enzyme.
The polypeptides and polynucleotides of the present invention, including modified GTP cyclohydrolase II enzymes, may be provided in an isolated form, and preferably are purified to homogeneity. As used herein, the term “isolated” means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, 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 may be part of a composition and still be isolated in that such vector or composition is not part of its natural environment. An isolated polypeptide is preferably greater than 80% pure, more preferably greater than 90% pure, even more preferably greater than 95% pure, most preferably greater than 99% pure. Purity may be determined according to methods known in the art, e.g., by SDS-PAGE and subsequent protein staining. Protein bands can then be quantified by densitometry. Further methods for determining the purity are within the level of ordinary skill.
The invention further relates to a polynucleotide comprising a nucleotide sequence which codes for a modified GTP cyclohydrolase II according to the invention. “Polynucleotide” as used herein refers to a polyribonucleotide or polydeoxyribonucleotide that may be unmodified RNA or DNA or modified RNA or DNA. Polynucleotides include but are not limited to single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is a mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. The term “polynucleotide” includes DNA or RNA that comprises one or more unusual bases, e.g., inosine, or one or more modified bases, e.g., tritylated bases.
The polynucleotide of the invention can easily be obtained by modifying a polynucleotide sequence which codes for a non-modified GTP cyclohydrolase II. Examples of such polynucleotide sequences encoding non-modified GTP cyclohydrolase II enzymes include but are not limited to the amino acid sequences in Table 4, in particular to SEQ ID NOs:2, 33, 35, 37, 39, 41, and 43. Non-limiting examples of polynucleotides encoding modified GTP cyclohydrolase II enzymes according to the invention are shown in SEQ ID NOs:6, 8, 10, 12, 14, 16, 18, 20, 22, 24 and 26.
Methods for introducing mutations, e.g., additions, deletions and/or substitutions into the nucleotide sequence coding for the non-modified GTP cyclohydrolase II include but are not limited to site-directed mutagenesis and PCR-based methods.
DNA sequences of the present invention can be constructed starting from genomic or cDNA sequences coding for GTP cyclohydrolase II enzymes known in the state of the art, as are available from, e.g., Genbank (Intelligenetics, California, USA), European Bioinformatics Institute (Hinston Hall, Cambridge, GB), NBRF (Georgetown University, Medical Centre, Washington D.C., USA) and Vecbase (University of Wisconsin, Biotechnology Centre, Madison, Wis., USA) or from the sequence information disclosed in Table 4 by methods of in vitro mutagenesis (see e.g. Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory Press, New York). Another possibility of mutating a given DNA sequence which is also preferred for the practice of the present invention is mutagenesis by using the polymerase chain reaction (PCR). DNA as starting material can be isolated by methods known in the art and described, e.g., in Sambrook et al. (Molecular Cloning) from the respective strains/organisms. It is, however, understood that DNA encoding a GTP cyclohydrolase II to be constructed/mutated in accordance with the present invention can also be prepared on the basis of a known DNA sequence, e.g. by construction of a synthetic gene by methods known in the art (as described, e.g., in EP 747483).
The polynucleotide of the invention may be an isolated polynucleotide, i.e. a polynucleotide that is substantially free from other nucleic acid sequences such as but not limited to other chromosomal and extrachromosomal DNA and RNA. Conventional nucleic acid purification methods known to people skilled in the art may be used to obtain isolated polynucleotides. The term also embraces recombinant polynucleotides and chemically synthesized polynucleotides.
In yet another embodiment the invention pertains to a functional polynucleotide in which a promoter, a ribosome-binding site, if necessary as in the case of bacterial cells, and a terminator are operably linked with a polynucleotide according to the invention. In yet a further embodiment the invention pertains to a vector or plasmid comprising such a polynucleotide. The vector or plasmid preferably comprises at least one marker gene. The term “operably linked” as used herein refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence, i.e., the coding sequence is under the transcriptional control of the promoter. Coding sequences may be operably linked to regulatory sequences in sense or anti-sense orientation. The term “expression” denotes the transcription of a DNA sequence into mRNA and/or the translation of mRNA into an amino acid sequence. The term “over-expression” means the production of a gene product in a modified organism (e.g., modified by transformation or transfection) that exceeds levels of production in the corresponding non-modified organism by deregulating the expression of the gene and/or by multiplying the gene itself inside of the organism.
Once complete DNA sequences of the present invention have been obtained, they may be integrated into vectors or directly introduced into the genome of a host organism by methods known in the art and described in, e.g., Sambrook et al. (s.a.) to (over-) express the encoded polypeptide in appropriate host systems. However, a man skilled in the art knows that also the DNA sequences themselves can be used to transform the suitable host systems of the invention to get (over-) expression of the encoded polypeptide.
Suitable host cells may be eukaryotic or prokaryotic cells. Examples of suitable host cells include but are not limited to bacterial cells such as cells of cyanobacteria, streptococci, staphylococci, enterococci, e.g., Bacilli as, e.g., Bacillus subtilis, or Streptomyces, as, e.g. Streptomyces lividans or Streptococcus pneumoniae, E. coli as, e.g., E. coli K12 strains, e.g. M15 or HB 101. The host cells may be a fungal cell including yeast cells, such as cells of Aspergilli, e.g. Aspergillus niger or Aspergillus oryzae, Trichoderma, e.g. Trichoderma reesei, Ashbya, e.g. Ashbya gossypii, Eremothecium, e.g. Eremothecium ashbyii, Saccharomyces, e.g. Saccharomyces cerevisiae, Candida, e.g. Candida flareri, Pichia, e.g. Pichia pastoris, Hansenula polymorpha, e.g. H. polymorpha (DSM 5215), and Kluyveromyces. A suitable host cell may further be selected from animal cells, including mammalian cells, such as for instance CHO, COS, HeLa, 3T3, BHK, 293, CV-1 and insect cells like Drosophila S2 and Spodoptera Sf9 cells; and plant cells such as cells of a gymnosperm or angiosperm.
Vectors which may be used for expression in fungi are known in the art and described e.g. in EP 420358, or by Cullen et al. (Bio/Technology 5, 369-376, 1987), Ward (in Molecular Industrial Mycology, Systems and Applications for Filamentous Fungi, Marcel Dekker, New York, 1991), Upshall et al. (Bio/Technology 5, 1301-1304, 1987), Gwynne et al. (Bio/Technology 5, 71-79, 1987), or Punt et al. (J. Biotechnol. 17, 19-34, 1991), and for yeast by Sreekrishna et al. (J. Basic Microbiol. 28, 265-278, 1988; Biochemistry 28, 4117-4125, 1989), Hitzemann et al. (Nature 293, 717-722, 1981) or in EP 183070, EP 183071, EP 248227, or EP 263311. Suitable vectors which may be used for expression in E. coli are known in the art as described by Sambrook et al. (s.a.). Vectors which may be used for expression in Bacilli are known in the art and described, e.g. in EP 207459 or EP 405370, by Yansura and Henner in Proc. Natl. Acad. Sci. USA 81, 439-443 (1984), or by Henner, Le Grice and Nagarajan in Meth. Enzymol. 185, 199-228, 1990. Vectors which maybe used for expression in H. polymnorpha are known in the art as described, e.g. in Gellissen et al., Biotechnology 9, 291-295, 1991.
Either such vectors already carry regulatory elements, e.g. promoters, or the polynucleotides of the present invention may be engineered to contain such elements. Suitable promoter elements which may be used are known in the art and are, e.g., for Trichoderma reesei the cbh1- or the pki1-promoter, for Aspergillus oryzae the amy-promoter, and for Aspergillus niger the glaA-, alcA-, aphA-, tpiA-, gpdA- and the pkiA-promoter. Suitable promoter elements which may be used for expression in yeast are known in the art and are, e.g., the pho5- or the gap-promoter for expression in Saccharomyces cerevisiae, and e.g. the aox1-promoter for Pichia pastoris or the FMD- or MOX promoter for H. polymorpha. 
Suitable promoters and vectors for bacterial expression include, e.g., a synthetic promoter described by Giacomini et al. (Gene 144, 17-24, 1994), the vegI promoter from Bacillus subtilis or the strong bacteriophage T5 promoter. Appropriate teachings for expression of the claimed (mutant) GTP cyclohydrolase II enzymes in bacteria, either by appropriate plasmids or through integration of GTP cyclohydrolase II-encoding DNA sequences into the chromosomal DNA, may be found in many places, e.g., U.S. Pat. No. 6,322,995.
Accordingly, vectors comprising a polynucleotide of the present invention, preferably for the expression of said polynucleotides in bacterial, fungal, animal or plant hosts, and such transformed bacteria or fungal, animal or plant hosts are also an object of the present invention.
The invention further relates to a method for producing riboflavin, a riboflavin precursor, FMN, FAD, or one or more derivatives thereof, comprising:
(a) culturing the host cell of the invention in a suitable medium under conditions that allow expression of the modified GTP cyclohydrolase II in said host cell; and
(b) optionally separating the product (riboflavin, a riboflavin precursor, FMN, FAD, or one or more derivatives thereof) from the medium.
Such a method can be used for the biotechnological production of either one or more of the following products: riboflavin, a riboflavin precursor, FMN, FAD, or one or more derivatives thereof. Such derivatives may include flavoproteins.
Methods of genetic and metabolic engineering of suitable host cells according to the present invention are known to the man skilled in the art. Similarly, (potentially) suitable purification methods for riboflavin, a riboflavin precursor, FMN, FAD, or one or more derivatives thereof are well known in the area of fine chemical biosynthesis and production.
It is understood that methods for biotechnological production of riboflavin, a riboflavin precursor, FMN, FAD, or one or more derivatives thereof according to the present invention are not limited to whole-cellular fermentation processes as described above, but may also use, e.g., permeabilized host cells, crude cell extracts, cell extracts clarified from cell remnants by, e.g., centrifugation or filtration, or even reconstituted reaction pathways with isolated enzymes. Also combinations of such processes are in the scope of the present invention. In the case of cell-free biosynthesis (such as with reconstituted reaction pathways), it is irrelevant whether the isolated enzymes have been prepared by and isolated from a host cell, by in vitro transcription/translation, or by still other means.
The invention further relates to a method for producing a modified GTP cyclohydrolase II of the invention comprising:
(a) culturing a host cell of the invention under conditions that allow expression of the modified GTP cyclohydrolase II of the invention; and
(b) recovering the modified GTP cyclohydrolase II from the cells or from the media.
The modified GTP cyclohydrolase II enzymes of the invention may be prepared from genetically engineered host cells comprising appropriate expression systems.
For recombinant production of the polypeptides of the invention, host cells may be genetically engineered to incorporate polynucleotides or vectors or plasmids of the invention. Introduction of a polynucleotide or vector into the host cell may be effected by standard methods known in the art such as calcium phosphate transfection, DEAE-dextran mediated transfection, microinjection, cationic lipid-mediated transfection, electroporation, transduction, ballistic introduction and infection.
A great variety of expression systems may be used to produce the modified GTP cyclohydrolase II enzymes of the invention. Such vectors include, among others, those described supra. Generally, any system or vector suitable to maintain, propagate or express polynucleotides and/or to express a polypeptide in a host may be used for expression in this regard.
In recombinant expression systems in eukaryotes, for secretion of a translated protein into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment, appropriate secretion signals may be incorporated into the expressed polypeptide. These signals may be endogenous to the polypeptide or they may be heterologous signals.
Polypeptides of the invention may be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxyapatite chromatography, and high performance liquid chromatography. Well-known techniques for protein refolding may be employed to regenerate active conformation when the polypeptide is denatured during isolation and/or purification.
GTP cyclohydrolase II enzymes of the present invention may also be expressed in plants according to methods as described, e.g., by Pen et al. in Bio/Technology 11, 811-814, 1994 or in EP 449375, preferably in seeds as described, e.g., in EP 449376. Some suitable examples of promoters and terminators include those from nopaline synthase (nos), octopine synthase (ocs) and cauliflower mosaic virus (CaMV) genes. One type of efficient plant promoter that may be used is a high-level plant promoter. Such promoters, in operable linkage with the genetic sequences of the present invention should be capable of promoting expression of a gene product of the present invention. High-level plant promoters that may be used in this invention include the promoter of the small subunit (ss) of the ribulose-1,5-bisphosphate carboxylase, for example from soybean, and the promoter of the chlorophyll a/b binding protein.
Where commercial production of the instant proteins is desired, a variety of culture methodologies may be applied. For example, large-scale production of a specific gene product, overexpressed from a recombinant microbial host may be achieved by both batch or continuous culture methodologies. Batch and fed-batch culturing methods are common and well known in the art, and examples have been described by Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989), Sinauer Associates, Inc., Sunderland, Mass., or Deshpande, Appl. Biochem. Biotechnol. 36, 227-234, 1992. Methods of modulating nutrients and growth factors for continuous culture processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology, and a variety of methods are detailed by Brock, supra.
Fermentation media may further contain suitable carbon substrates. Suitable substrates may include but are not limited to monosaccharides such as glucose and fructose, oligosaccharides such as lactose or sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpurified mixtures from renewable feedstocks. It is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism.
The invention further relates to a method for the preparation of a GTP cyclohydrolase II having increased specific activity, comprising the following steps:
(a) providing a polynucleotide encoding a first GTP cyclohydrolase II with a specific activity that, desirably, should be increased;
(b) introducing one or more mutation(s) into the polynucleotide sequence such that the mutated polynucleotide sequence encodes a modified GTP cyclohydrolase II comprising one or more mutation(s) when compared to the first GTP cyclohydrolase II wherein the one or more mutation(s) include 1, 2, 3, 4, 5, or 6 mutation(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308 and/or 347 of SEQ ID NO:2;
(c) optionally inserting the mutated polynucleotide in a vector or plasmid;
(d) introducing the polynucleotide or the vector or plasmid into a suitable host cell; and
(e) culturing the host cell under conditions that allow expression of the modified GTP cyclohydrolase II.
The present invention includes further the provision of a method for the preparation of a GTP cyclohydrolase II having increased specific activity, comprising the following steps:
(a) providing a polynucleotide encoding a first GTP cyclohydrolase II with a specific activity that, desirably, should be increased;
(b) providing the positions that have an effect on the specific activity;
(c) defining the optimal amino acid for replacement of a given amino acid of the wild-type GTP cyclohydrolase II as defined in (b) and introducing one or more mutations into the polynucleotide sequence of (a) at the positions defined in (b) such that the mutated polynucleotide sequence encodes a new GTP cyclohydrolase II;
(d) optionally inserting the mutated polynucleotide in a vector or plasmid;
(d) introducing the polynucleotide or the vector or plasmid into a suitable host cell; and
(e) culturing the host cell under conditions that allow expression of the modified GTP cyclohydrolase II.
In one embodiment, step (c) or the method described above is performed via saturated mutagenesis. However, it is understood that this may be not the only way to define the amino acid which should replace an amino acid at a given position of the wild-type GTP cyclohydrolase II in order to obtain a modified GTP cyclohydrolase II with increased specific activity.
The preparation of a modified GTP cyclohydrolase II having increased specific activity from a non-modified GTP cyclohydrolase II as described above, e.g., via saturated mutagenesis, includes, but is not limited to, the preparation of mutated GTP cyclohydrolase II proteins from non-modified proteins as in Table 4, in particular those identified by SEQ ID NOs:2, 33, 35, 37, 39, 41, and 43, such as for example non-modified GTP cyclohydrolase II proteins of Bacillus subtilis or Ashbya gossypii. The primers used for the PCR reaction are such that one primer, e.g., the sense primer, may contain a mutated nucleotide sequence and the other primer, e.g., the anti-sense primer, may contain the wild-type nucleotide sequence. PCR with these primer pairs and genomic DNA of the wild-type ribA may result in a PCR product carrying the particular mutation at a given position, depending on the mutated nucleotide sequence of the primer used. After purification of the resulting PCR products using standard methods like, e.g., the QIAquick PCR purification kit (Qiagen), the DNA may be cut with restriction enzymes such as BamHI and EcoRI, ligated into a suitable vector, e.g., pQE60, and transformed into a strain which is negative for GTP cyclohydrolase II. An example for such a strain is the E. coli strain Rib7 (Richter et al., J. Bacteriol. 175, 4045-4051, 1993) containing the plasmid pREP4. After confirmation of the correct sequence by DNA sequencing, the mutated RibA may be purified and characterized as described above. If Ashbya gossypii is used for the generation of a GTP cyclohydrolase II having increased specific activity, saturated mutagenesis has to be performed at amino acid residues/positions T126, G135, A141, L144, N182 and I221 corresponding to the respective residues V261, G270, A276, Q279, K308 and M347 of Bacillus subtilis GTP cyclohydrolase II as of SEQ ID NO:2 that were shown to have an impact on the specific activity of the latter enzyme (see Table 4).
The preferred embodiments of this method correspond to the preferred embodiments of the modified GTP cyclohydrolase II, the polynucleotides encoding them, the vectors and plasmids, the host cells, and the methods described herein. The first and second GTP cyclohydrolase II correspond to the non-modified and modified GTP cyclohydrolase II, respectively (see supra).
It is an object of the present invention to provide a polynucleotide comprising a nucleic acid sequence coding for a modified GTP cyclohydrolase II as described above, a vector, preferably an expression vector, comprising such a polynucleotide, a host cell which has been transformed by such a polynucleotide or vector, a process for the preparation of a GTP cyclohydrolase II of the present invention wherein the host cell as described before is cultured under suitable culture conditions and the GTP cyclohydrolase II is isolated from such host cell or the culture medium by methods known in the art, and a process for the biotechnological production of riboflavin, a riboflavin precursor, FMN, FAD, or one or more derivatives thereof based on a host cell which has been transformed by such a polynucleotide or vector, and/or which may have stably integrated such a polynucleotide into its chromosome(s).
It is also an object of the present invention to provide (i) a DNA sequence which codes for a GTP cyclohydrolase II carrying at least one of the specific mutations of the present invention and which hybridizes under standard conditions with any of the DNA sequences of the specific modified GTP cyclohydrolase II enzymes of the present invention, or (ii) a DNA sequence which codes for a GTP cyclohydrolase II carrying at least one of the specific mutations of the present invention but, because of the degeneracy of the genetic code, does not hybridize but which codes for a polypeptide with exactly the same amino acid sequence as a DNA sequence which hybridizes under standard conditions with any of the DNA sequences of the specific modified GTP cyclohydrolase II enzymes of the present invention, or (iii) a DNA sequence which is a fragment of such DNA sequences which maintains the activity properties of the polypeptide of which it is a fragment.
“Standard conditions” for hybridization mean in the context of the present invention the conditions which are generally used by a man skilled in the art to detect specific hybridization signals and which are described, e.g. by Sambrook et al., “Molecular Cloning”, second edition, Cold Spring Harbor Laboratory Press 1989, New York, or preferably so-called stringent hybridization and non-stringent washing conditions or more preferably so-called stringent hybridization and stringent washing conditions a man skilled in the art is familiar with and which are described, e.g., in Sambrook et al. (s.a.). A specific example of stringent hybridization conditions is overnight incubation (e.g., 15 hours) at 42° C. in a solution comprising: 50% fornamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 μg/ml of denatured, sheared salmon sperm DNA, followed by washing the hybridization support in 0.1×SSC at about 65° C.
It is furthermore an object of the present invention to provide a DNA sequence which can be obtained by the so-called polymerase chain reaction method (“PCR”) by PCR primers designed on the basis of the specifically described DNA sequences of the present invention. It is understood that the so obtained DNA sequences code for GTP cyclohydrolase II enzymes with at least the same mutation as the ones from which they are designed and show comparable activity properties.



The various embodiments of the invention described herein may be cross-combined.
Multiple sequence alignment was calculated by the program PILEUP of the GCG program package of 92 GTP cyclohydrolase II sequences found by the program BLASTN using standard databases as SWISS-PROT and TrEMBL (Candida guilliermondii, Ashbya gossypii, Saccharomyces cerevisiae, Neurospora crassa, Schizosaccharomyces pombe, Archaeoglobus fulgidus, Streptomyces coelicolor, Helicobacter pylori J99, Helicobacter pylori, Pyrococcus furiosus, Thermotoga maritima, Chlamydia muridarum, Chlamydia trachomatis, Chlamydia caviae GPIC, Arabidopsis thaliana, Lycopersicum exculentum, Oryza sativa, Alcaligenes eutrophus, Neisseria meningitidis (serogroup A), Neisseria meningitidis (serogroup B, two GTP cyclohydrolase II enzymes), Pseudomonas putida (two GTP cyclohydrolase II enzymes), Pseudomonas syringae (two GTP cyclohydrolase II enzymes), Actinobacillus actinomycetemcomitans (Haemophilus actinomycetemcomitans), Haemophilus influenzae, Pasteurella multocida, Escherichia coli, Escherichia coli O6, Salmonella typhimurium, Yersinia pestis, Buchnera aphidicola (subsp. Acyrthosiphon pisum) (Acyrthosiphon pisum symbiotic bacterium), Buchnera aphidicola (subsp. Schizaphis graminum), Wigglesworthia glossinidia brevipalpis, Buchnera aphidicola (subsp. Baizongia pistaciae), Mycobacterium leprae, Mycobacterium tuberculosis, Corynebacterium efficiens, Corynebacterium glutamicum, Corynebacterium ammoniagenes (Brevibacterium ammoniagenes), Staphylococcus aureus, Staphylococcus epidermidis, Actinobacillus pleuropneumoniae, Lactococcus lactis (Streptococcus lactis), Streptococcus agalactiae, Streptococcus pneumoniae, Clostridium acetobutylicum, Fusobacterium nucleatum, Anabaena spec., Synechocystis spec., Synechococcus elongatus (Thermosynechococcus elongatus), Bacillus amyloliquefaciens, Bacillus subtilis, Bacillus cereus, Bacillus halodurans, Clostridium perfringens, Clostridium tetani, Chlorobium tepidum, Aquifex aeolicus, Leptospira initerrogans, Deiniococcus radiodurans, Bacteroides thetaiotaomicron, Caulobacter crescentus, Coxiella burnetii, Rhizobium etli, Lactobacillus plantarum, Pseudomonas glumae, Streptomyces avermitilis, Photobacterium phosphoreum, Azospirillum brasilense, Agrobacterium tumefaciens, Rhizobium meliloti (Sinorhizobium meliloti), Brucella melitensis, Brucella suis, Rhizobium loti (Mesorhizobium loti), Nitrosomonas europaea, Ralstonia solanacearum (Pseudomonas solanacearum), Xanthomonas axonopodis, Xanthoinonas campestris, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio cholerae, Vibrio fischeri, Shewanella oneidensis, Photobacterium phosphoreum, Photobacterium leiognathi, Pseudomonas aeruginosa, Dehalospirillum multivorans, Xylella fastidiosa). Numbering relates to the alignment made. Some of the amino acid sequences code for an enzyme that has just GTP cyclohydrolase II activity like the enzymes from Ashbya gossypii, Streptomyces coelicolor, Helicobacter pylori J99, Heliobacter pylori, Arabidopsis thaliana, Alcaligenes eutrophus, Neisseria meningitidis (serogroup A), Neisseria meningitidis (serogroup B), Pseudomonas putida, Pseudomonas syringae, Actinobacillus actinomycetemcomitans (Haemophilus actinomycetemcomitans), Haemophilus influenzae, Pasteurella multocida, Escherichia coli, Escherichia coli O6, Salmonella typhimurium, Yersinia pestis, Buchnera aphidicola (subsp. Acyrthosiphon pisum) (Acyrthosiphon pisum symbiotic bacterium), Buchnera aphidicola (subsp. Schizaphis graminum), Wigglesworthia glossinidia brevipalpis, Buchnera aphidicola (subsp. Baizongia pistaciae), Pseudomonas glumae, Streptomyces avermitilis, or Photobacterium phosphoreum. Other enzymes like the RibA enzyme from B. subtilis contain, in addition, a domain having DHBP synthase activity. Positions that are homologous/equivalent to the amino acid residues found to have a positive effect on specific activity (amino acid residues 261, 270, 276, 279, 308, 347) and on protease sensitivity (196) of RibA from B. subtilis are discussed in one of the following examples. The numbering used for those positions is done according to the B. subtilis wild-type amino acid sequence.



The following non-limiting examples further illustrate the invention.
EXAMPLE 1
Measurement of GTP Cyclohydrolase II Activity and Determination of Specific Activity
The enzymatic assay used for measuring GTP cyclohydrolase II activity was adapted from Ritz et al. (J. Biol. Chem. 276, 22273-22277, 2001). The final assay buffer contained 50 mM Tris/HCl, pH 8.5, 10 mM MgCl2, 7.5 mM mercaptoethanol, 2.5 mM GTP and 0.1 mg/ml bovine serum albumin. After purification (see Example 5), the enzyme was kept in a buffer containing 50 mM Tris/HCl, pH 8.5, 10 mM MgCl2, 7.5 mM mercaptoethanol, and 10% glycerol. Substrate was added to the enzyme and the absorption at 310 nm, at which GTP shows no absorption, was followed over 20-30 min. The final reaction mixture contained between 0.02 and 0.04 mg/ml GTP cyclohydrolase II from B. subtilis or one of the mutants as shown in Table 1 or 2. An absorption coefficient of 6.28 [mM−1 cm−1] for DRAPP was used for the calculation of the activity. Protein determination was done with the Protein Assay from Bio-Rad (Cat. No. 500-0002, Bio-Rad Laboratories AG, Nenzlingerweg 2, CH-4153 Reinach, Switzerland).
According to the definition of “specific activity” given above, one unit is the amount of RibA that catalyzes the formation of 1 μmol DRAPP per minute under the conditions as described above. The specific activity is the amount of DRAPP that is formed by 1 mg of RibA per minute under the conditions as described above. Using the aforementioned definitions, the specific GTP cyclohydrolase II activity of the His6-tagged RibA protein of B. subtilis was 0.115 U/mg.
EXAMPLE 2
Testing of the Quality of the Enzymatic Assay
An optimal assay should fulfill a number of requirements, such as linearity with enzyme concentration and linearity with time. Using the conditions described in Example 1 and 22 μg enzyme, the increase in the absorption at 310 nm was followed over 25 min. To test in which range the assay is linear with the enzyme concentration, the dependence of the assay on increasing enzyme concentration (0-40 μg His6-tagged RibA) was tested. The assay proved to be linear over 25 min and between 0 and 40 μg His6-tagged RibA from B. subtilis. 
After this the dependence of the GTP cyclohydrolase II activity of His6-tagged RibA from B. subtilis on GTP concentration was tested. The conditions as described in Example 1 were used. However, the GTP concentration was varied from 0.05 to 2.5 mM final concentration. The data indicate a Km value for GTP of 0.07 mM and a specific activity of around 115 mU/mg protein at 37° C. for the GTP cyclohydrolase II activity of the His6-tagged RibA enzyme from B. subtilis. The experiments of this example showed that the GTP cyclohydrolase II activity assay, in fact, is linear with time and enzyme (GTP cyclohydrolase II) concentration, and that under the given conditions for Bacillus subtilis GTP cyclohydrolase II, a GTP concentration of 2.5 mM may be optimal to allow reliable measurements of the specific activity of the enzyme.
EXAMPLE 3
Isolation of Genomic DNA from Bacillus Subtilis 
B. subtilis was grown at 30° C. in Veal Infusion Broth (Becton Dickinson, Sparks, Md. 21152, USA) overnight. 1.5 ml culture was transferred into a 1.5 ml tube and centrifuged.
The cell pellet was resuspended in 0.5 ml suspension buffer (50 mM Tris/HCl, pH 7.5, 50 mM Na2EDTA, 15% sucrose and 1 mg/ml freshly added lysozyme). After 10 min incubation at room temperature 1 μl diethyloxydiformate was added. Then 10 μl of 10% SDS solution was added and the tube was inverted several times. The tube was incubated for 5 min at 70° C. to release the bacterial DNA. 50 μl 5 M potassium acetate was added, the tube was cooled on ice and left there for 45 min. After this, the sample was centrifuged for 30 min at 4° C. The supernatant was transferred into a new 1.5-ml tube, which was filled (up to 1.5 ml) with ethanol at room temperature. After 5 min centrifugation, the supernatant was discarded and the DNA pellet was dried. Then the DNA was washed with 70% and 96% ethanol and dissolved in 10 mM Tris/HCl, pH 7.5, 1 mM EDTA, and 10 μg/ml RNase A.
EXAMPLE 4
Construction of the Expression Plasmids for Expressing RibA Coding for GTP Cyclohydrolase II and DHBP Synthase from B. Subtilis and its Mutants
Cloning of the ribA gene (SEQ ID NO:1) of B. subtilis that codes for the GTP cyclohydrolase II and the DHBP synthase was done by PCR. Genomic DNA of B. subtilis was isolated according to Example 3. 100 ng of this DNA or of a template coding for a mutated form of the ribA gene were used for a PCR using primers RibA 1S (SEQ ID NO:27) and RibA 1AS (SEQ ID NO:28). The following PCR conditions were used: 2 μM of each primer, 0.2 mM of each nucleotide, 2.5 U of a proof-reading DNA polymerase (Stratagene, Gebouw Calif., 1101 CB Amsterdam Zuidoost, The Netherlands), and 100 ng genomic DNA in the appropriate buffer as supplied together with the DNA polymerase.
Temperature regulation was as follows:
Step 1: 3 min at 95° C.
Step 2: 30 sec at 95° C.
Step 3: 30 sec at 52° C.
Step 4: 60 sec at 72° C.
Steps 2 to 4 were repeated 30-times.
The PCR product of 1.3 kb was used as template for PCR 2, in which primer RibA 1S was replaced by primer RibA 2S (SEQ ID NO:29). The PCR product of this reaction (SEQ ID NO:3), encoding an N-terminally His6-tagged version of B. subtilis RibA (SEQ ID NO:4), was separated by agarose gel electrophoresis, eluted from the gel, digested with EcoRI and BamHI, and ligated into the EcoRI and BamHI digested vector pQE60 (Qiagen AG, Hilden, Germany). The plasmid was called pQE60ribANhis.
EXAMPLE 5
Characterization of the Wild-Type and the Mutant Enzymes
The generation of mutated enzymes was performed using methods described above and which are known to the skilled person. Mutants of RibA from B. subtilis that were further investigated are depicted in Table 1. All mutant genes were cloned into a pQE60 vector as described in Example 4. All final constructs contained an N-terminal His6-tag.







TABLE 1







Rib A mutants as defined by the amino acid exchanges compared


to the wild-type RibA protein of B. subtilis (the numbers define the


respective amino acid positions in SEQ ID NO: 2)











SEQ



SEQ ID NO
ID NO


Mutant
(DNA)
(protein)












RibA M347I
9
10


RibA G270R
23
24


RibA K220E, G270A
19
20


RibA Y196C, A276T, A282T
11
12


(PCR III)


RibA Y196C, A276T
5
6


RibA Y196C, V261A
7
8


RibA Y196C, V261A, A276T
25
26


RibA Y196C, A276T, A282T, M347I
13
14


RibA Y196C, A276T, Q279R, A282T, M347I
15
16


RibA Y196C, A276T, Q279R, A282T,
17
18


K308R, M347I (construct C)


RibA
21
22


Y196C, A276T, Q279R, A282T, K308R,


F325Y, M347I (construct E)









The RibA mutant enzymes were expressed from the plasmids of Example 4 and purified as described in “The QiaExpressionist”, Qiagen, Hilden, Germany, March 2001, edition 5. The enzymatic properties of the purified enzymes (RibA mutants) were analyzed as described in Examples 1 and 2. Table 2 compares the specific GTP cyclohydrolase II activities of the RibA mutants (see Table 1) to that of the GTP cyclohydrolase II of the wild-type RibA of B. subtilis. The activity was measured using the N-terminally His6-tagged enzyme versions of RibA as described in Example 4. The numbers define the respective amino acid positions in SEQ ID NO:2.







TABLE 2







Comparison of the specific GTP cyclohydrolase II activities of


mutated and wild-type (WT) B. subtilis RibAs


(all N-terminally His6-tagged)









specific activity



(in % relative to


Mutations
wild-type RibA)





WT
100


M347I
120


G270R
140


G270A, (K220E)
160


(Y196C), A276T, (A282T)
160


(Y196C), A276T
160


(Y196C), V261A
160


(Y196C), V261A, A276T
160


(Y196C), A276T, (A282T), M347I
180


(Y196C), A276T, Q279R, (A282T), M347I
185


(Y196C), A276T, Q279R, (A282T), K308R, M347I
201


(Y196C), A276T, Q279R, (A282T), K308R,
200


(F325Y), M347I









The amino acid replacements in parentheses have most probably no effect on GTP cyclohydrolase II activity of the mutants. Amino acid exchange Y196C reduces the protease sensitivity of RibA.
EXAMPLE 6
Construction of Recombinant B. Subtilis Strains Over-Expressing RibA Mutants that Show a Higher Specific GTP Cyclohydrolase II Activity
In the following example, the mutated ribA polynucleotide sequences of RibA Y196C,A276T,282T (PCR III), RibA Y196C,A276T,Q279R,A282T,K308R,M347I (construct C), and RibA Y196C,A276T,Q279R,A282T,K308R,F325Y,M347I (construct E) were first introduced into a vector containing the strong constitutive promoter PvegI, and then further manipulated in E. coli. Transformation of a natural competent B. subtilis microorganism with the polynucleotide sequence and flanking vector sequences resulted in a B. subtilis strain over-expressing the mutated ribA. Standard recombinant DNA techniques were used for the construction of the polynucleotide sequence and the B. subtilis strains. See, for example, Sambrook et al., Molecular Cloning. A Laboratory Manual (2nd Ed.), Cold Spring Harbor Laboratory Press (1989), and Harwood and Cutting, Molecular Biology Methods for Bacillus, John Wiley and Sons (1990).
To amplify the mutated ribA, a 1.2-kb DNA fragment containing the entire ribA coding sequence was amplified by PCR using DNA from a plasmid containing mutants PCR III, construct C or construct E, and RibANde+1 (SEQ ID NO:30) and RibA4AS (SEQ ID NO:31) as primers.
The reaction conditions for the PCR reaction consisted of 30 cycles of denaturation at 95° C. for 1 min, annealing at 52° C. for 1 min, and extension at 72° C. for 2 min. The Pfu Turbo DNA polymerase (Stratagene, Gebouw Calif., 1101 CB Amsterdam Zuidoost, The Netherlands) was used to minimize PCR-generated errors. The PCR products were purified using the QIAquick PCR purification kit (Qiagen), and doubly digested using NdeI and BamHI. The digested PCR products were cloned into the pXI16 vector (Huembelin et al., J. Ind. Microbiol. Biotechnol. 22, 1-7, 1999), which consists of suitable restriction sites for the cloning of polynucleotide sequences immediately downstream of the strong constitutive PvegI promoter from B. subtilis. The pXI16 vector also contains the cryT transcriptional terminator from B. thuringiensis, the sacB flanking sequences for homologous recombination into the B. subtilis genome by a double-crossover event, and an erythromycin-resistance marker. That each plasmid contained the mutated ribA was confirmed by DNA sequencing.
Each plasmid was digested with ApaI to remove the spacer region from the PvegI promoter, re-ligated and digested again with FspI, and transformed into natural competent B. subtilis 1012 cells. Transformants were selected on TBAB plates (Tryptose Blood Agar Base, Becton Dickinson, Sparks, Md. 21152, USA) containing erythromycin to a final concentration of 2 μg/ml. DNA sequencing verified that the mutated ribA polynucleotide sequences were correct in these strains. Overproduction of riboflavin was tested according to Example 7.
The mutated ribA polynucleotide sequences driven by the PvegI promoter were introduced into riboflavin over-producing B. subtilis strain RB50::(pRF69)n::(pRF93)m, which has been described in Perkins et al., J. Ind. Microbiol. Biotechnol. 22:8-18 (1999), by generalized transduction. Standard techniques using bacteriophage PBS1 were employed according to Harwood and Cutting, Molecular Biology Methods for Bacillus, John Wiley and Sons (1990). Transductants were selected for on TBAB plates containing erythromycin to a final concentration of 2 μg/ml. Transformants were checked by PCR analysis and DNA sequencing to verify correct insertion of the mutated ribA polynucleotide sequence.
EXAMPLE 7
Improved Production of Riboflavin Using a GTP Cyclohydrolase II with Increased Specific Activity
To test the in vivo effect of mutations affecting the specific activity of GTP cyclohydrolase II, the Bacillus subtilis GTP cyclohydrolase II (RibA) mutants PCR III, construct C, or construct E were introduced into riboflavin over-producing B. subtilis strains, such as strain RB50::(pRF69)n::(pRF93)m (Perkins et al, J. Ind. Microbiol. Biotechnol. 22, 8-18, 1999), e.g. in the sacB locus. The production of riboflavin was compared directly in two recombinant strains of B. subtilis that differ only by the presence or absence of the mutations in the ribA gene. Culturing of the Bacillus strains was done as described in Example 8.
EXAMPLE 8
Culture Conditions for Evaluating Riboflavin Production
Riboflavin production was tested in fed-batch cultivations of riboflavin-overproducing B. subtilis strain RB50::(pRF69)n::(pRF93)m in which the GTP cyclohydrolase II mutants PCR III, construct C, or construct E driven by the PvegI promoter were integrated in the sacB locus (see Example 6). Fermentation of the strains was done as described in EP 405370.
EXAMPLE 9
Analytical Methods for Determination of Riboflavin
For determination of riboflavin, the following analytical method can be used (Bretzel et al, J. Ind. Microbiol. Biotechnol. 22, 19-26, 1999).
The chromatographic system was a Hewlett-Packard 1100 System equipped with a binary pump, a column thermostat and a cooled autosampler. Both a diode array detector and a fluorescence detector were used in line. Two signals were recorded, UV at 280 nm and a fluorescence trace at excitation 446 nm, emission 520 nm.
A stainless-steel Supelcosil LC-8-DB column (150×4.6 mm, 3 μm particle size) was used, together with a guard cartridge. The mobile phases were 100 mM acetic acid (A) and methanol (B). A gradient elution according to the following scheme was used:












Time [min]
% A
% B

















0
98
2


6
98
2


15
50
50


25
50
50









The column temperature was set to 20° C., and the flow rate was 1.0 ml/min. The run time was 25 min.
Fermentation samples were diluted, filtered and analyzed without further treatment. Riboflavin was quantitated by comparison with an external standard. The calculations were based on the UV signal at 280 nm. Riboflavin purchased from Fluka (9471 Buchs, Switzerland) was used as standard material (purity≧99.0%).
EXAMPLE 10
Identification of Corresponding Residues in GTP Cyclohydrolase II Enzymes that are Homologous to Bacillus subtilis GTP Cyclohydrolase II
A multiple amino acid sequence alignment of 92 different GTP cyclohydrolase II enzymes found by the program BLASTN using standard databases such as SWISS-PROT and TrEMBL was calculated with the program “PILEUP” (GCG Wisconsin Package, version 10.2, Accelrys Inc., 9685 Scranton Road, San Diego, Calif. 92121-3752, USA) using the following parameters: gap creation penalty 8, gap extension penalty 2, and blosum62.cmp matrix (default parameters).
A homologous GTP cyclohydrolase II in the context of the present invention may show sequence similarity with any of the GTP cyclohydrolase II amino acid sequences shown in Table 4, which. serves as an example and is not meant to be a complete collection of all known GTP cyclohydrolase II enzymes. Homologous residues, i.e. residues of the different GTP cyclohydrolase II enzymes that are located at the same position in the amino acid sequence alignment, are expected to be similarly positioned in the 3D structure of each protein and to fulfill in each protein a comparable function structure-wise and function-wise. Amino acid residues homologous to the amino acid residues of the GTP cyclohydrolase II from B. subtilis are discussed in the Examples.
Amino acid residues of 92 different organisms corresponding to specific amino acid positions, i.e. positions that are homologous/equivalent to the amino acid residues found to have a positive effect on specific activity (amino acid residues 261, 270, 276, 279, 308, 347) of the amino acid sequence of Bacillus subtilis GTP cyclohydrolase II (SEQ ID NO:2) are summarized in Table 4, wherein the number in the left column defines the organism, starting with the name of the sequence used, the database accession number, and in parenthesis the source organism of the sequence:
(1) gch2_bacsu: SWISS-PROT: gch2_bacsu (Bacillus subtilis)
(2) gch2_cangu: geneseqp:aay69776 (Candida guilliermondii)
(3) gch2_ashgo: TrEMBL: CAA02912: (Ashbya gossypii (Eremothecium gosypii))
(4) gch2_yeast: SWISS-PROT: gch2_yeast (Saccharomyces cerevisiae)
(5) gch2_neucr: TrEMBL: Q871B3 (Neurospora crassa)
(6) gch2_schpo: TrEMBL: Q9P7M9 (Schizosaccharomyces pombe)
(7) gch2_arcfu: SWISS-PROT: gch2_arcfu (Archaeoglobus fulgidus)
(8) gch2_strco: SWISS-PROT: gch2_strco (Streptomyces coelicolor)
(9) gch2_helpj: SWISS-PROT: gch2_helpj (Helicobacter pylori J99)
(10) gch2_helpy: SWISS-PROT: gch2_helpy (Heliobacter pylori)
(11) gch2_pyrfu: TrEMBL: Q8U4L7 (Pyrococcus furiosus)
(12) gch2_thema: SWISS-PROT: gch2_thema (Thermotoga maritima)
(13) gch2_chlmu: SWISS-PROT: gch2_chlmu (Chlamydia muridarum)
(14) gch2_chltr: SWISS-PROT: gch2_chltr (Chlamydia trachomatis)
(15) gch2_chlca: TrEMBL: AAP05635 (Chlamydia caviae GPIC)
(16) gch2_chlpn: SWISS-PROT: gch2_chlpn (Chlamydia pneumoniae)
(17) gch2_arath: SWISS-PROT: gch2_arath (Arabidopsis thaliana)
(18) gch2_lyces: TrEMBL: CAC09119 (Lycopersicum esculentum)
(19) gch2_orysa: TrEMBL: AAO72560 (Oryza sativum)
(20) gch2_alceu: TrEMBL: Q9F184 (Alcaligenes eutrophus)
(21) gch2_neima: SWISS-PROT: gch2_neima (Neisseria meningitidis (serogroup A))
(22) gch2_neimb: SWISS-PROT: gch2_neimb (Neisseria meningitidis (serogroup B))
(23) gch2_psepk: SWISS-PROT: gch2_psepk (Pseudomonas putida (strain KT2440))
(24) gch2_psesm: SWISS-PROT: gch2_psesm (Pseudomonas syringae (pv. tomato))
(25) gch2_actac: TrEMBL: Q9JRR0 (Actinobacillus actinomycetemcomitans (Haemophilus actinomycetemcomitans))
(26) gch2_haein: SWISS-PROT: gch2_pasmu gch2_haein (Haemophilus influenzae)
(27) gch2_pasmu: SWISS-PROT: (Pasteurella multocida)
(28) gch2_ecO6: TrEMBL: Q8FHU5 (Escherichia coli O6)
(29) gch2—ecoli: SWISS-PROT: gch2—ecoli (Escherichia coli)
(30) gch2_salty: TrEMBL: Q8XFY7 (Salmonella typhimurium)
(31) gch2_yerpe: TrEMBL: Q8ZEF0 (Yersinia pestis)
(32) gch2_bucai: SWISS-PROT: gch2_bucai (Buchnera aphidicola (subsp. Acyrthosiphon pisum) (Acyrthosiphon pisum symbiotic bacterium))
(33) gch2_bucap: SWISS-PROT: gch2_bucap (Buchnera aphidicola (subsp. Schizaphis graminum))
(34) gch2_wigbr: SWISS-PROT: gch2_wigbr (Wigglesworthia glossinidia brevipalpis)
(35) gch2_bucbp: SWISS-PROT: gch2_wigbr (Buchnera aphidicola (subsp. Baizongia pistaciae))
(36) gch2_mycle: TrEMBL: Q9CCP4 (Mycobacterium leprae)
(37) gch2_myctu: SWISS-PROT: gch2_myctu (Mycobacterium tuberculosis)
(38) gch2_coref: TrEMBL: Q8FT57 (Corynebacterium efficiens)
(39) gch2_corgl: GENESEQP: AAB79913 (Corynebacterium glutamicum)
(40) gch2_coram: SWISS-PROT: gch2_coram (Corynebacterium ammoniagenes (Brevibacterium ammoniagenes))
(41) gch2_staau: TrEMBL: Q8NW14 (Staphylococcus aureus (strain MW2))
(42) gch2_staep: GENESEQP: ABP40248 (Staphylococcus epidermidis)
(43) gch2_actpl: SWISS-PROT: gch2_actpl (Actinobacillus pleuropneumoniae)
(44) gch2_lacla: TrEMBL: Q9CGU7 (Lactococcus lactis (subsp. lactis) (Streptococcus lactis))
(45) gch2_stcag: TrEMBL: Q8E658 (Streptococcus agalactiae (serotype III))
(46) gch2_stcpn: TrEMBL: Q8DRF1 (Streptococcus pneumoniae (strain ATCC BAA-255/R6))
(47) gch2_cloac: TrEMBL: Q97LG9 (Clostridium acetobutylicum)
(48) gch2_fusnu: TrEMBL: Q8RIR1 (Fusobacterium nucleatum (subsp. nucleatum))
(49) gch2_anasp: TrEMBL: Q8RIR1 (Anabaena sp. (strain PCC 7120))
(50) gch2_syny3: SWISS-PROT: gch2_syny3 (Synechocystis sp. (strain PCC 6803))
(51) gch2_synel: TrEMBL: Q8DI64 Synechococcus elongatus (Thermosynechococcus elongatus)
(52) gch2_bacam: SWISS-PROT: gch2_bacam (Bacillus amyloliquefaciens)
(53) gch2_bacce: TrEMBL: AAP11030 (Bacillus cereus ATCC 14579)
(54) gch2_bacha: TrEMBL: Q9KCL5 (Bacillus halodurans)
(55) gch2_clope: TrEMBL: Q8XMX0 (Clostridium perfringens)
(56) gch2_clote: TrEMBL: Q897Q8 (Clostridium tetani)
(57) gch2_chlte: TrEMBL: Q8KC35 (Chlorobium tepidum)
(58) gch2_aquae: SWISS-PROT: gch2_aquae (Aquifex aeolicus)
(59) gch2_lepin: TrEMBL: Q8F701 (Leptospira interrogans)
(60) gch2_deira: TrEMBL: Q9RXZ9 (Deinococcus radiodurans)
(61) gch2_bacth: TrEMBL: Q8A528 (Bacteroides thetaiotaomicron)
(62) gch2_caucr: TrEMBL: Q9A9S5 (Caulobacter crescentus)
(63) gch2_coxbu: TrEMBL: AAO90191 (Coxiella burnetii RSA 493)
(64) gch2_rhiet: TrEMBL: Q8KL38 (Rhizobium etli)
(65) gch2_lacpl: TrEMBL: Q88X17 (Lactobacillus plantarum)
(66) gch2_psegl: TrEMBL: Q8RS38 (Pseudomonas glumae)
(67) gch2_strav: TrEMBL: BAC71833 (Streptomyces avermitilis)
(68) gch2_phopo: SWISS-PROT: gch2_phopo (Photobacterium phosphoreum)
(69) gch2_azobr: SWISS-PROT: gch2_azobr (Azospirillum brasilense)
(70) gch2_agrtu: TrEMBL: Q8UHC9 (Agrobacterium tumefaciens (strain C58/ATCC 33970))
(71) gch2_rhime: TrEMBL: Q92RH2 (Rhizobium meliloti (Sinorhizobium meliloti))
(72) gch2_brume: TrEMBL: Q8YFL5 (Brucella melitensis)
(73) gch2_brusu: TrEMBL: Q8G298 (Brucella suis)
(74) gch2_rhilo: TrEMBL: Q985Z3 (Rhizobium loti (Mesorhizobium loti))
(75) gch2_braja: TrEMBL: Q89RZ7 (Bradyrhizobium japonicum)
(76) gch2_niteu: TrEMBL: CAD86468 (Nitrosomonas europaea ATCC 19718)
(77) gch2_ralso: TrEMBL: Q8Y1H7 (Ralstonia solanacearum (Pseudomonas solanacearum))
(78) gch2_neime: TrEMBL: Q9JZ77 (Neisseria meningitidis (serogroup B, second enzyme found))
(79) gch2_xanax: TrEMBL: Q8PPD7 (Xanthomonas axonopodis (pv. citri))
(80) gch2_xanca: TrEMBL: Q8PCM8 (Xanthomonas campestris (pv. campestris))
(81) gch2_vibpa: TrEMBL: Q87RU5 (Vibrio parahaemolyticus)
(82) gch2_vibvu: TrEMBL: Q8DF98 (Vibrio vulnificus)
(83) gch2_vibch: TrEMBL: Q9KPU3 (Vibrio cholerae)
(84) gch2_vibfi: TrEMBL: Q8G9G5 (Vibrio fischeri)
(85) gch2_sheon: TrEMBL: Q8EBP2 (Shewanella oneidensis)
(86) gch2_phoph: TrEMBL: Q8G9H7 (Photobacterium phosphoreum)
(87) ribb_phole: TrEMBL: Q93E93 (Photobacterium leiognathi)
(88) gch2_psepu: TrEMBL: Q88GB1 (Pseudomonas putida (strain KT2440, second enzyme found))
(89) gch2_psesy: TrEMBL: Q882G0 (Pseudomonas syringae (pv. Tomato, second enzyme found))
(90) gch2_pseae: TrEMBL: Q9HWX4 (Pseudomonas aeruginosa)
(91) ribb_dehmu: SWISS-PROT: ribb_dehmu (Dehalospirillum multivorans)
(92) gch2_xylfa: TrEMBL: Q87D69 (Xylella fastidiosa (strain Temecula1/ATCC 700964))







TABLE 4







Positions/amino acid residues corresponding to positions


V261, G270, A276, Q279, K308, and M347 of RibA of


B. subtilis as of SEQ ID NO: 2. The numbers in the left


column refer to the different organisms (see above).









SEQ ID NO



DNA; protein


















(1)
V261
G270
A276
Q279
K308
M347
1; 2


(2)
T181
G190
A196
L199
N228
I267


(3)
T126
G135
A141
L144
N182
I221
32; 33


(4)
N153
G162
A168
L171
N211
V250


(5)
T255
G264
A270
L273
N305
I344


(6)
T176
G185
A191
L194
N223
I262


(7)
V139
G248
A254
M257
K287
I326


(8)
A73
G82
A88
Q91
A121
V160


(9)
A60
G69
A75
R78
A106
M145


(10)
A60
G69
A75
R78
A106
M145


(11)
T151
G160
A166
T169
E297
I336


(12)
V245
G254
F260
Y263
S291
V330


(13)
V267
G276
A282
Y285
A315
V354


(14)
I267
G276
A282
Y285
A315
V354


(15)
I272
G281
A287
Y290
A320
I359


(16)
I272
G281
A287
Y290
A320
I359


(17)
I91
G100
S106
Q109
N139
M178


(18)
I299
G308
A314
Q317
N347
M386


(19)
I295
G304
A310
L313
N343
M382


(20)
V61
G70
A76
K79
R109
V148


(21)
A60
G69
A75
A78
H107
V146


(22)
A60
G69
A75
A78
H107
V146


(23)
A59
G68
A74
A77
E106
L145


(24)
A59
G68
A74
A77
E106
L145


(25)
A61
G70
A76
A79
S108
I147


(26)
A61
G70
A76
A79
S108
V147


(27)
A61
G70
A76
A79
S108
V147


(28)
A80
G89
A95
Q98
A127
V166


(29)
A59
G68
A74
Q77
A106
V145
34; 35


(30)
A59
G68
A74
H77
A106
V145


(31)
A59
G68
A74
R77
A106
V145


(32)
A57
G66
S72
R75
A104
I143


(33)
A59
G68
A74
R77
S106
I145


(34)
A59
G68
A74
H77
S106
I145


(35)
A60
G69
A75
E78
A107
I146


(36)
V279
G288
A294
M297
Q327
M366


(37)
V269
G278
A284
M287
Q317
M356


(38)
V281
G290
S296
M299
Q329
I368


(39)
V273
G282
S288
L291
Q321
L360
36; 37


(40)
V274
G283
S289
I292
S322
A361


(41)
I259
G268
S274
Y277
E305
I344


(42)
I263
G272
S276
Y279
E309
I348


(43)
A264
G273
A279
Q282
E311
I350


(44)
A262
G271
A277
K280
S309
L348


(45)
V261
G270
A276
Q279
H308
I347


(46)
V261
G270
A276
M279
H308
L347


(47)
V264
G273
A279
A282
M311
V350


(48)
I261
G270
A276
R279
N308
I347


(49)
A301
R310
A316
M319
S348
I387


(50)
A265
R274
A280
M283
S312
I351


(51)
A267
R276
A282
M285
S315
I353


(52)
V261
G270
A276
Q279
R308
M347
38; 39


(53)
V260
G269
A275
Q278
K307
L346
40; 41


(54)
V264
G273
A279
Q282
K311
M350
42; 43


(55)
V244
G253
A259
K262
K291
I330


(56)
A265
G274
A280
A283
N312
I351


(57)
T267
G276
A282
M285
N314
M353


(58)
V270
R279
A285
M288
E317
M356


(59)
I263
G272
A278
M281
N310
M349


(60)
A269
G278
A284
A287
A316
L355


(61)
I265
G274
A281
M283
K314
M351


(62)
A260
G269
S276
Q278
A307
V346


(63)
V265
G274
A280
E283
A311
I350


(64)
A283
G292
A298
A301
S330
V369


(65)
V262
G271
A277
K280
A309
V348


(66)
V70
G79
S85
L88
R117
V156


(67)
V66
G75
A81
R84
A112
L151


(68)
G61
G70
T76
I79
K108
I147


(69)
L250
G259
A265
E268
R297
V336


(70)
V264
—
Y274
K277
K304
I340


(71)
V264
—
I274
R277
K304
I340


(72)
V264
—
I275
R278
R305
I345


(73)
V264
—
I275
R278
R305
I345


(74)
V264
—
I274
A277
—
I340


(75)
I261
—
V271
H274
—
I330


(76)
L262
S271
A277
V280
D303
M338


(77)
L285
S294
A300
A303
Q327
M362


(78)
F263
S271
A277
H280
D303
L336


(79)
L262
G271
A277
A280
R304
L339


(80)
L262
G271
A277
A280
R304
L339


(81)
V261
S271
A277
R280
R303
M343


(82)
L261
S271
A277
R280
R303
M343


(83)
L261
S271
A277
R280
R303
M343


(84)
I261
S271
A277
R280
R303
M343


(85)
L260
S270
A276
R279
K302
M343


(86)
I262
—
A275
R278
K301
M341


(87)
I262
—
A275
R278
Q301
I339


(88)
L262
N272
A278
K281
R305
L342


(89)
L262
N272
A278
R281
R305
L342


(90)
L262
R270
A276
K279
H303
M339


(91)
L269
Y276
A282
Y285
—
I324


(92)
L230
G239
S245
T248
G277
I316









The examples shown in Table 4 serve as illustration of the principle. Corresponding residues can be determined for all other GTP cyclohydrolase II amino acid sequences that are homologous to any one of the sequences shown in Table 4.

## Claims

1. A method for producing riboflavin, a riboflavin precursor, FMN, FAD, or a derivative thereof comprising:
culturing a host cell in a suitable medium, the host cell comprising a polynucleotide comprising a nucleotide sequence which codes for a modified GTP cyclohydrolase II from Bacillus subtilis, wherein (i) the specific activity of the modified enzyme is increased in comparison to the corresponding non-modified enzyme and (ii) the amino acid sequence of the modified enzyme comprises one or more mutations(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308, and/or 347 of SEQ ID NO: 2 and combinations of the one or more mutations(s) thereof such that said modified enzyme includes from 1 to 6 position substitutions selected from: Alanine at an amino acid position corresponding to the position 261, Alanine or Arginine at an amino acid position corresponding to the position 270, Threonine at an amino acid position corresponding to the position 276, Arginine at an amino acid position corresponding to the position 279, Arginine at an amino acid position corresponding to the position 308, and Isoleucine at an amino acid position corresponding to the position 347; said modified enzyme exhibiting at least 98% identity to SEQ ID NO: 2, and
optionally separating riboflavin, a riboflavin precursor, FMN, FAD, or a derivative thereof from the medium.

2. A method for increasing the production of riboflavin, a riboflavin precursor, FMN, FAD, or a derivative thereof by introducing into a host cell a modified GTP cyclohydrolase II from Bacillus subtilis, wherein
(i) the specific activity of the modified enzyme is increased in comparison to the corresponding non-modified enzyme, and
(ii) the amino acid sequence of the modified enzyme comprises one or more mutations(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308, and/or 347 of SEQ ID NO: 2 and combinations of the one or more mutation(s) thereof such that said modified enzyme includes from 1 to 6 position substitutions selected from: Alanine at an amino acid position corresponding to the position 261, Alanine or Arginine at an amino acid position corresponding to the position 270, Threonine at an amino acid position corresponding to the position 276, Arginine at an amino acid position corresponding to the position 279, Arginine at an amino acid position corresponding to the position 308, and a sixth mutation comprises an Isoleucine at an amino acid position corresponding to the position 347, said modified enzyme exhibiting at least 98% identity to SEQ ID NO: 2.

3. A method for increasing the production of riboflavin, a riboflavin precursor, FMN, FAD, or a derivative thereof by introducing into a host cell a polynucleotide comprising a nucleotide sequence which codes for a modified GTP cyclohydrolase II from Bacillus subtilis, wherein
(i) the specific activity of the modified enzyme is increased in comparison to the corresponding non-modified enzyme, and
(ii the amino acid sequence of the modified enzyme comprises one or more mutations(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308, and/or 347 of SEQ ID NO: 2 and combinations of the one or more mutation(s) thereof such that said modified enzyme includes from 1 to 6 position substitutions selected from: Alanine at an amino acid position corresponding to the position 261, Alanine or Arginine at an amino acid position corresponding to the position 270, Threonine at an amino acid position corresponding to the position 276, Arginine at an amino acid position corresponding to the position 279, Arginine at an amino acid position corresponding to the position 308, and a sixth mutation comprises an Isoleucine at an amino acid position corresponding to the position 347, said modified enzyme exhibiting at least 98% identity to SEQ ID NO: 2.

4. A method for producing riboflavin, a riboflavin precursor, FMN, FAD, or a derivative thereof comprising:
culturing a host cell in a suitable medium, the host cell comprising a polynucleotide comprising a nucleotide sequence which codes for a modified GTP cyclohydrolase II from Bacillus subtilis, wherein (i) the specific activity of the modified enzyme is increased in comparison to the corresponding non-modified enzyme and (ii) the amino acid sequence of the modified enzyme consisting of one or more mutations(s) on amino acid position(s) corresponding to positions 261, 270, 276, 279, 308, and/or 347 of SEQ ID NO: 2 and combinations of the one or more mutations(s) thereof such that said modified enzyme includes from 1 to 6 position substitutions selected from: Alanine at an amino acid position corresponding to the position 261; Alanine or Arginine at an amino acid position corresponding to the position 270; Threonine at an amino acid position corresponding to the position 276; Arginine at an amino acid position corresponding to the position 279; Arginine at an amino acid position corresponding to the position 308, and Isoleucine at an amino acid position corresponding to the position 347; said modified enzyme exhibiting at least 98% identity to SEQ ID NO: 2, and
optionally separating riboflavin, a riboflavin precursor, FMN, FAD, or a derivative thereof from the medium.