WO2010072902A1 - Conversion of hexuronic acid to hexaric acid - Google Patents

Conversion of hexuronic acid to hexaric acid Download PDF

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WO2010072902A1
WO2010072902A1 PCT/FI2009/051029 FI2009051029W WO2010072902A1 WO 2010072902 A1 WO2010072902 A1 WO 2010072902A1 FI 2009051029 W FI2009051029 W FI 2009051029W WO 2010072902 A1 WO2010072902 A1 WO 2010072902A1
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host
acid
nucleotide sequence
enzyme
seq
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PCT/FI2009/051029
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French (fr)
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Hannu Boer
Satu Hildich
Peter Richard
Merja Penttilä
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Valtion Teknillinen Tutkimuskeskus
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Priority to US13/141,736 priority Critical patent/US8895273B2/en
Priority to PL09796407T priority patent/PL2376620T3/en
Priority to BRPI0923653-8A priority patent/BRPI0923653B1/en
Priority to EP09796407.6A priority patent/EP2376620B1/en
Publication of WO2010072902A1 publication Critical patent/WO2010072902A1/en

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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
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/40—Preparation of oxygen-containing organic compounds containing a carboxyl group including Peroxycarboxylic acids
    • C12P7/44—Polycarboxylic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0006—Oxidoreductases (1.) acting on CH-OH groups as donors (1.1)
    • 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
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/40—Preparation of oxygen-containing organic compounds containing a carboxyl group including Peroxycarboxylic acids
    • C12P7/58—Aldonic, ketoaldonic or saccharic acids

Definitions

  • the present invention relates to a method and microbial host strain for converting a hexuronic acid to a hexaric acid.
  • the invention relates to the conversion of D-galacturonic acid to meso-galactaric acid (mucic acid).
  • D-galacturonic acid is the major component of pectin, a low price raw material enriched e.g. in sugar beet pulp and citrus peel, and a carbon source for microorganisms living on decaying plant material.
  • D- glucuronic acid and D-mannuronic acid are components for example in woody materials and algae.
  • D-galacturonate D-galacturonic acid
  • the isomerase pathway that is present in e.g. Escherichia coir. This pathway consists of five enzymes converting D-galacturonate to pyruvate and D- glyceraldehyde-3-phosphate.
  • D-galacturonic acid is oxidized to mucic acid in some bacteria.
  • these bacteria could be used for the fermentation of D-galacturonic acid to mucic acid. The most likely reason for this is that the mucic acid is immediately metabolized further.
  • Mucic acid is currently a speciality chemical. It is made from galactose by oxidation with nitric acid. If produced at low price, it has the potential for a wider use. It is listed as one of the 30 most potential products produced from biomass listed in a study of the American NREL.
  • D-galacturonic acid is a cheap raw material, which is enriched in sugar beet pulp and citrus fruit peel
  • a method for catabolizing D-galacturonic acid (D-galacturonate) is needed.
  • a cheap method for producing mucic acid is needed.
  • new methods for catabolizing other hexaric acids, such as D- glucuronic acid and mannuronic acid are needed.
  • biomatehals comprising sugars, sugar acids and their derivatives.
  • Another aim of the invention is to provide methods and means for degrading and utilising biomaterials comprising hexuronic acids.
  • a further aim of the present invention is provide a method for catabolizing D- galacturonic acid.
  • an aim of the present invention is to provide a method for degrading biomaterial comprising D-galacturonic acid, such as pectin.
  • Still a further aim of the present invention is to provide a method for converting D- galacturonic acid to mucic acid.
  • One further aim of the invention is to provide a method for degrading and utilising biomaterial comprising D-glucuronic acid
  • One further aim of the invention is to provide a method for degrading and utilising biomaterial comprising D-mannuronic acid.
  • Still a further aim of the present invention is to provide a method for converting D- glucuronic acid to D-glucahc acid and/or D-mannuronic acid to D-mannaric acid.
  • the present invention is based on the idea that a microbial host can be ge- netically modified to convert hexuronic acid to hexaric acid. This can be achieved by introducing a nucleotide sequence encoding uronate dehydrogenase enzyme (EC 1.1.1.203) into the host strain and express said nucleotide sequence in the host strain.
  • a recombinant microbial strain can be used to degrade and utilise biomaterials comprising hexuronic acids.
  • the host is a eukaryotic host.
  • the host is a fungus host, more preferably a filamentous fungus host.
  • a fungus host naturally consuming hexuronic acid is genetically modified so that it can not consume it any more.
  • the fungus host is genetically modified to produce uronate dehydrogenase enzyme (EC 1.1.1.203) and the host is capable of oxidizing hexuronic acid to hexaric acid. More specifically the fungus host is capable of converting D- galacturonic acid to mucic acid. The fungus host is also capable of converting D-glucuronic acid to D-glucaric acid and D- mannuronic acid to D-mannahc acid.
  • mucic acid is made from galactose by oxidation with nitric acid.
  • the new process would be a fermentation in which only air is utilised for the oxidation.
  • the process would be cheaper, since no chemicals are used.
  • Galacturonic acid is cheaper than galactose. With this method mucic acid can become a cheap bulk product.
  • Figure 1 shows the bacterial pathway for D-galacturonic acid catabolism.
  • the first three metabolites are represented in Fischer projection.
  • the C1 of the meso- galactarate (mucic acid) in this representation is the C6 of the 3-deoxy-2-keto-L- threo-hexarate.
  • the D-galacturonate dehydrogenase and the 2,5 dioxovalerate dehydrogenase are using NAD as a cofactor.
  • Figure 2 shows the fungal pathway for D-galacturonic acid catabolism.
  • the metabolites are represented in Fischer projection, which means that the C1 of the D- galacturonate becomes the C6 of the L-galactonate.
  • the D-galacturonate reductase can be specific for their NADPH requirement or unspecific accepting NADH of NADPH depending on the organism.
  • Figure 3 shows the open reading frame of uro1 gene from Agrobacte ⁇ um tumefa- ciens.
  • Figure 4 shows the amino acid sequence encoded by uro1 gene.
  • Figure 5 shows the plasmid pRSET-A-53-pyrG_A Figure 6.
  • the ATCC1015-pyrG (parental strain) and mutant strains (two clones obtained) were grown on a medium in the presence of 2 % D-galacturonic acid asa sole carbon source. The mutant strains were not able to grow under these conditions.
  • Figure 7 shows plasmid GUDH_A-tum.
  • Figure 8 shows plasmid pCL2-Amfds+GU-DH
  • Figure 9 shows the nucleotide sequence encoding uronate dehydrogenase from
  • Figure 10 shows the encoded amino acid sequence.
  • Figure 11 shows plasmid URO-DH.
  • Figure 12 shows plasmid pCL2-AMDS+URO-DH
  • the expression "uronate dehydrogenase enzyme” designates an enzyme classified as EC 1.1.1 .203 by the enzyme classification.
  • D-galacturonic acid (D-galacturonate) is known to be catabolized through the following pathways:
  • Bacterial pathway for D-galacturonic acid catabolism The isomerase pathway that is present in e.g. Escherichia coir. This pathway consists of five enzymes converting D-galacturonate to pyruvate and D- glyceraldehyde-3-phosphate. The intermediate metabolites are D-tagaturonate, D- altronate, 3-Deoxy-D-eryf/?ro-hex-2-ulosonate and 3-Deoxy-D-erythro-hex-2- ulosonate-6-phosphate.
  • the enzymes are uronate isomerase (EC 5.3.1 .12), NADH-utilizing D-tagaturonate reductase (EC 1.1.1.5), altronate dehydratase (EC 4.2.1.7), 3-Deoxy-D-eryf/?ro-hex-2-ulosonate kinase (EC 2.7.1.45) and 3-Deoxy-D- eryf/?ro-hex-2-ulosonate-6-phosphate aldolase (EC 4.1.2.14).
  • the oxidative pathway that is present in e.g. Agrobacterium tumefaciens In this bacterial pathway D-galacturonic acid is first oxidized to meso-galactahc acid (mucic acid). This was described for Pseudomonas and for Agrobacterium tume- faciens ( Figure 1 ). An NAD dependend dehydrogenase is induced in A. tumefaciens cells growing on D-galacturonic acid. The partially purified enzyme showed activity with D-galacturonic and D-glucuronic acid (Chang and Feingold 1969). The immediate reaction product is probably a galactahc acid lactone (or D-glucaric acid lactone), which hydrolyses spontaneously.
  • the hydrolysed reaction product is in general the more stable form; the reverse reaction of the D-galacturonate dehydrogenase is consequently not observed.
  • the reverse reaction is only observed at acidic pH were galactahc acid lactone is present (Wagner and Hollmann 1976).
  • meso-Galactahc acid (mucic acid) undergoes a dehydratation in the next step, and the reaction product is 3-Deoxy-2-keto-L-f/?reo-hexaric acid (Chang and Feingold 1970).
  • the following steps involve a dehydratation and a decarboxylation and the reaction product is 2-ketoglutarate semialdehyde (2,5-dioxovalerate) (Chang and Feingold 1970).
  • the dehydratation and decarboxylation is executed by a single en- zyme (EC 4.2.1.41 ) which was described in more detail in Pseudomonas acido- vorans (Jeffcoat 1975).
  • 2-Ketoglutarate semialdehyde is subsequently oxidized to 2-ketoglutarate which is a metabolite in numerous pathways. Only the enzyme activities of these enzymes have been described. The corresponding genes have been identified in neither A. tumefaciens nor P. acidovorans or any other microorganism.
  • jecorina gar2
  • the second enzyme in this pathway a dehydratase, splits a water molecule from L-galactonic acid to generate 3-Deoxy-L-threo-hex-2-ulosonate (2-keto-3-deoxy-L-galactonic acid) (Kuorelahti et al. 2006). This enzyme reaction is not reversible. A deletion of the corresponding gene, lgd 1 , in the mould H.
  • jecorina prevented the mould from growing on D-galacturonic acid, however when grown on a dif- ferent carbon source, the deletion strain was converting D-galacturonate to L-galactonate (Kuorelahti et al. 2006).
  • the third enzyme in the D- galacturonic acid pathway is the 3-Deoxy-L-threo-hex-2-ulosonate aldolase which is splitting the substrate 3-Deoxy-L-threo-hex-2-ulosonate into pyruvate and L-glyceraldehyde (Hilditch et al. 2007).
  • L-Glyceraldehyde is converted to glycerol by the fourth enzyme of the pathway, an NADPH dependent reductase.
  • a gene coding for an enzyme with this activity was identified in H. jecorina (Liepins et al. 2006).
  • This enzyme, GLD1 in H. jecorina was not reversible, i.e. the purified enzyme did not exhibit activity with glycerol and NADP.
  • Martens-Uzonova analysed the tran- scriptome (the transcription of all genes) in the mould A. niger. In this work different carbon sources were compared including D-galacturonic acid, poly- galacturonic acid and sugar beet pulp.
  • a nucleotide sequence encoding uronic acid dehydrogenase is meant a gene encoding said enzyme, or a shortened or modified form of said gene being a functional equivalent of said gene.
  • nucleotide sequence includes both genome and cDNA.
  • a nucleotide sequence encoding uronate dehydrogenase enzyme EC 1.1.1.203 of the present invention can be isolated from any organism producing this enzyme comprising eukaryotes and including animals (and man), plants, fungi, yeasts or prokaryotes including bacteria.
  • a nucleotide sequence encoding uro- nate dehydrogenase enzyme of the present invention is isolated from a microbial source, such as from bacteria or fungi, in particular from bacteria.
  • a nucleotide sequence encoding uronate dehydrogenase enzyme of the present invention is obtainable from genus Agrobacterium, more preferably from A. tumefaciens.
  • a nucleotide sequence encoding the enzyme is obtainable from a commercial culture collection strain C 58, ATCC, American Type Culture Collection.
  • a nucleotide sequence encoding uronate dehydrogenase enzyme is ob- tainable from genus Pseudomonas.
  • a nucleotide sequence encoding the enzyme is available as Gen- Bank accession number EU377538.
  • nucleotide sequence encoding uronate dehydrogenase enzyme of the present invention is not restricted to the genus Agrobacte ⁇ um or to the species A. tumefaciens or is not restricted to genus or species of Pseudomonas.
  • a person skilled in the art can find and isolate a nucleotide sequence encoding uronate dehydrogenase enzyme of the present in- vention from other genera of bacteria or fungi or from other organisms.
  • Organisms capable of producing uronate dehydrogenase enzyme can be screened, the activity on various substrates can be determined, and the enzyme characterized.
  • Nucleotide sequences encoding uronate dehydrogenase enzyme in various organisms can be isolated and the amino acid sequences encoded by the nucleotide sequences can be compared with the amino acid sequence of the uronate dehydrogenase enzyme isolated and characterized in the Examples here.
  • a person skilled in the art can also identify a conserved region in the nucleotide or amino acid sequence and clone a gene fragment using PCR techniques. After se- quencing the fragment the complete gene can be obtained for example by using cDNA library in a vector as described by Richard et al. (2001 ).
  • a nucleotide sequence encoding uronate dehydrogenase enzyme can be identified also by nucleic acid hybridization.
  • Standard molecular biology methods can be used in the cloning of the uronate dehydrogenase enzyme i.e. in the isolation and enzyme treatments of DNA, in E. coli transformations, the isolation of a fragment comprising the uronate dehydrogenase gene by amplification in a PCR reaction (Coen D M, 2001 ) and in the techniques for codon change.
  • the basic methods used are described in the stan- dard molecular biology handbooks, e.g. Sambrook et al. (1989) and Sambrook and Russell (2001 ). Insertion of the nucleotide sequence under a strong promoter in an expression vector, transfer of the vector into suitable host cells and cultivation of the host cells in conditions provoking production of said enzyme. Methods for protein production by recombinant technology in different host systems are well known in the art (Gellissen, 2005).
  • a homologous nucleotide sequence is meant a nucleotide sequence originat- ing from the same species as the host.
  • a heterologous nucleotide sequence is meant a nucleotide sequence from another species as the host or from other genera as the host. If the host organism is prokaryotic host, for example a bacterial host, such as E. coli, Agrobacte ⁇ um or Pseudomonas, the nucleotide sequence encoding uronate dehydrogenase may be homologous. If the host organism is a eukaryotic organism, for example a fungus, the heterologous nucleotide sequence may mean a nucleotide sequence from a prokaryote, such as from bacteria.
  • nucleotide sequence of a gene do not significantly change the catalytic properties of the encoded protein.
  • many changes in the nucleotide sequence do not change the amino acid sequence of the encoded protein.
  • an amino acid sequence may have variations, which do not change the functional properties of a protein, in particular they do not prevent an enzyme from carrying out its catalytic function.
  • Such variations in the nucleotide sequence or DNA molecules or in an amino acid sequence are known as "functional equivalents", because they do not significantly change the function of the gene to encode a protein with a particular function, e.g. catalyzing a particular reaction or, respectively, change the particular function of the protein.
  • functional equivalents including fragments, of the nucleotide sequence SEQ ID NO:3 or 19, and of the amino acid sequence SEQ ID NO:4 or 20, respectively, are encompassed within the scope of invention.
  • nucleotide sequences that are capable of hybridizing with the identified sequences under intermediate or high stringency conditions.
  • intermediate stringency hydhdisation condi- tions can be performed in a hybridization mixture containing 6xSSC (0.9 M NaCI in 0.09 M sodium citrate, pH 7), 0.5% sodium dodecyl sulfate (SDS), 5x Denhardt ' s solution and 100 ⁇ /ml of Herring Sperm DNA at 50 ° C.
  • High stringency hybridization can be performed for example in the same hybridization mix at 68 ° C.
  • identity is here meant the identity between two amino acid sequences compared to each other from the first amino acid encoded by the corresponding gene to the last amino acid.
  • the identity of the full-length sequences is measured by using Needleman-Wunsch global alignment program at EMBOSS (European Molecular Biology Open Software Suite; Rice et al., 2000) program package, version 2.9.0, with the following parameters: EMBLOSUM62, Gap penalty 10.0, Extend penalty 0.5.
  • enzymes or polypeptides which comprise amino acid sequences which have uronate dehydrogenase activity and which show at least 65 % identity to the amino acid sequence SEQ ID NO:4 or
  • Preferred enzymes comprise amino acid sequences which show at least 70 %, more preferably at least 75 %, even more preferably at least 80 % identity. Still more preferable the amino acid sequences show at least 85 %, more preferably at least 90 %, still more preferably at least 95 %, most preferably at least 98 % identity to the amino acid sequence SEQ ID NO:4 or SEQ ID NO:20.
  • a nucleotide sequence encoding uronate dehydrogenase is identified and expressed in a host microorganism.
  • the host may be prokaryotic or eukaryotic host.
  • the host is eukaryotic, more preferably a fungal host, most preferably a filamentous fungal host.
  • the nucleotide sequence encoding uronate dehydrogenase encodes preferably uronate dehydrogenase of the oxidative pathway for uronic acid catabo- lism of bacteria.
  • the invention is not restricted to genetically modifying moulds or yeasts.
  • the nucleic acid sequence encoding the uronate dehydrogenase enzyme can be expressed in any organism, such as bacteria, plants or higher eukaryotes by applying the genetic tools suitable and known in the art for that particular organism.
  • the microorganism should therefore be interpreted broadly to include also cell of higher organisms.
  • the present invention was exemplified by identifying and expressing a nucleotide sequence encoding uronic acid dehydrogenase in a fungal microorganism.
  • the recombinant organism was shown to be able to convert D-galacturonic acid to mucic acid (meso-galactaric acid) and D-glucuronic acid to sacchraric acid (D- glucaric acid).
  • the nucleotide sequence encoding uronic acid dehydrogenase was from bacterial origin.
  • uronate dehydrogenase in a fungal host is of advantage, since many fungal hosts, in particular moulds, produce pectinolytic enzymes.
  • Suitable fungal hosts are host strains from for example Fusa ⁇ um, Aspergillus and Hy- pocrea (earlier T ⁇ choderma) genera, preferably Aspergillus and Hypocrea.. More specifically suitable host strains belong to H. jecorina or A. niger species.
  • the production of pectinolytic enzymes would facilitate the making of D-galacturonic acid from pectin.
  • Suitable expression and production host systems are for example the production system developed for the fungus host Trichoderma (EP 244 234) (species of Hypocrea were earlier classified to Trichoderma), or Aspergillus production system, such as A. oryzae or A. niger (WO 9708325 and WO 9533836, US 5,843,745, US 5,770,418), or the production system developed for Fusarium, such as F. ox- ysporum (Malardier et al., 1989).
  • the host organism of the present invention might be naturally utilizing hexuronic acids. To prevent the natural pathway from competing for hexuronic acid the competing pathways can be knocked out.
  • the nucleotide sequence encoding the enzyme can be inactivated for example by preventing its expression or by mutation or deletion of the coding sequence. These techniques typically makes use of the nucleotide sequence of the coding sequence or of the nucleotide sequence adjacent to the coding sequence.
  • the coding sequence of the enzyme can be inactivated in any microorganism having said nucleotide sequence.
  • the knocking out of a natural pathway for utilisation of D-galacturonic acid can be done for example by deleting the D-galacturonic acid reductase.
  • gar1 and gaaA deletion mutants survive in the presence of D- galacturonic acid. It could have been expected that such a deletion causes D- galacturonic acid to be toxic similar to a pgi1 deletion in S. cerevisiae.
  • the pgi1 gene codes for the phosphofructo isomerase, the deletion of which results in glucose toxicity.
  • the immediate reaction product of uronic acid dehydrogenase is probably the galactarate lactone (Wagner and Hollmann 1976). The lactone is hydrolysing to galactarate spontaneously; however it might be ad- vantageous to coexpress a lactonase that would facilitate the hydrolysis of the lactone.
  • the transport of hexuronic acid into the cell might slow down the conversion of hexuronic acids to hexaric acids.
  • the D-galacturonic acid dehydrogenase is expressed in a host, which is not naturally utilising D-galacturonic acid, there is no need to knock out competing pathways.
  • the transport of D- galacturonic acid into the cell might slow down the conversion of D-galacturonic acid to mucic acid.
  • the expression of genes coding for D-galacturonic acid transport molecules can facilitate the conversion of uronic acids.
  • the host is yeast, such as S. cerevisiae
  • the introduction of a transporter to facilitate the transport of D-galacturonic acid, D- glucuronic acid and7or D-mannuronic acid or into the cell is recommended.
  • nucleic acid sequence encoding the uronate dehydrogenase enzyme is introduced into a host.
  • nucleotide sequence is typically operable linked to regulatory regions facilitating the expression of the nucleotide sequence, such as a promoter and signal sequence.
  • the vector can be for example a virus, such as a bacteriophage or a plasmid.
  • Suitable biomaterial for the invention is biomass comprising sugar, sugar acids or derivatives thereof, in particular comprising hexuronic acids.
  • Suitable biomaterial is for example sugar beet pulp, which comprises pectin. Also other pectin comprising materials may be used.
  • Other suitable biomaterials are effluents and side streams of pulp and paper industry or biomaterial comprising algae.
  • a microbial host strain genetically modified to express uronate dehydrogenase enzyme (EC 1 .1 .1 .203) is contacted with a biomaterial comprising hexuronic acid in order to convert at least a portion of the hexuronic acid to hexaric acid.
  • the conversion products are recovered.
  • biomass comprising a sugar acid or a deriva- tive thereof is fermented by a microorganism capable of converting hexuronic acid to hexaric acid and the desired compounds produced are recovered.
  • the present invention is directed to a method, which comprises cultivating a genetically modified microorganism under conditions allowing expression of the protein in the presence of hexuronic acids.
  • the present invention also comprises methods for recovery of the enzyme protein o orr r reeccoovveerrvy o off t thhee c coonnvveerrssiioonn o prroodduuccttss..
  • the invention is not only restricted to the oxidation of D-galacturonic acid to mucic acid.
  • D-glucuronic acid as well as D-mannuronic acid which is the principal component of alginate, can be oxidised to D-glucahc and D-mannahc acid respectively.
  • the uronate dehydrogenase enzyme can be used by growing the host organism on a substrate comprising hexuronic acids, such as D-galacturonic acid, D- glucuronic acid or D-mannuronic acid.
  • the culture conditions can be made suitable for the growth and proliferation of the host organism.
  • the invention is further directed to an enzyme preparation comprising the uronate dehydrogenase enzyme.
  • Such a preparation may be a crude cell extract of the genetically modified organism, a spent culture medium or the enzyme may be further purified from the cell extract or from the culture medium, whereby the prepara- tion comprises at least the enzyme in purified form.
  • the preparation may also comprise other enzymes taking part in the catabolism of sugars, or sugar acids or their derivatives.
  • the uronate dehydrogenase enzyme can be used as an enzyme preparation.
  • the term "enzyme preparation" denotes here to any enzyme product, which contains at least uronate dehydrogenase enzyme.
  • an enzyme preparation may be a spent culture medium or filtrate containing one or more uronate dehydrogenase optionally with other enzymes, an isolated uronate dehydrogenase enzyme or a mixture of one or more uronate dehydrogenase enzymes.
  • such a preparation may contain additives, such as mediators, stabilizers, buffers, preservatives, surfactants and/or culture medium components. Preferred additives are such, which are commonly used in enzyme preparations intended for the application, where the enzyme preparation is used.
  • the enzyme preparation may be in the form of liquid, powder or granulate.
  • the enzyme preparation may comprise in addition to uronate dehydrogenase, one or more other enzymes, which may be for example pectinolytic enzymes, amylases and/or cellulases. Alternatively, before, during or after the uronate dehydrogenase treatment of the present invention, another enzyme treatment may be carried out.
  • a commercial culture collection strain CS58 of Agrobacterium tumefaciens (Rhizo- bium radiobacter) was grown in a minimal medium containing D-galacturonic acid. The cells were lysed by sonication and the protein extract was then bound to a DEAE column and eluted with a linear salt gradient. The fractions were tested for D-galacturonic acid dehydrogenase activity using D-galacturonic acid and NAD reaction as the substrates by measuring the NADH production by following the absorption at 340 nm. The active fractions were concentrated and applied to a non-denaturating PAGE. After separation the active fraction was identified using zymogram staining.
  • the active fractions were identified and separated on an SDS-PAGE.
  • a 32 kDa protein band was identified as the D-galacturonic acid dehydrogenase.
  • the protein band was cut from the gel, digested with trypsin and the resulting peptides were analyzed using MALDI TOF.
  • the following peptide masses were obtained : 665.4160, 966.4224, 1020.4779, 1029.5153, 1407.4625, 1720.6669, 1740.7902 and 2082.9321. These peptide masses were then used to identify the corresponding gene in the A. tumefaciens genome.
  • the open reading frame was then amplified by PCR introducing EcoRI and BamHI restrictions sites.
  • the following primers were used ⁇ '-CACAGCAAAGACGCAGAATTCGCTTGGAAG-S' (SEQ ID NO:1 ) and 5 1 -GGCTTGGGATCCCGCTGATCATTCAGCTC-3 1 (SEQ ID NO: 2).
  • the gene was called uro1 and the sequence of the open reading frame is SEQ ID NO:3 in the sequence listing.
  • the sequence SEQ ID NO:3 encodes the amino acid sequence SEQ ID NO:4.
  • the PCR product was then ligated to a TOPO vector (Invitrogen).
  • the EcoRI - BamHI fragment was released from the TOPO vector and ligated to a yeast expression vector.
  • the expression vector was a multicopy expression vector for S. cerevisiae containing the URA3 for selection and the constitutive TPI promoter.
  • the plasmid was derived from the pYX212 plasmid (R&D Systems); it was modi- fied to have a Bam ⁇ restriction site in the multiple cloning site.
  • the derived vector was transfected to the Saccharomyces cerevisiae strain CEN. PK.
  • the S. cerevisiae strain resulting from the Example 1 was then disintegrated by vortexing with glass beads and the yeast extract analysed for D-galacturonic acid dehydrogenase activity.
  • a similar strain but with an empty plasmid was used.
  • To assay the D-galacturonic acid dehydrogenase activity the crude cell extract was mixed with 0.5 mM NAD and 4 mM D-galacturonic acid in a 50 mM Tris pH 7.5 buffer containing 0.5 mM MgC ⁇ . The activity was 0.12 units per mg of extracted protein. One unit is the activity that forms 1 ⁇ mol of product per minute. In the control strain no activity could be detected.
  • the D-galacturonic acid dehydrogenase with a histidine-tag at the N-terminal end was produced in a similar manner as in the Example 1 , except that the histidine- tag was introduced by PCR.
  • the histidine tag was introduced by PCR.
  • the following primers were used 5 1 - CCGGAATTCACCATGCACCACCATCACCATCACATGGCGAT- GAAACGGCTTCTTG -3' (SEQ ID NO:5) in sense direction and 5 1 - GGCTTGGGATCCCGCTGATCATTCAGCTC-S 1 (SEQ ID NO:6) in anti-sense.
  • the activity was measured as described in the Example 2.
  • the histidine tagged protein exhibited the same activity as the non-tagged protein in the yeast extract.
  • the histidine-tagged D-galacturonic acid dehydrogenase was then purified using a Ni-NTA-agarose (Qiagen) according to the instructions of the manufacturer. The purified enzyme gave a single band in an SDS PAGE.
  • the protein was active with D-galacturonic acid and D-glururonic acid (GIcUA).
  • the purified protein was then used to estimate the Michaelis-Menten constants.
  • Km (GIcUA) 1.1 mM Vmax (GIcUA 221 units per mg of protein) and for NAD a Km of 0.9 mM and a Vmax of 145 units per mg of protein were estimated.
  • a deletion cassette was constructed. To obtain the deletion cassette 1.5 kb areas of genomic DNA from both sides of the D- galacturonic acid reductase gene were cloned by PCR from H. jecorina genomic
  • gar1 5f GTAACGCCAGGGTTTTCCCAGTCACGACGAAGCTTATATCCACCGT- GTCCCAG (SEQ ID NO:7)
  • gar1 5r ATCCACTTAACGTTACTGAAATCTCCAACGACGCAGTTGTTTGAG-
  • CAAC (SEQ ID NO:8) gar1 3f: CTCCTTCAATATCATCTTCTGTCTCCGACTTGCATTGGTCAGAGCG-
  • GTA (SEQ ID NO:9) gar1 3r: GCGGATAACAATTTCACACAGGAAACAGCAAGCTTAAGCAGTGGAT-
  • the other elements for the construction of the deletion cassette were the hph (hy- gromycin B phosphotransferase) gene under Aspergillus trpC promoter and the elements for replication and selection in yeast and E. coli.
  • the hph containing fragment was obtained by PCR using the pCSN44 as a template and using the following primers:
  • hphF GTCGGAGACAGAAGATGATATTGAAGGAGC (SEQ ID NO:11 )
  • hphR GTTGGAGATTTCAGTAACGTTAAGTGGAT SEQ ID NO:12
  • the fragment for replication and selection in S. cerevisiae and E. coli was obtained by digesting the pRS426 with the restriction enzymes EcoRI and Xhol to release a 5,7 kb fragment.
  • the two fragments obtained by PCR that contained the flanking regions for homologous recombination were combined with the other fragments. All four DNA fragments were then transformed to the S. cerevisiae strain FY834.
  • the single plasmid obtained through homologues recombination was isolated from the S. cerevisiae strain and amplified in E. coli.
  • pCSN44, pRS426 and FY834 were obtained from Jay C. Dunlap.
  • the deletion cassette 4520 bp containing the gar1 flanking regions and the hygromycin B resistance, was then released by Hind ⁇ digestion and transformed to the H. jecorina strain QM6a. Transformants were selected for the resistance to hygromycin. Strains with a successful deletion were identified by colony PCR. To test if the mutant strains were still able to catabolise D-galacturonic acid a growth experiment was performed. The QM6a and mutant strain were grown on a medium in the presence and absence of 1 % D- galacturonic acid as described previously (Kuorelahti et al.
  • the QM6a After inoculating 10 7 spores per 50 ml the QM6a produced a dry mass of about 3 g/l in the presence and about 0.24 g/l in the absence of D-galacturonic acid after 5 days of incubation.
  • the mutant strains produced 0.4 - 0.6 g/l in the presence of D-galacturonic acid and about 0.24 g/l in the absence of D-galacturonic acid under similar condi- tions.
  • a ga ⁇ deletion strain from example 4 was used to express the A. tumefaciens D- galacturonic acid dehydrogenase uro1 from example 1.
  • the BamHI fragment containing the uro1 was released from the TOPO vector described in the Example 1 and the uro1 gene was ligated to the BamH ⁇ site of the modified pAN53-1 Notl vec- tor described by Kuorelahti et al., 2006. It was checked that the orientation of the uro1 was suitable for transcription.
  • the resulting plasmid was then cotransformed into the gar1 deletion strain with a selection plasmid pTOC202 that has the A.
  • nidulans amdS gene coding for acetamidase as a marker Transformants were selected for growth in the presence of acetamide. The transformants were also verified by PCR and by testing the crude extract of the mycelia for D-galacturonic acid dehydrogenase activity. The activity in the transformants were 1.3 - 1.5 nkat per mg of extracted protein. In the control strain no activity was detected. The transformants were also used for a fermentation experiment to convert D- galacturonic acid to mucic acid. For that purpose mutant and control strains were tested as described in Example 4 except that the medium contained 1 % D-xylose in addition to the 1 % D-galacturonic acid.
  • the D-xylose was added to allow the strains to grow since the mutant strain is unable to grow on D-galacturonic acid. After 3 days the mutant strains expressing the uro1 had produced between 1 and 1.3 g/l of mucic acid while the control strain, which only contained the gar1 deletion, did not produce detectable amounts of mucic acid.
  • deletion cassette For the deletion of the GaaA gene in Aspergillus niger a deletion cassette was constructed. To obtain the deletion cassette 1.5 kb areas of genomic DNA from both sides of the D-galacturonic acid dehydrogenase gene were cloned by PCR from A. niger genomic DNA. The following primers were used:
  • gaaA-5-F TATACTCGAGTGAATTGCACTCTTCGTACCG (SEQ ID NO: 13)
  • gaaA-5-R TATACCATGGTGTGATTGCTGTGGTGTAAAT
  • gaaA-3-F TATACCATGGCCGTTTATGATTCTGGTCCATC
  • SEQ ID NO: 15 gaaA-3-R: TATAGAATTCTCGAGTTAATTCCCTTAGCG (SEQ ID NO: 16)
  • the other element for the construction of the deletion cassette was the pyrG (orotidine-5'-phosphate decarboxylase) gene from Aspergillus niger.
  • the pyrG fragment containing its own promoter and terminator was obtained by PCR from A. niger genomic DNA. The following primers were used:
  • pyrG-del-F_n TATACCCGGGTGATTGAGGTGATTGGCGAT (SEQ ID NO: 17)
  • pyrG-del-R_n TATACCCGGGTTATCACGCGACGGACAT (SEQ ID NO: 18)
  • the Gaa/A-deletion fragments were first inserted into pRSET-A vector (Xhol-EcoRI sites) by conventional restriction-ligation cloning approach.
  • the pyrG DNA fragment was inserted into ⁇ /col site (Klenow polymerase and Antarctic phosphatase treated) created between the two gaaA deletion frag- ments.
  • Resulting construct (Fig. 3) was confirmed by restriction digestion and sequencing.
  • the deletion cassette, 4854 bp containing the gaaA flanking regions and the pyrG gene was then released by Nhe ⁇ digestion and transformed to an A. niger strain where the pyrG gene was deleted.
  • Transformants were selected for the growth in the absence of uracil. Strains with a successful deletion were identified by PCR. To test if the mutant strains were still able to catabolise D-galacturonic acid a growth experiment was performed. The ATCC1015-pyrG (parental strain) and mutant strains (two clones obtained) were grown on a medium in the presence of 2% D-galacturonic acid as a sole carbon source. The mutant strains were not able to grow under these conditions (Fig. 4).
  • the gaaA deletion strain from example 6 was used to express the A. tumefaciens D-galacturonic acid dehydrogenase uro1.
  • the uro1 gene was codon optimized for the expression in A. niger.
  • Apa ⁇ -Ech 36Il fragment from the p-GU-DH plasmid (Fig. 6) containing the uro1 gene was ligated to the Apa ⁇ -Spe ⁇ (Klenow filled-in) sites of the modified pCL2 vector containing A. nidulans amdS gene as a selection marker.
  • the resulting plasmid (Fig. 7) was then transformed into the gaaA deletion strain. Transformants were selected for the growth in presence of acetamide as a sole nitrogen source.
  • the transformants were also verified by PCR and by testing the crude extract of the mycelia for D-galacturonic acid dehydrogenase activity.
  • the crude extract of the transformants showed D-galacturonic acid dehydrogenase activity while in the control strain no activity was detected.
  • the transformants were also used for a fermentation experiment to convert D-galacturonic acid to mucic acid. For that purpose mutant and control strains were tested as described in Example 5. After 3 days the mutant strains expressing the uro1 had produced mucic acid while the control strain, which only contained the gaaA deletion, did not produce detectable amounts of mucic acid.
  • the DNA coding for uronate dehydrogenase was custom-synthesised by GE- NEART.
  • the DNA sequence is in the Sequence Listing SEQ ID NO: 19. It codes for the amino acid sequence SEQ ID NO:20.
  • the open reading frame was released by digestion with ⁇ /col and Spe ⁇ .
  • the resulting fragment was then ligated to the ⁇ /col and Nhe ⁇ sites of the pYX212 (R&D Systems) which is a multicopy yeast expression vector with PGK1 promotor and URA3 selection marker.
  • the resulting vector was then transfected to the S. cere- visiae strain CEN. PK as in the Example 1.
  • the enzyme activity was then tested as in Example 2.
  • the uronate dehydrogenase showed activity with NAD and D- galacturonic acid and with NAD and D-glucuronic acid.
  • D-galacturonic acid transporter from Aspergillus niger (Martens-Uzonova, 2008) was synthesised and a vector for the expression in S. cerevisiae was constructed.
  • the resulting plasmid was transformed to the yeast strain already containing the uronate dehydrogenase from Agrobacterium tumefaciens or from Pseudomonas. Fermentation in the presence of D-galacturonic acid resulted in the production of mucic acid.
  • the gaaA deletion strain from example 6 was used to express the uronate dehydrogenase from Pseudomonas (from example 8).
  • the gene was codon optimized for the expression in A. niger.
  • Apa ⁇ -Spe ⁇ fragment from the p-URO-DH plasmid (Fig.7) containing the uronate dehydrogenase gene was ligated to the Apa ⁇ -Spe ⁇ sites of the modified pCL2 vector containing A. nidulans amdS gene as a selection marker.
  • the resulting plasmid (Fig. 8) was then transformed into the gaaA deletion strain. Transformants were selected for the growth in the presence of acetamide as a sole nitrogen source.
  • the transformants were also verified by PCR and by testing the crude extract of the mycelia for D-galacturonic acid dehydrogenase activity.
  • the crude extract of the transformants showed D-galacturonic acid dehy- drogenase activity while in the control strain no activity was detected.
  • the transformants were also used for a fermentation experiment to convert D-galacturonic acid to mucic acid. For that purpose mutant and control strains were tested as described in Example 5. After 3 days the mutant strains expressing the uronate dehydrogenase had produced mucic acid while the control strain, which only con- tained the gaaA deletion, did not produce detectable amounts of mucic acid.

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Abstract

The present invention relates to a method and microbial host strain for converting a hexuronic acid to a hexaric acid. In particular, the invention relates to the con- version of D-galacturonic acid to meso-galactaric acid (mucic acid). The invention also concerns an isolated nucleotide sequence. According to the present method a microbial host strain genetically modified to express uronate dehydrogenase enzyme (EC 1.1.1.203)is contacted with a biomaterial comprising hexuronic acid and the conversion products are recovered. By using the recombinant microorganisms of the present invention it is possible to treat biomaterials comprising hexuronic acids and thereby decrease the amount of hexuronic acids released to the environment.

Description

CONVERSION OF HEXURONIC ACID TO HEXARIC ACID
Field of the Invention
The present invention relates to a method and microbial host strain for converting a hexuronic acid to a hexaric acid. In particular, the invention relates to the conversion of D-galacturonic acid to meso-galactaric acid (mucic acid).
Description of Related Art
Biological waste material from industry including agriculture and pulp and paper industry contains sugars and their derivatives such as sugar acids. The conversion of such waste to useful products has been of interest and a challenge in the field of biotechnology for a long time. D-galacturonic acid is the major component of pectin, a low price raw material enriched e.g. in sugar beet pulp and citrus peel, and a carbon source for microorganisms living on decaying plant material. D- glucuronic acid and D-mannuronic acid are components for example in woody materials and algae.
There are at least three different pathways known for the catabolism of D- galacturonic acid (D-galacturonate):
1 ) The isomerase pathway that is present in e.g. Escherichia coir. This pathway consists of five enzymes converting D-galacturonate to pyruvate and D- glyceraldehyde-3-phosphate.
2) The oxidative pathway that is present in e.g. Agrobacterium tumefaciens: In this bacterial pathway D-galacturonic acid is first oxidized to meso-galactaric acid (mucic acid). This was described for Pseudomonas and for Agrobacterium tumefaciens (Figure 1 ). An NAD dependent dehydrogenase is induced in A. tumefaciens cells growing on D-galacturonic acid. The enzyme has been partially purified and has shown activity with D-galacturonic and D-glucuronic acid (Chang and Feingold 1969).
3) The eukaryotic pathway that is present in Aspergillus niger and Hypocrea jecorina (Figure 2) (earlier Trichoderma reesei): In the first step of this pathway D-galacturonic acid is reduced to L-galactonic acid by an NADPH utilizing reductase in Hypocrea jecorina, GAR1 (Kuorelahti et al . 2005 and WO2006/128965). The enzyme is reversible and specific for NADPH. In Aspergillus niger a D-galacturonic acid reductase, GAAA, was identified that could use NADPH and NADH, however NADPH had a higher affinity (Mar- tens-Uzonova 2008). A gene ortholog of the A. niger gaak exists also in H. jecorina, gar2, however according to Martens-Uzonova (2008) it is not known whether it is functional.
Sugar beet pulp and citrus fruit peel are currently dried and used as cattle feed. However, since drying is very energy consuming alternative uses for biomaterial comprising hexuronic acids, in particular D-galacturonic acid, would be desirable. Also in pulp and paper industry new treatment methods for side streams comprising sugars and sugar acids are needed.
As described above in the oxidative pathway D-galacturonic acid is oxidized to mucic acid in some bacteria. However, there are no reports that these bacteria could be used for the fermentation of D-galacturonic acid to mucic acid. The most likely reason for this is that the mucic acid is immediately metabolized further.
Mucic acid is currently a speciality chemical. It is made from galactose by oxidation with nitric acid. If produced at low price, it has the potential for a wider use. It is listed as one of the 30 most potential products produced from biomass listed in a study of the American NREL.
Since D-galacturonic acid is a cheap raw material, which is enriched in sugar beet pulp and citrus fruit peel, a method for catabolizing D-galacturonic acid (D-galacturonate) is needed. In particular, a cheap method for producing mucic acid is needed. Furthermore, new methods for catabolizing other hexaric acids, such as D- glucuronic acid and mannuronic acid, are needed.
Summary of the Invention
It is an aim of the present invention to provide novel methods and means for utilisation of biomatehals comprising sugars, sugar acids and their derivatives.
Another aim of the invention is to provide methods and means for degrading and utilising biomaterials comprising hexuronic acids.
A further aim of the present invention is provide a method for catabolizing D- galacturonic acid. In particular, an aim of the present invention is to provide a method for degrading biomaterial comprising D-galacturonic acid, such as pectin.
Still a further aim of the present invention is to provide a method for converting D- galacturonic acid to mucic acid.
One further aim of the invention is to provide a method for degrading and utilising biomaterial comprising D-glucuronic acid
One further aim of the invention is to provide a method for degrading and utilising biomaterial comprising D-mannuronic acid.
Still a further aim of the present invention is to provide a method for converting D- glucuronic acid to D-glucahc acid and/or D-mannuronic acid to D-mannaric acid.
The present invention is based on the idea that a microbial host can be ge- netically modified to convert hexuronic acid to hexaric acid. This can be achieved by introducing a nucleotide sequence encoding uronate dehydrogenase enzyme (EC 1.1.1.203) into the host strain and express said nucleotide sequence in the host strain. A recombinant microbial strain can be used to degrade and utilise biomaterials comprising hexuronic acids. According to one preferred embodiment of the invention the host is a eukaryotic host. Preferably the host is a fungus host, more preferably a filamentous fungus host.
Furthermore, according to another preferred embodiment of the invention a fungus host naturally consuming hexuronic acid, is genetically modified so that it can not consume it any more. The fungus host is genetically modified to produce uronate dehydrogenase enzyme (EC 1.1.1.203) and the host is capable of oxidizing hexuronic acid to hexaric acid. More specifically the fungus host is capable of converting D- galacturonic acid to mucic acid. The fungus host is also capable of converting D-glucuronic acid to D-glucaric acid and D- mannuronic acid to D-mannahc acid.
Currently mucic acid is made from galactose by oxidation with nitric acid. The new process would be a fermentation in which only air is utilised for the oxidation. The process would be cheaper, since no chemicals are used. Galacturonic acid is cheaper than galactose. With this method mucic acid can become a cheap bulk product.
By using the recombinant microorganisms of the present invention it is possible to treat biomaterials comprising hexuronic acids and thereby decrease the amount of hexuronic acids released to the environment.
Other objects, details and advantages of the present invention will become apparent from the following drawings, detailed description and examples.
Brief Description of the Drawings
Figure 1 shows the bacterial pathway for D-galacturonic acid catabolism. The first three metabolites are represented in Fischer projection. The C1 of the meso- galactarate (mucic acid) in this representation is the C6 of the 3-deoxy-2-keto-L- threo-hexarate. In this pathway the D-galacturonate dehydrogenase and the 2,5 dioxovalerate dehydrogenase are using NAD as a cofactor. Figure 2 shows the fungal pathway for D-galacturonic acid catabolism. The metabolites are represented in Fischer projection, which means that the C1 of the D- galacturonate becomes the C6 of the L-galactonate. The D-galacturonate reductase can be specific for their NADPH requirement or unspecific accepting NADH of NADPH depending on the organism.
Figure 3 shows the open reading frame of uro1 gene from Agrobacteήum tumefa- ciens.
Figure 4 shows the amino acid sequence encoded by uro1 gene.
Figure 5 shows the plasmid pRSET-A-53-pyrG_A Figure 6. The ATCC1015-pyrG (parental strain) and mutant strains (two clones obtained) were grown on a medium in the presence of 2 % D-galacturonic acid asa sole carbon source. The mutant strains were not able to grow under these conditions. Figure 7 shows plasmid GUDH_A-tum. Figure 8 shows plasmid pCL2-Amfds+GU-DH
Figure 9 shows the nucleotide sequence encoding uronate dehydrogenase from
Pseudomonas.
Figure 10 shows the encoded amino acid sequence.
Figure 11 shows plasmid URO-DH. Figure 12 shows plasmid pCL2-AMDS+URO-DH
Detailed Description of the Preferred Embodiments
Definitions
In connection with the present invention, the expression "uronate dehydrogenase enzyme" designates an enzyme classified as EC 1.1.1 .203 by the enzyme classification.
D-galacturonic acid (D-galacturonate) is known to be catabolized through the following pathways:
1 ) Bacterial pathway for D-galacturonic acid catabolism: The isomerase pathway that is present in e.g. Escherichia coir. This pathway consists of five enzymes converting D-galacturonate to pyruvate and D- glyceraldehyde-3-phosphate. The intermediate metabolites are D-tagaturonate, D- altronate, 3-Deoxy-D-eryf/?ro-hex-2-ulosonate and 3-Deoxy-D-erythro-hex-2- ulosonate-6-phosphate. The enzymes are uronate isomerase (EC 5.3.1 .12), NADH-utilizing D-tagaturonate reductase (EC 1.1.1.5), altronate dehydratase (EC 4.2.1.7), 3-Deoxy-D-eryf/?ro-hex-2-ulosonate kinase (EC 2.7.1.45) and 3-Deoxy-D- eryf/?ro-hex-2-ulosonate-6-phosphate aldolase (EC 4.1.2.14).
2) Oxidative pathway for D-galacturonic acid catabolism in bacteria:
The oxidative pathway that is present in e.g. Agrobacterium tumefaciens: In this bacterial pathway D-galacturonic acid is first oxidized to meso-galactahc acid (mucic acid). This was described for Pseudomonas and for Agrobacterium tume- faciens (Figure 1 ). An NAD dependend dehydrogenase is induced in A. tumefaciens cells growing on D-galacturonic acid. The partially purified enzyme showed activity with D-galacturonic and D-glucuronic acid (Chang and Feingold 1969). The immediate reaction product is probably a galactahc acid lactone (or D-glucaric acid lactone), which hydrolyses spontaneously. The hydrolysed reaction product is in general the more stable form; the reverse reaction of the D-galacturonate dehydrogenase is consequently not observed. The reverse reaction is only observed at acidic pH were galactahc acid lactone is present (Wagner and Hollmann 1976). meso-Galactahc acid (mucic acid) undergoes a dehydratation in the next step, and the reaction product is 3-Deoxy-2-keto-L-f/?reo-hexaric acid (Chang and Feingold 1970).
The following steps involve a dehydratation and a decarboxylation and the reaction product is 2-ketoglutarate semialdehyde (2,5-dioxovalerate) (Chang and Feingold 1970). The dehydratation and decarboxylation is executed by a single en- zyme (EC 4.2.1.41 ) which was described in more detail in Pseudomonas acido- vorans (Jeffcoat 1975). 2-Ketoglutarate semialdehyde is subsequently oxidized to 2-ketoglutarate which is a metabolite in numerous pathways. Only the enzyme activities of these enzymes have been described. The corresponding genes have been identified in neither A. tumefaciens nor P. acidovorans or any other microorganism.
3) Eucaryotic pathway for D-galacturonic acid catabolism in fungi:
The eukaryotic pathway that is present in Aspergillus niger and Hypocrea jecorina (Figure 2): In the first step of this pathway D-galacturonic acid is reduced to L-galactonic acid by an NADPH utilizing reductase in Hypocrea jecoria, GAR1 (Kuorelahti et al. 2005 and WO2006/128965). The enzyme is reversible and specific for NADPH. In Aspergillus niger a D-galacturonic acid reductase, GAAA, was identified that could use NADPH and NADH, however NADPH had a higher affinity (Martens-Uzonova 2008). A gene ortholog of the A. niger gaaA exists also in H. jecorina, gar2, however it is not known whether it is functional (Martens-Uzonova 2008). The second enzyme in this pathway, a dehydratase, splits a water molecule from L-galactonic acid to generate 3-Deoxy-L-threo-hex-2-ulosonate (2-keto-3-deoxy-L-galactonic acid) (Kuorelahti et al. 2006). This enzyme reaction is not reversible. A deletion of the corresponding gene, lgd 1 , in the mould H. jecorina prevented the mould from growing on D-galacturonic acid, however when grown on a dif- ferent carbon source, the deletion strain was converting D-galacturonate to L-galactonate (Kuorelahti et al. 2006). The third enzyme in the D- galacturonic acid pathway is the 3-Deoxy-L-threo-hex-2-ulosonate aldolase which is splitting the substrate 3-Deoxy-L-threo-hex-2-ulosonate into pyruvate and L-glyceraldehyde (Hilditch et al. 2007). The deletion of the aldolase gene, Igd1 , in Hypocrea jecorina resulted in a strain unable to grow on D- galacturonic acid as a carbon source (Hilditch et al. 2007), however when grown on a different carbon source D-galacturonic acid was converted to 3- Deoxy-L-threo-hexulosonate (Hilditch et al. 2007). L-galactonic acid did not accumulate probably due to the activity of the L-galactonate dehydratase. Pyruvate can be metabolised trough different pathways whereas L- glyceraldehyde is not a metabolite of any known pathway.
L-Glyceraldehyde is converted to glycerol by the fourth enzyme of the pathway, an NADPH dependent reductase. A gene coding for an enzyme with this activity was identified in H. jecorina (Liepins et al. 2006). This enzyme, GLD1 in H. jecorina, was not reversible, i.e. the purified enzyme did not exhibit activity with glycerol and NADP. Martens-Uzonova analysed the tran- scriptome (the transcription of all genes) in the mould A. niger. In this work different carbon sources were compared including D-galacturonic acid, poly- galacturonic acid and sugar beet pulp. It was noticed that the four genes of this catabolic pathway, here they are called gaaA, gaaB, gaaC and gaaD, were upregulated during growth on pectin and D-galacturonic acid (Martens- Uzonova 2008). Besides the genes required for catabolism and genes cod- ing for pectinolytic enzymes also 3 genes coding for potential transport proteins were identified to be upregulated. It was suggested that these transporter proteins play a role in uptake of D-galacturonic acid (Martens- Uzonova 2008).
By " a nucleotide sequence encoding uronic acid dehydrogenase" is meant a gene encoding said enzyme, or a shortened or modified form of said gene being a functional equivalent of said gene.
The terms "nucleotide sequence", "nucleic acid sequence" and "DNA molecule" include both genome and cDNA.
A nucleotide sequence encoding uronate dehydrogenase enzyme EC 1.1.1.203 of the present invention can be isolated from any organism producing this enzyme comprising eukaryotes and including animals (and man), plants, fungi, yeasts or prokaryotes including bacteria. Preferably a nucleotide sequence encoding uro- nate dehydrogenase enzyme of the present invention is isolated from a microbial source, such as from bacteria or fungi, in particular from bacteria.
According to a preferred embodiment of the invention a nucleotide sequence encoding uronate dehydrogenase enzyme of the present invention is obtainable from genus Agrobacterium, more preferably from A. tumefaciens. According to a most preferred embodiment of the invention a nucleotide sequence encoding the enzyme is obtainable from a commercial culture collection strain C 58, ATCC, American Type Culture Collection. According to another preferred embodiment of the invention a nucleotide sequence encoding uronate dehydrogenase enzyme is ob- tainable from genus Pseudomonas. According to a most preferred embodiment of the invention a nucleotide sequence encoding the enzyme is available as Gen- Bank accession number EU377538.
The origin of a nucleotide sequence encoding uronate dehydrogenase enzyme of the present invention is not restricted to the genus Agrobacteήum or to the species A. tumefaciens or is not restricted to genus or species of Pseudomonas. By using the description provided herein, a person skilled in the art can find and isolate a nucleotide sequence encoding uronate dehydrogenase enzyme of the present in- vention from other genera of bacteria or fungi or from other organisms.
Organisms capable of producing uronate dehydrogenase enzyme can be screened, the activity on various substrates can be determined, and the enzyme characterized. Nucleotide sequences encoding uronate dehydrogenase enzyme in various organisms can be isolated and the amino acid sequences encoded by the nucleotide sequences can be compared with the amino acid sequence of the uronate dehydrogenase enzyme isolated and characterized in the Examples here. A person skilled in the art can also identify a conserved region in the nucleotide or amino acid sequence and clone a gene fragment using PCR techniques. After se- quencing the fragment the complete gene can be obtained for example by using cDNA library in a vector as described by Richard et al. (2001 ). A nucleotide sequence encoding uronate dehydrogenase enzyme can be identified also by nucleic acid hybridization.
Standard molecular biology methods can be used in the cloning of the uronate dehydrogenase enzyme i.e. in the isolation and enzyme treatments of DNA, in E. coli transformations, the isolation of a fragment comprising the uronate dehydrogenase gene by amplification in a PCR reaction (Coen D M, 2001 ) and in the techniques for codon change. The basic methods used are described in the stan- dard molecular biology handbooks, e.g. Sambrook et al. (1989) and Sambrook and Russell (2001 ). Insertion of the nucleotide sequence under a strong promoter in an expression vector, transfer of the vector into suitable host cells and cultivation of the host cells in conditions provoking production of said enzyme. Methods for protein production by recombinant technology in different host systems are well known in the art (Gellissen, 2005).
By "a homologous nucleotide sequence" is meant a nucleotide sequence originat- ing from the same species as the host. By "a heterologous nucleotide sequence" is meant a nucleotide sequence from another species as the host or from other genera as the host. If the host organism is prokaryotic host, for example a bacterial host, such as E. coli, Agrobacteήum or Pseudomonas, the nucleotide sequence encoding uronate dehydrogenase may be homologous. If the host organism is a eukaryotic organism, for example a fungus, the heterologous nucleotide sequence may mean a nucleotide sequence from a prokaryote, such as from bacteria.
It is evident that small variations in the nucleotide sequence of a gene do not significantly change the catalytic properties of the encoded protein. For example many changes in the nucleotide sequence do not change the amino acid sequence of the encoded protein. Also an amino acid sequence may have variations, which do not change the functional properties of a protein, in particular they do not prevent an enzyme from carrying out its catalytic function. Such variations in the nucleotide sequence or DNA molecules or in an amino acid sequence are known as "functional equivalents", because they do not significantly change the function of the gene to encode a protein with a particular function, e.g. catalyzing a particular reaction or, respectively, change the particular function of the protein. Thus such functional equivalents, including fragments, of the nucleotide sequence SEQ ID NO:3 or 19, and of the amino acid sequence SEQ ID NO:4 or 20, respectively, are encompassed within the scope of invention.
Within the scope of the present invention are also nucleotide sequences that are capable of hybridizing with the identified sequences under intermediate or high stringency conditions. For example, intermediate stringency hydhdisation condi- tions can be performed in a hybridization mixture containing 6xSSC (0.9 M NaCI in 0.09 M sodium citrate, pH 7), 0.5% sodium dodecyl sulfate (SDS), 5x Denhardt's solution and 100 μ/ml of Herring Sperm DNA at 50°C. High stringency hybridization can be performed for example in the same hybridization mix at 68°C. By the term "identity" is here meant the identity between two amino acid sequences compared to each other from the first amino acid encoded by the corresponding gene to the last amino acid. The identity of the full-length sequences is measured by using Needleman-Wunsch global alignment program at EMBOSS (European Molecular Biology Open Software Suite; Rice et al., 2000) program package, version 2.9.0, with the following parameters: EMBLOSUM62, Gap penalty 10.0, Extend penalty 0.5.
Within the scope of the present invention are enzymes or polypeptides which comprise amino acid sequences which have uronate dehydrogenase activity and which show at least 65 % identity to the amino acid sequence SEQ ID NO:4 or
SEQ ID NO:20. Preferred enzymes comprise amino acid sequences which show at least 70 %, more preferably at least 75 %, even more preferably at least 80 % identity. Still more preferable the amino acid sequences show at least 85 %, more preferably at least 90 %, still more preferably at least 95 %, most preferably at least 98 % identity to the amino acid sequence SEQ ID NO:4 or SEQ ID NO:20.
According to one preferred embodiment of the present invention a nucleotide sequence encoding uronate dehydrogenase is identified and expressed in a host microorganism. The host may be prokaryotic or eukaryotic host. Preferably the host is eukaryotic, more preferably a fungal host, most preferably a filamentous fungal host. The nucleotide sequence encoding uronate dehydrogenase encodes preferably uronate dehydrogenase of the oxidative pathway for uronic acid catabo- lism of bacteria.
The invention is not restricted to genetically modifying moulds or yeasts. The nucleic acid sequence encoding the uronate dehydrogenase enzyme can be expressed in any organism, such as bacteria, plants or higher eukaryotes by applying the genetic tools suitable and known in the art for that particular organism. The microorganism should therefore be interpreted broadly to include also cell of higher organisms.
The present invention was exemplified by identifying and expressing a nucleotide sequence encoding uronic acid dehydrogenase in a fungal microorganism. The recombinant organism was shown to be able to convert D-galacturonic acid to mucic acid (meso-galactaric acid) and D-glucuronic acid to sacchraric acid (D- glucaric acid). The nucleotide sequence encoding uronic acid dehydrogenase was from bacterial origin.
The expression of uronate dehydrogenase in a fungal host is of advantage, since many fungal hosts, in particular moulds, produce pectinolytic enzymes. Suitable fungal hosts are host strains from for example Fusaήum, Aspergillus and Hy- pocrea (earlier Tήchoderma) genera, preferably Aspergillus and Hypocrea.. More specifically suitable host strains belong to H. jecorina or A. niger species. The production of pectinolytic enzymes would facilitate the making of D-galacturonic acid from pectin.
Suitable expression and production host systems are for example the production system developed for the fungus host Trichoderma (EP 244 234) (species of Hypocrea were earlier classified to Trichoderma), or Aspergillus production system, such as A. oryzae or A. niger (WO 9708325 and WO 9533836, US 5,843,745, US 5,770,418), or the production system developed for Fusarium, such as F. ox- ysporum (Malardier et al., 1989).
The cloning of genes coding for the uronate dehydrogenase in two different species of filamentous fungi and a yeast was exemplified in the examples. The same approach can be used with other filamentous fungi, yeast or any microorganism.
The host organism of the present invention might be naturally utilizing hexuronic acids. To prevent the natural pathway from competing for hexuronic acid the competing pathways can be knocked out. The nucleotide sequence encoding the enzyme can be inactivated for example by preventing its expression or by mutation or deletion of the coding sequence. These techniques typically makes use of the nucleotide sequence of the coding sequence or of the nucleotide sequence adjacent to the coding sequence. The coding sequence of the enzyme can be inactivated in any microorganism having said nucleotide sequence. The knocking out of a natural pathway for utilisation of D-galacturonic acid can be done for example by deleting the D-galacturonic acid reductase.
It is therefore still another embodiment of this invention that in addition to the het- erologous expression of uronate dehydrogenase the endogenous pathway for hexuronate catabolism is interrupted. The interruption of this catabolic pathway has been exemplified by deleting D-galacturonic acid reductase, more specifically gar1 in H. jecorina and the gaaA gene in Aspergillus niger. These two genes have a low sequence homology and different kinetic properties. The gaaA has a close homologue called gar2 in H. jecorina (Martens-Uzonova 2008). Because of the redundancy of homologue sequences it was unexpected that the single deletion of gar1 or gaaA was sufficient to bring the catabolism to a halt. Another unexpected result was that the gar1 and gaaA deletion mutants survive in the presence of D- galacturonic acid. It could have been expected that such a deletion causes D- galacturonic acid to be toxic similar to a pgi1 deletion in S. cerevisiae. In the yeast S. cerevisiae the pgi1 gene codes for the phosphofructo isomerase, the deletion of which results in glucose toxicity. The immediate reaction product of uronic acid dehydrogenase is probably the galactarate lactone (Wagner and Hollmann 1976). The lactone is hydrolysing to galactarate spontaneously; however it might be ad- vantageous to coexpress a lactonase that would facilitate the hydrolysis of the lactone.
If the uronate dehydrogenase is expressed in a host, which is not naturally utilising hexuronic acids, there is no need to knock out competing pathways. However, here the transport of hexuronic acid into the cell might slow down the conversion of hexuronic acids to hexaric acids. If for example the D-galacturonic acid dehydrogenase is expressed in a host, which is not naturally utilising D-galacturonic acid, there is no need to knock out competing pathways. Here the transport of D- galacturonic acid into the cell might slow down the conversion of D-galacturonic acid to mucic acid. In this case the expression of genes coding for D-galacturonic acid transport molecules can facilitate the conversion of uronic acids. For example, if the host is yeast, such as S. cerevisiae, the introduction of a transporter to facilitate the transport of D-galacturonic acid, D- glucuronic acid and7or D-mannuronic acid or into the cell is recommended.
The enzyme activity of the uronate dehydrogenase has been described previously by Chang and Feingold (1969) and references therein. Chang and Feingold (1969) described a partly purified NAD-dependent dehydrogenase, which had activity with D-galacturonic and D-glucuronic acid.
In the present description there has been described a different procedure for the purification of the enzyme. In this description has been used the technique of tryp- tic digestion of the purified protein and subsequent MALDI-ToF analysis to identify the sizes of the protein fragments. Since the genome sequence of this organism was known, the knowledge of the protein fragments enabled us to identify the cor- responding gene. It is believed that a gene sequence coding for a uronate dehydrogenase has been described here the first time. There is an entry in the NCBI sequence database (National Center for Biotechnology Information, USA, www.ncbi.nlm.nih.gov) with the GenBank accession number EU377538 which describes an uronate dehydrogenase from Pseudomonas syringae pv. tomato str. DC3000 with the EC number EC 1.1.1.203. This database entry did not contain any further details to substantiate that the gene was indeed a uronate dehydrogenase.
Within the scope of the present invention are also genetic constructions compris- ing a suitable vector which can be used when the nucleic acid sequence encoding the uronate dehydrogenase enzyme is introduced into a host. In the construction the nucleotide sequence is typically operable linked to regulatory regions facilitating the expression of the nucleotide sequence, such as a promoter and signal sequence. The vector can be for example a virus, such as a bacteriophage or a plasmid.
In the examples strong and constitutive promoters were used for the expression of the uronate dehydrogenase. Other more or less strong promoters or regulated promoters can be used. Suitable biomaterial for the invention is biomass comprising sugar, sugar acids or derivatives thereof, in particular comprising hexuronic acids. Suitable biomaterial is for example sugar beet pulp, which comprises pectin. Also other pectin comprising materials may be used. Other suitable biomaterials are effluents and side streams of pulp and paper industry or biomaterial comprising algae.
According to an embodiment of the invention, in the method of converting hexuronic acid to hexaric acid, a microbial host strain genetically modified to express uronate dehydrogenase enzyme (EC 1 .1 .1 .203) is contacted with a biomaterial comprising hexuronic acid in order to convert at least a portion of the hexuronic acid to hexaric acid. The conversion products are recovered.
Thus, according to this embodiment, biomass comprising a sugar acid or a deriva- tive thereof is fermented by a microorganism capable of converting hexuronic acid to hexaric acid and the desired compounds produced are recovered.
In another embodiment, the present invention is directed to a method, which comprises cultivating a genetically modified microorganism under conditions allowing expression of the protein in the presence of hexuronic acids.
The present invention also comprises methods for recovery of the enzyme protein o orr r reeccoovveerrvy o off t thhee c coonnvveerrssiioonn o prroodduuccttss..
The invention is not only restricted to the oxidation of D-galacturonic acid to mucic acid. D-glucuronic acid as well as D-mannuronic acid, which is the principal component of alginate, can be oxidised to D-glucahc and D-mannahc acid respectively.
The uronate dehydrogenase enzyme can be used by growing the host organism on a substrate comprising hexuronic acids, such as D-galacturonic acid, D- glucuronic acid or D-mannuronic acid. The culture conditions can be made suitable for the growth and proliferation of the host organism. The invention is further directed to an enzyme preparation comprising the uronate dehydrogenase enzyme. Such a preparation may be a crude cell extract of the genetically modified organism, a spent culture medium or the enzyme may be further purified from the cell extract or from the culture medium, whereby the prepara- tion comprises at least the enzyme in purified form. The preparation may also comprise other enzymes taking part in the catabolism of sugars, or sugar acids or their derivatives.
The uronate dehydrogenase enzyme can be used as an enzyme preparation. The term "enzyme preparation" denotes here to any enzyme product, which contains at least uronate dehydrogenase enzyme. Thus, such an enzyme preparation may be a spent culture medium or filtrate containing one or more uronate dehydrogenase optionally with other enzymes, an isolated uronate dehydrogenase enzyme or a mixture of one or more uronate dehydrogenase enzymes. In addition to the uro- nate dehydrogenase activity, such a preparation may contain additives, such as mediators, stabilizers, buffers, preservatives, surfactants and/or culture medium components. Preferred additives are such, which are commonly used in enzyme preparations intended for the application, where the enzyme preparation is used. The enzyme preparation may be in the form of liquid, powder or granulate.
The enzyme preparation may comprise in addition to uronate dehydrogenase, one or more other enzymes, which may be for example pectinolytic enzymes, amylases and/or cellulases. Alternatively, before, during or after the uronate dehydrogenase treatment of the present invention, another enzyme treatment may be carried out.
The invention is illustrated by the following non-limiting examples. It should be understood, however, that the embodiments given in the description above and in the example are for illustrative purposes only, and that various changes and modifica- tions are possible within the scope of the claims. Example 1
Cloning and expression of the D-galacturonic acid dehydrogenase in a heterologous host
A commercial culture collection strain CS58 of Agrobacterium tumefaciens (Rhizo- bium radiobacter) was grown in a minimal medium containing D-galacturonic acid. The cells were lysed by sonication and the protein extract was then bound to a DEAE column and eluted with a linear salt gradient. The fractions were tested for D-galacturonic acid dehydrogenase activity using D-galacturonic acid and NAD reaction as the substrates by measuring the NADH production by following the absorption at 340 nm. The active fractions were concentrated and applied to a non-denaturating PAGE. After separation the active fraction was identified using zymogram staining.
The active fractions were identified and separated on an SDS-PAGE. A 32 kDa protein band was identified as the D-galacturonic acid dehydrogenase. The protein band was cut from the gel, digested with trypsin and the resulting peptides were analyzed using MALDI TOF. The following peptide masses were obtained : 665.4160, 966.4224, 1020.4779, 1029.5153, 1407.4625, 1720.6669, 1740.7902 and 2082.9321. These peptide masses were then used to identify the corresponding gene in the A. tumefaciens genome. The open reading frame was then amplified by PCR introducing EcoRI and BamHI restrictions sites. The following primers were used δ'-CACAGCAAAGACGCAGAATTCGCTTGGAAG-S' (SEQ ID NO:1 ) and 51-GGCTTGGGATCCCGCTGATCATTCAGCTC-31 (SEQ ID NO: 2). The gene was called uro1 and the sequence of the open reading frame is SEQ ID NO:3 in the sequence listing. The sequence SEQ ID NO:3 encodes the amino acid sequence SEQ ID NO:4.
The PCR product was then ligated to a TOPO vector (Invitrogen). The EcoRI - BamHI fragment was released from the TOPO vector and ligated to a yeast expression vector. The expression vector was a multicopy expression vector for S. cerevisiae containing the URA3 for selection and the constitutive TPI promoter. The plasmid was derived from the pYX212 plasmid (R&D Systems); it was modi- fied to have a Bam\λ\ restriction site in the multiple cloning site. The derived vector was transfected to the Saccharomyces cerevisiae strain CEN. PK.
Example 2 Characterization of the enzyme activity
The S. cerevisiae strain resulting from the Example 1 was then disintegrated by vortexing with glass beads and the yeast extract analysed for D-galacturonic acid dehydrogenase activity. In a control experiment a similar strain but with an empty plasmid was used. To assay the D-galacturonic acid dehydrogenase activity the crude cell extract was mixed with 0.5 mM NAD and 4 mM D-galacturonic acid in a 50 mM Tris pH 7.5 buffer containing 0.5 mM MgC^. The activity was 0.12 units per mg of extracted protein. One unit is the activity that forms 1 μmol of product per minute. In the control strain no activity could be detected.
Example 3
Characterization of the purified histidine-tagged D-galacturonic acid dehydrogenase
The D-galacturonic acid dehydrogenase with a histidine-tag at the N-terminal end was produced in a similar manner as in the Example 1 , except that the histidine- tag was introduced by PCR. To introduce the histidine tag the following primers were used 51- CCGGAATTCACCATGCACCACCATCACCATCACATGGCGAT- GAAACGGCTTCTTG -3' (SEQ ID NO:5) in sense direction and 51- GGCTTGGGATCCCGCTGATCATTCAGCTC-S1 (SEQ ID NO:6) in anti-sense.
After the expression of the histidine-tagged protein in S. cerevisiae as described in the Example 1 the activity was measured as described in the Example 2. The histidine tagged protein exhibited the same activity as the non-tagged protein in the yeast extract. The histidine-tagged D-galacturonic acid dehydrogenase was then purified using a Ni-NTA-agarose (Qiagen) according to the instructions of the manufacturer. The purified enzyme gave a single band in an SDS PAGE.
The protein was active with D-galacturonic acid and D-glururonic acid (GIcUA). The purified protein was then used to estimate the Michaelis-Menten constants. For D-galacturonic acid a Km of 0.5 mM and a Vmax of 124 units per mg of protein (Km (GIcUA) = 1.1 mM Vmax (GIcUA 221 units per mg of protein) and for NAD a Km of 0.9 mM and a Vmax of 145 units per mg of protein were estimated.
Example 4
Deletion of the D-galacturonic acid reductase in H. jecorina
For the deletion of the gaή gene a deletion cassette was constructed. To obtain the deletion cassette 1.5 kb areas of genomic DNA from both sides of the D- galacturonic acid reductase gene were cloned by PCR from H. jecorina genomic
DNA. The following primers were used: gar1 5f: GTAACGCCAGGGTTTTCCCAGTCACGACGAAGCTTATATCCACCGT- GTCCCAG (SEQ ID NO:7) gar1 5r: ATCCACTTAACGTTACTGAAATCTCCAACGACGCAGTTGTTTGAG-
CAAC (SEQ ID NO:8) gar1 3f: CTCCTTCAATATCATCTTCTGTCTCCGACTTGCATTGGTCAGAGCG-
GTA (SEQ ID NO:9) gar1 3r: GCGGATAACAATTTCACACAGGAAACAGCAAGCTTAAGCAGTGGAT-
GACTTGCTG (SEQ ID NO:10)
The other elements for the construction of the deletion cassette were the hph (hy- gromycin B phosphotransferase) gene under Aspergillus trpC promoter and the elements for replication and selection in yeast and E. coli. The hph containing fragment was obtained by PCR using the pCSN44 as a template and using the following primers:
hphF GTCGGAGACAGAAGATGATATTGAAGGAGC (SEQ ID NO:11 ) hphR GTTGGAGATTTCAGTAACGTTAAGTGGAT (SEQ ID NO:12)
to produce a PCR fragment of 1.447 bp. The fragment for replication and selection in S. cerevisiae and E. coli was obtained by digesting the pRS426 with the restriction enzymes EcoRI and Xhol to release a 5,7 kb fragment. The two fragments obtained by PCR that contained the flanking regions for homologous recombination were combined with the other fragments. All four DNA fragments were then transformed to the S. cerevisiae strain FY834. The single plasmid obtained through homologues recombination was isolated from the S. cerevisiae strain and amplified in E. coli. pCSN44, pRS426 and FY834 were obtained from Jay C. Dunlap. The deletion cassette, 4520 bp containing the gar1 flanking regions and the hygromycin B resistance, was then released by Hind\\\ digestion and transformed to the H. jecorina strain QM6a. Transformants were selected for the resistance to hygromycin. Strains with a successful deletion were identified by colony PCR. To test if the mutant strains were still able to catabolise D-galacturonic acid a growth experiment was performed. The QM6a and mutant strain were grown on a medium in the presence and absence of 1 % D- galacturonic acid as described previously (Kuorelahti et al. 2006) After inoculating 107 spores per 50 ml the QM6a produced a dry mass of about 3 g/l in the presence and about 0.24 g/l in the absence of D-galacturonic acid after 5 days of incubation. The mutant strains produced 0.4 - 0.6 g/l in the presence of D-galacturonic acid and about 0.24 g/l in the absence of D-galacturonic acid under similar condi- tions.
Example 5
Expression of the A. tumefaciens D-galacturonic acid dehydrogenase in the
H. jecorina D-galacturonic acid reductase deletion strain.
A gaή deletion strain from example 4 was used to express the A. tumefaciens D- galacturonic acid dehydrogenase uro1 from example 1. The BamHI fragment containing the uro1 was released from the TOPO vector described in the Example 1 and the uro1 gene was ligated to the BamH\ site of the modified pAN53-1 Notl vec- tor described by Kuorelahti et al., 2006. It was checked that the orientation of the uro1 was suitable for transcription. The resulting plasmid was then cotransformed into the gar1 deletion strain with a selection plasmid pTOC202 that has the A. nidulans amdS gene coding for acetamidase as a marker. Transformants were selected for growth in the presence of acetamide. The transformants were also verified by PCR and by testing the crude extract of the mycelia for D-galacturonic acid dehydrogenase activity. The activity in the transformants were 1.3 - 1.5 nkat per mg of extracted protein. In the control strain no activity was detected. The transformants were also used for a fermentation experiment to convert D- galacturonic acid to mucic acid. For that purpose mutant and control strains were tested as described in Example 4 except that the medium contained 1 % D-xylose in addition to the 1 % D-galacturonic acid. The D-xylose was added to allow the strains to grow since the mutant strain is unable to grow on D-galacturonic acid. After 3 days the mutant strains expressing the uro1 had produced between 1 and 1.3 g/l of mucic acid while the control strain, which only contained the gar1 deletion, did not produce detectable amounts of mucic acid.
Example 6
Deletion of the Aspergillus niger D-galacturonic acid dehydrogenase
For the deletion of the GaaA gene in Aspergillus niger a deletion cassette was constructed. To obtain the deletion cassette 1.5 kb areas of genomic DNA from both sides of the D-galacturonic acid dehydrogenase gene were cloned by PCR from A. niger genomic DNA. The following primers were used:
gaaA-5-F: TATACTCGAGTGAATTGCACTCTTCGTACCG (SEQ ID NO: 13) gaaA-5-R: TATACCATGGTGTGATTGCTGTGGTGTAAAT (SEQ ID NO: 14) gaaA-3-F: TATACCATGGCCGTTTATGATTCTGGTCCATC (SEQ ID NO: 15) gaaA-3-R: TATAGAATTCTCGAGTTAATTCCCTTAGCG (SEQ ID NO: 16)
The other element for the construction of the deletion cassette was the pyrG (orotidine-5'-phosphate decarboxylase) gene from Aspergillus niger. The pyrG fragment containing its own promoter and terminator was obtained by PCR from A. niger genomic DNA. The following primers were used:
pyrG-del-F_n: TATACCCGGGTGATTGAGGTGATTGGCGAT (SEQ ID NO: 17) pyrG-del-R_n: TATACCCGGGTTATCACGCGACGGACAT (SEQ ID NO: 18) The Gaa/A-deletion fragments (gaaA flanking regions) were first inserted into pRSET-A vector (Xhol-EcoRI sites) by conventional restriction-ligation cloning approach. The pyrG DNA fragment was inserted into Λ/col site (Klenow polymerase and Antarctic phosphatase treated) created between the two gaaA deletion frag- ments. Resulting construct (Fig. 3) was confirmed by restriction digestion and sequencing. The deletion cassette, 4854 bp containing the gaaA flanking regions and the pyrG gene, was then released by Nhe\ digestion and transformed to an A. niger strain where the pyrG gene was deleted.
Transformants were selected for the growth in the absence of uracil. Strains with a successful deletion were identified by PCR. To test if the mutant strains were still able to catabolise D-galacturonic acid a growth experiment was performed. The ATCC1015-pyrG (parental strain) and mutant strains (two clones obtained) were grown on a medium in the presence of 2% D-galacturonic acid as a sole carbon source. The mutant strains were not able to grow under these conditions (Fig. 4).
Example 7
Expression of the A. tumefaciens D-galacturonic acid dehydrogenase in the
A. niger D-galacturonic acid reductase deletion strain.
The gaaA deletion strain from example 6 was used to express the A. tumefaciens D-galacturonic acid dehydrogenase uro1. The uro1 gene was codon optimized for the expression in A. niger. Apa\-Ech 36Il fragment from the p-GU-DH plasmid (Fig. 6) containing the uro1 gene was ligated to the Apa\-Spe\ (Klenow filled-in) sites of the modified pCL2 vector containing A. nidulans amdS gene as a selection marker. The resulting plasmid (Fig. 7) was then transformed into the gaaA deletion strain. Transformants were selected for the growth in presence of acetamide as a sole nitrogen source. The transformants were also verified by PCR and by testing the crude extract of the mycelia for D-galacturonic acid dehydrogenase activity. The crude extract of the transformants showed D-galacturonic acid dehydrogenase activity while in the control strain no activity was detected. The transformants were also used for a fermentation experiment to convert D-galacturonic acid to mucic acid. For that purpose mutant and control strains were tested as described in Example 5. After 3 days the mutant strains expressing the uro1 had produced mucic acid while the control strain, which only contained the gaaA deletion, did not produce detectable amounts of mucic acid.
Example 8 Expression of uronate dehydrogenase from Pseudomonas
The DNA coding for uronate dehydrogenase was custom-synthesised by GE- NEART. The codes for the same amino acid as the gene with the GenBank accession number EU377538. The DNA sequence is in the Sequence Listing SEQ ID NO: 19. It codes for the amino acid sequence SEQ ID NO:20.
The open reading frame was released by digestion with Λ/col and Spe\. The resulting fragment was then ligated to the Λ/col and Nhe\ sites of the pYX212 (R&D Systems) which is a multicopy yeast expression vector with PGK1 promotor and URA3 selection marker. The resulting vector was then transfected to the S. cere- visiae strain CEN. PK as in the Example 1. The enzyme activity was then tested as in Example 2. The uronate dehydrogenase showed activity with NAD and D- galacturonic acid and with NAD and D-glucuronic acid.
Example 9
Expression of a transporter gene for D-galacturonic acid in S. cerevisiae in combination with the expression of uronate dehydrogenase.
For the expression of a D-galacturonic acid transporter in S. cerevisiae a gene coding for a
D-galacturonic acid transporter from Aspergillus niger (Martens-Uzonova, 2008) was synthesised and a vector for the expression in S. cerevisiae was constructed. The resulting plasmid was transformed to the yeast strain already containing the uronate dehydrogenase from Agrobacterium tumefaciens or from Pseudomonas. Fermentation in the presence of D-galacturonic acid resulted in the production of mucic acid. Example 10
Expression of uronate dehydrogenase from Pseudomonas in the A. niger
D-galacturonic acid reductase deletion strain.
The gaaA deletion strain from example 6 was used to express the uronate dehydrogenase from Pseudomonas (from example 8). The gene was codon optimized for the expression in A. niger. Apa\-Spe\ fragment from the p-URO-DH plasmid (Fig.7) containing the uronate dehydrogenase gene was ligated to the Apa\-Spe\ sites of the modified pCL2 vector containing A. nidulans amdS gene as a selection marker. The resulting plasmid (Fig. 8) was then transformed into the gaaA deletion strain. Transformants were selected for the growth in the presence of acetamide as a sole nitrogen source. The transformants were also verified by PCR and by testing the crude extract of the mycelia for D-galacturonic acid dehydrogenase activity. The crude extract of the transformants showed D-galacturonic acid dehy- drogenase activity while in the control strain no activity was detected. The transformants were also used for a fermentation experiment to convert D-galacturonic acid to mucic acid. For that purpose mutant and control strains were tested as described in Example 5. After 3 days the mutant strains expressing the uronate dehydrogenase had produced mucic acid while the control strain, which only con- tained the gaaA deletion, did not produce detectable amounts of mucic acid.
References:
Chang YF, Feingold DS (1969) Hexuronic acid dehydrogenase of Agrobacteήum tumefaciens. J Bacterid. 99:667-673
Chang YF, Feingold DS (1970) D-glucaric acid and galactahc acid catabolism by
Agrobacterium tumefaciens. J Bacterid. 102:85-96 Coen D. M. 2001 The polymerase chain reaction, published in Ausubel F M, Brent
R, Kingston R E, More D D, Seidman J G, Smith K. and Struhl K (eds.) Cur- rent protocols in molecular biology. John Wiley & Sons. Inc., Hoboken,
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Germany. Hilditch S, Berghall S, Kalkkinen N, Penttila M, Richard P (2007) The missing link in the fungal D-galacturonate pathway: identification of the L-threo-3-deoxy- hexulosonate aldolase. J Biol Chem. 282:26195-26201
Jeffcoat R (1975) Studies on the subunit structure of 4-deoxy-5-oxoglucarate hy- dro-lyase (decarboxylating) from Pseudomonas acidovorans. Biochem J.
145:305-309
Kuorelahti S, Jouhten P, Maaheimo H., Penttila M, Richard P (2006) L-galactonate dehydratase is part of the fungal path for D-galacturonic acid catabolism. MoI. Microbiol. 61 :1060-1068 Kuorelahti S, Kalkkinen N, Penttila M, Londesborough J, Richard P (2005) Identification in the mold Hypocrea jecorina of the first fungal D-galacturonic acid reductase. Biochemistry 44:11234-11240
Liepins J, Kuorelahti S, Penttila M, Richard P (2006) Enzymes for the NADPH- dependent reduction of dihydroxyacetone and D-glyceraldehyde and L- glyceraldehyde in the mould Hypocrea jecorina. Febs J. 273:4229-4235.
Malardier L, MJ Daboussi, J Julien, F Roussel, C Scazzocchio and Y Brygoo. 1989. Gene 15:147-156.
Martens-Uzonova E (2008) Assessment of the pectinolytic network of Aspergillus niger by functional genomics. Insight from the transchptome. In. PhD thesis, University of Wageningen, Wageningen
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Wagner G, Hollmann S (1976) Uronic acid dehydrogenase from Pseudomonas syringae. Purification and properties. Eur J Biochem. 61 :589-596

Claims

Claims
1. A method for converting hexuronic acid to hexaric acid, which comprises contacting a microbial host strain genetically modified to express uronate dehydro- genase enzyme (EC 1 .1 .1 .203) with a biomaterial comprising hexuronic acid and recovering the conversion products.
2. The method according to claim 1 , wherein the host is a eukaryotic host.
3. The method according to claim 1 or 2, wherein the host is a fungal host, preferably a fungal host being naturally capable of degrading pectin.
4. The method according to any one of claims 1 to 3, wherein the host belongs to Aspergillus or Hypocrea genera.
5. The method according to any one of claims 1 to 4, wherein D-galacturonic acid is converted to mucic acid.
6. The method according to any one of claims 1 to 5, wherein the endogenous pathway for hexuronate catabolism has been interrupted in the host.
7. The method according to claim 6, wherein the endogenous pathway of D- galacturonic acid reductase has been deleted.
8. The method according to any one of claims 1 to 3, wherein the host is a yeast host, preferably belonging to Saccharomyces genus.
9. The method according to any one of claims 1 to 8, wherein the host expresses a heterologous, preferably bacterial nucleotide sequence encoding uronate dehy- drogenase enzyme (EC 1.1.1.203).
10. The method according to claim 9, wherein the nucleotide sequence encoding uronate dehydrogenase enzyme (EC 1.1.1.203) originates from Pseudomonas or Agrobacteήum genera.
11. The method according to any one of claims 1 to 10, wherein the host expresses hexuronic acid transport molecules.
12. A method for treating biomatehal comprising hexuronic acids, which comprises that a microbial host strain genetically modified to express uronate dehydrogenase enzyme (EC 1.1.1.203), is contacted with said biomaterial under suitable culture conditions.
13. A microbial host strain, characterized in that the host strain has been geneti- cally modified to express uronate dehydrogenase enzyme (EC 1.1.1.203) and said host strain is capable of converting hexuronic acid to hexaric acid.
14. The host according to claim 15, wherein the host is a eukaryotic host.
15. The host according to claim 15 or 16, wherein the host is a fungal host, preferably a fungal host being naturally capable of degrading pectin.
16. The host according to any one of claims 13 to 15, wherein the host belongs to Aspergillus or Hypocrea genera.
17. The host according to any one of claims 13 to 16, wherein the host is capable of converting D-galacturonic acid to mucic acid.
18. The host according to any one of claims 13 to 17, wherein the endogenous pathway for hexuronate catabolism has been interrupted in the host.
19. The host according to claim 18, wherein the endogenous pathway of D- galacturonic acid reductase has been deleted.
20. The host according to any one of claims 13 to 19, wherein the host is a yeast host, preferably belonging to Saccharomyces genus.
21. The host according to any one of claims 13 to 20, wherein the host has been genetically modified to express a nucleotide sequence selected from the group comprising:
(a) a nucleotide sequence encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 4 or SEQ ID NO:20;
(b) a nucleotide sequence comprising the coding sequence of the nucleotide sequence SEQ ID NO:3 or SEQ ID NO:19; (c) a nucleotide sequence the coding sequence of which differs from the coding sequence of the nucleotide sequence of (a) or (b) due to the degeneracy of the genetic code;
(d) a nucleotide sequence which hybridizes under stringent conditions to any one of the sequences (a), (b) or (c); and
(e) an isolated nucleotide sequence encoding a polypeptide having uro- nate dehydrogenase enzyme (EC 1.1.1.203) activity and having an amino acid sequence which shows at least 80 % identity to the sequence of SEQ ID NO: 4 or SEQ ID NO:20.
22. An isolated nucleotide sequence encoding an enzyme having the enzymatic activity of uronate dehydrogenase enzyme (EC 1.1.1.203), which comprises that the nucleotide sequence is selected from the group comprising: a. an isolated nucleotide sequence encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 4; b. an isolated nucleotide sequence comprising the coding sequence of the nucleotide sequence SEQ ID NO:3; c. an isolated nucleotide sequence the coding sequence of which differs from the coding sequence of the nucleotide sequence of (a) or (b) due to the degeneracy of the genetic code; d. a nucleotide sequence which hybridizes under stringent conditions to any one of the sequences (a), (b) or (c); and e. an isolated nucleotide sequence encoding a polypeptide having uronate dehydrogenase enzyme (EC 1.1.1.203) activity and having an amino acid sequence which shows at least 80 % identity to the sequence of SEQ ID NO: 4.
23. An enzyme encoded by the nucleotide sequence of claim 22.
PCT/FI2009/051029 2008-12-23 2009-12-22 Conversion of hexuronic acid to hexaric acid WO2010072902A1 (en)

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BRPI0923653-8A BRPI0923653B1 (en) 2008-12-23 2009-12-22 method for converting d-galacturonic acid to mesogalactonic acid, method for treating biomaterial comprising d-galacturonic acid and eukaryotic microbial host strain
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US9528133B2 (en) 2012-09-21 2016-12-27 Synthetic Genomics, Inc. Compositions and methods for producing chemicals and derivatives thereof
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WO2012125027A1 (en) * 2011-03-14 2012-09-20 Dsm Ip Assets B.V. Yeast strains that ferment uronic acids
KR101835130B1 (en) 2011-07-25 2018-04-19 포항공과대학교 산학협력단 Method for the production of D-glucaric acid from green seaweed
WO2013151428A1 (en) 2012-04-04 2013-10-10 Stichting Dienst Landbouwkundig Onderzoek Catalytic oxidation of uronic acids to aldaric acids
US9506090B2 (en) 2012-09-21 2016-11-29 Synthetic Genomics, Inc. Method for synthesizing FDCA and derivates thereof
US9528133B2 (en) 2012-09-21 2016-12-27 Synthetic Genomics, Inc. Compositions and methods for producing chemicals and derivatives thereof
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WO2017198908A1 (en) 2016-05-20 2017-11-23 Teknologian Tutkimuskeskus Vtt Oy Improved meso-galactaric acid production from galacturonic acid with genetically modified fungal cells
CN109477078A (en) * 2016-05-20 2019-03-15 芬兰国家技术研究中心股份公司 It is carried out using genetically modified fungal cell improved from the generation of the meso galactosaccharic acid of galacturonic acid
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