Patent Grant
10920253
This application is a § 371 National Stage Application of PCT/EP2015/055254, filed 13 Mar. 2015, which claims priority to EP 14161723.3, filed 26 Mar. 2014 and EP 14176885.3, filed 14 Jul. 2014. All of these documents (PCT/EP2015/055254, EP 14161723.3 and EP 14176885.3) are hereby incorporated by reference in their entirety.
The present invention relates to a method for the enzymatic production of acetyl phosphate from formaldehyde said method making use of a phosphoketolase or of a sulfoacetaldehyde acetyltransferase, as well as to the use of a phosphoketolase or of a sulfoacetaldehyde acetyltransferase or of a microorganism expressing a phosphoketolase or a sulfoacetaldehyde acetyltransferase for the production of acetyl phosphate from formaldehyde.
For the past several decades, practitioners of metabolic engineering have endeavoured to explore biological solutions for the production of chemicals, thus, providing alternatives to more traditional chemical processes. In general, biological solutions allow for the utilization of renewable feedstocks (e.g. sugars) and compete with existing petrochemical based processes. A multi-step, biological solution for the production of a chemical typically comprises a microorganism as the catalyst for the conversion of feedstock to a target molecule. A complete set of enzyme reactions for the production of a particular target molecule can be grouped into those belonging to central carbon pathways and those belonging to the product specific pathway. The reactions belonging to central carbon and product specific pathways are linked in that redox (typically, NAD(P)H) and energetic (typically, ATP) constraints of every enzyme reaction must be accounted for in an overall balance contributing to the competitiveness of the process. Historically, central carbon pathways of heterotrophs growing on sugars have been described as the Embden-Meyerhoff-Parnas pathway (EMPP; i.e., “glycolysis”), the pentose phosphate pathway (PPP), the Entner-Doudoroff pathway (EDP), and the phosphoketolase pathway (PKP) (see Gottschalk (1986), Bacterial Metabolism, 2nd Edition, Springer-Verlag, New York). Each central pathway or combinations of central pathways offer advantages and disadvantages with respect to a specific target molecule. In order to provide competitive bioprocesses, recombinant microorganisms with modifications involving the EMPP, PPP and EDP have been described (M. Emmerling et al., Metab. Eng. 1:117 (1999); L. O. Ingram et al., Appl. Environ. Microbiol. 53: 2420 (1987); C. T. Trinh et al., Appl. Environ. Microbiol. 74:3634 (2008)). More recently, recombinant microorganisms with modifications involving the PKP have been described (see Sonderegger et al. Appl. Environ. Microbiol. 70 (2004), 2892-2897, U.S. Pat. No. 7,253,001, Chinen et al. J. Biosci. Bioeng. 103 (2007), 262-269, U.S. Pat. No. 7,785,858; Fleige et al., Appl. Microbiol. Cell Physiol. 91 (2011), 769-776).
The EMPP (glycolysis) converts 1 mol glucose to 2 mol pyruvate (PYR). When acetyl-CoA is desired, 1 mol PYR can be converted to 1 mol of acetyl-CoA (AcCoA) with the concomitant generation of 1 mol CO2 and 1 mol NADH. The sum of the reactions is given in Equation 1.
glucose+2ADP+2H3PO4+2CoA+4NAD+→2acetyl-CoA+2CO2+2ATP+2H2O+4NADH+4H+ (Equation 1)
The PPP provides a means to convert 1 mol glucose to 1 mol CO2 and 2 mol NADPH, with the concomitant generation of 0.67 mol fructose-6-phosphate (F6P) and 0.33 mol glyceraldehyde-3-phosphate (GAP). The F6P and GAP thus formed must be metabolized by other reaction pathways, e.g. by the EMPP. The EDP converts 1 mol glucose to 1 mol GAP and 1 mol PYR with the concomitant generation of 1 mol NADPH. As with the PPP, the GAP thus formed must be metabolized by other reaction pathways. The PKP provides a means to convert 1 mol glucose to 1 mol GAP and 1.5 mol acetyl phosphate (AcP). When acetyl-CoA is desired, 1 equivalent of AcP plus 1 equivalent coenzyme A (CoA) can be converted to 1 equivalent acetyl-CoA and 1 equivalent inorganic phosphate (Pi) by the action of phosphotransacetylase.
Various approaches have been described in the art for genetically modifying microorganisms so as to be able to convert various feedstocks such as liquefied cornflour, glycerol or syngas (a mixture of hydrogen and carbon monoxide) or compounds such as methane into desired compounds, such as liquid fuels or butanol (see, e.g., WO2012/053905 and Peralta-Yahya et al., Nature 488 (2012), 320-328). Conrado and Gonzalez (Science 343 (2014), 621-623) discuss, for example, possible options for converting methane into liquid fuels and mention in this context that methanotrophs can convert formaldehyde into pyruvate either through the ribulose monophosphate (RuMP) cycle, which uses formaldehyde directly, or through the Calvin-Benson-Bassham-(CBB) CO2-fixation cycle from fully oxidized formaldehyde. However, the efficiency of such processes is said to be low and the processes are said to involve high metabolic energy losses.
In view of the increasing demand for processes which make use of renewable resources for producing all sorts of compounds, it is desirable to provide means and methods which allow for an efficient production of central metabolites, such as acetyl-CoA, or their precursors, thereby building a platform for developing further processes to convert these metabolites into useful compounds.
Thus, there is a need to provide methods, comprising central carbon and product specific pathways, that maximize the conversion of feedstock to product by best accommodating the redox and energetic constraints of enzyme reactions, thereby allowing the energetically efficient production of precursors of acetyl-CoA, one of the most central metabolites in catabolism of many organisms, in particular of microorganisms which can be used for the production of numerous industrially important compounds from renewable resources. Applicants have addressed this need by providing the embodiments as defined in the claims.
There is a need to provide methods allowing the energetically efficient production of precursors of acetyl-CoA, one of the most central metabolites in catabolism of many organisms, in particular of microorganisms which can be used for the production of numerous industrially important compounds from renewable resources. The present invention addresses this need by providing the embodiments as defined in the claims.
Thus, the present invention relates to method for the production of acetyl phosphate from formaldehyde by making use of a phosphoketolase or of a sulfoacetaldehyde acetyltransferase.
The present inventor surprisingly found that enzymes which are classified as phosphoketolases are capable of catalyzing the formation of acetyl phosphate from formaldehyde and phosphate according to the following reaction scheme:
2CH2O+phosphate→acetyl phosphate+H2O
This reaction is strongly exergonic, dissipating more energy than ATP hydrolysis under physiological conditions.
Different types of phosphoketolases are known and all of them can be employed in the method according to the invention. Generally, phosphoketolases are classified into two types based on substrate preference as regards their naturally catalyzed reaction: xylulose-5-phosphate (X5P) phosphoketolases, which are classified in EC 4.1.2.9 and which naturally use X5P and fructose-6-phosphate (F6P) as a substrate but which prefer X5P, and X5P/fructose-6-phosphate (F6P) phosphoketolases, which are classified in 4.1.2.22 and which can use both X5P and F6P with comparable activities as substrate (Suzuki et al., J. Biol. Chem. 44 (2010), 34279-34287). In the following, the term “phosphoketolase” always refers to both types.
Thus, X5P phosphoketolases are enzymes which are classified in EC 4.1.2.9 and which are capable of catalyzing the following reaction:
D-xylulose-5-phosphate+phosphate→D-glyceraldehyde-3-phosphate+acetyl-phosphate+H2O
The other type of phosphoketolases which are classified in EC 4.1.2.22 are generally referred to as fructose-6-phosphate phosphoketolases and are naturally capable of catalyzing the following reaction:
D-Fructose-6-phosphate+phosphate→acetyl phosphate+D-erythrose 4-phosphate+H2O
There are also cases in which a phosphoketolase is assigned to both types of phosphoketolases, e.g., in the case of the phosphoketolase from Nitrolancetus hollandicus Lb, or where an identified phosphoketolase has not yet been assigned to any of the two types but is simply generally classified as a phosphoketolases. The term “phosphoketolase” when used herein also refers to all these phosphoketolases.
Thus, in one embodiment of the method according to the present invention the enzymatic conversion of formaldehyde and phosphate into acetyl phosphate according to the above shown reaction scheme is achieved by making use of a phosphoketolase which is classified as a phosphoketolases in EC 4.1.2.9. This enzyme has been identified in a variety of organisms, in particular microorganisms such as bacteria and fungi. In one preferred embodiment the phosphoketolase (EC 4.1.2.9) originates from a prokaryotic organism, preferably a bacterium. The enzyme has, for example, been described to occur in Lactococcus lactis, Lactobacillus plantarum (Uniprot Accession numbers: Q88S87; Q88U67), Lactobacillus pentosus (Uniprot Accession number: Q937F6), Lactobacillus reuteri, Bifidobacterium animalis (Uniprot Accession number: A0PAD9), Bifidobacterium animalis subsp. lactis (Uniprot Accession number: Q9AEM9), Butyrovibrio fibrisolvens, Fibrobacter intestinalis, Fibrobacter succinogenes, Leuconostoc mesenteroides, Oenococcus oeni, Starkeya novella, Thiobacillus sp., Thermobispora bispora (strain ATCC 19993/DSM 43833/CBS 139.67/JCM 10125/NBRC 14880/R51; Uniprot Accession number D6YAD9), Thermobaculum terrenum (strain ATCC BAA-798/YNP1; Uniprot Accession number D1CI63) and Nitrolancetus hollandicus Lb (Uniprot Accession number I4EJ52).
In another preferred embodiment the phosphoketolase (EC 4.1.2.9) originates from a eukaryotic organism, preferably a fungus, e.g. a yeast, such as S. cerevisiae. The enzyme has, for example, been described to occur in Emericella nidulans (Uniprot Accession number: Q5B3G7), Metarhizium anisopliae (Uniprot Accession number: C1K2N2), Candida boidinii, Candida curvata, Candida famata, Candida humicola, Candida parapsilosis, Candida parapsilosis NCYC 926, Candida tropicalis, Cyberlindnera jadinii, Cyberlindnera saturnus, Debaromyces robertsiae, Fusarium oxysporum, Kluyveromyces marxianus, Kluyveromyces phaseolosporus, Lipomyces starkeyi, Ogataea angusta, Pachysolen tannophilus, Priceomyces medius, Saccharomyces cerevisiae, Rhodospiridium toruloides, Rhodotorula glutinis, Rhodotorula graminis, Penicillium chrysogenum, Trichosporon cutaneum and Yarrowia lipolytica.
The enzymatic activity of a phosphoketolase (EC 4.1.2.9) can be assessed with methods known to a person skilled in the art. Such methods are, e.g., described in Meile et al. (J. Bacteriol. 183 (2001), 2929-2936) and in Suzuki et al (Acta Cryst. F66 (2010), 941-943).
The phosphoketolase (EC 4.1.2.9) is structurally and functionally well defined. For example, Petrareanu et al. (Acta Crystallographica F66 (2010), 805-807) describe the X-ray crystallographic analysis of the xylulose-5-phosphate phosphoketolase from Lactococcus lactis.
In another embodiment of the method according to the present invention the enzymatic conversion of formaldehyde and phosphate into acetyl phosphate according to the above shown reaction scheme is achieved by making use of a phosphoketolase which is classified as a fructose-6-phosphate phosphoketolase in EC 4.1.2.22. This enzyme has been identified in a variety of organisms, in particular microorganisms such as bacteria and fungi. In one preferred embodiment the fructose-6-phosphate phosphoketolase (EC 4.1.2.22) originates from a prokaryotic organism, preferably a bacterium. The enzyme has, for example, been described to occur in Bifidobacterium adolescentis, Bifidobacterium animalis subsp. lactis (Uniprot Accession number: Q9AEM9), Bifidobacterium longum, Bifidobacterium pseudolongum, in particular Bifidobacterium pseudolongum subsp. globosum, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium dentium, Bifidobacterium mongoliense, Bifidobacterium bombi, Cupriavidus necator, Gardnerella vaginalis, Gluconacetobacter xylinus, Lactobacillus paraplantarum, Leuconostoc mesenteroides and Nitrolancetus hollandicus Lb (Uniprot Accession number 14EJ52).
In another preferred embodiment the fructose-6-phosphate phosphoketolase (EC 4.1.2.22) originates from a eukaryotic organism, preferably a fungus, e.g. a yeast, such as S. pastorianus. The enzyme has, for example, been described to occur in Candida sp., Candida sp. 107, Candida tropicalis, Rhodotorula glutinis, Rhodotorula graminis and Saccharomyces pastorianus.
The enzyme is structurally and functionally well defined. For example, Suzuki et al. (Acta Crystallographica F66 (2010), 941-943; J. Biol. Chem. 285 (2010), 34279-34287) describe the overexpression, crystallization and X-ray analysis of the phosphoketolase from Bifidobacterium breve. The gene encoding the xylulose-5-phosphate/fructose-6-phosphate phosphoketolase from Bidifobacterium lactis is e.g. described in Meile et al. (J. Bacteriol. 183 (2001), 2929-2936).
The enzymatic activity of a fructose-6-phosphate phosphoketolase (EC 4.1.2.22) can be assessed with methods known to a person skilled in the art. Such methods are, e.g., described in Meile et al. (J. Bacteriol. 183 (2001), 2929-2936) and in Suzuki et al. (Acta Cryst. F66 (2010), 941-943).
Other phosphoketolases which have not yet been classified into EC 4.2.1.9 or EC 4.2.1.22 and which can be used in the method according to the present invention are, e.g. the phosphoketolase from Thermosynechococcus elongatus (strain BP-1; Uniprot Accession number: Q8DJN6), the phosphoketolase from Bacillus coagulans 36D1 (Uniprot Accession number: G2TIL0), the phosphoketolase from Lactococcus lactis subsp. lactis (Strain KF147; Uniprot Accession number: A9QST6; SEQ ID NO: 3), the phosphoketolase from Bifidobacterium pseudolongum subsp. globosum (Uniprot Accession number: Q6R2Q6; SEQ ID NO: 1) and the phosphoketolase from Clostridium acetobutylicum (Strain ATCC 824; Uniprot Accession number: Q97JE3; Servisky et al. (J. Ind. Microbiol. Biotechnol. 39 (2012), 1859-1867); SEQ ID NO: 2).
In the appended Examples it is shown that the phosphoketolases of Bifidobacterium pseudolongum subsp. globosum (Uniprot Accession number: Q6R2Q6; SEQ ID NO: 1), of Clostridium acetobutylicum (Strain ATCC 824; Uniprot Accession number: Q97JE3; SEQ ID NO: 2) and of Lactococcus lactis subsp. lactis (Strain KF147; Uniprot Accession number: A9QST6; SEQ ID NO: 3) are capable of converting formaldehyde and phosphate into acetyl phosphate and H2O.
In a preferred embodiment, the phosphoketolase employed in the method of the invention has an amino acid sequence as shown in any one of SEQ ID NOs: 1 to 3 or shows an amino acid sequence which is at least x % homologous to any one of SEQ ID NOs: 1 to 3 and has the activity of a phosphoketolase with x being an integer between 30 and 100, preferably 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 wherein such an enzyme is capable of converting formaldehyde and phosphate into acetyl phosphate as set forth herein above.
Preferably, the degree of identity is determined by comparing the respective sequence with the amino acid sequence of any one of the above-mentioned SEQ ID NOs. When the sequences which are compared do not have the same length, the degree of identity preferably either refers to the percentage of amino acid residues in the shorter sequence which are identical to amino acid residues in the longer sequence or to the percentage of amino acid residues in the longer sequence which are identical to amino acid residues in the shorter sequence. The degree of sequence identity can be determined according to methods well known in the art using preferably suitable computer algorithms such as CLUSTAL.
When using the Clustal analysis method to determine whether a particular sequence is, for instance, 80% identical to a reference sequence default settings may be used or the settings are preferably as follows: Matrix: blosum 30; Open gap penalty: 10.0; Extend gap penalty: 0.05; Delay divergent: 40; Gap separation distance: 8 for comparisons of amino acid sequences. For nucleotide sequence comparisons, the Extend gap penalty is preferably set to 5.0.
Preferably, the degree of identity is calculated over the complete length of the sequence.
It has been described that a multiple alignment of phosphoketolase sequences shows several highly conserved regions and two of these regions are used as signature patterns for phosphoketolases (prosite.expasy.org/PDOC60002). The first signature pattern is E-G-G-E-L-G-Y (SEQ ID NO:9) and the second signature pattern is G-x(3)-[DN]-x-P-x(2)-[LIVFT]-x(3)-[LIVM]-x-G-D-G-E (SEQ ID NO:10). The function of the first signature pattern is not yet known while the second signature pattern corresponds to the thiamine pyrophosphate binding site. Thus, in a preferred embodiment, a phosphoketolase as defined herein above has an amino acid sequence which contains at least one of the two above mentioned signature patterns, preferably at least the second signature pattern, and even more preferably both signature patterns.
Sequence comparisons show that the overall sequence identity between phosphoketolases from different origins can be as low as around 26%. For example, Meile et al. (J. Biol. Chem. 183 (2001), 2929-2936) reports that the D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase gene (xfp) of Bifidobacterium lactis revealed identities of 26% to 55% to sequences in the genomes of other organisms.
Whether a chosen phosphoketolase is capable of catalyzing the conversion of formaldehyde and phosphate into acetyl phosphate and H2O can, e.g., be assessed by an assay as set forth in the appended Examples.
The term “phosphate” as used in connection with the method of the invention refers to a compound which is acceptable as a phosphate source for the enzyme employed in the method for the conversion of formaldehyde and phosphate into acetyl phosphate and H2O. One possibility is the provision of phosphate in the form of phosphoric acid, i.e. H3PO4. However, also other forms are conceivable, in particular salts of phosphoric acid (H3PO4) in which one, two or three of the hydrogen atoms are replaced by other ions, such as sodium ions. Phosphoketolases are thiamine diphosphate-dependent enzymes, i.e. they require thiamine diphosphate (also referred to as ThDP or TPP) as a cofactor. Therefore, it is advantageous that in a method according to the invention TPP is provided during the reaction. Moreover, some phosphoketolases require ions, such as Mg2+ or Ca2+ as cofactors. In such a case, the method according to the invention also includes the presence of such ions during the conversion as described above.
The enzymatic conversion of formaldehyde and phosphate into acetyl phosphate according to the above shown reaction scheme can also be achieved by making use of a sulfoacetaldehyde acetyltransferase (EC 2.3.3.15). Sulfoacetaldehyde acetyltransferases (EC 2.3.3.15) are enzymes which can catalyze the following reaction:
2-sulfoacetaldehyde+phosphate→acetyl phosphate+sulfite
The enzyme has been identified in a variety of organisms, in particular bacteria. In one preferred embodiment the sulfoacetaldehyde acetyltransferase (EC 2.3.3.15) originates from a prokaryotic organism, preferably a bacterium. The enzyme has, for example, been described to occur in Castellaniella defragans (Uniprot Accession number: Q84H44; previously Alcaligenes defragans (Ruff et al., Biochem. J. 369 (2003), 275-285)), Alcaligenes xylosoxydans xylosoxydans (Uniprot Accession number: Q84H41), Desulfonispora thiosulfatigenes (Uniprot Accession number: Q93PS3), Rhizobium meliloti (strain 1021) (Uniprot Accession number: Q92UW6), Ruegeria pomeroyi (Uniprot Accession number: Q5LMK2), Cupriavidus necator (Uniprot Accession number: Q0K022), Roseovarius nubinhibens (Uniprot Accession number: A3SR25), Acinetobacter sp. and Pseudomonas aeruginosa.
In principle any sulfoacetaldehyde acetyltransferase (EC 2.3.3.15) can be employed in the conversion of formaldehyde and phosphate into acetyl phosphate according to a method of the invention.
Sulfoacetaldehyde acetyltransferases are, like phosphoketolases, thiamine pyrophosphate (TPP)-dependent enzymes and therefore are characterized in that they contain a TPP binding domain. Among the sulfoacetaldehyde acetyltransferases known, the TPP binding domain is highly conserved (see, e.g., Ruff et al., Biochem. J. 369 (2003), 275-285). Overall, the known sulfoacetaldehyde acetyltransferases show a high degree of sequence conservation near the N-terminus, including the TPP binding domain (see Ruff et al., loc. cit.). Sequence divergence can be observed in the N-terminus of the enzymes itself and in a region near amino acid 400 of the C. defragans enzyme. Ruff et al. (loc. cit.) describe that sulfoacetaldehyde acetyltransferases form 3 subgroups (see FIG. 4 of said publication). Subgroups 2 and 3 are said to show a TPP binding domain conforming with the PROSITE consensus sequence (L/I/V/M/F)(G/S/A)X5PX4(L/I/V/M/F/Y/W)X(L/I/V/M/F)XGD(G/S/A)(G/S/A/C), while subgroup slightly deviates from the consensus sequence: (L/I/V/M/F)(G/S/A)X5PX4(L/I/V/M/F/Y/W)X(L/1/V/M/F/Y)XGD(G/S/A)(G/S/A/C).
Apart from these regions, the sequence identity between the different sulfoacetaldehyde acetyltransferases can be rather low (down to about 44%).
In a preferred embodiment, the sulfoacetaldehyde acetyltransferase employed in a method according to the present invention is the sulfoacetaldehyde acetyltransferase of C. defragans showing the amino acid sequence as depicted in SEQ ID NO:4 or the sulfoacetaldehyde acetyltransferase of Alcaligenes xylosoxydans xylosoxydans showing the amino acid sequence as depicted in SEQ ID NO:5 or the sulfoacetaldehyde acetyltransferase of Desulfonispora thiosulfatigenes showing the amino acid sequence as depicted in SEQ ID NO:6 or the sulfoacetaldehyde acetyltransferase of Rhizobium meliloti (strain 1021) showing the amino acid sequence as depicted in SEQ ID NO:7 or the sulfoacetaldehyde acetyltransferase of Roseovarius nubinhibens showing the amino acid sequence as depicted in SEQ ID NO:8 or showing a related amino acid sequence.
Thus, in a preferred embodiment, the sulfoacetaldehyde acetyltransferase employed in the method of the invention has an amino acid sequence as shown in any one of SEQ ID NOs: 4 to 8 or shows an amino acid sequence which is at least x % homologous to any one of SEQ ID NOs: 4 to 8 and has the activity of a sulfoacetaldehyde acetyltransferase ith x being an integer between 30 and 100, preferably 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 wherein such an enzyme is capable of converting formaldehyde and phosphate into acetyl phosphate as set forth herein above. Preferably, the degree of identity is determined as described above.
The enzymatic activity of a sulfoacetaldehyde acetyltransferase (EC 2.3.3.15) can be assessed with methods known to a person skilled in the art. Such methods are, e.g., described in Ruff et al. (Biochem. J. 369 (2003), 275-285).
The acetyl phosphate produced according to a method of the present invention can be further converted into desired molecules such as acetate or acetyl-Coenzyme A (also referred to as acetyl-CoA) which is a central metabolite in most organisms.
The hydrolysis of acetyl phosphate into acetate in vitro occurs spontaneously since acetyl phosphate is rather unstable.
Acetyl phosphate can also be converted, in vitro or in vivo, enzymatically into acetate, e.g. by making use of an acetate kinase (EC 2.7.2.1), a propionate kinase (EC 2.7.2.15), a butyrate kinase (EC 2.7.2.7) or an acetate kinase (diphosphate) (EC 2.7.2.12).
Acetate kinase is an enzyme which catalyzes the following reaction:
ATP+acetateADP+acetyl phosphate.
Since this reaction is reversible, the enzyme can be employed to convert acetyl phosphate into acetate. The reaction may be pushed into the direction of acetate by continuously removing ATP from the reaction, e.g. by further enzymatic conversion or by removal from the reaction by means and methods known to the person skilled in the art. This enzyme occurs in a large variety of organism, in particular in prokaryotes, eukaryotes and archae. It is an important enzyme in glycolysis and the enzyme levels are normally increased in the presence of excess glucose. In principle any acetate kinase (EC 2.7.2.1) can be used to convert acetyl phosphate into acetate in a method according to the invention.
Also propionate kinase (EC 2.7.2.15) has been described to be able to convert acetyl phosphate into acetate according to the reaction scheme:
ATP+acetateADP+acetyl phosphate.
This enzyme is found in Enterobacteriaceae, such as E. coli or Salmonella enteric subsp. enterica serovar. thyphimurium.
The conversion of acetyl phosphate into acetate can also be achieved by making use of a butyrate kinase (EC 2.7.2.7). Butyrate kinases are enzymes which catalyze the following reaction:
ATP+butanoateADP+butanoyl phosphate
However, it has been shown for some butyrate kinases, e.g. for those from Clostridium butyricum and from Clostridium acetobutylicum, that they can also catalyze the reaction:
ATP+acetateADP+acetyl phosphate
Thus, any butyrate kinase which is also capable of catalyzing the reversible conversion of ATP+acetate into ADP+acetyl phosphate can be employed in a method of the present invention for converting acetyl phosphate into acetate.
Moreover, the conversion of acetyl phosphate into acetate can also be achieved by making use of an acetate kinase (diphosphate) (EC 2.7.2.12). Acetate kinases (diphosphate) (EC 2.7.2.12) are enzymes which catalyze the following reaction:
Diphosphate+acetateH3PO4+acetyl phosphate.
This enzyme has been described to occur in Entamoeba histolytica.
The enzymatic hydrolysis of acetyl phosphate into acetate and H3PO4 can also be achieved by making use of an acylphosphatase (EC 3.6.1.7). Acylphosphatase (AcP; EC 3.6.1.7) is a cytosolic enzyme (with a molecular weight of about 10 kDa) widely expressed in eukaryotic and prokaryotic organisms (both mesophilic and extremophilic). AcP can be found in many tissues of vertebrate species in the skeletal muscles and in the heart as muscle-type AcP (MT-AcP) and in erythrocytes, brain and testis as (organ) common-type AcP (CT-AcP) (Zuccotti et al., Acta Cryst. 61 (2005), 144-146). Acylphosphatases catalyze the following reaction:
Acetyl phosphate+H2O→acetate+H3PO4
This enzyme has been described in a large variety of organisms. Preferably, an acylphosphatase employed in a method according to the present invention is derived from Gallus gallus, Cavia porcellus (Liguri et al., Biochem. J. 217 (1984), 499-505), Homo sapiens, Sus scrofa, Bos taurus, Oryctolagus cuniculus, Equus acallus or Pyrococcus hirokoshii (Miyazoo et al., Acta Crystallographica D60 (2004), 1135-1136).
The structural and functional characteristics of these enzymes have already been studied in detail and are described, e.g., in Liguri et al. (Biochem. J. 217 (1984), 499-505), Miyazoo et al. (Acta Crystallographica D60 (2004), 1135-1136) and in Taddei et al. (FEBS Letters 362 (1995), 175-179).
The conversion of acetyl phosphate into acetyl-CoA (in vitro or in vivo) can be achieved enzymatically, e.g. by the use of phosphate acetyltransferase (EC 2.3.1.8). This enzyme naturally catalyzes the following reaction:
acetyl-CoA+H3PO4CoA+acetyl phosphate
The enzyme occurs in a multitude of organisms, i.e. in prokayotes, eukaryotes and archae. In principle any known phosphate acetyltransferase (EC 2.3.1.8) can be employed for this conversion.
The formaldehyde converted according to a method of the present invention into acetyl phosphate can be provided externally to the reaction or can be provided by another chemical or enzymatic reaction.
The chemical production of formaldehyde has been known for a long time and generally formaldehyde is industrially produced by the catalytic oxidation of methanol. The most common catalysts in this context are silver metal or a mixture of an iron and molybdenum or vanadium oxides. In the commonly used formox process, methanol and oxygen react at approximately 250 to 400° C. in the presence of iron oxide in combination with molybdenum and/or vanadium to produce formaldehyde according to the following chemical equation:
2CH3OH+O2→2CH2O+2H2O
The silver-based catalyst usually operates at a higher temperature, about 650° C. Two chemical reactions on it simultaneously produce formaldehyde: that shown above and the dehydrogenation reaction:
CH3OH→H2CO+H2
Formaldehyde can also be generated by oxidation of methane. Moreover, it has been described that formaldehyde (and methanol) can be produced by a reaction of carbon monoxide and hydrogen on neutral Fe2S2 clusters in gas phase (see Yin et al., Phys. Chem. Chem. Phys. 15 (2013), 4699-4706).
In a preferred embodiment a method of the present invention further comprises the step of providing the formaldehyde to be converted by the enzymatic conversion of methanol. Enzymes which catalyze the conversion of methanol into formaldehyde are known and include, e.g. methanol dehydrogenase (EC 1.1.1.244). Methanol dehydrogenase (EC 1.1.1.244) catalyzes the following reaction:
Methanol+NAD+formaldehyde+NADH+H+
This enzyme has been identified in the methylotrophic Bacillus species Bacillus methanolicus (Arfman et al., Arch. Microbiol. 152 (1989), 280-288). Enzymes which can also catalyze the conversion of methanol into formaldehyde are enzymes classified as EC 1.1.2.7 (methanol dehydrogenase (cytochrome c)). These enzymes are type II PQQ-containing alcohol dehydrogenases, i.e. NAD(P)-independent methanol dehydrogenases. Such enzymes are, for example, known from several proteobacteria such as Methylobacterium extorquens, Methylophilus methylotrophus or Hyphomicrobium denitrificans. Moreover, also alcohol oxidases (EC 1.1.3.13) can be employed for the conversion of methanol into formaldehyde. Alcohol oxidases (EC 1.1.3.13) are enzymes which catalyze the following reaction:
Primary alcohol+O2→aldehyde+H2O2
These enzymes have been identified in a large variety of organisms, e.g., methylotrophic yeast such as Pichia, Candida and Hansenula, that use methanol as a sole carbon and energy source (Hartner and Glieder, Microbial Cell Factories 5 (2006), 39) and in some fungi, e.g. Aspergillus (Kumar and Goswami, Appl. Microbiol. Biotechnol. 72 (2006), 906-911). Arnaud et al. (FEBS 296 (1992), 259-262) describe that purified terminal oxidase of Pseudomonas nautica strain 617 reduces CO to formaldehyde.
The methanol which can be converted into formaldehyde can itself be provided by enzymatic reactions from methane. In particular, the conversion of methane to methanol is, e.g., catalyzed by methane monooxygenase (MMO). Two types of this enzyme have been described, i.e. EC 1.14.13.25 methane monooxygenase (soluble) and EC 1.14.18.3 methane monooxygenase (particulate). The catalyzed reactions are:
CH4+NADH+H++O2→CH3OH+NAD+H2O (with NADH as co-factor)
CH4+NADPH+H++O2→CH3OH+NADP+H2O (with NADPH as co-factor)
Corresponding enzymes have been identified, e.g., in methanotrophic bacteria such as Methylococcus capsulatus (Pilkington and Dalton, Methods Enzymology 188 (1990), 181-190) and Methylosinus trichosporium (Fox et al., J. Biol. Chem. 266 (1991), 540-550). These enzymes have been characterized by in vitro studies, including cristal structure analysis (Sazinsky et al., Biochemistry 43 (2004), 16263-16276).
The method according to the present invention may be carried out in vitro or in vivo. An in vitro reaction is understood to be a reaction in which no cells are employed, i.e. an acellular reaction. Thus, in vitro preferably means in a cell-free system. The term “in vitro” in one embodiment means in the presence of isolated enzymes (or enzyme systems optionally comprising possibly required cofactors). In one embodiment, the enzymes employed in the method are used in purified form.
For carrying out the method in vitro the substrates for the reaction and the enzymes are incubated under conditions (buffer, temperature, co-substrates, co-factors etc.) allowing the enzymes to be active and the enzymatic conversion to occur. The reaction is allowed to proceed for a time sufficient to produce the respective product. The production of the respective products can be measured by methods known in the art, such as liquid chromatography (HPLC) possibly linked to mass spectrometry detection.
The enzymes may be in any suitable form allowing the enzymatic reaction to take place. They may be purified or partially purified or in the form of crude cellular extracts or partially purified extracts. It is also possible that the enzymes are immobilized on a suitable carrier.
The Examples illustrate in vitro reactions according to the invention using phosphoketolases from different origins.
In another embodiment the method according to the invention is carried out in culture, in the presence of an organism, preferably a microorganism, producing at least a phosphoketolase or a sulfoacetaldehyde acetyltransferase and optionally enzymes which are necessary for providing formaldehyde or for further converting the produced acetyl phosphate into other compounds, such as acetate or acetyl-CoA, as described herein above. A method which employs a microorganism for carrying out a method according to the invention is referred to as an “in vivo” method. The formaldehyde may either be provided externally or may be produced by the employed microorganism expressing the phosphoketolase or the sulfoacetaldehyde acetyltransferase itself. Such a microorganism expresses at least one enzyme necessary for the enzymatic production of formaldehyde as described herein above. It is also possible to co-culture a microorganism which is capable of producing formaldehyde and a microorganism which expresses a phosphoketolase and/or a sulfoacetaldehyde acetyltransferase so as to convert the formaldehyde produced by the first microorganism.
Thus, in such embodiments of the invention, a microorganism that produces at least a phosphoketolase or a sulfoacetaldehyde acetyltransferase as described above is used. It is possible to use a microorganism which naturally produces the phosphoketolase or the sulfoacetaldehyde acetyltransferase or a microorganism which had been genetically modified so that it expresses (or overexpresses) a phosphoketolase and/or the sulfoacetaldehyde acetyltransferase. Thus, the microorganism can be a microorganism which naturally expresses a phosphoketolase and/or a sulfoacetaldehyde acetyltransferase, i.e. which naturally has in its genome a nucleotide sequence encoding a phosphoketolase or a sulfoacetaldehyde acetyltransferase and which expresses it/them. The expression may occur constitutively or in an induced or regulated manner. Microorganisms that inherently, i.e. naturally, have phosphoketolase activity or sulfoacetaldehyde acetyltransferase activity are known in the art and any of them can be used in the context of the present invention.
In another embodiment the microorganism can be a microorganism which has been genetically modified by the introduction of a nucleic acid molecule containing a nucleotide sequence encoding a phosphoketolase or a sulfoacetaldehyde acetyltransferase. The nucleic acid molecule can be stably integrated into the genome of the microorganism or may be present in an extrachromosomal manner, e.g. on a plasmid.
Such a genetically modified microorganism can, e.g., be a microorganism that does not naturally have phosphoketolase activity or sulfoacetaldehyde acetyltransferase activity and has been genetically modified to express a phosphoketolase or a sulfoacetaldehyde acetyltransferase or a microorganism which naturally has phosphoketolase activity or sulfoacetaldehyde acetyltransferase activity and which has been genetically modified, e.g. by transformation with a nucleic acid, e.g. a vector, encoding a phosphoketolase or a sulfoacetaldehyde acetyltransferase in order to increase the phosphoketolase activity or sulfoacetaldehyde acetyltransferase activity in said microorganism and/or by insertion of a promoter in front of the endogenous nucleotide sequence encoding the enzyme in order to increase the respective activity in said microorganism.
However, the invention preferably excludes naturally occurring microorganisms as found in nature expressing an enzyme as described above at levels as they exist in nature. Instead, the microorganism of the present invention and employed in a method of the present invention is preferably a non-naturally occurring microorganism, whether it has been genetically modified to express (including overexpression) an exogenous enzyme of the invention not normally existing in its genome or whether it has been engineered to overexpress an exogenous enzyme.
Thus, the enzymes and (micro)organisms employed in connection with the present invention are preferably non-naturally occurring enzymes or (microorganisms), i.e. they are enzymes or (micro)organisms which differ significantly from naturally occurring enzymes or microorganism and which do not occur in nature. As regards the enzymes, they are preferably variants of naturally occurring enzymes which do not as such occur in nature. Such variants include, for example, mutants, in particular prepared by molecular biological methods, which show improved properties, such as a higher enzyme activity, higher substrate specificity, higher temperature resistance and the like. As regards the (micro)organisms, they are preferably genetically modified organisms as described herein above which differ from naturally occurring organisms due to a genetic modification. Genetically modified organisms are organisms which do not naturally occur, i.e., which cannot be found in nature, and which differ substantially from naturally occurring organisms due to the introduction of a foreign nucleic acid molecule.
By overexpressing an exogenous or endogenous enzyme as described herein above, the concentration of the enzyme is substantially higher than what is found in nature, which can then unexpectedly force the reaction of the present invention which uses a non-natural for the respective enzyme. Preferably, the concentration of the overexpressed enzyme is at least 5%, 10%, 20%, 30% or 40% of the total host cell protein.
A “non-natural” substrate is understood to be a molecule that is not acted upon by the respective enzyme in nature, even though it may actually coexist in the microorganism along with the endogenous enzyme. This “non-natural” substrate is not converted by the microorganism in nature as other substrates are preferred (e.g. the “natural substrate”). Thus, the present invention contemplates utilizing a non-natural substrate with the enzymes described above in an environment not found in nature.
Thus, it is also possible in the context of the present invention that the microorganism is a microorganism which naturally does not have phosphoketolase activity or sulfoacetaldehyde acetyltransferase activity but which is genetically modified so as to comprise a nucleotide sequence allowing the expression of a phosphoketolase or a sulfoacetaldehyde acetyltransferase. Similarly, the microorganism may also be a microorganism which naturally has phosphoketolase activity or sulfoacetaldehyde acetyltransferase activity but which is genetically modified so as to enhance the phosphoketolase activity or sulfoacetaldehyde acetyltransferase activity, e.g. by the introduction of an exogenous nucleotide sequence encoding a phosphoketolase or a sulfoacetaldehyde acetyltransferase or by the introduction of a promoter for the endogenous gene encoding the enzyme to increase endogenous production to overexpressed (non-natural) levels.
If a microorganism is used which naturally expresses a phosphoketolase or a sulfoacetaldehyde acetyltransferase, it is possible to modify such a microorganism so that the respective activity is overexpressed in the mircroorganism. This can, e.g., be achieved by effecting mutations in the promoter region of the corresponding gene or introduction of a high expressing promoter so as to lead to a promoter which ensures a higher expression of the gene. Alternatively, it is also possible to mutate the gene as such so as to lead to an enzyme showing a higher activity.
By using microorganisms which express a phosphoketolase or a sulfoacetaldehyde acetyltransferase, it is possible to carry out the method according to the invention directly in the culture medium, without the need to separate or purify the enzymes.
In one embodiment the organism employed in the method according to the invention is a microorganism which has been genetically modified to contain a foreign nucleic acid molecule encoding a phosphoketolase or a sulfoacetaldehyde acetyltransferase. The term “foreign” or “exogenous” in this context means that the nucleic acid molecule does not naturally occur in said microorganism. This means that it does not occur in the same structure or at the same location in the microorganism. In one preferred embodiment, the foreign nucleic acid molecule is a recombinant molecule comprising a promoter and a coding sequence encoding the respective enzyme in which the promoter driving expression of the coding sequence is heterologous with respect to the coding sequence. “Heterologous” in this context means that the promoter is not the promoter naturally driving the expression of said coding sequence but is a promoter naturally driving expression of a different coding sequence, i.e., it is derived from another gene, or is a synthetic promoter or a chimeric promoter. Preferably, the promoter is a promoter heterologous to the microorganism, i.e. a promoter which does naturally not occur in the respective microorganism. Even more preferably, the promoter is an inducible promoter. Promoters for driving expression in different types of organisms, in particular in microorganisms, are well known to the person skilled in the art.
In a further embodiment the nucleic acid molecule is foreign to the microorganism in that the encoded enzyme is not endogenous to the microorganism, i.e. is naturally not expressed by the microorganism when it is not genetically modified. In other words, the encoded enzyme is heterologous with respect to the microorganism. The foreign nucleic acid molecule may be present in the microorganism in extrachromosomal form, e.g. as a plasmid, or stably integrated in the chromosome. A stable integration is preferred. Thus, the genetic modification can consist, e.g. in integrating the corresponding gene(s) encoding the enzyme(s) into the chromosome, or in expressing the enzyme(s) from a plasmid containing a promoter upstream of the enzyme-coding sequence, the promoter and coding sequence preferably originating from different organisms, or any other method known to one of skill in the art.
The term “microorganism” in the context of the present invention refers to bacteria, as well as to fungi, such as yeasts, and also to algae and archaea. In one preferred embodiment, the microorganism is a bacterium. In principle any bacterium can be used. Preferred bacteria to be employed in the process according to the invention are bacteria of the genus Bacillus, Clostridium, Corynebacterium, Pseudomonas, Zymomonas or Escherichia. In a particularly preferred embodiment the bacterium belongs to the genus Escherichia and even more preferred to the species Escherichia coli. In another preferred embodiment the bacterium belongs to the species Pseudomonas putida or to the species Zymomonas mobilis or to the species Corynebacterium glutamicum or to the species Bacillus subtilis.
It is also possible to employ an extremophilic bacterium such as Thermus thermophilus, or anaerobic bacteria from the family Clostridiae.
In another preferred embodiment the microorganism is a fungus, more preferably a fungus of the genus Saccharomyces, Schizosaccharomyces, Aspergillus, Trichoderma, Kluyveromyces or Pichia and even more preferably of the species Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus niger, Trichoderma reesei, Kluyveromyces marxianus, Kluyveromyces lactis, Pichia pastoris, Pichia torula or Pichia utilis.
In another embodiment, the method according to the invention makes use of a photosynthetic microorganism expressing at least a phosphoketolase and/or a sulfoacetaldehyde acetyltransferase. Preferably, the microorganism is a photosynthetic bacterium, or a microalgae. In a further embodiment the microorganism is an algae, more preferably an algae belonging to the diatomeae.
It is also conceivable to use in the method according to the invention a combination of microorganisms wherein different microorganisms express different enzymes as described above.
In a particularly preferred embodiment the microorganism employed in a method according to the present invention is a methanotrophic or methylotrophic bacterium or a methanotrophic or methylotrophic yeast. Such microorganisms are preferably employed in a method according to the present invention since they have naturally the capability of metabolizing methanol and/or methane in order to produce formaldehyde via the enzymatic reactions described herein above. Methanotrophic bacteria and their possible uses are, e.g. described in Jiang et al. (Biochemical Engineering J. 49 (2010), 277-288), Schrader et al. (Trends in Biotechnology 27 (2008), 107-115), Chistoserdova et al. (Anu. Rev. Microbiol. 63 (2009), 477-499) and Kalyuzhnaya et al. (Nature Commun. 4 (2013). The diversity of these bacteria is, e.g. described in Chistoserdova et al. (loc. cit.) and in Jiang et al. (loc. cit.). Schrader et al. (loc. cit.) and Kalyuzhnaya et al. (loc. cit.) describe the use of such microorganisms as catalysts for methane conversion. Finally, Schrader et al. (loc. cit.) also describe genetic tools allowing to manipulate the metabolism of methylotrophic bacteria (such as Methylobacterium extorquens) for the formation of a desired product. Examples of methanotroph or methylotrophic bacteria include but are not limited to bacteria of the family Methylophilaceae, and bacteria of the genus Methylobacter, Methylobacterium (e.g. Methylobacterium extorquens Methylobacterium organophilum and Methylobacterium rhodesianum), Methylobacillus (e.g. Methylobacillus flagellatus and Methylobacillus glycogenes), Methylomonas (e.g Methylomonas methanica), Methylosoma, Methylomicrobium (e.g. Methylomicrobium alcaliphilum), Methylothermus, Methylohalobius, Methylosarcina, Methylosphaera, Methylocystis, Methylosinus (e.g. Methylosinus trichosporium), Methylocapsa, Methylocella, Methylococcus (e.g. Methylococcus capsulatus), Methylocaldum, Methylophilus (e.g. Methylophilus methylotrophus), Methylacidiphilum, Hyphomicrobium (e.g. Hyphomicrobium methylovorum or Hyphomicrobium zavarzinii), Bacillus (e.g. Bacillus methanolicus), Pseudomonas, Paracoccus (e.g. Paracoccus denitrificans), Silicibacter (e.g. Silicibacter pomeroyi), or Granulibacter (e.g. Granulibacter bethesdensis).
In a preferred embodiment the microorganism employed in a method according to the present invention is a microorganism which expresses a methanol dehydrogenase (MDH) and in particular a pyrroloquinoline-quinone (PQQ)-containing enzyme (quinoprotein) which catalyzes the ocidation of methanol to formaldehyde (Anthony, Adv. Microbila Physiol. 27 (1986), 113-120; Duine and Frank, Methanol dehydrogenase: A quinoprotein; In: Microbial Growth on C1 Compounds; Ed. Dalton, H., Heyden & Son Ltd., London (1981), 31-41; Duine et al., Eur. J. Biochem. 108 (1980), 187-192).
In a particularly preferred embodiment the microorganism employed in a method according to the present invention is a microorganism of the genus Acidomonas, preferably of the species Acidomonas methanolica (former name: Acetobacter methanolicus). Acidomonas methanolica is a unique acetic acid bacterium which is capable of growing on methanol as a sole carbon source. This bacterium is particularly useful in a method according to the present invention since it takes up methanol efficiently. The methanol is converted by such a bacterium into formaldehyde due to the expression of a methanol dehydrogenase (encoded by the MxaF gene; see, e.g. Suzuki et al., J. Gen. Appl. Microbiol. 55 (2009), 101-110). A draft genomic DNA sequence of this organism has been reorted by Higashiura et al. (FEMS Microbiol. Lett. 351 (2014), 9-13). The methanol dehydrogenase of Acidomonas methanolica is a quinoprotein and its properties have been described in detail (Frébortova et al., Biochim. Biophys. Acta 1363 (1998), 24-34).
Other examples are bacteria belonging to the Verrucomicrobia phylum or bacteria of the order Burkholderiales, in particular of the families Comamonadaceae or Rhodocyclaceae, e.g. of the genus Methylibium (e.g. Methylibium petroleiphilum) and Burkholderia (e.g. Burkholderia phymatum). Further examples are filamentous bacteria, for example of the genus Crenothrix (e.g. Crenothrix polyspora), of the genus Clonothrix (e.g. Clonothrix fusca) or of the genus Beggiatoa (e.g. Beggiatoa alba).
Methanotrophic or methylotrophic yeast include, e.g., yeasts of the genus Pichia, preferably Pichia pastoris), of the genus Candida (e.g. Candida boidinii), of the genus Ogataea, of the geus Kuraishia, of the genus Komagatealla (see, e.g. Yurimoto et al., Intern. J. Microbiol. 2011 (2011), ID 101298), of the genus Sporobolomyces (e.g. Sporobolomyces roseus strain Y) or of the genus Rhodotorula (e.g. Rhodotorula glutinis strain CY), of the genus Hansenula (e.g. Hansenula polymorpha)
The genetic modification of microorganisms to express an enzyme of interest will also be further described in detail below.
The phosphoketolase and/or sulfoacetaldehyde acetyltransferase used in the method according to the invention can be a naturally occurring phosphoketolase or sulfoacetaldehyde acetyltransferase or it can be a phosphoketolase/sulfoacetaldehyde acetyltransferase which is derived from a naturally occurring phosphoketolase/sulfoacetaldehyde acetyltransferase, e.g. by the introduction of mutations or other alterations which, e.g., alter or improve the enzymatic activity, the stability, etc.
Methods for modifying and/or improving the desired enzymatic activities of proteins are well-known to the person skilled in the art and include, e.g., random mutagenesis or site-directed mutagenesis and subsequent selection of enzymes having the desired properties or approaches of the so-called “directed evolution”.
For example, for genetic modification in prokaryotic cells, a nucleic acid molecule encoding phosphoketolase or a sulfoacetaldehyde acetyltransferase can be introduced into plasmids which permit mutagenesis or sequence modification by recombination of DNA sequences. Standard methods (see Sambrook and Russell (2001), Molecular Cloning: A Laboratory Manual, CSH Press, Cold Spring Harbor, N.Y., USA) allow base exchanges to be performed or natural or synthetic sequences to be added. DNA fragments can be ligated by using adapters and linkers complementary to the fragments. Moreover, engineering measures which provide suitable restriction sites or remove surplus DNA or restriction sites can be used. In those cases, in which insertions, deletions or substitutions are possible, in vitro mutagenesis, “primer repair”, restriction or ligation can be used. In general, a sequence analysis, restriction analysis and other methods of biochemistry and molecular biology are carried out as analysis methods. The resulting phosphoketolase/sulfoacetaldehyde acetyltransferase variants are then tested for the desired activity, e.g., enzymatic activity, with an assay as described above and in particular for their increased enzyme activity.
As described above, the microorganism employed in a method of the invention or contained in the composition of the invention may be a microorganism which has been genetically modified by the introduction of a nucleic acid molecule encoding a phosphoketolase and/or a sulfoacetaldehyde acetyltransferase. Thus, in a preferred embodiment, the microorganism is a recombinant microorganism which has been genetically modified to have an increased phosphoketolase activity and/or an increased sulfoacetaldehyde acetyltransferase activity. This can be achieved e.g. by transforming the microorganism with a nucleic acid encoding a phosphoketolase and/or a sulfoacetaldehyde acetyltransferase. A detailed description of genetic modification of microorganisms will be given further below. Preferably, the nucleic acid molecule introduced into the microorganism is a nucleic acid molecule which is heterologous with respect to the microorganism, i.e. it does not naturally occur in said microorganism.
In the context of the present invention, an “increased activity” means that the expression and/or the activity of an enzyme, in particular of the phosphoketolase or the sulfoacetaldehyde acetyltransferase, in the genetically modified microorganism is at least 10%, preferably at least 20%, more preferably at least 30% or 50%, even more preferably at least 70% or 80% and particularly preferred at least 90% or 100% higher than in the corresponding non-modified microorganism. In even more preferred embodiments the increase in expression and/or activity may be at least 150%, at least 200% or at least 500%. In particularly preferred embodiments the expression is at least 10-fold, more preferably at least 100-fold and even more preferred at least 1000-fold higher than in the corresponding non-modified microorganism.
The term “increased” expression/activity also covers the situation in which the corresponding non-modified microorganism does not express a corresponding enzyme, e.g. a phosphoketolase or a sulfoacetaldehyde acetyltransferase, so that the corresponding expression/activity in the non-modified microorganism is zero. Preferably, the concentration of the overexpressed enzyme is at least 5%, 10%, 20%, 30%, or 40% of the total host cell protein.
Methods for measuring the level of expression of a given protein in a cell are well known to the person skilled in the art. In one embodiment, the measurement of the level of expression is done by measuring the amount of the corresponding protein. Corresponding methods are well known to the person skilled in the art and include Western Blot, ELISA etc. In another embodiment the measurement of the level of expression is done by measuring the amount of the corresponding RNA. Corresponding methods are well known to the person skilled in the art and include, e.g., Northern Blot.
Methods for measuring the enzymatic activity of the phosphoketolase or sulfoacetaldehyde acetyltransferase are known in the art and have already been described above.
In the context of the present invention the term “recombinant” means that the microorganism is genetically modified so as to contain a nucleic acid molecule encoding an enzyme as defined above as compared to a wild-type or non-modified microorganism. A nucleic acid molecule encoding an enzyme as defined above can be used alone or as part of a vector.
The nucleic acid molecules can further comprise expression control sequences operably linked to the polynucleotide comprised in the nucleic acid molecule. The term “operatively linked” or “operably linked”, as used throughout the present description, refers to a linkage between one or more expression control sequences and the coding region in the polynucleotide to be expressed in such a way that expression is achieved under conditions compatible with the expression control sequence.
Expression comprises transcription of the heterologous DNA sequence, preferably into a translatable mRNA. Regulatory elements ensuring expression in fungi as well as in bacteria, are well known to those skilled in the art. They encompass promoters, enhancers, termination signals, targeting signals and the like. Examples are given further below in connection with explanations concerning vectors.
Promoters for use in connection with the nucleic acid molecule may be homologous or heterologous with regard to its origin and/or with regard to the gene to be expressed. Suitable promoters are for instance promoters which lend themselves to constitutive expression. However, promoters which are only activated at a point in time determined by external influences can also be used. Artificial and/or chemically inducible promoters may be used in this context.
The vectors can further comprise expression control sequences operably linked to said polynucleotides contained in the vectors. These expression control sequences may be suited to ensure transcription and synthesis of a translatable RNA in bacteria or fungi.
In addition, it is possible to insert different mutations into the polynucleotides by methods usual in molecular biology (see for instance Sambrook and Russell (2001), Molecular Cloning: A Laboratory Manual, CSH Press, Cold Spring Harbor, N.Y., USA), leading to the synthesis of polypeptides possibly having modified biological properties. The introduction of point mutations is conceivable at positions at which a modification of the amino acid sequence for instance influences the biological activity or the regulation of the polypeptide.
Moreover, mutants possessing a modified substrate or product specificity can be prepared. Preferably, such mutants show an increased activity. Alternatively, mutants can be prepared the catalytic activity of which is abolished without losing substrate binding activity.
Furthermore, the introduction of mutations into the polynucleotides encoding an enzyme as defined above allows the gene expression rate and/or the activity of the enzymes encoded by said polynucleotides to be reduced or increased.
For genetically modifying bacteria or fungi, the polynucleotides encoding an enzyme as defined above or parts of these molecules can be introduced into plasmids which permit mutagenesis or sequence modification by recombination of DNA sequences. Standard methods (see Sambrook and Russell (2001), Molecular Cloning: A Laboratory Manual, CSH Press, Cold Spring Harbor, N.Y., USA) allow base exchanges to be performed or natural or synthetic sequences to be added. DNA fragments can be connected to each other by applying adapters and linkers to the fragments. Moreover, engineering measures which provide suitable restriction sites or remove surplus DNA or restriction sites can be used. In those cases, in which insertions, deletions or substitutions are possible, in vitro mutagenesis, “primer repair”, restriction or ligation can be used. In general, a sequence analysis, restriction analysis and other methods of biochemistry and molecular biology are carried out as analysis methods.
Thus, in accordance with the present invention a recombinant microorganism can be produced by genetically modifying fungi or bacteria comprising introducing the above-described polynucleotides, nucleic acid molecules or vectors into a fungus or bacterium.
The polynucleotide encoding the respective enzyme, in particular a phosphoketolase or a sulfoacetaldehyde acetyltransferase, is expressed so as to lead to the production of a polypeptide having any of the activities described above, e.g. phosphoketolase activity or sulfoacetaldehyde acetyltransferase activity. An overview of different expression systems is for instance contained in Methods in Enzymology 153 (1987), 385-516, in Bitter et al. (Methods in Enzymology 153 (1987), 516-544) and in Sawers et al. (Applied Microbiology and Biotechnology 46 (1996), 1-9), Billman-Jacobe (Current Opinion in Biotechnology 7 (1996), 500-4), Hockney (Trends in Biotechnology 12 (1994), 456-463), Griffiths et al., (Methods in Molecular Biology 75 (1997), 427-440). An overview of yeast expression systems is for instance given by Hensing et al. (Antonie van Leuwenhoek 67 (1995), 261-279), Bussineau et al. (Developments in Biological Standardization 83 (1994), 13-19), Gellissen et al. (Antonie van Leuwenhoek 62 (1992), 79-93, Fleer (Current Opinion in Biotechnology 3 (1992), 486-496), Vedvick (Current Opinion in Biotechnology 2 (1991), 742-745) and Buckholz (Bio/Technology 9 (1991), 1067-1072).
Expression vectors have been widely described in the literature. As a rule, they contain not only a selection marker gene and a replication-origin ensuring replication in the host selected, but also a bacterial or viral promoter, and in most cases a termination signal for transcription. Between the promoter and the termination signal there is in general at least one restriction site or a polylinker which enables the insertion of a coding DNA sequence. The DNA sequence naturally controlling the transcription of the corresponding gene can be used as the promoter sequence, if it is active in the selected host organism. However, this sequence can also be exchanged for other promoter sequences. It is possible to use promoters ensuring constitutive expression of the gene and inducible promoters which permit a deliberate control of the expression of the gene. Bacterial and viral promoter sequences possessing these properties are described in detail in the literature. Regulatory sequences for the expression in microorganisms (for instance E. coli, S. cerevisiae) are sufficiently described in the literature. Promoters permitting a particularly high expression of a downstream sequence are for instance the T7 promoter (Studier et al., Methods in Enzymology 185 (1990), 60-89), IacUV5, trp, trp-lacUV5 (DeBoer et al., in Rodriguez and Chamberlin (Eds), Promoters, Structure and Function; Praeger, N.Y., (1982), 462-481; DeBoer et al., Proc. Natl. Acad. Sci. USA (1983), 21-25), Ip1, rac (Boros et al., Gene 42 (1986), 97-100). Inducible promoters are preferably used for the synthesis of polypeptides. These promoters often lead to higher polypeptide yields than do constitutive promoters. In order to obtain an optimum amount of polypeptide, a two-stage process is often used. First, the host cells are cultured under optimum conditions up to a relatively high cell density. In the second step, transcription is induced depending on the type of promoter used. In this regard, a tac promoter is particularly suitable which can be induced by lactose or IPTG (=isopropyl-β-D-thiogalactopyranoside) (deBoer et al., Proc. Natl. Acad. Sci. USA 80 (1983), 21-25). Termination signals for transcription are also described in the literature.
The transformation of the host cell with a polynucleotide or vector as described above can be carried out by standard methods, as for instance described in Sambrook and Russell (2001), Molecular Cloning: A Laboratory Manual, CSH Press, Cold Spring Harbor, N.Y., USA; Methods in Yeast Genetics, A Laboratory Course Manual, Cold Spring Harbor Laboratory Press, 1990. The host cell is cultured in nutrient media meeting the requirements of the particular host cell used, in particular in respect of the pH value, temperature, salt concentration, aeration, antibiotics, vitamins, trace elements etc.
When the method according to the invention is carried out in vivo by using an organism/microorganism providing the respective enzyme activities, the organism, preferably microorganism, is cultivated under suitable culture conditions allowing the occurrence of the enzymatic reaction. The specific culture conditions depend on the specific organism/microorganism employed but are well known to the person skilled in the art. The culture conditions are generally chosen in such a manner that they allow the expression of the genes encoding the enzymes for the respective reactions. Various methods are known to the person skilled in the art in order to improve and fine-tune the expression of certain genes at certain stages of the culture such as induction of gene expression by chemical inducers or by a temperature shift.
In another embodiment, the method of the invention comprises the step of providing the organism, preferably the microorganism carrying the respective enzyme activity or activities in the form of a (cell) culture, preferably in the form of a liquid cell culture, a subsequent step of cultivating the organism, preferably the microorganism in a fermenter (often also referred to a bioreactor) under suitable conditions allowing the expression of the respective enzyme and further comprising the step of effecting an enzymatic conversion of a method of the invention as described herein above. Suitable fermenter or bioreactor devices and fermentation conditions are known to the person skilled in the art. A bioreactor or a fermenter refers to any manufactured or engineered device or system known in the art that supports a biologically active environment. Thus, a bioreactor or a fermenter may be a vessel in which a chemical/biochemical process like the method of the present invention is carried out which involves organisms, preferably microorganisms and/or biochemically active substances, i.e., the enzyme(s) described above derived from such organisms or organisms harbouring the above described enzyme(s). In a bioreactor or a fermenter, this process can either be aerobic or anaerobic. These bioreactors are commonly cylindrical, and may range in size from litres to cubic metres, and are often made of stainless steel. In this respect, without being bound by theory, the fermenter or bioreactor may be designed in a way that it is suitable to cultivate the organisms, preferably microorganisms, in, e.g., a batch-culture, feed-batch-culture, perfusion culture or chemostate-culture, all of which are generally known in the art.
The culture medium can be any culture medium suitable for cultivating the respective organism or microorganism.
The present invention also relates to a composition containing
The phosphoketolase/sulfoacetaldehyde acetyltransferase can be a phosphoketolase/sulfoacetaldehyde acetyltransferase as defined above in connection with the method according to the invention. The microorganism contained in the composition can be any suitable microorganism which expresses a phosphoketolase and/or a sulfoacetaldehyde acetyltransferase, in particular a microorganism as described herein above in connection with the method according to the invention.
The present invention furthermore relates to the use of a phosphoketolase or of a sulfoacetaldehyde acetyltransferase or of a microorganism expressing a phosphoketolase and/or sulfoacetaldehyde acetyltransferase for the production of acetyl phosphate from formaldehyde. As regards the phosphoketolase/sulfoacetaldehyde acetyltransferase and the microorganism, the same applies as has been set forth above in connection with a method according to the invention.
In this specification, a number of documents including patent applications are cited. The disclosure of these documents, while not considered relevant for the patentability of this invention, is herewith incorporated by reference in its entirety. More specifically, all referenced documents are incorporated by reference to the same extent as if each individual document was specifically and individually indicated to be incorporated by reference.
The invention will now be described by reference to the following examples which are merely illustrative and are not to be construed as a limitation of the scope of the present invention.
The sequences of phosphoketolases inferred from the genomes of prokaryotic organisms were generated by oligonucleotide concatenation to fit the codon usage of E. coli (genes were commercially synthesized by GeneArt®). A stretch of 6 histidine codons was inserted after the methionine initiation codon to provide an affinity tag for purification. The genes thus synthesized were cloned in a modified pUC18 expression vector (New England Biolabs) containing a modified Multiple Cloning Sites (MCS). The genes of interest were cloned at Pacl and Notl restriction sites.
Competent MG1655 E. coli cells were transformed with these vectors using standard heat shock procedure. The transformed cells were grown in LB-ampicillin medium for 24 h at 30° C., 160 rpm shaking.
The cells were collected by centrifugation at 4° C., 10,000 rpm for 20 min and the pellets were stored at −80° C.
Protein Purification and Concentration
The pellets from 200 ml of cultured cells were thawed on ice and resuspended in 3 ml of 50 mM Tris-HCl pH 7.5 containing 300 mM NaCl, 5 mM MgCl2, 1 mM DTT and 10 mM Imidazole. 10 μl of lysonase (Merck) was added. Cells were incubated 10 minutes at room temperature and then returned to ice for 20 minutes. Cell lysis was completed by sonication for 2×30 seconds. The bacterial extracts were then clarified by centrifugation at 4° C., 10,000 rpm for 20 min. The clarified bacterial lysates were loaded on PROTINO-1000 Ni-TED column (Macherey-Nagel) allowing adsorption of 6-His tagged proteins. Columns were washed and the enzymes of interest were eluted with 4 ml of 50 mM Tris-HCl pH 7.5 containing 300 mM NaCl, 5 mM MgCl2, 1 mM DTT, 250 mM Imidazole. Eluates were then concentrated, desalted on Amicon Ultra-4 10 kDa filter unit (Millipore) and enzymes were resuspended in 50 mM Tris-HCl pH 7.5. Enzyme preparation was complemented with 10% glycerol prior to long-term storage. Protein concentrations were quantified by direct UV 280 nm measurement on the NanoDrop 1000 spectrophotometer (Thermo Scientific). The purity of proteins thus purified varied from 70% to 90%.
Acetyl phosphate is particularly unstable to hydrolysis, releasing acetate. Therefore, the enzyme-catalyzed production of acetate from formaldehyde was monitored using Mass Spectrometry (MS) and HPLC analysis.
Mass Spectrometry (MS) Analysis
The enzymatic reactions were carried out under the following conditions: 50 mM Sodium phosphate pH 7.5
1 mM Thiamine pyrophosphate (TPP)
10 mM MgCl2
50 mM Formaldehyde (Sigma)
The pH was adjusted to 7.5
Phosphoketolase (PKT) concentration was 10 mg/ml.
Control assays were performed in which either no enzyme was added, or no formaldehyde was added. The enzymatic reactions were run in total volume of 0.2 ml for 40 hours with shaking at 37° C. Typically, an aliquot of 200 μl reaction was removed, centrifuged and the supernatant was transferred into a clean vial. The MS spectra were obtained on Ion Trapp Mass Spectrometer (Esquire 3000, Bruker) in negative ion mode by direct injection of sample using a syringe pump operated at a flow rate of 2 ml/h. The presence of acetate was evaluated. MS analysis showed an [M-H]− ion at m/z 59.4, corresponding to acetate, from the enzymatic sample but not from the controls (
HPLC-Based Analysis
The enzymatic reactions were carried out under the following conditions:
50 mM Sodium phosphate pH 7.5
5 mM Thiamine pyrophosphate (TPP)
5 mM MgCl2
1.9 mM L-cysteine hydrochloride
23 mM Sodium fluoride
50 mM Formaldehyde (Sigma)
The pH was adjusted to 7.5
Phosphoketolase (PKT) was added at concentration of 5 mg/ml.
Control reactions consisting of (a) formaldehyde and phosphate without enzyme, (b) formaldehyde and enzyme without phosphate were run in parallel.
The enzymatic reactions were run in total volume of 0.3 ml for 48 hours with shaking at 37° C. and stopped by a 5-min incubation at 80° C. The assays tubes were then centrifuged and 100 μl of the clarified supernatant was transferred into a clean vial. Commercial sodium acetate (Sigma-Aldrich) was used as reference. HPLC analyses were performed using a 1260 Inifinity LC System (Agilent), equipped with a refractometer detector and a column heating module. 10 μl sample was separated on Hi-Plex H column (300×7.7 mm, 8 μm particle size, column temp. 65° C.) equipped with a PL Hi-Plex H Guard Column (50×7.7 mm). The mobile phase consisted of aqueous sulfuric acid (5.5 mM) was run with a flow rate of 0.6 ml/min. Retention time of acetate under these conditions was 18.4 min.
The results of HPLC analysis are shown in Table 1.
pseudolongum subsp.
globosum (Uniprot Q6R2Q6;
acetobutylicum (strain ATCC
These data indicate that production of acetate from formaldehyde takes place in the presence of phosphate and phosphoketolase proceeding through the formation of acetyl phosphate.
Acetyl phosphate is particularly unstable to hydrolysis, releasing acetate. Therefore, the enzyme-catalyzed production of acetate from formaldehyde is monitored using HPLC analysis.
HPLC-Based Analysis
The enzymatic reactions are carried out under the following conditions:
50 mM sodium phosphate pH 7.5
5 mM thiamine pyrophosphate (TPP)
5 mM MgCl2
1.9 mM L-cysteine hydrochloride
23 mM sodium fluoride
50 mM formaldehyde (Sigma-Aldrich)
1-10 mg/ml of enzyme
The following enzymes are used in this study:
Sulfoacetaldehyde acetyltransferase from Alcaligenes xylosoxydans xylosoxydans (Uniprot Accession number: Q84H41)
Sulfoacetaldehyde acetyltransferase from Roseovarius nubinhibens ISM (Uniprot Accession number: A3SR25)
Sulfoacetaldehyde acetyltransferase from Castellaniella defragans (Uniprot Accession Number: Q84H44)
Sulfoacetaldehyde acetyltransferase from Desulfonispora thiosulfatigenes (Uniprot Accession Number: Q93PS3)
Control reactions consisting of (a) formaldehyde and phosphate without enzyme, (b) formaldehyde and enzyme without phosphate are run in parallel.
The enzymatic reactions are conducted in a total volume of 0.3 ml for 48 hours with shaking at 37° C. and stopped by a 5-min incubation at 80° C. The assays tubes are then centrifuged and 100 μl of the clarified supernatant is transferred into a clean vial. Commercial sodium acetate (Sigma-Aldrich) is used as reference. HPLC analyses are performed using a 1260 Inifinity LC System (Agilent), equipped with a refractometer detector and a column heating module. 10 μl sample is separated on Hi-flex H column (300×7.7 mm, 8 μm particle size, column temp. 65° C.) equipped with a PL Hi-flex H Guard Column (50×7.7 mm). The mobile phase, consisting of aqueous sulfuric acid (5.5 mM) is run with a flow rate of 0.6 ml/min. Retention time of acetate under these conditions is 18.4 min.
| Number | Date | Country | Kind |
|---|---|---|---|
| 14161723 | Mar 2014 | EP | regional |
| 14176885 | Jul 2014 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2015/055254 | 3/13/2015 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2015/144447 | 10/1/2015 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 7253001 | Wahlbom et al. | Aug 2007 | B2 |
| 20120222148 | Turano et al. | Aug 2012 | A1 |
| Number | Date | Country |
|---|---|---|
| 2006016705 | Feb 2006 | WO |
| Entry |
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| Number | Date | Country | |
|---|---|---|---|
| 20170107546 A1 | Apr 2017 | US |
