Patent Grant
11505811
The present invention relates to a novel method for the preparation of 2,4-dihydroxybutyrate (2,4-DHB) from homoserine comprising a two-step pathway:
The carboxylic acids cited within the present application are equally named under their salt (e.g. 2,4-dihydroxyburyrate) or acid forms (e.g. 2,4-dihydroxybutyric acid).
2,4-dihydroxybutyric acid (equally 2,4-DHB or DHB) is a compound of considerable economic interest. DHB can be readily converted into α-hydroxy-γ-butyrolactone in aqueous media by adjusting the appropriate pH. α-hydroxy-γ-butyrolactone is a prominent precursor for the production of the methionine substitute 2-hydroxy-4-(methylthio)-butyrate (HMTB) (US 2009/318715) which has a large market in animal nutrition. At present, α-hydroxy-γ-butyrolactone is derived from γ-butryolactone by a multi-stage process that implies halogenation of the γ-butryolactone in position α, and subsequent substitution of the halogen atom by a hydroxyl group in alkaline medium (US 2009/318715).
From growing oil prices the need for the production of DHB from renewable resources arises. Microorganisms are capable of transforming biomass-derived raw material, e.g. sugars or organic acids, into a large variety of different chemical compounds (Werpy & Petersen, 2004). With the growing body of biochemical and genomic information it is possible to modify microorganisms such that they overproduce naturally occurring metabolic intermediates with high yield and productivity (Bailey, 1991). Optimization of production microorganisms often requires rational engineering of metabolic networks which ensures, among others, overexpression of enzymes required for the biosynthesis of the metabolite of interest, and alleviation of product feedback inhibition. Another possibility is the implementation of novel enzymatic systems that catalyze the production of a metabolite of interest.
Metabolic engineering approaches and enzymatic catalyses require detailed knowledge of the biochemistry and regulation of the metabolic pathway leading to the metabolite of interest. In the case of DHB production, this information is not available. Only few studies report the occurrence of DHB in patients with succinic semialdehyde dehydrogenase deficiency (Shinka et al., 2002) without, however, identifying enzymatic reactions implicated in DHB production. The zymotic or enzymatic production of DHB, therefore, requires (i) the identification of a thermodynamically feasible pathway which transforms an accessible precursor into DHB, (ii) the identification or construction of enzymes that are capable to catalyze individual reaction steps in the pathway and (iii) the functional expression of the pathway enzymes in an appropriate production organism. The present invention has as an objective to satisfy these needs.
Accordingly, one object of the present invention is a method of preparation of 2,4-DHB from homoserine comprising a two-step pathway (see
The first and/or the second step(s) of the method of the invention can be catalyzed either by an enzyme encoded by an endogenous or a heterologous gene.
In the description, enzymatic activities are also designated by reference to the genes coding for the enzymes having such activity. The use of the denomination of the genes is not limited to a specific organism, but covers all the corresponding genes and proteins in other organisms (e.g. microorganisms, functional analogues, functional variants and functional fragments thereof as long as they retain the enzymatic activity).
Within a further aspect of the invention, the enzyme converting the primary amino group of homoserine to a carbonyl group to obtain OHB can be homoserine transaminase, homoserine dehydrogenase, or homoserine oxidase.
Within a further aspect of the invention, the enzyme having homoserine transaminase activity can be identified among enzymes having aspartate transaminase (EC2.6.1.1) activity, branched-chain-amino-acid transaminase (EC2.6.1.42) activity, or aromatic-amino-acid transaminase (EC2.6.1.57) activity.
Within a further aspect of the invention, the homoserine transaminase can be the branched-chain-amino-acid transaminase from Escherichia coli, Ec-IlvE, and Lactococcus lactis, Ll-BcaT, the aromatic-amino-acid transaminases from E. coli, Ec-TyrB, L. lactis, Ll-AraT, and Saccharomyces cerevisiae, Sc-Aro8, or the aspartate transaminase from E. coli, Ec-AspC.
The second step of the method of the present invention is catalysed by an enzyme having OHB reductase activity. Within a further aspect of the invention, the enzyme having OHB reductase activity can be identified among enzymes having 2-hydroxyacid dehydrogenase activity, in particular among enzymes having lactate dehydrogenase (Ldh) (EC1.1.1.27, EC1.1.1.28), malate dehydrogenase (Mdh) (EC1.1.1.37, EC1.1.1.82, EC1.1.1.299) activity, or branched chain (D)-2-hydroxyacid dehydrogenase (EC1.1.1.272, EC1.1.1.345) activity. More specifically, the enzyme having homoserine transaminase activity is encoded by genes ilvE, tyrB, aspC, araT, bcaT, or ARO8.
In an even more specific aspect, the enzyme having homoserine transaminase activity is encoded by sequence set forth in SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67 or SEQ ID NO: 69 or any sequence sharing a homology of at least 50% with said sequences or corresponds to SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70 or any sequence sharing a homology of at least 50% with said sequences.
Within a further aspect of the invention, the OHB reductase enzyme can be the (L)-lactate dehydrogenase from Lactococcus lactis (Ll-LdhA), from Oryctalagus cuniculus (Oc-LldhA), from Geobacillus stearothermophilus (Gs-Lldh), or from Bacillus subtilis (Bs-Ldh), the (D)-lactate dehydrogenase from Escherichia coli (Ec-LdhA), the (L)-malate dehydrogenase from Escherichia coli (Ec-Mdh), or the branched chain (D)-2-hydroxyacid dehydrogenase from Lactococcus lactis (Ll-PanE).
In an even more specific aspect of the invention the OHB reductase enzyme is represented by the amino acid sequences SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 288, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID NO: 116 or SEQ ID NO: 118 or any sequence sharing a homology of at least 50% with said sequences, or is encoded by the nucleic acid sequences represented by SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 287, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 101, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 113, SEQ ID NO: 115 or SEQ ID NO: 117 or any sequence sharing a homology of at least 50% with said sequences.
In a further aspect, the invention also deals with the use of an enzyme reducing OHB to 2,4-DHB as above described.
Proteins sharing substantial homology with the above enzymes are also another aspect of the invention such as functional variants or functional fragments.
The expression “substantial homology” covers homology with respect to structure and/or amino acid components and/or biological activity.
More generally, within the meaning of the invention the homology between two protein sequences can be determined by methods well known by the skilled man in the art. It is generally defined as a percentage of sequence identity between a reference sequence and the sequence of a protein of interest.
As used herein, “percent (%) sequence identity” with respect to the amino acid or nucleotide sequences identified herein is defined as the percentage of amino acid residues or nucleotides in a candidate sequence that are identical with the amino acid residues or nucleotides in an enzyme sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Methods for performing sequence alignment and determining sequence identity are known to the skilled artisan, may be performed without undue experimentation, and calculations of identity values may be obtained with definiteness. See, for example, Ausubel, et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 19 (Greene Publishing and Wiley-Interscience, New York); and the ALIGN program (Dayhoff (1978) in Atlas of Protein Sequence and Structure 5:Suppl. 3 (National Biomedical Research Foundation, Washington, D.C.). A number of algorithms are available for aligning sequences and determining sequence identity and include, for example, the homology alignment algorithm of Needleman et al. (1970) J. Mol. Biol. 48:443; the local homology algorithm of Smith, et al. (1981) Adv. Appl. Math. 2:482; the search for similarity method of Pearson, et al. (1988) Proc. Natl. Acad. Sci. 85:2444; the Smith-Waterman algorithm (Meth. Mol. Biol. 70:173-187 (1997); and BLASTP, BLASTN, and BLASTX algorithms (see Altschul, et al. (1990) J. Mol. Biol. 215:403-410). Computerized programs using these algorithms are also available, and include, but are not limited to: ALIGN or Megalign (DNASTAR) software, or WU-BLAST-2 (Altschul, et al., Meth. Enzym., 266:460-480 (1996)); or GAP, BESTFIT, BLAST (Altschul, et al.), supra, FASTA, and TFASTA, available in the Genetics Computing Group (GCG) package, Version 8, Madison, Wis., USA; and CLUSTAL in the PC/Gene program by Intelligenetics, Mountain View, Calif. Those skilled in the art can determine appropriate parameters for measuring alignment, including algorithms needed to achieve maximal alignment over the length of the sequences being compared. Preferably, the sequence identity is determined using the default parameters determined by the program. Specifically, sequence identity can be determined by the Smith-Waterman homology search algorithm (Meth. Mol. Biol. 70:173-187 (1997)) as implemented in MSPRCH program (Oxford Molecular) using an affine gap search with the following search parameters: gap open penalty of 12, and gap extension penalty of 1. Preferably, paired amino acid comparisons can be carried out using the GAP program of the GCG sequence analysis software package of Genetics Computer Group, Inc., Madison, Wis., employing the blosum 62 amino acid substitution matrix, with a gap weight of 12 and a length weight of 2. With respect to optimal alignment of two amino acid sequences, the contiguous segment of the variant amino acid sequence may have additional amino acid residues or deleted amino acid residues with respect to the reference amino acid sequence. The contiguous segment used for comparison to the reference amino acid sequence will include at least 20 contiguous amino acid residues, and may be 30, 40, 50, or more amino acid residues. Corrections for increased sequence identity associated with inclusion of gaps in the derivative's amino acid sequence can be made by assigning gap penalties.
The enzymes according to the present invention having the same activity (either OHB reductase, or the enzyme converting the primary amino group of homoserine to a carbonyl group to obtain OHB) share at least about 50%, 70% or 85% amino acid sequence identity, preferably at least about 85% amino acid sequence identity, more preferably at least about 90% amino acid sequence identity, even more preferably at least about 95% amino acid sequence identity and yet more preferably 98% amino acid sequence identity. Preferably, any amino acid substitutions are “conservative amino acid substitutions” using L-amino acids, wherein one amino acid is replaced by another biologically similar amino acid. Conservative amino acid substitutions are those that preserve the general charge, hydrophobicity/hydrophilicity, and/or steric bulk of the amino acid being substituted. Examples of conservative substitutions are those between the following groups: Gly/Ala, Val/Ile/Leu, Lys/Arg, Asn/Gln, Glu/Asp, Ser/Cys/Thr, and Phe/Trp/Tyr. A derivative may, for example, differ by as few as 1 to 10 amino acid residues, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue.
The term functional variant encompasses enzymes that may present substantial sequence modifications when compared to the sequences specifically described within the present application but that still retain the original enzymatic activity.
It also means that the sequence of the enzyme may comprise less amino acids than the original one but said truncated enzyme still retains the original enzymatic activity.
According to an aspect of the invention, the activity of the enzyme catalyzing the first and/or the second step of the method of the present invention is enhanced. This enhancement can be measured by an enzymatic assay as described in Examples 1 or 4.
Improvement of said enzymes can be obtained by at least one mutation, said mutation(s) (i) improving the activity and/or substrate affinity of the mutated enzyme for homoserine or OHB respectively, and or (ii) decreasing the activity and/or substrate affinity of the mutated enzyme for their natural substrate.
Within the present invention, the expression “improve the activity and/or substrate affinity” means that the enzyme before mutation, was either
In a still further aspect the invention encompasses the nucleotide sequences encoding the enzymes catalyzing the first and the second step of the method of the invention.
In an even more specific aspect of the invention the OHB reductase enzyme is encoded by the nucleic acid sequences represented by SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 287, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 101, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO: 113, SEQ ID NO: 115 or SEQ ID NO: 117 or any sequence sharing a homology of at least 50% with said sequences.
The OHB reductase according to the invention corresponds in a specific aspect to (L)-lactate dehydrogenase A comprising at least one mutation when a compared to the wild type enzyme in at least one of the positions V17, Q85, E89, I226, or A222. These positions are conserved in the lactate dehydrogenase family, and they are defined in this text by reference to the Lactococcus lactis (L)-lactate dehydrogenase A (SEQ ID NO: 6). The skilled man in the art will then easily identify the corresponding amino acid residues in other lactate dehydrogenases by an alignment of the corresponding amino acid sequences. Therefore, the invention also provides for changes of these amino acids in other lactate dehydrogenase enzymes. 2
The OHB reductase according to the invention corresponds in a specific aspect to (L)-malate dehydrogenase comprising at least one mutation when compared to the wild type enzyme in at least one of the positions I12, R81, M85, D86, V93, G179, T211, or M227. These positions are conserved in the malate dehydrogenase family, and they are defined in this text by reference to the sequence of the E. coli (L)-malate dehydrogenase (SEQ ID NO: 2). The man skilled in the art will easily identify the corresponding amino acid residues in other malate dehydrogenases by an alignment of the corresponding amino acid sequences. Therefore, the invention also provides for changes of these amino acids in other malate dehydrogenase enzymes.
In accordance with this invention, a “nucleic acid sequence” refers to a DNA or RNA molecule in single or double stranded form, preferably a DNA molecule. An “isolated DNA”, as used herein, refers to a DNA which is not naturally-occurring or no longer in the natural environment wherein it was originally present, e.g., a DNA coding sequence associated with other regulatory elements in a chimeric gene, a DNA transferred into another host cell, or an artificial, synthetically-made DNA sequence having a different nucleotide sequence compared to any naturally-occurring DNA sequence.
The present invention also relates to a chimeric gene comprising, functionally linked to one another, at least one promoter which is functional in a host organism, a polynucleotide encoding anyone of the enzymes catalyzing first and second step of the method as defined according to the invention, and a terminator element that is functional in the same host organism. The various elements which a chimeric gene may contain are, firstly, elements regulating transcription, translation and maturation of proteins, such as a promoter, a sequence encoding a signal peptide or a transit peptide, or a terminator element constituting a polyadenylation signal and, secondly, a polynucleotide encoding a protein. The expression “functionally linked to one another” means that said elements of the chimeric gene are linked to one another in such a way that the function of one of these elements is affected by that of another. By way of example, a promoter is functionally linked to a coding sequence when it is capable of affecting the expression of said coding sequence. The construction of the chimeric gene according to the invention and the assembly of its various elements can be carried out using techniques well known to those skilled in the art. The choice of the regulatory elements constituting the chimeric gene depends essentially on the host organism in which they must function, and those skilled in the art are capable of selecting regulatory elements which are functional in a given host organism. The term “functional” is intended to mean capable of functioning in a given host organism.
The promoters which the chimeric gene according to the invention may contain are either constitutive or inducible. By way of example, the promoters used for expression in bacteria may be chosen from the promoters mentioned below. For expression in Escherichia coli mention may be made of the lac, trp, lpp, phoA, recA, araBAD, prou, cst-I, tetA, cadA, nar, tac, trc, lpp-lac, Psyn, cspA, PL, PL-9G-50, PR-PL, T7, [lambda]PL-PT7, T3-lac, T5-lac, T4 gene 32, nprM-lac, VHb and the protein A promoters or else the Ptrp promoter (WO 99/64607). For expression in Gram-positive bacteria such as Corynebacteria or Streptomyces, mention may be made of the PtipA or PS1 and PS2 (FR91/09870) promoters or those described in application EP0629699A2. For expression in yeasts and fungi, mention may be made of the K. lactis PLAC4 promoters or the K. lactis Ppgk promoter (patent application FR 91/05294), the Trichoderma reesei tef1 or cbh1 promoter (WO 94/04673), the Penicillium funiculosum his, csl or apf promoter (WO 00/68401) and the Aspergillus niger gla promoter.
According to the invention, the chimeric gene may also comprise other regulatory sequences, which are located between the promoter and the coding sequence, such as transcription activators (enhancers).
As such, the chimeric gene of the invention comprises in a specific embodiment at least, in the direction of transcription, functionally linked, a promoter regulatory sequence which is functional in a host organism, a nucleic acid sequence encoding a polynucleotide encoding anyone of the enzymes catalyzing first and second step of the method as defined according to the invention and a terminator regulatory sequence which is functional in said host organism.
The present invention also relates to a cloning and/or expression vector comprising a chimeric gene according to the invention or a nucleic acid sequence of the invention. The vector according to the invention is of use for transforming a host organism and expressing in this organism anyone of the enzymes catalyzing the first and/or the second step(s) of the method of the present invention. This vector may be a plasmid, a cosmid, a bacteriophage or a virus. Preferentially, the transformation vector according to the invention is a plasmid. Generally, the main qualities of this vector should be able to maintain itself and to self-replicate in the cells of the host organism, in particular by virtue of the presence of an origin of replication, and to express anyone of the enzymes catalyzing the first and/or the second step(s) of the method of the present invention therein. For the purpose of stable transformation of a host organism, the vector may also integrate into the genome. The choice of such a vector, and also the techniques of insertion of the chimeric gene according to the invention into this vector are part of the general knowledge of those skilled in the art. Advantageously, the vector used in the present invention also contains, in addition to the chimeric gene according to the invention, a chimeric gene encoding a selectable marker. This selectable marker makes it possible to select the host organisms which are effectively transformed, i.e. those which incorporated the vector. According to a particular embodiment of the invention, the host organism to be transformed is a bacterium, a yeast, a fungus. Among the selectable markers which can be used, mention may be made of markers containing genes for resistance to antibiotics, such as, for example, the hygromycinphosphotransferase gene. Other markers may be genes to complement an auxotrophy, such as the pyrA, pyrB, pyrG, pyr4, arg4, argB and trpC genes, the molybdopterin synthase gene or that of acetamidase. Mention may also be made of genes encoding readily identifiable enzymes such as the GUS enzyme, or genes encoding pigments or enzymes regulating the production of pigments in the transformed cells. Such selectable marker genes are in particular described in patent applications WO 91/02071, WO 95/06128, WO 96/38567 and WO 97/04103.
The present invention also relates to modified microorganisms.
More specifically, the modified microorganism of the invention allows the preparation of 2,4-DHB from homoserine by a two-step pathway comprising:
The enzymes involved in the two steps are those above described.
The term “microorganism” is intended to mean any lower unicellular organism into which the chimeric gene(s), nucleic acid(s) or vector(s) according to the invention may be introduced in order to produce 2,4-DHB. Preferably, the host organism is a microorganism, in particular a fungus, for example of the Penicillium, Aspergillus and more particularly Aspergillusflavus, Chrysosporium or Trichoderma genus, a yeast, in particular of the Saccharomycetaceae, Pichiaceae or Schizosaccharomycetaceae, most preferentially Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces marxianus, or Pichia jadinii, Pichia stipitis or Pichia pastoris, a bacterium, preferentially selected among Enterobacteriaceae, Clostridiaceae, Bacillaceae, Streptomycetaceae, Streptococcaceae, Methylobacteriacae, and Corynebacteriaceae, most preferentially Escherichia coli, Bacillus subtilis, Corynebacterium glutamicum, Clostridium acetobutylicum, Methylobacterium extorquens or Lactococcus lactis.
The present invention also relates to modified microorganisms containing at least one chimeric gene according to the invention, either integrated into their genome or carried on an extra-chromosomal genetic element, for example a plasmid. In a more specific aspect of the invention, the transformed host organism comprises a nucleic acid of the invention encoding a polypeptide converting the primary amino acid group of homoserine to a carbonyl group to obtain OHB and/or a nucleic acid encoding a polypeptide reducing OHB in 2,4-DHB or a chimeric gene comprising a nucleic acid encoding a polypeptide converting the primary amino acid group of homoserine to a carbonyl group to obtain OHB, and/or a OHB reductase or an expression vector comprising a nucleic acid encoding a polypeptide converting the primary amino acid group of homoserine to a carbonyl group to obtain OHB, or a polypeptide having a OHB reductase activity.
Within a further aspect of the invention, the synthetic pathway for the conversion of homoserine into DHB is expressed in a microorganism with enhanced production of homoserine. Enhanced production of homoserine in microorganisms can be achieved by (i) overexpressing the enzymes aspartate kinase, aspartate semialdehyde dehydrogenase, and homoserine dehydrogenase, (ii) by rendering the aspartate kinase enzyme insensitive to product inhibition that can be brought about by lysine, methionine, or threonine, and (iii) by deletion of metabolic pathways that branch off the homoserine biosynthesis pathway. Overexpression of aspartate kinase, aspartate semialdehyde dehydrogenase, and homoserine dehydrogenase can be achieved by expressing the enzymes from a multicopy plasmid under the control of an appropriate constitutive or inducible promoter. Alternatively, overexpression of said enzymes can be achieved by deletion of transcriptional repressors that limit the transcription of genes coding for aspartate kinase, aspartate semialdehyde dehydrogenase, and homoserine dehydrogenase. Aspartate kinases can be rendered insensitive to inhibition by aspartate-derived amino acids by introducing appropriate mutations into their amino acid sequences. Entry points into metabolic pathways that branch off the homoserine biosynthesis pathway are catalyzed by enzymes having O-succinyl homoserine or O-acetyl homoserine synthase activity (entry into methionine biosynthesis), homoserine kinase activity (entry into threonine biosynthesis), or diaminopimelate decarboxylase activity (entry into lysine biosynthesis). Deletion of genes encoding proteins having said enzymatic activities avoids formation aspartate-derived amino acids and therefore aids homoserine formation.
Accordingly, deletion of the genes metA, thrB, and lysA in E. coli attenuates pathways that branch of the homoserine biosynthetic pathway. The increase of enzymatic activities of the homoserine pathway in E. coli can be achieved, for instance, by the overexpression of the bifunctional aspartate kinase-homoserine dehydrogenase mutant thrA S345F (insensitive to threonine inhibition) and asd (both genes from E. coli); or by the overexpression of the monofunctional aspartate kinase mutant lysC E250K (insensitive to lysine), asd (both genes from E. coli), and the homoserine dehydrogenase gene HOM6 from S cerevisiae.
The microorganism of the invention may also have attenuated capacity to export homoserine which increases the intracellular availability of this amino acid. In order to achieve decreased homoserine export from the cells, permeases capable of exporting homoserine can be deleted. Such permeases may be identified by overexpressing genomic libraries in the microorganism and cultivating said microorganism at inhibitory concentrations of homoserine or structurally similar amino acids such as threonine, leucine, or aspartate (Zakataeva et al. 1999/FEBS Lett/452/228-232). Genes whose overexpression confers growth at increased concentrations of either of said amino acids are likely to participate in homoserine export.
In a further aspect, the microorganism of the invention being Escherichia coli carries deletions in the homoserine efflux transporters rhtA, rhtb, and/or rhtC.
Efficient production of DHB can be ensured by optimizing carbon flux repartitioning in the metabolic network of the host organism with respect to the optimization of cofactor supply for DHB synthesis, and attenuation of competing pathways that cause formation of metabolic by-products other than DHB. An important tool for strain improvement provides constraint-based flux balance analysis. This method allows calculating the theoretical yield of a given metabolic network depending on cultivation conditions, and facilitates identification of metabolic targets for overexpression or deletion. The experimental techniques used for overexpression and deletion of the metabolic target reaction are described (Example 8).
Accordingly, the microorganism of the invention may also exhibit enzymatic activities chosen among phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, isocitrate lyase, pyruvate carboxylase, and hexose symporter permease which is increased, and/or at least one of the enzymatic activities chosen among lactate dehydrogenase, alcohol dehydrogenase, acetate kinase, phosphate acetyltransferase, pyruvate oxidase, isocitrate lyase, fumarase, 2-oxoglutarate dehydrogenase, pyruvate kinase, malic enzyme, phosphoglucose isomerase, phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, pyruvate-formate lyase, succinic semialdehyde dehydrogenase, sugar-transporting phosphotransferase, ketohydroxyglutarate aldolase, homoserine-O-succinyl transferase, homoserine kinase, homoserine efflux transporter, diaminopimelate decarboxylase, and/or methylglyoxal synthase which is (are) decreased.
In a further aspect, the microorganism of the invention being Escherichia coli overexpresses at least one of the genes chosen among ppc, pck, aceA, galP, asd, thrA, metL, lysC all E. coli; pycA from L. lactis, and/or has at least one of the genes deleted chosen among ldhA, adhE, ackA, pta, poxB, focA, pfIB, sad, gabABC, sfcA, maeB, ppc, pykA, pykF, mgsA, sucAB, ptsl, ptsG, pgi, fumABC, aldA, lldD, icIR, metA, thrB, lysA, eda, rhtA, rhtB, rhtC.
The present invention also encompasses a method of production of 2,4-DHB comprising the steps of
Product separation and purification is very important factor enormously affecting overall process efficiency and product costs. Methods for product recovery commonly comprise the steps cell separation, as well as product purification, concentration and drying, respectively.
Cell Separation
Ultrafiltration and centrifugation can be used to separate cells from the fermentation medium. Cell separation from fermentation media is often complicated by high medium viscosity. Therefore, we can add additives such as mineral acids or alkali salts, or heating of the culture broth to optimize cell separation.
Product Recovery
A variety of ion-exchange chromatographic methods can be applied for the separation of DHB either before or after biomass removal. They include the use of primary cation exchange resins that facilitate separation of products according to their isoelectric point. Typically, the resin is charged with the solution, and retained product is eluted separately following increase of pH (e.g. by adding ammonium hydroxide) in the eluent. Another possibility is the use of ion-exchange chromatography using fixed or simulated moving bed resins. Different chromatographic steps may have to be combined in order to attain adequate product purity. Those purification methods are more economical compared with a costly crystallization step, also providing additional advantages and flexibility regarding the form of final product.
Product Concentration and Drying
The purification process can also comprise a drying step which may involve any suitable drying means such as a spray granulator, spray dryer, drum dryer, rotary dryer, and tunnel dryer. Concentrated DHB solutions can be obtained by heating fermentation broths under reduced pressure by steam at 130° C. using a multipurpose concentrator or thin film evaporator.
The following non limiting examples illustrate the invention.
Construction of plasmids containing wild-type genes coding for lactate dehydrogenase or malate dehydrogenase:
The genes coding for (L)-malate dehydrogenase in Escherichia coli, Ec-mdh (SEQ ID NO: 1), (D)-lactate dehydrogenase in E. coli, Ec-ldhA (SEQ ID NO: 3), (L)-lactate dehydrogenase of Lactococcus lactis, Ll-ldhA (SEQ ID NO: 5), (L)-lactate dehydrogenase of Bacillus subtilis, Bs-ldh (SEQ ID NO: 7), (L)-lactate dehydrogenase of Geobacillus stearothermophilus, Gs-ldh (SEQ ID NO: 9), the two isoforms of the (L)-lactate dehydrogenase of Oryctalagus cuniculus, Oc-ldhA (SEQ ID NO: 11 and SEQ ID NO: 13), were amplified by PCR using the high-fidelity polymerase Phusion™ (Fermentas) and the primers listed in Table 1. Genomic DNAs of E. coli MG1655, L. lactis IL1403, and B. subtilis strain 168 were used as the template. The genes Oc-ldhA, and Gs-ldh were codon-optimized for expression in E. coli and synthesized by MWG Eurofins. The primers introduced restriction sites (Table 1) upstream of the start codon and downstream of the stop codon, respectively, facilitating the ligation of the digested PCR products into the corresponding sites of the pET28a+ (Novagen) expression vector using T4 DNA ligase (Fermentas). Ligation products were transformed into E. coli DH5a cells (NEB). The resulting pET28-Ec-mdh, pET28-Ec-ldhA, pET28-Ll-ldhA, pET28-Bs-ldh, pET28-Gs-ldh, and pET28-Oc-ldhA plasmids were isolated and shown by DNA sequencing to contain the correct full-length sequence of the E. coli mdh, E. coli ldhA, L. lactis ldhA, B. subtilis ldh, G. stearothermophilus ldh, and O. cuniculus ldhA genes, respectively. The corresponding protein sequences are represented by SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12 and SEQ ID NO: 14, respectively.
Expression of enzymes: E. coli BL21 (DE3) star cells were transformed with the appropriate plasmids using standard genetic protocols (Sambrook, Fritsch, & Maniatis, 1989). Enzymes with an N-terminal hexa-His tag were expressed in 50 mL LB cultures that were inoculated from an overnight culture at OD600 of 0.1 and grown to OD600 of 0.6 before protein expression was induced by addition of 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) to the culture medium. After 15 h of protein expression, cells were harvested by centrifugation at 4000 g at 4° C. for 10 min and discarding the supernatant. Cell pellets were stored at −20° C. until further analysis. Growth and protein expression were carried out at 25° C. Culture media contained 50 μg/mL kanamycin.
Purification of enzymes: Frozen cell pellets of expression cultures were resuspended in 0.5 mL of breakage buffer (50 mM Hepes, 300 mM NaCl, pH 7.5) and broken open by four successive rounds of sonication (sonication interval: 20 s, power output: 30%, sonicator: Bioblock Scientific, VibraCell™ 72437). Cell debris was removed by centrifuging the crude extracts for 15 min at 4° C. at 4000 g and retaining the clear supernatant. RNA and DNA were removed from the extracts by adding 15 mg/mL streptomycin sulfate (Sigma), centrifuging the samples at 13000 g for 10 min at 4° C. and retaining the supernatant. Clear protein extract was incubated for 1 h at 4° C. with 0.75 mL (bed volume) of Talon™ Cobalt affinity resin (Clontech). The suspension was centrifuged at 700 g in a table top centrifuge and supernatant was removed. The resin was washed with 10 bed volumes of wash buffer (50 mM Hepes, 300 mM NaCl, 15 mM Imidazole, pH 7.5) before proteins were eluted with 0.5 mL of elution buffer (50 mM Hepes, 300 mM NaCl, 250 mM Imidazole, pH 7.5). Purity of eluted enzymes was verified by SDS-PAGE analysis. Protein concentrations were estimated with the method of Bradford (Bradford (1976, Anal. Biochem. 72: 248-54). To stabilize the lactate dehydrogenase enzymes, the elution buffer was systematically exchanged by 100 mM phosphate buffer adjusted to pH 7. The protein sample was transferred to an Amicon™ Ultra centrifugal filter (cut-off 10 kDa), and centrifuged during 8 min at 4000 g at 4° C. to remove the buffer. The protein was diluted into phosphate buffer and the procedure was repeated 4 times.
Enzymatic assays: The reaction mixture contained 60 mM Hepes (pH 7), 50 mM potassium chloride, 5 mM MgCl2, 0.25 mM NADH, (optionally 5 mM fructose-1,6-bisphosphate) (all products from Sigma), and appropriate amounts of purified malate or lactate dehydrogenase or cell extract. Reactions were started by adding appropriate amounts of 2-oxo-4-hydroxybutyrate (OHB), pyruvate, or oxaloacetate (OAA). Enzymatic assays were carried out at 37° C. in 96-well flat bottomed microtiter plates in a final volume of 250 μL. The reactions were followed by the characteristic absorption of NADH at 340 nm (εNADH=6.22 mM−1 cm−1) in a microplate reader (BioRad 680XR).
OHB was synthesized by incubating 125 mM homoserine with snake venom (L)-amino acid oxidase (1.25 U/mL, Sigma) and catalase (4400 U/mL, Sigma) in 100 mM Tris buffer at pH 7.8 for 90 min at 37° C. Subsequently, the reaction mixture was purified on an Amicon™ Ultra centrifugal filter with a cut-off of 10 kDa to eliminate the enzymes (method adapted from Wellner & Lichtenberg, 1971).
OHB was quantified by mixing 100 μL of the tested solution with 1 mL of a solution containing 1 M sodium arsenate and 1 M boric acid at pH 6.5. The mixture was incubated at room temperature for 30 min and the absorbance at 325 nm was used to quantify OHB. The relation between absorbance and concentration of the ketone was calibrated using pyruvate solutions of known concentrations (method adapted from (Wellner & Lichtenberg, 1971)). The typical OHB yield of the method was 90%.
Results: The kinetic parameters are listed in Table 2 for the tested enzymes on their natural substrates and OHB. Significant OHB reductase activity was found for all lactate dehydrogenases of different biological origin. Malate dehydrogenase, Mdh, of E. coli only had very minor activity on OHB. The branched chain 2-oxo-acid dehydrogenase, PanE, from L. lactis also had significant activity on OHB.
aNatural substrates for Mdh and Ldh are oxaloacetate and pyruvate, respectively
bWhen enzymes could not be saturated, maximum specific activity refers to the activity estimated at 20 mM substrate concentration
Site-directed mutagenesis of the L. lactis ldhA gene was carried out using the pET28-Ll-ldhA plasmid as the template. Point mutations to change the amino acid sequence were introduced by PCR (Phusion 1U, HF buffer 20% (v/v), dNTPs 0.2 mM, direct and reverse primers 0.04 μM each, template plasmid 30-50 ng, water) using the oligonucleotide pairs listed in Table 3. The genes mutated by PCR contained a new restriction site listed in Table 3 (introduced using silent mutations) in addition to the functional mutation to facilitate identification of mutated clones. The PCR products were digested by DpnI at 37° C. for 1 h to remove template DNA, and transformed into competent E. coli DH5α (NEB) cells. The mutated plasmids were identified by restriction site analysis and were verified to carry the desired mutations by DNA sequencing.
L. lactis (nnk denotes a degenerated codon
Mutant enzymes were expressed, purified and tested for OHB and pyruvate reductase activity as described in Example 1. The activity measurements for both substrates are summarized in
The mutation Q85N in Ll-Ldh was combined with mutation I226V. It was demonstrated that this exchange had a major positive impact on substrate affinity for OHB.
Site-directed mutagenesis of the mdh gene from E. coli was carried out as described in Example 2 using the primers listed in Table 5. Plasmid pET28-Ec-mdh was used as the template.
Mutant enzymes were expressed, purified and tested for OHB and oxaloacetate reductase activity as described in Example 1. The activity measurements on OHB and oxaloacetate are summarized in
The mutation R81A in Ec-Mdh was combined with additional changes in the protein sequence. The results are listed in Table 6. It was demonstrated that the introduction of mutations M85Q, M85E, I12V, D86S or G179D result in an increased activity on OHB.
aactivity was measured at 0.5 mM oxaloacetate
bactivity was measured at 20 mM OHB
The genes coding for different transaminases in E. coli, S. cerevisiae, and L. lactis were amplified by PCR using the high-fidelity polymerase Phusion™ (Finnzymes) and the primers listed in Table 7. Genomic DNA of E. coli MG1655, S. cerevisiae BY4741, and L. lactis IL1403 were used as the templates. The primers introduced restriction sites (Table 7) upstream of the start codon and downstream of the stop codon, respectively, facilitating the ligation of the digested PCR products into the corresponding sites of the pET28a+(Novagen) expression vector using T4 DNA ligase (Biolabs). Ligation products were transformed into E. coli DH5a cells. The resulting plasmids were isolated and shown by DNA sequencing to contain the correct full-length sequence of the corresponding genes. The references to the corresponding protein sequences are listed in Table 7.
Enzymes were expressed and purified as described in Example 1, and tested for homoserine transaminase activity under the conditions described below.
Enzymatic assays: Transaminase activity of several candidate aminotransferases was quantified with 2-oxoglutarate as the amino group acceptor. Transaminase reactions were carried out using homoserine and the preferred amino acid of the enzymes. The reactions were followed by the amino acid-dependent oxidation of NADH in the coupled dehydrogenase reaction.
Transaminase Assays (Reaction Scheme)
Transaminase: Amino acid+2-oxoglutarate→2-oxo-acid+glutamate
Dehydrogenase: 2-oxo-acid+NADH→2-hydroxy-acid+NAD+
The reaction mixture contained 60 mM Hepes (pH 7), 50 mM potassium chloride, 5 mM MgCl2, 4 mM 2-oxoglutarate, 0.1 mM pyridoxal-5′-phosphate (PLP), 0.25 mM NADH, (optionally 5 mM fructose-1,6-bisphosphate) (all products from Sigma), 4 Units/mL of auxiliary 2-hydroxyacid dehydrogenase, and appropriate amounts of purified aminotransferase or cell extract. The auxiliary dehydrogenase enzyme was purified PanE from L. lactis in case of the amino acids phenylalanine and leucine (Chambellon, Rijnen, Lorquet, Gitton, van HylckamaVlieg, Wouters, & Yvon, 2009), malate dehydrogenase (Sigma) in case of aspartate, and rabbit muscle (L)-lactate dehydrogenase (Sigma) when homoserine was used as the starting substrate. Reactions were started by adding 50 mM of the amino acid.
Enzymatic assays were carried out at 37° C. in 96-well flat bottomed microtiter plates in a final volume of 250 μL. The reactions were followed by the characteristic absorption of NAD(P)H at 340 nm (εNADPH=6.22 mM−1 cm−1) in a microplate reader (BioRad 680XR).
Results: The kinetic parameters of different aminotransferases are listed in Table 8. Significant homoserine transaminase activity was found for the listed transaminase enzymes.
Construction of the Plasmids pTAC-op-HMS1 and pACT3-op-HMS1
The plasmid pET28-LYSCwt was constructed by amplifying the lysC gene by PCR using high fidelity polymerase Phusion™ (Finnzymes) and the direct and reverse primers 5′ CACGAGGTACATATGTCTGAAATTGTTGTCTCC3′ (SEQ ID NO: 71) and 5′ CTTCCAGGGGATCCAGTATTTACTCAAAC3′ (SEQ ID NO: 72) that introduced a NdeI and BamHI restriction sites upstream of the start codon and downstream of the stop codon, respectively. Genomic DNA from E. coli MG1655 was used as the template. The PCR product was digested with NdeI and BamHI, ligated into the corresponding sites of the pET28a (Novagen) expression vector using T4 DNA ligase (Biolabs), and transformed into E. coli DH5a cells. The resulting pET28-LYSCwt plasmid was isolated and shown by DNA sequencing to contain the full-length lysC gene having the correct sequence (SEQ ID NO: 73).
Site-directed mutagenesis of lysC to alleviate inhibition by lysine was carried out using the pET28-LYSCwt plasmid as the template. A point mutation to change the amino acid sequence in position 250 from glutamate to lysine (E250K, SEQ ID NO: 36) was introduced by PCR (Phusion 1U, HF buffer 20% (v/v), dNTPs 0.2 mM, direct and reverse primers 0.04 μM each, template plasmid 50 ng, water) using the oligonucleotides 5′ GCGTTTGCCGAAGCGGCAAAGATGGCCACTTTTG3′ (SEQ ID NO: 74) and 5′ CAAAAGTGGCCATCTTTGCCGCTTCGGCAAACGC3′ (SEQ ID NO: 75). The PCR product (SEQ ID NO: 35) was digested by DpnI at 37° C. for 1 h to remove template DNA, and transformed into competent E. coli DH5 α (NEB) cells. The mutated plasmid pET28-LYSC* was identified by restriction site analysis and verified to carry the desired mutations by DNA sequencing.
The plasmid pET28-ASDwt was constructed by amplifying the asd gene of E. coli by PCR using high fidelity polymerase Phusion™ (Finnzymes) and the direct and reverse primers 5′ TATAATGCTAGCATGAAAAATGTTGGTTTTATCGG3′ (SEQ ID NO: 76) and 5′ TATAATGGA-TCCTTACGCCAGTTGACGAAGC3′ (SEQ ID NO: 77) that introduced a NheI and BamHI restriction site upstream of the start codon and downstream of the stop codon, respectively. Genomic DNA from E. coli DH5 α was used as the template. The PCR product was digested with NheI and BamHI, ligated into the corresponding sites of the pET28a (Novagen) expression vector using T4 DNA ligase (Biolabs), and transformed into E. coli DH5a cells. The resulting pET28-ASDwt plasmid was isolated and shown by DNA sequencing to contain the full-length asd gene having the correct sequence (SEQ ID NO: 98).
The plasmid pET28-HOM6 wt was constructed by amplifying the HOM6 gene of S. cerevisiae by PCR using high fidelity polymerase Phusion™ (Finnzymes) and the direct and reverse primers 5′ TATAATCATATGAGCACTAAAGTTGTTAATG3′ (SEQ ID NO: 78) and 5′ TATAATGGATC-CCTAAAGTCTTTGAGCAATC3′ (SEQ ID NO: 79) that introduced a NdeI and BamHI restriction site upstream of the start codon and downstream of the stop codon, respectively. Genomic DNA from S. cerevisiae BY4741 was used as the template. The PCR product was digested with NdeI and BamHI, ligated into the corresponding sites of the pET28a (Novagen) expression vector using T4 ligase (Biolabs), and transformed into E. coli DH5a cells. The resulting pET28-HOM6 wt plasmid was isolated and shown by DNA sequencing to contain the full-length HOM6 gene having the correct sequence (SEQ ID NO: 97).
The plasmid pET28-LYSC* was used as the backbone for the construction of the pTAC-op-HMS plasmid that enabled the expression of lysine-insensitive aspartate kinase, aspartate semialdehyde dehydrogenase, and homoserine dehydrogenase from an inducible tac promoter.
The asd gene was obtained by PCR from pET28-asdwt. The whole coding region and part of the upstream region comprising the pET28 ribosome binding site (rbs) and the in-frame N-terminal His-Tag were amplified by PCR using high fidelity polymerase Phusion™ (Finnzymes) and the direct and reverse primers 5′ TATAAGGATCCGTTTAACTTTAAGAAGGAGATATACCATGGG3′ (SEQ ID NO: 80) and 5TATAAGAATTCTTACGCCAGTTGACGAAG3′ (SEQ ID NO: 81) that introduced a BamHI and EcoRI restriction site upstream of the rbs and downstream of the stop codon, respectively. The PCR product was digested with BamHI and EcoRI, ligated into the corresponding sites of pET28-LYSC*, using T4 DNA ligase (Biolabs), and transformed into E. coli DH5a cells. The resulting pET28-LYSC*-ASD plasmid was isolated and shown by DNA sequencing to have the correct sequence.
The HOM6 gene was obtained by PCR from pET28-HOM6 wt. The whole coding region and part of the upstream region comprising the pET28 ribosome binding site and the in-frame N-terminal His-Tag were amplified by PCR using high fidelity polymerase Phusion™ (Finnzymes), the direct primer 5′ TATAAGCGGCCGCGTTTAACTTTAAGAAGGAGATAT3′ (SEQ ID NO: 82), and the reverse primer 5′ TATAAACTCGAGCCTAAAGTCTTTGAGCAAT3′ (SEQ ID NO: 83) that introduced a NotI and a PspXI restriction site upstream of the rbs and downstream of the stop codon, respectively. The PCR product was digested with NotI and PspXI, ligated into the corresponding sites of pET28-LYSC*-ASD, using T4 DNA ligase (Biolabs), and transformed into E. coli DH5a cells. The resulting pET28-op-HMS1 plasmid was isolated and shown by DNA sequencing to have the correct sequence.
The 5′ upstream promoter region simultaneously regulating the expression of the three genes (i.e. the T7 promoter in pET28a+) can be replaced with any other promoter, inducible or constitutive, by digesting the plasmids with SphI and XbaI and cloning another promoter region with suitable restriction sites.
In the present non-exclusive example, the T7 promoter of the pET28a+ backbone was replaced by the artificial IPTG-inducible tac promoter (de Boer et al., 1983). The tac promoter was obtained from plasmid pEXT20 (Dykxhoorn et al., 1996) by digesting this plasmid with SphI and XbaI. The DNA fragment containing the promoter was purified and cloned into SphI and XbaI digested pET28-op-HMS1 obtaining pTAC-op-HMS1. The resulting pTAC-op-HMS plasmid was isolated and shown by DNA sequencing to have the correct sequence.
The operon containing the coding sequences of lysC*, asd, and HOM6 was PCR amplified from the plasmid pTAC-op-HMS1 using the primers 5′-TATAAAGATCTTAGAAATAATTTTGTTTA-3′ (SEQ ID NO: 84) and 5′-TATAATCTAGACTAAAGTCTTTGAGCAAT-3′ (SEQ ID NO: 85) which introduced a BgIII and a XbaI restriction site at the 5′ and the 3′ end, respectively, of the PCR fragment. The fragment was purified, digested with BgIII and XbaI and cloned into the corresponding sites of pACT3 (Dykxhoorn et al., 1996) to obtain the vector pACT3-op-HMS1. The resulting pACT3-op-HMS1 plasmid was isolated and shown by DNA sequencing to have the correct sequence.
Construction of the Plasmids pEXT20-op-HMS2 and pACT3-op-HMS2
The plasmid pET28-thrAwt was constructed by amplifying the E. coli thrA gene encoding bifunctional enzyme aspartate kinase/homoserine dehydrogenase I by PCR using high fidelity polymerase Phusion™ (Finnzymes) and the direct and reverse primers 5′-TATAATCATATGCGAGTGTTGAAGTTCG-3′ (SEQ ID NO: 86) and 5′-TATAATGGATCCTCAGACTCCTAACTTCCA-3′ (SEQ ID NO: 87) that introduced a NdeI and BamHI restriction sites upstream of the start codon and downstream of the stop codon, respectively. Genomic DNA from E. coli MG1655 was used as the template. The PCR product was digested with NdeI and BamHI, ligated into the corresponding sites of the pET28a+(Novagen) expression vector using T4 DNA ligase (Biolabs), and transformed into NEB 5-alpha competent E. coli cells (NEB). The resulting pET28-thrAwt plasmid was isolated and shown by DNA sequencing to contain the full-length thrA gene having the correct sequence (SEQ ID NO: 88). The corresponding protein is represented by SEQ ID NO: 89.
An aspartate kinase/homoserine dehydrogenase with strongly decreased sensitivity for inhibition by threonine was constructed by site directed mutagenesis, replacing serine in position 345 with phenylalanine (S345F). Site-directed mutagenesis was carried out using the direct and reverse primers 5′-TGTCTCGAGCCCGTATTTTCGTGGTGCTG-3′ (SEQ ID NO: 90) and 5′-CAGCACCACGAAAATACGGGCTCGAGACA-3′ (SEQ ID NO: 91) and the pET28-thrAwt plasmid as the template. A single point mutation to change the amino acid sequence was introduced by PCR (Phusion 1U, HF buffer 20% (v/v), dNTPs 0.2 mM, direct and reverse primers 0.04 μM each, template plasmid 30-50 ng, water). Plasmids created by PCR contained a new restriction site for XhoI (underlined) introduced by silent mutation in addition to the functional mutation to facilitate identification of mutated clones. The PCR products were digested by DpnI at 37° C. for 1 h to remove template DNA, and transformed into DH5a competent E. coli cells (NEB). The mutated plasmid pET_Ec_thrA_S345F was identified by restriction site analysis and verified to carry the desired mutation by DNA sequencing.
The thrAS345F coding region of the bifunctional E. coli aspartate kinase/homoserine dehydrogenase was obtained by PCR using the plasmid pET_Ec_thrA_S345F as the template (SEQ ID NO: 92). The whole coding region was amplified by PCR using high fidelity polymerase Phusion™ (Finnzymes) and the direct and reverse primers 5′-TATAATGAGCTCGTTTAACTTTAAGAAGGAGATATACCATGCGAGTGTTGA AGTTCGGCG-3′ (SEQ ID NO: 93) and 5′-TATAATCCCGGGTCAGACTCCTAACTTCCA-3′ (SEQ ID NO: 94) that introduced a SacI and XmaI restriction site (underlined) upstream of the start codon and downstream of the stop codon, respectively. The direct primer includes the ribosome binding site (bold face) sequence of pET28. The PCR product was digested with SacI and XmaI, ligated into the corresponding sites of either pEXT20 or pACT3 (Dykxhoorn, St Pierre, & Linn, 1996), using T4 DNA ligase (Biolabs), and transformed into E. coli DH5a cells. The resulting pEXT20-op-HMS2_step1 and pACT3-op-HMS2_step1 plasmids were isolated and shown by DNA sequencing to have the correct sequence.
Escherichia coli aspartate semialdehyde dehydrogenase asd was amplified by PCR using high fidelity polymerase Phusion™ (Finnzymes) and the direct and reverse primers 5′-TATAATCCCGGGGTTTAACTTTAAGAAGGAGATATACCATGAAAAATGTTG GTTTTATCGGC-3′ (SEQ ID NO: 95) and 5′-TATAATGGATCCTTACGCCAGTTGACGAAG-3′ (SEQ ID NO: 96) that introduced a XmaI and BamHI restriction site upstream of the start codon and downstream of the stop codon, respectively (SEQ ID NO: 98). The direct primer includes the ribosome binding site sequence of pET28. Genomic DNA of E coli MG1655 was used as the template. The PCR product was digested with XmaI and BamHI, ligated into the corresponding sites of pEXT20-op-HMS2_step1 and pACT3-op-HMS2_step1, directly downstream the E. coli thrA gene, using T4 DNA ligase (Biolabs), and transformed into E. coli DH5a cells. The resulting pEXT20-op-HMS2 and pACT3-op-HMS2 plasmids were isolated and shown by DNA sequencing to have the correct sequence.
The plasmid pACT3-pck harbouring the PEP carboxykinase encoding pck gene of E. coli was constructed by amplifying the pck coding sequence using genomic DNA from E. coli MG1655 as the template and the forward and reverse primers, respectively, 5′ TATAATCCCGGGATGCGCGTTAACAATGGTTTGACC3′ (SEQ ID NO: 119) and 5′ TATAATTCTAGATTACAGTTTCGGACCAGCCG3′ (SEQ ID NO: 120). The DNA fragment was digested with XmaI and XbaI, ligated into the corresponding sites of the pACT3 expression vector (Dykxhoorn et al., 1996) using T4 DNA ligase (Biolabs), and transformed into E. coli DH5a cells. The transformants were selected on solid LB medium containing chloramphenicol (25 μg/mL). The resulting plasmid was isolated and correct insertion of the pck gene was verified by sequencing. Plasmids pACT3-aceA, pACT3-ppc, pACT3-galP, pACT3-pck and pACT3-pycA harbouring, respectively, aceA, ppc, galP, or pck (all E. coli) or pycA from Lactococcus lactis were constructed analogously using the primers listed in Table 9.
The coding sequence of the branched chain amino transferase, IlvE, from E. coli was PCR amplified using the forward and reverse primers 5′-ACAATTTCACACAGGAAACAGAATTCGAGCTCGGTACCGTTTAACTTTAAG AAGGAGATATACCATGACCACGAAGAAAGCTGATTAC-3′ (SEQ ID NO: 131) and 5′-GGATAACTTTTTTACGTTGTTTATCAGCCATGGTATATCTCCTTCTTAAAGT TAAACGGATCCTTATTGATTAACTTG-3′ (SEQ ID NO: 132), respectively, and plasmid pET28-Ec-ilvE (Example 4) as the template. The coding sequence of lactate dehydrogenase, LdhA, from L. lactis was PCR amplified using the forward and reverse primers 5′-TAATATGGATCCGTTTAACTTTAAGAAGGAGATATACCATGGCTGATAAAC AACGTAAAAAAGTTATCC-3′ (SEQ ID NO: 133) and 5′-CAATGCGGAATATTGTTCGTTCATGGTATATCTCCTTCTTAAAGTTAAACTC TAGATTAGTTTTTAACTGCAGAAGCAAATTC-3′ (SEQ ID NO: 134), respectively, and plasmid pET28-Ll-ldhA (Example 1) as the template. The amplified PCR fragments were fused in an overlap extension PCR by adding 150 ng of each fragment to 50 μL of the reaction mix and running a PCR using primers 5′-ACAATTTCACACAGGAAACAGAATTCGAGCTCGGTACCGTTTAACTTTAAG AAGGAGATATACCATGACCACGAAGAAAGCTGATTAC-3′ (SEQ ID NO: 135) and 5′-CAATGCGGAATATTGTTCGTTCATGGTATATCTCCTTCTTAAAGTTAAACTC TAGATTAGTTTTTAACTGCAGAAGCAAATTC-3′ (SEQ ID NO: 136). The resulting PCR fragment was purified, digested with Kpnl and XbaI, and ligated into the corresponding sites of pEXT20 (Dykxhoorn, St Pierre, & Linn, 1996) using T4 DNA ligase (Fermentas). The ligation product was transformed into E. coli DH5a. The resulting plasmid pEXT20-DHB was isolated and shown by DNA sequencing to contain the correct full-length coding sequences of Ec-ilvE and Ll-ldhA. The plasmid was then transformed into E. coli MG1655-derived mutant strains and tested regarding DHB production.
Several genes were disrupted in E. coli strain MG1655 in order to optimise carbon flux repartitioning and cofactor supply for DHB production. Gene deletions were carried out using phage transduction method, or the lambda red recombinase method according to Datsenko et al. (Datsenko & Wanner, 2000).
Protocol for Introduction of Gene Deletions Using the Phage Transduction Method:
Strains carrying the desired single deletions were obtained from the Keio collection (Baba et al., 2006). Phage lysates of single deletion mutants were prepared by inoculating 10 mL of LB medium containing 50 μg/mL kanamycin, 2 g/L glucose, and 5 mM CaCl2 with 100 μL of overnight precultures. Following an incubation of 1 h at 37° C., 200 μL of phage lysate prepared from the wild-type MG1655 strain were added, and cultures were incubated for another 2-3 h until cell lysis had completed. After addition of 200 μL chloroform, cell preparations were first vigorously vortexted and then centrifuged for 10 min at 4500×g. The clear lysate was recovered and stored at 4° C.
The receptor strain was prepared for phage transduction by an overnight cultivation at 37° C. in LB medium. A volume of 1.5 mL of the preculture was centrifuged at 1500×g for 10 min. The supernatant was discarded and the cell pellet was resuspended in 600 μl of a solution containing 10 mM MgSO4 and 5 mM CaCl2. The transduction was carried out by mixing 100 μL of the solution containing the receptor strain with 100 μL of lysate and incubating this mixture at 30° C. for 30 min. Thereafter, 100 μL of a 1M sodium citrate solution were added followed by vigorous vortexing. After addition of 1 mL LB medium, the cell suspension was incubated at 37° C. for 1 h before spreading the cells on LB agar dishes containing 50 μg/mL kanamycin. Clones able to grow in presence of the antibiotic were confirmed by colony PCR to contain the desired deletion using the primers listed in Table 11. After the introduction of each gene deletion, the antibiotic marker was removed as described above following the method of (Cherepanov & Wackernagel, 1995). The deletions ΔldhA, ΔadhE, ΔmetA, ΔthrB, ΔrhtB, and ΔlldD were successively introduced by the described method.
Protocol for Introduction of Gene Deletions Using the Lambda-Red Recombinase Method:
The deletion cassettes were prepared by PCR using high fidelity polymerase Phusion™ (Finnzymes), and the FRT-flanked kanamycin resistance gene (kan) of plasmid pKD4 as the template (Datsenko & Wanner, 2000). Sense primers contained sequences corresponding to the 5′ end of each targeted gene (underlined) followed by 20 bp corresponding to the FRT-kan-FRT cassette of pKD4. Anti-sense primers contained sequences corresponding to the 3′ end region of each targeted gene (underlined) followed by 20 bp corresponding to the cassette. The primers are described in Table 10. PCR products were digested with DpnI and purified prior to transformation.
E. coli MG1655 strain was rendered electro-competent by growing the cells to an OD600 of 0.6 in LB liquid medium at 37° C., concentrating the cells 100-fold, and washing them twice with ice-cold 10% glycerol. The cells were transformed with plasmid pKD46 (Datsenko & Wanner, 2000) by electroporation (2.5 kV, 200 Ω, 25 μF, in 2 mm gap cuvettes). Transformants were selected at 30° C. on ampicillin (100 μg/mL) LB solid medium.
Disruption cassettes were transformed into electro-competent E. coli strains harbouring the lambda Red recombinase-expressing plasmid pKD46. The cells were grown at 30° C. in liquid SOB medium containing ampicillin (100 μg/mL). The lambda red recombinase system was induced by adding 10 mM arabinose when OD600 of the cultures reached 0.1. Cells were further grown to an OD600 of 0.6 before they were harvested by centrifugation, washed twice with ice-cold 10% glycerol, and transformed with the disruption cassette by electroporation. After an overnight phenotypic expression at 30° C. in LB liquid medium, cells were plated on solid LB medium containing 25 μg/mL kanamycin. Transformants were selected after cultivation at 30° C.
The gene replacement was verified by colony PCR using Crimson Taq polymerase (NEB). A first reaction was carried out with the flanking locus-specific primers (see Table 11) to verify simultaneous loss of the parental fragment and gain of the new mutant specific fragment. Two additional reactions were done by using one locus-specific primer together with one of the corresponding primers k1rev, or k2 for (see Table 11) that align within the FRT-kanamycin resistance cassette (sense locus primer/k1rev and k2for/reverse locus primer).
The resistance gene (FRT-kan-FRT) was subsequently excised from the chromosome using the FLP recombinase-harbouring plasmid pCP20 (Cherepanov & Wackernagel, 1995) leaving a scar region containing one FRT site. pCP20 is an ampicillin and CmR plasmid that shows temperature-sensitive replication and thermal induction of FLP recombinase synthesis. Kanamycin resistant mutants were transformed with pCP20, and ampicillin-resistant transformants were selected at 30° C. Transformants were then grown on solid LB medium at 37° C. and tested for loss of all antibiotic resistances. Excision of the FRT-kanamycin cassette was analysed by colony PCR using crimson taq polymerase and the flanking locus-specific primers (Table 11). Multiple deletions were obtained by repeating the above described steps.
gaaggttgcgcctacactaagcatagttgttgatgagtgtaggctggagctgcttc
ttaaaccagttcgttcgggcaggtttcgcctttttcatgggaattagccatggtcc
atggctgttactaatgtcgctgaacttaacgcactcgtagagcgtgtgtaggctggagctgcttc
ttaagcggattttttcgcttttttctcagctttagccggagcagccatatgaatatcctccttag
atgtcgagtaagttagtactggttctgaactgcggtagttcttcagtgtaggctggagctgcttc
tcaggcagtcaggcggctcgcgtcttgcgcgataaccagttcttccatatgaatatcctccttag
ttactccgtatttgcataaaaaccatgcgagttacgggcctataagtgtaggctggagctgcttc
atagattgagtgaaggtacgagtaataacgtcctgctgctgttctcatatgaatatcctccttag
gtgtcccgtattattatgctgatccctaccggaaccagcgtcggtgtgtaggctggagctgcttc
ttactgctgctgtgcagactgaatcgcagtcagcgcgatggtgtacatatgaatatcctccttag
atgaaacaaacggttgcagcttatatcgccaaaacactcgaatcggtgtaggctggagctgcttc
ttaccttagccagtttgttttcgccagttcgatcacttcatcacccatatgaatatcctccttag
atgaccattactccggcaactcatgcaatttcgataaatcctgccgtgtaggctggagctgcttc
tcagatccggtctttccacaccgtctggatattacagaattcgtgcatatgaatatcctccttag
atgaaacttaacgacagtaacttattccgccagcaggcgttgattgtgtaggctggagctgcttc
ttaaagaccgatgcacatatatttgatttctaagtaatcttcgatcatatgaatatcctccttag
atggaccagaagctgttaacggatttccgctcagaactactcgatgtgtaggctggagctgcttc
tcaggtgtgtttaaagctgttctgctgggcaataccctgcagtttcatatgaatatcctccttag
atggataagaagcaagtaacggatttaaggtcggaactactcgatgtgtaggctggagctgcttc
tcaggtatgtttaaagctgttctgttgggcaataccctgcagtttcatatgaatatcctccttag
atggctacatcagtacagacaggtaaagctaagcagctcacattagtgtaggctggagctgcttc
ttagtgtttcttgtcattcatcacaatatagtgtggtgaacgtgccatatgaatatcctccttag
atggaaccaaaaacaaaaaaacagcgttcgctttatatcccttacgtgtaggctggagctgcttc
ttagatggaggtacggcggtagtcgcggtattcggcttgccagaacatatgaatatcctccttag
atggatgaccagttaaaacaaagtgcacttgatttccatgaatttgtgtaggctggagctgcttc
ttacagcggttgggtttgcgcttctaccacggccagcgccaccatcatatgaatatcctccttag
atgaacgaacaatattccgcattgcgtagtaatgtcagtatgctcgtgtaggctggagctgcttc
ttagccggtattacgcatacctgccgcaatcccggcaatagtgaccatatgaatatcctccttag
atgtccagaaggcttcgcagaacaaaaatcgttaccacgttaggcgtgtaggctggagctgcttc
ttactctaccgttaaaatacgcgtggtattagtagaacccacggtcatatgaatatcctccttag
atgaaaaagaccaaaattgtttgcaccatcggaccgaaaaccgaagtgtaggctggagctgcttc
ttacaggacgtgaacagatgcggtgttagtagtgccgctcggtaccatatgaatatcctccttag
atggaactgacgactcgcactttacctgcgcggaaacatattgcggtgtaggctggagctgcttc
ttacttcagacggtccgcgagataacgctgataatcggggatcagcatatgaatatcctccttag
atggtcgcacccattcccgcgaaacgcggcagaaaacccgccgttgtgtaggctggagctgcttc
tcagcgcattccaccgtacgccagcgtcacttccttcgccgctttcatatgaatatcctccttag
atggaaagtaaagtagttgttccggcacaaggcaagaagatcaccgtgtaggctggagctgcttc
ttacatgttttcgatgatcgcgtcaccaaactctgaacatttcagcatatgaatatcctccttag
atgcagaacagcgctttgaaagcctggttggactcttcttacctcgtgtaggctggagctgcttc
ttattcgacgttcagcgcgtcattaaccagatcttgttgctgtttcatatgaatatcctccttag
atgagtagcgtagatattctggtccctgacctgcctgaatccgtagtgtaggctggagctgcttc
ctacacgtccagcagcagacgcgtcggatcttccagcaactctttcatatgaatatcctccttag
gtgcaaacctttcaagccgatcttgccattgtaggcgccggtggcgtgtaggctggagctgcttc
tcagccattcgccttctccttcttattggctgcttccgccttatccatatgaatatcctccttag
atggctgagatgaaaaacctgaaaattgaggtggtgcgctataacgtgtaggctggagctgcttc
ttagcgtggtttcagggtcgcgataagaaagtctttcgaactttccatatgaatatcctccttag
atgacgactaaacgtaaaccgtatgtacggccaatgacgtccaccgtgtaggctggagctgcttc
ttaccagtacagggcaacaaacaggattacgatggtggcaaccaccatatgaatatcctccttag
atgattaatccaaatccaaagcgttctgacgaaccggtattctgggtgtaggctggagctgcttc
ttagattgtaacgacaccaatcagcgtgacaactgtcaggatagccatatgaatatcctccttag
atgatttcaggcattttagcatccccgggtatcgctttcggtaaagtgtaggctggagctgcttc
ttagcagattgttttttcttcaatgaacttgttaaccagcgtcatcatatgaatatcctccttag
atgtttaagaatgcatttgctaacctgcaaaaggtcggtaaatcggtgtaggctggagctgcttc
ttagtggttacggatgtactcatccatctcggttttcaggttatccatatgaatatcctccttag
gtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtcgtgtaggctggagctgcttc
tcactgcccgctttccagtcgggaaacctgtcgtgccagctgcatcatatgaatatcctccttag
atgattatttccgcagccagcgattatcgcgccgcagcgcaacgcgtgtaggctggagctgcttc
ctatgccgcattccctttcgccatgggagccagtgccgcaggcaacatatgaatatcctccttag
atgaaaaacatcaatccaacgcagaccgctgcctggcaggcactagtgtaggctggagctgcttc
ttaaccgcgccacgctttatagcggttaatcagaccattggtcgacatatgaatatcctccttag
atgccgattcgtgtgccggacgagctacccgccgtcaatttcttggtgtaggctggagctgcttc
ttaatccagcgttggattcatgtgccgtagatcgtatggcgtgatcatatgaatatcctccttag
atggttaaagtttatgccccggcttccagtgccaatatgagcgtcgtgtaggctggagctgcttc
ttagttttccagtactcgtgcgcccgccgtatccagccggcaaatcatatgaatatcctccttag
atgccacattcactgttcagcaccgataccgatctcaccgccgaagtgtaggctggagctgcttc
ttaaagcaattccagcgccagtaattcttcgatggtctggcgacgcatatgaatatcctccttag
atgaaaaactggaaaacaagtgcagaatcaatcctgaccaccggcgtgtaggctggagctgcttc
ctcgatcgggcattttgacttttacagcttagcgccttctacagccatatgaatatcctccttag
atggctatcgacgaaaacaaacagaaagcgttggcggcagcactggtgtaggctggagctgcttc
ttaaaaatcttcgttagtttctgctacgccttcgctatcatctaccatatgaatatcctccttag
atgaaaaatgttggttttatcggctggcgcggtatggtcggctccgtgtaggctggagctgcttc
ttacgccagttgacgaagcatccgacgcagcggctccgcggcccccatatgaatatcctccttag
The plasmid co-expressing aspartate kinase, aspartate semialdehyde dehydrogenase, and homoserine dehydrogenase (pACT3-op-HMS1) was transformed together with the plasmid expressing the homoserine transaminase and the OHB reductase (pEXT20-DHB) into the optimized host strains. Transformants were selected on solid LB medium containing chloramphenicol (25 μg/mL) and ampicillin (100 μg/mL). Non-exclusive examples of constructed strains are listed in Table 12.
It is understood that removal of the lacI gene from the backbone of the above described plasmids along with the genomic deletion of lacI in the host strain may render protein expression from above described plasmids constitutive.
Strains and cultivation conditions: Experiments were carried out with strains listed in Table 12. All cultivations were carried out at 37° C. on an Infors rotary shaker running at 170 rpm. Overnight cultures (3 mL medium in test tube) were inoculated from glycerol stocks and used to adjust an initial OD600 of 0.05 in 100 mL growth cultures cultivated in 500 mL shake flasks. IPTG was added at a concentration of 1 mmol/L when OD600 in the growth cultures reached 0.8. One liter culture medium contained, 20 g glucose, 18 g Na2HPO4*12 H2O, 3 g KH2PO4, 0.5 g NaCl, 2 g NH4Cl, 0.5 g MgSO4*7 H2O, 0.015 CaCl2*2 H2O, 1 mL of 0.06 mol/L FeCl3 stock solution prepared in 100 times diluted concentrated HCl, 2 mL of 10 mM thiamine HCl stock solution, 20 g MOPS and 1 mL of trace element solution (containing per liter: 0.04 g Na2EDTA*2H2O, 0.18 g CoCl2*6 H2O, ZnSO4*7 H2O, 0.04 g Na2MoO4*2 H2O, 0.01 g H3BO3, 0.12 g MnSO4*H2O, 0.12 g CuCl2*H2O.). Medium pH was adjusted to 7 and medium was filter-sterilized. The antibiotics kanamycin sulphate, ampicillin, and chloramphenicol were added at concentrations of 50 mg/L, 100 mg/L, and 25 mg/L, respectively, when necessary.
Estimation of DHB concentration by LC-MS analyses: Liquid anion exchange chromatography was performed on an ICS-3000 system from Dionex (Sunnyvale, USA) equipped with an automatic eluent (KOH) generator system (RFIC, Dionex), and an autosampler (AS50, Dionex) holding the samples at 4° C. Analytes were separated on an lonPac AS11 HC (250×2 mm, Dionex) column protected by an AG11 HC (50×2 mm, Dionex) pre-column. Column temperature was held at 25° C., flow rate was fixed at 0.25 mL/min, and analytes were eluted applying the KOH gradient described earlier (Groussac E, Ortiz M & Francois J (2000): Improved protocols for quantitative determination of metabolites from biological samples using high performance ionic-exchange chromatography with conductimetric and pulsed amperometric detection. Enzyme. Microb. Technol. 26, 715-723). Injected sample volume was 15 μL. For background reduction, an ASRS ultra II (2 mm, external water mode, 75 mA) anion suppressor was used. Analytes were quantified using a mass-sensitive detector (MSQ Plus, Thermo) running in ESI mode (split was ⅓, nitrogen pressure was 90 psi, capillary voltage was 3.5 kV, probe temperature was 450° C.).
Results:
After 24 h cultivation, the DHB concentration in the supernatant of different strains was quantified by LC-MS analyses. The strains ECE73, ECE74, ECE75, and ECE76 had produced 0 mg/L, 3.7 mg/L, 0.67 mg/L, and 11.9 mg/L of DHB, respectively.
This is a Continuation of application Ser. No. 14/414,331 filed Jan. 12, 2015, which in turn is a National Stage Application of PCT/EP2013/064619 filed Jul. 10, 2013, which claims the benefit of U.S. Provisional Application No. 61/670,405 filed Jul. 11, 2012. The disclosure of the prior applications is hereby incorporated by reference herein in their entireties.
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| Number | Date | Country | |
|---|---|---|---|
| 20200131542 A1 | Apr 2020 | US |
| Number | Date | Country | |
|---|---|---|---|
| 61670405 | Jul 2012 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 14414331 | US | |
| Child | 16740598 | US |
