Cell able to produce poly l-lactic acid
11697831 · 2023-07-11
Assignee
Inventors
- Danilo Porro (Cernusco sul Naviglio, IT)
- Paola Branduardi (Milan, IT)
- Stefano Bertacchi (Milan, IT)
- Nadia Maria Berterame (Milan, IT)
Cpc classification
C12N9/1029
CHEMISTRY; METALLURGY
C12Y203/01
CHEMISTRY; METALLURGY
International classification
Abstract
Disclosed is the production by fermentation of poly D-lactic acid (PDLA) and poly L-lactic acid (PLLA). In particular, there is provided engineered (prokaryotic or eukaryotic) cells for the direct synthesis of PLLA polymers and engineered eukaryotic cells for the direct synthesis of PDLA polymers starting from a carbon source, including residual biomasses of the different production chains.
Claims
1. A cell able to produce poly-L-lactic acid (PLLA), wherein said cell comprises: (i) a L-lactate dehydrogenase enzyme encoded by the Lactobacillus plantarum L-lactate dehydrogenase ldh 1 gene having the nucleotide sequence of SEQ ID NO:4, wherein said L-lactate dehydrogenase enzyme catalyzes the conversion of pyruvate into L-lactate; (ii) an acyl-CoA transferase enzyme which is a propionyl-CoA transferase enzyme encoded by a gene having the nucleotide sequence of SEQ ID NO:2, wherein said gene is a mutated form of the Clostridium propionicum propionyl-CoA transferase gene, and wherein said acyl-CoA transferase enzyme catalyzes the synthesis of L-lactoyl-CoA by thioesterification of L-lactate; and (iii) a polyhydroxyalkanoate synthase enzyme encoded by a gene having the nucleotide sequence of SEQ ID NO:3, wherein said gene is a mutated form of the Pseudomonas resinovorans polyhydroxyalkanoate synthase C1 gene, and wherein said polyhydroxyalkanoate synthase enzyme catalyzes the polymerization of L-lactoyl-CoA into PLLA; wherein said cell able to produce PLLA is a yeast cell.
2. The cell according to claim 1, wherein said yeast is Saccharomyces cerevisiae.
3. The cell according to claim 1, further containing one or more genes responsible for sugar internalization and/or catabolism.
4. The cell according to claim 1, wherein the genes encoding the pyruvate decarboxylase and/or alcohol dehydrogenase enzymes, involved in ethanol formation, are partially or completely deleted.
5. The cell according to claim 1, further containing one or more genes responsible for sugar internalization and/or catabolism.
6. The cell according to claim 1, further containing one or more genes responsible for sugar internalization and/or catabolism.
7. A method for producing poly-L-lactic acid (PLLA), which comprises the following steps: (i) cultivating the cell according to claim 1 in a culture medium containing a carbon source; (ii) recovering the cell mass containing the polymer; and (iii) extracting PLLA from the cells.
8. The method according to claim 7, wherein said carbon source is selected from hexose sugar monomers; pentose sugar monomers; and disaccharides.
9. The method according to claim 7, wherein the culture medium is not supplemented with lactic acid.
10. A method for producing poly-L-lactic acid (PLLA), which comprises the following steps: (i) cultivating the cell according to claim 1 in a culture medium containing a carbon source; and (ii) recovering the cell mass containing the polymer.
11. The method of claim 8, wherein the hexose and/or pentose sugar monomers are selected from the group consisting of glucose, fructose, galactose, mannose, xylose, and arabinose, and wherein the disaccharides are selected from the group consisting of lactose and saccharose.
12. The method according to claim 8, wherein the culture medium is not supplemented with lactic acid.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DESCRIPTION OF THE PREFERRED EMBODIMENTS
(13) Definitions
(14) The term “biomass” defines any substance of organic origin that can regenerate in times compatible with its consumption, destined for the production of bioenergy and/or biofuels and/or biomaterials. This contrasts with fossil biomasses, whose regeneration times exceed their consumption by several orders of magnitude.
(15) “Residual biomass” means the biodegradable fraction of waste and/or residues of biological origin from agriculture (including vegetable and/or animal compounds) and/or from forestry and/or related industries, including fishing and/or aquaculture, mowing and pruning from public and private green areas, as well as the biodegradable part of industrial and/or urban waste.
(16) The “production yield” is defined as the ratio between the quantity of product obtained and the quantity of substrate consumed.
(17) The term “vector” indicates a DNA construct comprising a DNA sequence that is linked to a control sequence capable of leading to the expression of the aforementioned DNA in a suitable host. In this invention the typical plasmid vector used has: a) or an origin of replication which allows the effective replication of the plasmid so that in each cell of the selected host there are tens of copies of the plasmid vector, or a DNA sequence which allows the integration of the plasmid vector in a chromosome of each cell of the chosen host; b) a selection marker such that a cell correctly transformed with the plasmid vector can be selected; c) a DNA sequence comprising recognition sites for restriction enzymes in order to introduce exogenous DNA into the plasmid vector by a process called ligation.
(18) As generally reported in the state of the art, in order to express the gene inserted in the host cell, the coding sequence must be correctly and functionally related to regulatory elements of transcription, translation and expression functioning in the selected expression host.
(19) The term “transformation” here used means that the DNA, once introduced into the cell, can replicate outside of chromosomes or as part of an entire chromosome.
EXAMPLES
(20) Example 1: Construction of the recombinant vector pTEFLEU2-ldhA harboring the ldhA gene.
(21) The coding sequence of the ldhA gene was amplified by PCR using as a template the genomic DNA of E. coli and specific oligonucleotides (SEQ ID NO: 5; SEQ ID NO: 6). It is as follows: after 30 seconds of denaturation at 98° C., 25 cycles (denaturation of 10 seconds at 98° C., annealing of 30 seconds at 72° C. and elongation of 60 seconds at 72° C.), followed by a final elongation of 2 minutes at 72° C. The PCR product and the pTEFLEU2 target vector were digested with the EcoRI and XhoI restriction enzymes and after their ligation, the recombinant pTEFLEU2-ldhA vector was obtained (
(22) Example 2: Construction of the recombinant vector pTEFLEU2-ldh1 harboring the ldh1 gene.
(23) The ldh1 gene of L. plantarum (SEQ ID NO: 4) was excised from the vector p022TLP (Branduardi et al., 2006) by digestion with the EcoRI restriction enzyme. The DNA fragment corresponding to the ldh1 gene having EcoRI ends was ligated with the target vector pTEFLEU2, after its digestion with EcoRI, leading to the obtainment of the recombinant expression vector pTEFLEU2-ldh1 (
(24) Example 3: Construction of the recombinant pYX212-Pct540 vector harboring the Pct540 gene.
(25) The coding sequence of the mutated version of the Pct gene of C. propionicum, Pct540 (SEQ ID NO: 3), preceded by the sequence of the pTDH3 promoter of S. cerevisiae (SEQ ID NO: 7) have been synthesized de novo and cloned by the manufacturing company into the pEX-A2 vector (Eurofins Genomics), obtaining the pEX-A2-Pct540 vector. In particular, the sequence of the Pct540 gene has codon usage optimized for yeast cells. The pEX-A2-Pct540 vector was linearized with the restriction enzyme BglI, and the pTDH3-Pct540 DNA fragment was excised from the aforementioned linearized vector, by digestion with the restriction enzymes KpnI and NheI. The pTDH3-Pct540 fragment with KpnI/NheI ends was cloned in the target vector pYX212 (R&D Systems, Inc., Wiesbaden, D), digested with the restriction enzymes KpnI and NheI and therefore lacking the pTPI promoter of S. cerevisiae. The ligation of the two DNA fragments led to the obtainment of the recombinant expression vector pYX212-Pct540 (
(26) Example 4: Construction of the recombinant vector pYX022-PhaC1437Pre harboring the PhaC1437Pre gene.
(27) The coding sequence of the mutated version of the PhaC1 gene of P. resinovorans, or PhaC1437Pre (SEQ ID NO: 3), preceded by the sequence of the pADH1 promoter of S. cerevisiae (SEQ ID NO: 8) have been synthesized de novo and cloned by the manufacturing company into the pEX-K4 vector (Eurofins Genomics). In particular, the PhaC1437Pre gene sequence has codon usage optimized for yeast cells. The pADH1-PhaC1437Pre DNA fragment was excised by the pEX-K4 vector by digestion with the restriction enzymes AatII and NheI. The pADH1-PhaC1437Pre fragment with AatII/NheI ends was cloned in the target vector pYX022 (R&D Systems, Inc., Wiesbaden, D), digested with the restriction enzymes AatII and NheI and therefore lacking the pTPI promoter of S. cerevisiae. The ligation of the two DNA fragments led to the obtainment of the recombinant expression vector pYX022-PhaC1437Pre (
(28) Example 5: Construction of the recombinant strain of S. cerevisiae for the production of PDLA.
(29) The CEN.PK laboratory strain of S. cerevisiae was transformed with the vectors pTEFLEU2-ldhA, pYX212-Pct540 and pYX022-PhaC1437Pre, described respectively in examples 1, 3, 4. The graphic representation of the metabolic pathway for PDLA synthesis starting from glucose via pyruvate, D-lactate and D-lactoyl-CoA, in the recombinant strain is shown in
(30) Example 6: Construction of the recombinant strain of S. cerevisiae for the production of PLLA.
(31) The S. cerevisiae CEN.PK laboratory strain was transformed with the vectors pTEFLEU2-ldh1, pYX212-Pct540 and pYX022-PhaC1437Pre, described respectively in examples 2, 3, 4. The graphic representation of the metabolic pathway for PLLA synthesis starting from glucose via pyruvate, L-lactate and L-lactyl-CoA, in the recombinant strain is shown in
(32) Example 7: Construction of the recombinant strain of S. cerevisiae as a negative control for PLA synthesis.
(33) The S. cerevisiae CEN.PK laboratory strain was transformed with the pTEFLEU2-ldhA and pYX212-Pct540 vectors. The aforementioned recombinant strain lacks the polyhydroxyalkanoate synthase activity and it is therefore used in the following examples as a negative control for PDLA and PLLA production. In fact, independently of the stereochemistry of lactate, the absence of polyhydroxyalkanoate synthase activity does not allow the polymerization of lactyl-CoA monomers.
(34) Example 8: Cell growth trend and production of the main extracellular metabolites over time in the engineered strain for PDLA production, in the engineered strain for PLLA production and in the control strain.
(35) Cells of the CEN.PK pTEFLEU2-ldhA, pYX212-Pct540, pYX022-PhaC1437Pre strain engineered for the production of PDLA, of the CEN.PK pTEFLEU2-ldh1, pYX212-Pct540, pYX022-PhaC1437Pre strain engineered for the production of PLLA and CEN.PK pTEFLEU2-ldhA, pYX212-Pct540 strain (used as a control) were grown in the presence of glucose 20 g/L and Yeast Nitrogen Base (YNB) 6.7 g/L. The cells were inoculated at an optical density of 0.05 (OD 660 nm) in 20 mL of medium in 100 mL flasks and incubated at 30° C. on an orbital shaker at 160 rpm. Cell growth was monitored by measuring OD at 660 nm at regular time intervals. The extracellular concentration of glucose, acetate, ethanol and glycerol was determined by HPLC using H.sub.2SO.sub.4 5 mN as a mobile phase and a Rezex ROA H+ column (8%) 300×7.8 mm with styrene sulfonate-divinylbenzene matrix (Phenomenex).
(36) As shown in
(37) A carbon flux redirection in cells transformed with the genes encoding the enzymatic activities necessary for the production of PDLA and PLLA is demonstrated by these experiments.
(38) Example 9: Evaluation of PDLA production or alternatively PLLA production by Nile red staining.
(39) The cells of the CEN.PK strain engineered for PDLA production, of the engineered strain for PLLA production and of the control strain expressing only the ldha and Pct540 genes were grown as described in Example 8. The production of PDLA or alternatively of PLLA was evaluated by staining with Nile red dye. Nile red is generally used to evaluate in live cells the accumulation of aliphatic biopolymers, such as PHA or co-polymers of D-lactic acid and other hydroxy acids, as reported in literature, by way of example, by Spiekermann et al., 1999; Glorenflo et al., 1999; Yang et al., 2010. Specifically, after 24, 48 and 72 hours from the inoculum, 0.3 OD of cells of the strains were collected and after centrifugation washed with 1 mL of phosphate buffer (PBS; NaH.sub.2PO.sub.4 53 mM, Na.sub.2HPO.sub.4 613 mM, 75 mM NaCl). After centrifugation, they were resuspended in 1 mL of 35% (v/v) cold ethanol and incubated in ice for 20 minutes in order to permeabilize the cells to Nile red. The cells were washed again with 1 mL of PBS, and, after the addition of Nile red at the final concentration of 31.4 μM, they were incubated for 5 minutes in the dark in ice. Subsequently, the samples were analyzed by flow cytometry (FACS), using a Beckman Coulter FC-500 flow cytometer (Beckman Coulter, Fullerton, Calif., USA) equipped with an argon ion laser (excitation wavelength 488 nm, laser power 20 mW). The fluorescence emission of Nile red is acquired through a 670 nm filter (FL3 channel), in a logarithmic scale. The operating parameters were set to analyze 20 thousand cells for each sample excluding cellular debris. The data were subsequently analyzed using the Flowing software program (see website at flowingsoftware.com).
(40) The dot plots show that almost all the cells engineered for the production of PDLA (panel B) and for the production of PLLA (panel C) are positive to Nile red staining. In particular, the maximum percentage of cells positive to the staining is 84% in the engineered strain for PDLA production and 97% in the PLLA-engineered strain. On the contrary, as can be observed in panel A, in the control cells expressing only the ldhA and Pct540 genes, the percentage of staining positive cells is negligible and attributable to the interaction of Nile red with structural components of the cell, such as cell membranes (Mukherjee et al., 2007).
(41) Given the direct correlation between the fluorescence emission of Nile red and the presence of aliphatic polymers, the reported data demonstrate that the metabolic engineering aimed at producing PDLA (
(42) Therefore, the synthesis of PDLA in eukaryotic cells by means of a one-step production, without the addition of lactate as substrate, without any mandatory need to attenuate or eliminate the ability to consume lactic acid as carbon source and without any mandatory need to increase the productivity of intracellular Coenzyme A (CoA) donor is described here for the first time. Furthermore, the direct synthesis of PLLA by cells is described for the first time. In literature no examples report wild-type or engineered cells capable of polymerizing hydroxy acids, and lactic acid among them, with a chiral center in L configuration. In particular, it has been described here for the first time that the enzyme polyhydroxyalkanoate synthase is able to polymerize hydroxy acid monomers with L configuration of the chiral center.
(43) In addition, the cells of the CEN.PK strain engineered for PDLA production, of the engineered strain for PLLA production and of the control strain expressing only the ldha and Pct540 genes were grown on agar plates with molasses 20 g/L as carbon source, supplement with Nile red dye 0.5 μg/mL. After 4 days of incubation at 30° C., cell growth was observed in all the strains but only the strain engineered for PDLA production and that one engineered for PLLA production were able to accumulate intracellularly PDLA or PLLA, respectively, they indeed resulted stained with Nile red when exposed to UV light.
(44) Example 10: Analysis of PDLA or alternatively of PLLA by GC-MS analysis.
(45) In order to evaluate the composition of the polymer accumulated in the cells (example 9) a gas chromatography mass spectrometry (GC-MS) analysis was performed.
(46) The cells of the engineered strain for PDLA production, of the engineered strain for PLLA production and of the control strain expressing only the ldha and Pct540 genes were pre-inoculated in the presence of glucose 50 g/L and YNB 6.7 g/L. The preinoculum was performed in 100 mL of medium in 500 mL flasks incubated at 30° C. on an orbital shaker at 160 rpm. After 24 hours of growth, cells were inoculated into a 2 L bioreactor at an initial OD660 of 0.2. The operating volume of the media used in the bioreactor is 1.5 L and its composition is: glucose 50 g/L and YNB 13.4 g/L.
(47) Growth parameters are: constant temperature of 30° C.; amount of dissolved oxygen greater than 25% with an air flow of 1 vvm (volume of air per volume of culture medium); pH maintained at 5 with additions, if necessary, of NaOH 4M and H3PO4 at 25% (v/v). Agitation is dependent on the percentage of oxygen dissolved in the media.
(48) After 48 hours from the inoculum, cells were collected by centrifugation and subjected to lyophilization and then to acid methanolysis in order to break the cells and depolymerize the lactic acid polymer into methyl lactate monomer units. Methanolysis was performed according to the following protocol adapted by Braunegg et al. (1978): the cells were dissolved in a solution of methanol acidified with sulfuric acid (3% v/v) and chloroform in a 1:1 ratio; the mixture was heated in microwave at a power of 300 W, for 200 minutes at 120° C. The solution resulting from the methanolysis of the cells was analyzed by GC-MS.
(49) This instrument consists of a Clarus 500 gas chromatograph (PerkinElmer) and a Clarus 560 mass spectrometer (PerkinElmer). The GC is equipped with an Elite-5MS capillary column (PerkinElmer). The temperature conditions in which the gas chromatographic analysis was carried out are the following: 70° C. for 5 minutes, increase of 10° C./minute up to 150° C., increase of 20° C./minute to reach 300° C., maintained for 14.5 minutes. The sample was injected at an initial temperature of 250° C., maintained for 10 minutes.
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SITOGRAPHY
(56) website appearing at european-bioplastics.org
(57) appearing at brenda-enzymes.org
(58) website appearing at flowingsoftware.com