Highly efficient L-lactate production using engineered Escherichia coli with dissimilar temperature optima for L-lactate formation and cell growth
© Niu et al.; licensee BioMed Central Ltd. 2014
Received: 28 January 2014
Accepted: 11 May 2014
Published: 29 May 2014
L-Lactic acid, one of the most important chiral molecules and organic acids, is produced via pyruvate from carbohydrates in diverse microorganisms catalyzed by an NAD+-dependent L-lactate dehydrogenase. Naturally, Escherichia coli does not produce L-lactate in noticeable amounts, but can catabolize it via a dehydrogenation reaction mediated by an FMN-dependent L-lactate dehydrogenase. In aims to make the E. coli strain to produce L-lactate, three L-lactate dehydrogenase genes from different bacteria were cloned and expressed. The L-lactate producing strains, 090B1 (B0013-070, ΔldhA::diflldD::P ldh -ldh Lca), 090B2 (B0013-070, ΔldhA::diflldD::P ldh -ldh Strb) and 090B3 (B0013-070, ΔldhA::diflldD::P ldh -ldh Bcoa) were developed from a previously developed D-lactate over-producing strain, E. coli strain B0013-070 (ack-ptappspflBdldpoxBadhEfrdA) by: (1) deleting ldhA to block D-lactate formation, (2) deleting lldD to block the conversion of L-lactate to pyruvate, and (3) expressing an L-lactate dehydrogenase (L-LDH) to convert pyruvate to L-lactate under the control of the ldhA promoter. Fermentation tests were carried out in a shaking flask and in a 25-l bioreactor. Strains 090B1, 090B2 or 090B3 were shown to metabolize glucose to L-lactate instead of D-lactate. However, L-lactate yield and cell growth rates were significantly different among the metabolically engineered strains which can be attributed to a variation between temperature optimum for cell growth and temperature optimum for enzymatic activity of individual L-LDH. In a temperature-shifting fermentation process (cells grown at 37°C and L-lactate formed at 42°C), E. coli 090B3 was able to produce 142.2 g/l of L-lactate with no more than 1.2 g/l of by-products (mainly acetate, pyruvate and succinate) accumulated. In conclusion, the production of lactate by E. coli is limited by the competition relationship between cell growth and lactate synthesis. Enzymatic properties, especially the thermodynamics of an L-LDH can be effectively used as a factor to regulate a metabolic pathway and its metabolic flux for efficient L-lactate production.
The enzymatic thermodynamics was used as a tool for metabolic regulation. ► minimizing the activity of L-lactate dehydrogenase in growth phase improved biomass accumulation. ► maximizing the activity of L-lactate dehydrogenase improved lactate productivity in production phase.
L-Lactic acid, one of the two lactic acid optical isomers, is produced via pyruvate from carbohydrates in diverse microorganisms catalyzed by an NAD+-dependent L-lactate dehydrogenase . L-Lactic acid is generally supplemented to foods or feeds as an excellent sour agent or pH modulator . L-Lactic acid is also an important precursor for synthesis of chiral compounds such as chiral drugs and chiral pesticides [3, 4] and, more importantly, as a monomer for the synthesis of poly-L-lactic acid, a bio-degradable and environmental friendly polymer [2, 5].
In contrast to past applications of racemic lactic acid, L-lactic acid as a monomer for poly-L-lactic acid synthesis must possess the highest optical purity and chemical purity [6, 7], Recently L-lactate production by microbial has been extensively investigated for this reason.
In previous works, metabolically engineered E. coli has been shown to be a suitable host for large-scale production of D-lactic acid or L-lactic acid, and several metabolically-engineered E. coli strains have been successfully constructed for efficient synthesis of D-lactic acid or L-lactic acid of high optical [8–12]. For L-lactic acid formation, E. coli strains are usually genetically modified to: (1) create a pathway for L-lactic acid formation, (2) block the pathway for L-lactic acid catabolism, and (3) construct/block pathways connected with intermediates for L-lactic acid [12–16].
Generally, L-lactate (and some other organic acids) is formed during cell growth, which negatively affects cell activity and cell growth and, as a consequence, exerts a detrimental effect on L-lactate titer and yield. The L-lactic acid synthesis pathway being less active during cell growth could be positive for cell growth and finally for L-lactic acid titer and yield as this strategy has been confirmed to be effective in D-lactate synthesis in E. coli [11, 17, 18].
It is expected that effectively controlling intracellular lactate dehydrogenase activity is crucial to achieve efficient lactate synthesis under fermentation process. Here, we described a new strategy to assess this proposal by engineering an L-lactate synthesis pathway in E. coli with temperature optima different between cell growth and a heterologously expressed bacterial L-lactate dehydrogenase. The strain expressed an L-lactate dehydrogenase from a thermophilic bacterium showed robust growth at its temperature optimum and was more efficient in fermenting glucose to L-lactate with less by-products formation at an elevated temperature.
Materials and methods
Strains and plasmids used in this study
Source or reference
Escherichia coli B0013-070
B0013, Δack-pta, Δpps, ΔpflB, Δdld, ΔpoxB, ΔadhE, ΔfrdA
E. coli B0013-080C
E. coli B0013-090B1
B0013-080C, ΔlldD:: ldhA p-ldh Lca
E. coli B0013-090B2
B0013-080C, ΔlldD:: ldhA p-ldh Strb
E. coli B0013-090B3
B0013-080C, ΔlldD:: ldhA p-ldh Bcoa
Bacillus coagulans B1821
Lactobacillus casei B1192
Steptococcus. bovis 1.1624
Source or reference
dif Gm, bla
bla; TA cloning vector
bla; P ldhA , T ldhA
To construct the 090B1, 090B2 and 090B3, ldhA in strain 070 encoding a D-lactate dehydrogenase for conversion of pyruvate to D-lactate was deleted followed by placing ldhAp-ldh Lca, ldhAp-ldh Strb or ldhA p-ldh Bcoa expression cassette which encodes an L-lactate dehydrogenase under the control of ldhA promoter for conversion of pyruvate to L-lactate from different microorganisms in the middle of the chromosomal lldD gene in strain 080C (070, ΔldhA::dif).
Deletion of ldhA to obtain E. coli B0013-080C
The ldhA' gene was cloned from the genomic DNA of E. coli B0013-070 using PCR amplification and the primers LdhA1 and LdhA2. The PCR product was purified and cloned into pMD18-T simple vector to yield plasmid pMD-ldhA'. This plasmid was digested with Sal I and Kpn I and blunted by incubation with Pfu DNA polymerase, which was then ligated with a selectable marker (GmR with dif sites flanked) isolated from pSK-dif GmR , to yield a hybrid plasmid pMD-ldhA::Gm, in which a 212 bp fragment in the middle of ldhA in pMD-ldhA was removed and replaced with dif Gm. The deletion cassette, ldhA'-dif Gm-dif-ldhA', was recovered from pMD-ldhA::Gm with Eco RI digestion and agarose gel isolation. The deletion cassette was electro-transformed into strain B0013-070 and ldhA disruption mutant was selected by the method described previously [10, 11]. The resulting recombinant strain was designated 080C (B0013-070, ΔldhA::dif).
Expression of ldh and disruption of lldD
The E. coli ldhA gene was cloned from the genomic DNA of B0013-070 using PCR amplification and the primers LdhA3 and LdhA4. The resulting 1.6-kb PCR fragment, which included the promoter, the structural region of the ldhA gene and the terminator, was inserted into the pMD18-T simple vector to create pMD-ldhA. The reverse PCR fragment from plasmid pMD-ldhA was amplified using the primers RldhA1 and RldhA2. The amplified fragment was then self-ligated to create an expression plasmid, pLDHex. The ldh Bcoa gene encoding a Bacillus coagulans L-LDH was recovered from the genome by PCR amplification with primers BcoaLDH1 and BcoaLDH4. After digestion with Bam HI and Eco RI, this 885-bp fragment was cloned into the Bgl II and Eco RI sites of pLDHex to create pLDH-ldhBcoa. A selectable marker, dif Gm (GmR with dif sites flanked) isolated from pSK-dif GmR , was subcloned into the Eco RV site of pLDH-ldhBcoa to create pLDH-ldhBcoa-Gm. Similarly, pLDH-ldhStrb-Gm was created by cloning a 1,464-bp ldh Strb (encoding a Streptococcus bovis L-LDH) digested with Bam HI and Eco RI into the Bgl II and Eco RI sites of pLDHex followed by inserting dif Gm into the Eco RV site. For development of pLDH-ldhLca-Gm, PCR amplified 1.26-kb fragment of ldh lca (encoding a Lactobacillus casei L-LDH) was first cloned into the Bgl II and Pst I sites of pLDHex to yield pLDH-ldhLca followed by insertion of dif Gm from pSK-dif GmR  into the Eco RV site. Meanwhile, the whole length of lldD was amplified from the genomic DNA of E. coli B0013 with primers LldD1 and LldD2. The resulting PCR 1154-bp fragment was cloned into pMD18-T simple vector to create pMD-lldD. Afterwards, the ldh expression cassette (P ldhA -ldh-Gm) was isolated from pLDH-ldhLca-Gm, pLDH-ldhStrb-Gm, or pLDH-ldhBcoa-Gm with Bam HI digestion and gel purification and cloned into the Bam HI sites of pMD-lldD to create pMD-lldD::P ldhA -ldh Lca-Gm, pMD-lldD::P ldhA -ldh Strb-Gm, or pMD-lldD::P ldhA -ldh Bcoa-Gm, in which a 39-bp Bam HI-fragment was deleted in the middle of lldD. These plasmids were digested with Sma I and the resulting deletion/expression cassettes were gel isolated and electroporated into strain B0013-080C The recombinants were selected by the method described previously [10, 18]. The resulting recombinant strains were designated 090B1 (B0013-080C, ΔlldD::P ldhA -ldh Lca), 090B2 (B0013-080C, ΔlldD::P ldhA -ldh Strb), and 090B3 (B0013-080C, ΔlldD::P ldhA -ldh Bcoa).
Primers used in this study
Sequence (5'-3') restriction sites are italic/underlined
CTTGAATTC a AAGCTT aGCTGCCGGAAATCATCATTTTTT
EcoR Ia, Hin dIIIa
Measurement of LDH activity
Strains (stored as glycerol stocks at −80°C) were first grown on Luria-Bertani (LB) plates for approximately 24 h at 37°C and then the colonies were transferred to 50 ml of LB medium in a 250-ml flask. After growing while shaking at 200 rpm for 7 h, the cells were collected and crude cell extracts were prepared using the bacterial soluble total protein preparation kit (GENMED Scientifics Inc., Arlington, MA, USA). The extracts were assayed for LDH activity using a kit to colorimetrically determine the total bacterial LDH activity (GENMED Scientifics Inc., Arlington, MA, USA) at pH 6.5 and at the same temperature as that of incubation (25°C ~ 50°C). One unit of the overall LDH activity was defined as the amount of enzyme required to transform 1 μmole NADH to NAD+ per minute. The protein concentration in the crude extracts was determined using the Bradford method, and bovine serum albumin was used as the standard. The LDH activity was divided by the corresponding protein concentration to calculate the specific LDH activity. The assays are performed in triplicates.
Flask fermentation experiments
The flask fermentation experiments were carried out according to the previous publication [10, 17] in 250 ml flasks with the working volume of 50 ml. Briefly, cells were grown in 50 ml of LB medium in a 250 ml flask at 37°C with shaking (200 rpm) for 8–10 h until cell density (OD600) of 2.0-2.5 was reached. Cells were collected by centrifugation and resuspended in a modified M9 medium and then inoculated into 50 ml of the modified M9 medium complemented with 5 g/l glucose in a 250 ml flask with the initial cell density (OD600) of 0.05. For cell growth experiments, the cultivation was carried out at shaking speed of 200 rpm and at different temperatures. For lactate fermentation, the cultivation was first carried out at 37°C and 200 rpm for 12 h, then 30 g/l glucose was added followed by stationary cultivation (anaerobic fermentation) for lactate formation at different temperatures. Calcium carbonate with a final concentration of 75 g/l was added for neutralization. Sampling was carried out during the cultivation. Modified M9 medium contained (per liter): 15.11 g Na2HPO4 · 12H2O, 3 g KH2PO4, 1 g NH4Cl, 0.5 g NaCl. One ml of filter-sterilized 1 M MgSO4, and 1 ml of filter-sterilized trace element solution containing (per liter) 2.4 g FeCl3 · 6H2O, 0.3 g CoCl2 · 6H2O, 0.15 g CuCl2 · 2H2O, 0.3 g ZnCl2, 0.3 g Na2MO4 · 2H2O, 0.075 g H3BO3, 0.495 g MnCl2 · 4H2O was added to a liter of the final medium.
Fed-batch fermentation in bioreactor
A fed-batch fermentation experiment in bioreactor was carried out according to the method described [10, 11, 21]. A 25-l bioreactor (Bioflow110; New Brunswick Scientific Co., Inc., Edison, NJ), initially containing 11 l of the modified M9 medium as above in the “Flask fermentation experiments”, was used for L-lactate production from glucose. The two-phase fed-batch process was started by inoculating 600 ml fresh inoculum prepared by pre-culturing cells in LB medium as described above. The cells were cultivated in the aerobic condition followed by anaerobic fermentation. Anaerobic fermentation for L-lactate formation was initiated by ceasing air sparging and reducing agitation to 100 rpm when the cell density (OD600) reached about 30 (which is equal to about 11.4 g/l dry cell weight (DCW)). During the aerobic phase, glucose was supplemented with 30 g/l for cell growth and the culture was grown at pH 7.0 controlled by automatically feeding 25% (w/v) NH4OH solution and the dissolved oxygen tension controlled above 30% of saturation. During the anaerobic phase, the pH was controlled at 7.0 by the addition of 25% (w/v) Ca(OH)2. The residual glucose concentration was maintained above 10 g/l by adding glucose in four batches (649.5 g of glucose was added in total). The fermentations were stopped when the glucose was exhausted.
Cultivation conditions for exploiting growth properties
Strains B0013-090B1, B0013-090B2 or B0013-090B3 heterologously expressing an L-lactate dehydrogenase (L-LDH) were examined for their growth rate and L-LDH activity. A shake flask fermentation test was carried out in a 250-ml flask with working volume of 50 ml at various temperatures from 25°C to 50°C for up to 14 h. The cell density was analyzed with the method as described below in the “Analytical methods”. The intracellular lactate dehydrogenase activities in strains B0013-090B1, B0013-090B2 and B0013-090B3 grown for 7 h were determined.
The cell mass was estimated by measuring the optical density at 600 nm (if CaCO3 or Ca(OH)2 had been added during fermentation, samples were pretreated with 1 M HCl at 20-fold of the sample volume to remove the suspended substances), and the dry weight of the cells was calculated using a standard curve (1OD 600 = 0.38 g/l DCW) . The glucose concentration was estimated using a glucose biosensor . Samples were pretreated with H2SO4 (at 5% of the sample volume) to release organic acids that precipitated with CaCO3 or Ca(OH)2 during fermentation. Organic acid concentrations were measured by HPLC as described previously . Organic acid and ethanol concentrations were measured by HPLC equipped with UV (210 nm) and refractive index detectors, using a Shodex SH-1011 column (Shodex SH-1011 H610009; Showa Denko K.K., Kawasaki, Japan) with 0.01 M H2SO4 as eluent (0.6 ml/min; 50°C). Lactic acid isomeric purity was measured by HPLC using a chiral column (CLC-L; Advanced Separation Technologies Inc., Whippany, NJ, USA), at room temperature, equilibrated with 1 ml/min of 5 mM CuSO4 as the mobile phase and detected at 254 nm with a UV detector.
Metabolic engineering of E. coli B0013 to produce L-lactate
Lactate formation in flask fermentation
L- lactate (g/l)a
Yield of L-/D-lactate (%, w/w, based on total supplied glucose)
20.16 ± 0.90
0.02 ± 0.00
16.19 ± 0.92
0.03 ± 0.00
25.59 ± 1.08
0.03 ± 0.00
0.00 ± 0.00
27.27 ± 1.06
0.00 ± 0.00
0.01 ± 0.00
A flask fermentation experiment was carried out at 37°C to evaluate the performances of the engineered strains. The results are summarized in Table 3. The total amounts of lactate produced by strain B0013-090B1, B0013-090B2 and B0013-090B3 was 20.16, 16.19 and 25.59 g/l from 35.0 g/l of glucose (5 g/l of glucose in LB medium and 30 g/l of glucose was added afterwards), respectively, while the total lactate produced by B0013-070 and B0013-080C was 27.27 g/l and 0.02 g/l respectively. The percentage of L-lactate in the total lactate produced by B0013-090B1, B0013-090B2 or B0013-090B3 was above 99.9%, while nearly no L-lactate was produced by B0013-070 and B0013-080C. These results indicated that all three L-lactate dehydrogenases were functionally expressed and capable of catalyzing L-lactate formation, and that D-lactate formation can be blocked thoroughly by deleting the ldhA gene. It is interesting to note that conversion efficiency of L-lactate and cell growth rate were obviously different among the recombinant E. coli strains carrying a different L-lactate dehydrogenase.
Temperature as a factor for variation in cell growth and L-lactate synthesis
L-Lactate production in a bioreactor using temperature as an adjustable parameter
Comparison of fermentation data (mean ± range of duplicate experiments) from the bioreactor experiments
Overall volumetric lactate productivity (g/l h)a
Oxygen-limited volumetric lactate productivity (g/l h)b
Oxygen-limited specific lactate productivity (g/g h)c
Oxygen-limited specific glucose consumption rate (g/g h)d
Aerobic biomass yield (g/100 g glucose)e
Oxygen-limited lactate yield (g/100 g glucose)f
Lactate titer (g/l)
Yield (g/100 g glucose) (The molar yield)g
2.67 ± 0.10
3.46 ± 0.23
0.42 ± 0.00
0.50 ± 0.01
36.9 ± 0.2
83.0 ± 1.2
106.8 ± 1.1
5.8 ± 0.1
74.3 ± 1.2 (1.49 ± 0.02)
0.6 ± 0.1
0.3 ± 0.0
0.0 ± 0.0
4.66 ± 0.12
6.77 ± 0. 30
0.98 ± 0.10
0.97 ± 0. 04
36.8 ± 0.1
97.0 ± 0.5
142.2 ± 0.7
4.9 ± 0.3
87.0 ± 2.1 (1.74 ± 0.04)
0.4 ± 0.1
0.1 ± 0.1
0.1 ± 0.2
Metabolic engineering are focusing mainly on the manipulation of directly-related metabolic pathways, which is obtained by introduction and/or amplification of product-oriented pathways or by deletion or attenuation of competing pathways [22, 23]. Currently, metabolic engineers tend to finely exploit a pathway or a reaction to make it compatible with the cell physiological properties [11, 17, 24–26].
Generally, cell growth depends on the synthesis of acetyl-CoA from pyruvate, which also acts as the precursor of lactate. Expression of a lactate dehydrogenase results in a certain percentage of pyruvate converted to lactate, thereby limiting metabolic flux for cell synthesis and eventually retarding cell growth. Specific to E. coli, intracellular activity level of the lactate dehydrogenase depends not only on the transcription and translation levels of its encoding gene, which is mainly affected by the unique cellular microenvironment in E. coli, but also on its original native biochemical properties as well. Due to these concerns, fine control of the transcription and translation of ldhA encoding NAD+-dependent D-lactate dehydrogenase and the intracellular activity level of the D-lactate dehydrogenase in D-lactate production was found to significantly improve both lactate yield and cell growth rate [11, 17]. In that case, a novel strategy has been developed for finely-regulating lactate dehydrogenase expression in E. coli, in which a gene encoding a lactate dehydrogenase was under the control of a thermo-induced promoter [11, 24]. In a bioreactor experiment using scaled-up conditions, strain B0013-070B produced 122.8 g/l D-lactate with an increased oxygen-limited productivity of 0.89 g/g h .
Most enzymes have a native temperature optimum but some have a broader plateau in activity for a certain temperature range. On the other hand, the enzymes belonging to the same super-family originating from different (micro-)organisms carry out the same reaction yet may show the different temperature optima. The effect of temperature on the activity of an enzyme are complex and can be considered as two forces acting simultaneously but in opposite directions. As the temperature is raised, the rate increases, but at the same time there exists a progressive inactivation (denaturation) of the enzyme protein. From the metabolic engineering’s point of view, temperature may become one of the most important factors that can be used to control the enzyme activity in a pathway and hence finely regulate the metabolic flux. In present case we used temperature to optimize the cell growth and L-lactate production.
In present studies, three L-lactate dehydrogenases with different temperature optima were functionally expressed in E. coli. The recombinant E. coli strain harboring an L-LDH from B. coagulans exhibited lower L-LDH activity at 37°C or below thus allowing robust cell growth at this temperature (Figures 2, 3). On the other hand, the enzyme showed higher activity at 42°C or above, which allowed cells to convert pyruvate to L-lactate efficiently, and the L-lactate titer reached 142.2 g/l (Figure 4, Table 4). To our knowledge this is the highest level of L-lactate production by recombinant E. coli cells ever reported.
The recombinant E. coli cells expressing an L-LDH from L. casei displayed a slow growth phenotype during the aerobic phase at 37°C, which can be attributed to the insufficient supply of substrate for cell growth due to channeling of metabolic flux by the effects of higher L-lactate dehydrogenase activity at the growth temperature (Figures 2, 3). Normal growth of the recombinant cells expressing the L-LDH from B. coagulans or Str. bovis was observed at 37°C, consistent with the lower activity of L-lactate dehydrogenase at this temperature (Figures 2, 3). These observations strongly suggest that it would be essential to either investigate the enzymatic properties or use a combination of promoter, temperature or pH conditions of a specific target enzyme before engineering a metabolic pathway. Different requirements for cell growth and target product formation conferred by a target enzyme can be utilized to rationally design and construct efficient metabolic pathways. Additionally, the desired enzymatic properties of a specific enzyme referred to a specific pathway or a reaction can be obtained either by cloning of genes obtained from microorganisms of extensive bio-diversity [27, 28] and/or by gene manipulation in the laboratory using modern molecular tools [29, 30].
In conclusion, the rapid growth characteristics and clearly defined metabolic pathway information in E. coli make it one of the most excellent lactate producers. The scale-up production of lactate by E. coli was limited by the competition relationship between cell growth and lactate synthesis in which lactate dehydrogenase activity is a critical factor. Furthermore, as described in present studies, properties, especially the thermodynamics of an enzyme can be effectively used as a powerful alternative tool to finely regulate a metabolic pathway and its metabolic flux by controlling temperature during cultivation/fermentation. This approach is convenient and economical to operate in any biotechnological process.
This work is partly supported by the Science and Technology Development Foundation of Tianjin Higher Education (20130628), the program for Changjiang Scholars and Innovative Research Team in University (IRT1166), SA-China Joint Project (CS06-L11). We thankfully thank Prof. Xiaoguang Liu from Tianjin University of Science and Technology for his assistance and kind revision in manuscript preparation.
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