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Directed Evolution of Soluble α-1,2-Fucosyltransferase Using Kanamycin Resistance Protein as a Phenotypic Reporter for Efficient Production of 2'-Fucosyllactose
1Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi 16419, Republic of Korea
2Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
3Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea
J. Microbiol. Biotechnol. 2022; 32(11): 1471-1478
Published November 28, 2022 https://doi.org/10.4014/jmb.2209.09018
Copyright © The Korean Society for Microbiology and Biotechnology.
Abstract
Keywords
Graphical Abstract
Introduction
Human milk oligosaccharides (HMOs) have multiple beneficial functions, such as the regulation of the human immune system and protection against pathogens, including viruses, bacteria, and protozoa [1]. Among the various oligosaccharides present in HMOs, 2'-fucosyllactose (Fuc-α1,2-Gal-β1,4-Glc; 2'-FL) is highly abundant and has attracted great interest as a functional food ingredient because of its pharmaceutical and nutraceutical properties [2, 3]. However, the milk of some women (non-secretor) does not contain 2'-FL owing to genetic variation [4].
A biosynthetic approach based on in vitro enzymatic reactions or metabolically engineered microorganisms is commonly considered an efficient and sustainable method for producing 2'-FL on a large scale [5]. Since in vitro multienzyme catalysis requires purified reagents and enzymes that increase production costs, production of 2'-FL using engineered microbes has been proven to be cost effective [5, 6]. In engineered
Fusion protein technologies [13], chaperone co-expression [14], directed evolution [15], promoter optimization [16], and machine learning [17] have been used to improve solubility of target proteins. We previously developed an inducible plasmid display system to improve the solubility of α-1,2-fucosyltransferase from
To overcome this limitation, we used a biosensor that links protein solubility to antimicrobial resistance. For such a system to be viable, the antibiotic resistance of cells containing the biosensor should be directly correlated with FucT2 solubility. To this end, aminoglycoside-3'-phosphotransferase (
-
Fig. 1. A schematic diagram representing overall process of directed evolution.
FucT2 mutant libraries were generated via a combination of error-prone PCR and DNA shuffling. The expression of the fusion protein (FucT2-KanR) consisting of FucT2 and kanamycin (Kan) resistance protein (KanR) was under the transcriptional control of the
PBAD promoter. The amino acid sequence of the linker was KSAAGT. Kan-resistantE. coli Top10 cells expressing FucT2-KanR were isolated from solid LB medium containing 2 g/l L-arabinose and 10–200 μg/ml Kan. Finally, the solubility and activity of FucT2 mutants were characterized, or they were used as substrates for the next round of evolution.
In this study, a protein solubility-based selection strategy for directed evolution was developed to allow for a high-throughput analysis of complex libraries within a short time and to enhance 2'-FL production in recombinant
Materials and Methods
Strains and Plasmids
All the strains and plasmids used in this study are listed in Table 1.
-
Table 1 .
Escherichia coli strains and plasmids used in this study.Name Description Reference E. coli TOP10 F– mcrA Δ(mrr-hsdRMS-mcrBC ) Φ80lacZ ΔM15 ΔlacX74 recA1 ara D139 Δ(ara-leu )7697 galU galK rpsL (StrR)endA1 nupG Invitrogen (USA) ΔL M15 BL21 star (DE3) Δ lacZYA Tn7::lacZΔM15 [11] Plasmids pSel2 PBAD promoter-KanR expression system, ColEI origin, AmpR[42] pSel2-FucT2 pSel2 + wild type FucT2 This study pSel2-FucT2mut pSel2 + FucT2 mutants This study pColAduet-1 Two T7 promoters, ColA origin, KanRNovagen (Germany) pColAduet-FucT2 pColAduet + wild type FucT2 from H. pylori AP Technology (Republic of Korea) pColAduet-FucT2mut pColAduet + FucT2 mutants This study
pColAduet-FucT2 and pColAduet-FucT2mut plasmids were designed to contain the genes encoding wild-type (WT) FucT2 and its mutants, respectively, for production of 2'-FL in
Kanamycin Sensitivity Assay
Construction of FucT2 Mutant Library
To construct a primary FucT2 mutant library, the gene coding for FucT2 was amplified with pSel2-FucT2 I FW and BW primers using a GeneMorph II Random Mutagenesis Kit (Agilent Technologies, USA) according to the manufacturer’s instructions. The resulting PCR products were ligated with the pSel2 plasmid to construct an intermediate plasmid, and additional mutations were introduced using a JBS DNA-Shuffling Kit (Jena Bioscience, Germany), as specified by the manufacturer. Briefly, the primary FucT2 mutant library present in the intermediate plasmid was amplified using Pfu polymerase (Elpis Biotech, Korea). The products were purified using a gel-prep kit (Elpis-Biotech) and digested with DNase I. The digested DNA fragments were reassembled using Taq polymerase (Elpis-Biotech) without primers, and reassembled
Selection of FucT2 Mutants with Improved Solubility
105–106
Preparation of Proteins
Analysis of Protein Expression
Protein samples were separated using 12% (w/v) sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then transferred to polyvinylidene difluoride membranes. In immunoblot assays, His6-fusion proteins were detected using an anti-polyhistidine antibody (Sigma-Aldrich), as specified by the manufacturer. Band intensities were quantified using densitometry software (GelAnalyzer 19.1, Hungary).
Culture Conditions and Analytical Methods
Lactose, glycerol, and 2'-FL concentrations were determined using high-performance liquid chromatography (Waters Corporation, USA). Metabolites were separated using a Rezex ROA-Organic Acid H+ column (Phenomenex, USA) in isocratic mode at a constant temperature (50°C) and a flow rate of 0.6 ml/min in 0.01 N H2SO4, and then passed through a refractive index detector (Fig. S1).
Statistical Analysis
Statistical methods were not used to determine sample size. Randomization and blind tests were not performed to evaluate the experimental procedures and results. Each experiment was performed in triplicate. Numerical analyses were performed using GraphPad Prism 5 (GraphPad Software Inc., San Diego, CA, USA). The Student’s
Results
Expression of an Insoluble FucT2-KanR Fusion Protein Comprising FucT2 and Kanamycin Resistance Protein
To construct an expression plasmid (pSel2-FucT2) for the fusion protein (FucT2-KanR) consisting of FucT2 and kanamycin resistance protein (KanR), the coding sequence of FucT2 was cloned into the pSel2 plasmid containing the
-
Fig. 2. The loss of Kan resistance owing to FucT2 insolubility.
(A) Western blot analysis was used to confirm the expression of FucT2-KanR. Cell lysates were prepared from recombinant
E. coli Top10 containing pSel2 and pSel2-FucT2 and fractionated into total (T) and soluble (S) fractions. (B, C) RecombinantE. coli Top10 containing pSel2 (B) and pSel2-FucT2 (C) were streaked on selection medium containing various concentrations of Kan.
To determine the minimum concentration of kanamycin that completely inhibits the growth of the
Construction of a FucT2 Mutant Library and Selection of FucT2 Mutants
In this study, a combination of error-prone PCR and DNA shuffling was used to obtain FucT2 variants with improved solubility. A primary FucT2 mutant library constructed via error-prone PCR (Fig. S3B) was re-amplified using Pfu polymerase (lane 2, Fig. S3C). After digesting the resulting PCR products with DNase I (lane 3, Fig. S3C), DNA fragments were reassembled into a full-length gene in the absence of primers (lane 4, Fig. S3C). The 903-bp DNA fragments containing FucT2 mutant libraries were amplified with pSel2-FucT2 I FW and BW primers and then ligated into the pSel2 plasmid to construct pSel2-FucT2mut (lane 5, Fig. S3C).
Fifteen large colonies of
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Table 2 . A list of FucT2 mutants isolated from five rounds of directed evolution process.
aDel: amino acid deletion
Soluble Expression of FucT2 via KanR-Mediated Directed Evolution
F#1-5, F#1-13, and F#2-11 mutants were selected from the first and second rounds of directed evolution. Before measuring the expression of WT FucT2 and its mutants selected via directed evolution using KanR as a biosensor motif, colony-forming units (CFUs) of
-
Fig. 3. Validation of KanR-mediated directed evolution for improving the expression of soluble FucT2.
(A) Recombinant
E. coli Top10 expressing wild-type (WT) FucT2 and its mutants (F#1-5, F#1-13, and F#2-11) were grown on selection medium with and without 25 μg/ml Kan. (B) Western blot analysis was used to confirm FucT2-KanR expression. Cell lysates were prepared from recombinantE. coli Top10 expressing WT FucT2 and its mutants, and divided into total (T) and soluble (S) fractions. (C) Comparison of relative expression of soluble FucT2-KanR detected in Fig. 3B.
Next, we evaluated whether the expression of soluble FucT2 could be enhanced via KanR-mediated directed evolution. Although total expression of the F#2-11 mutant was slightly lower than that of the WT FucT2, and F#1-5 and F#1-13 mutants, the expression of soluble FucT2-KanR by the F#1-5, F#1-13, and F#2-11 mutants was significantly higher than that by the WT (Fig. 3B). The decrease in total expression level of the F#2-11 mutant is likely due to the dynamic transtriptional response of
Enhanced Production of 2'-FL by Engineered E. coli Expressing FucT2 Mutants with Improved Solubility
An engineered
-
Fig. 4. Comparison of 2'-FL production in engineered
E. coli strains expressing wild-type (WT) FucT2 (A) and F#1-5 (B), F#2-11 (C), and F#3-1 (D) mutants. At the mid-exponential growth phase, IPTG and lactose were added at final concentrations of 0.1 mM and 5 g/l, respectively. Results are the mean of duplicate experiments and error bars indicate standard deviation.
Discussion
α-1,2-Fucosyltransferase is the rate-limiting enzyme in
The overall process of directed evolution consists of generating a mutant library and high-throughput screening and/or selection (HTSS). Although mutant libraries with controllable numbers of mutations can be generated via modern mutagenesis techniques, such as error-prone PCR and DNA shuffling, the real bottleneck for solubility engineering lies in establishing HTSS for mutant isolation [25]. Using a biosensor of protein solubility may overcome such bottlenecks, thereby increasing the probability of selecting desired mutants. A typical biosensor of protein solubility consists of target and phenotypical reporter proteins [26]. Since these two are expressed as a fusion protein, the activity of the reporter is affected by the solubility of the target protein. Chloramphenicol acetyltransferase (CAT), which confers resistance to chloramphenicol, is a frequently used reporter protein owing to its easily detectable enzymatic activity [27]. Cells expressing insoluble and/or unstable proteins fused to CAT were unable to grow in the presence of chloramphenicol, whereas mutants with improved solubility and/or stability could be isolated from solid medium containing chloramphenicol. Examples of successful applications of CAT-based biosensors include isolation of mitochondrial Acytochrome P450 [28], imidazole glycerol phosphate synthase [29], and interleukin-15 [30] mutants with improved solubility and/or stability. In addition to CAT, green fluorescent protein (GFP) has been used as a phenotypical reporter protein. In recent studies, the solubility and/or stability of L-serine/L-threonine exchanger [31] and esterase [32] were significantly improved via the GFP-mediated directed evolution coupled with fluorescence size-exclusion chromatography analysis and fluorescence-activated cell sorting, respectively. In this system, variants with high levels of soluble protein expression can confer GFP with strong fluorescence, whereas low stability and/or solubility of target proteins results in improper folding of GFP which in turn lead to a decrease in the intensity of fluorescence.
For the biosensor with CAT to be viable, the activity of CAT should be solely dependent on FucT2 solubility. However, CAT activity in the fusion protein is dependent on its quaternary structure in addition to the solubility of target proteins because the homotrimeric CAT is catalytically active only as a trimer [33]. Therefore, KanR was employed in this study as an alternative phenotypic reporter. Although KanR thermodynamically favors dimers of identical subunits, dimerization does not affect its activity [34].
We noted that a single round of the overall directed evolution process enabled the expression of soluble FucT2, which resulted in a significant increase in 2'-FL production. However, the increase in FucT2 activity was not proportional to the extent of FucT2 solubility. Although the mechanism remains to be investigated, we hypothesize that one of the reasons for this might be due to the activity-solubility trade-offs, or rather, the negative correlation between activity and solubility [35, 36]. Since amino acids in enzymes have multiple roles, the adjustment of one physical parameter could influence other properties [37, 38]. Among seven FucT2 mutants with improved solubility, only three (F#1-5, F#1-13, and F# 2-11) exhibited higher activity than that of the WT FucT when expressed in ΔL M15 pBCGW strain (Fig. S5). In addition, the activity of KanR was not directly proportional to the expression level of soluble FucT2-KanR by the mutants. These results are consistent with those of previous studies that reported a decrease in enzyme activity of the mutants with improved solubility and/or stability [37-39]. In our ongoing research, we are striving to identify the key mutations that play crucial roles in solubility enhancement and/or mutations that enhance solubility without negatively affecting activity. The FucT2 structure predicted using AlphaFold [40], an artificial intelligence method for predicting protein structures, showed that the key mutation sites (V33, G84, D120, and I287) were present on the surface of FucT2 (Fig. S6). A previous study reported that hydrophobic amino acids on the surface of recombinant proteins played an important role in the formation of inclusion body [41]. Therefore, we speculated that the V33M, G84R, D120N, and I287M mutations enhanced expression level of soluble FucT2 by decreasing formation of inclusion body.
In conclusion, in this study, we aimed to enhance the expression of soluble FucT2 via directed evolution for the efficient production of 2'-FL. To this end, KanR was employed in this study as a phenotypic reporter, whose activity is affected by the solubility of FucT2. Three FucT2 mutants (F#1-5, #F2-11, and F#3-1) with improved solubility and activity were successfully isolated. Finally, ΔL M15 pBCGW strain expressing F#1-5, #F2-11, and F#3-1 produced 0.27–0.31 g/l 2'-FL, showing a 1.46–1.72 fold increase in 2'-FL titer, compared to those of the control strain. Therefore, our approach could be applied to other biotransformation processes that include highly unstable and insoluble enzymes.
Supplemental Materials
Acknowledgments
This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2017R1A6A1A03015642 and NRF-2020R1A2C2101964). This research was also supported by the Chung-Ang University Graduate Research Scholarship (Academic Scholarship for College of Biotechnology and Natural Resources) in 2022.
Conflict of Interest
The authors have no financial conflicts of interest to declare.
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Related articles in JMB
Article
Research article
J. Microbiol. Biotechnol. 2022; 32(11): 1471-1478
Published online November 28, 2022 https://doi.org/10.4014/jmb.2209.09018
Copyright © The Korean Society for Microbiology and Biotechnology.
Directed Evolution of Soluble α-1,2-Fucosyltransferase Using Kanamycin Resistance Protein as a Phenotypic Reporter for Efficient Production of 2'-Fucosyllactose
Jonghyeok Shin1,2†, Seungjoo Kim1†, Wonbeom Park1, Kyoung Chan Jin3, Sun-Ki Kim3*, and Dae-Hyuk Kweon1*
1Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon, Gyeonggi 16419, Republic of Korea
2Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
3Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea
Correspondence to:Sun-Ki Kim, skkim18@cau.ac.kr
Dae-Hyuk Kweon, dhkweon@skku.edu
†These authors contributed equally to this paper.
Abstract
2'-Fucosyllactose (2'-FL), the most abundant fucosylated oligosaccharide in human milk, has multiple beneficial effects on human health. However, its biosynthesis by metabolically engineered Escherichia coli is often hampered owing to the insolubility and instability of α-1,2-fucosyltransferase (the rate-limiting enzyme). In this study, we aimed to enhance 2'-FL production by increasing the expression of soluble α-1,2-fucosyltransferase from Helicobacter pylori (FucT2). Because structural information regarding FucT2 has not been unveiled, we decided to improve the expression of soluble FucT2 in E. coli via directed evolution using a protein solubility biosensor that links protein solubility to antimicrobial resistance. For such a system to be viable, the activity of kanamycin resistance protein (KanR) should be dependent on FucT2 solubility. KanR was fused to the C-terminus of mutant libraries of FucT2, which were generated using a combination of error-prone PCR and DNA shuffling. Notably, one round of the directed evolution process, which consisted of mutant library generation and selection based on kanamycin resistance, resulted in a significant increase in the expression level of soluble FucT2. As a result, a batch fermentation with the ΔL M15 pBCGW strain, expressing the FucT2 mutant (F#1–5) isolated from the first round of the directed evolution process, resulted in the production of 0.31 g/l 2'-FL with a yield of 0.22 g 2'-FL/g lactose, showing 1.72- and 1.51-fold increase in the titer and yield, respectively, compared to those of the control strain. The simple and powerful method developed in this study could be applied to enhance the solubility of other unstable enzymes.
Keywords: 2&prime,-fucosyllactose, &alpha,-1,2-fucosyltransferase, directed evolution, solubility biosensor, kanamycin resistance, Escherichia coli
Introduction
Human milk oligosaccharides (HMOs) have multiple beneficial functions, such as the regulation of the human immune system and protection against pathogens, including viruses, bacteria, and protozoa [1]. Among the various oligosaccharides present in HMOs, 2'-fucosyllactose (Fuc-α1,2-Gal-β1,4-Glc; 2'-FL) is highly abundant and has attracted great interest as a functional food ingredient because of its pharmaceutical and nutraceutical properties [2, 3]. However, the milk of some women (non-secretor) does not contain 2'-FL owing to genetic variation [4].
A biosynthetic approach based on in vitro enzymatic reactions or metabolically engineered microorganisms is commonly considered an efficient and sustainable method for producing 2'-FL on a large scale [5]. Since in vitro multienzyme catalysis requires purified reagents and enzymes that increase production costs, production of 2'-FL using engineered microbes has been proven to be cost effective [5, 6]. In engineered
Fusion protein technologies [13], chaperone co-expression [14], directed evolution [15], promoter optimization [16], and machine learning [17] have been used to improve solubility of target proteins. We previously developed an inducible plasmid display system to improve the solubility of α-1,2-fucosyltransferase from
To overcome this limitation, we used a biosensor that links protein solubility to antimicrobial resistance. For such a system to be viable, the antibiotic resistance of cells containing the biosensor should be directly correlated with FucT2 solubility. To this end, aminoglycoside-3'-phosphotransferase (
-
Figure 1. A schematic diagram representing overall process of directed evolution.
FucT2 mutant libraries were generated via a combination of error-prone PCR and DNA shuffling. The expression of the fusion protein (FucT2-KanR) consisting of FucT2 and kanamycin (Kan) resistance protein (KanR) was under the transcriptional control of the
PBAD promoter. The amino acid sequence of the linker was KSAAGT. Kan-resistantE. coli Top10 cells expressing FucT2-KanR were isolated from solid LB medium containing 2 g/l L-arabinose and 10–200 μg/ml Kan. Finally, the solubility and activity of FucT2 mutants were characterized, or they were used as substrates for the next round of evolution.
In this study, a protein solubility-based selection strategy for directed evolution was developed to allow for a high-throughput analysis of complex libraries within a short time and to enhance 2'-FL production in recombinant
Materials and Methods
Strains and Plasmids
All the strains and plasmids used in this study are listed in Table 1.
-
Table 1 .
Escherichia coli strains and plasmids used in this study..Name Description Reference E. coli TOP10 F– mcrA Δ(mrr-hsdRMS-mcrBC ) Φ80lacZ ΔM15 ΔlacX74 recA1 ara D139 Δ(ara-leu )7697 galU galK rpsL (StrR)endA1 nupG Invitrogen (USA) ΔL M15 BL21 star (DE3) Δ lacZYA Tn7::lacZΔM15 [11] Plasmids pSel2 PBAD promoter-KanR expression system, ColEI origin, AmpR[42] pSel2-FucT2 pSel2 + wild type FucT2 This study pSel2-FucT2mut pSel2 + FucT2 mutants This study pColAduet-1 Two T7 promoters, ColA origin, KanRNovagen (Germany) pColAduet-FucT2 pColAduet + wild type FucT2 from H. pylori AP Technology (Republic of Korea) pColAduet-FucT2mut pColAduet + FucT2 mutants This study
pColAduet-FucT2 and pColAduet-FucT2mut plasmids were designed to contain the genes encoding wild-type (WT) FucT2 and its mutants, respectively, for production of 2'-FL in
Kanamycin Sensitivity Assay
Construction of FucT2 Mutant Library
To construct a primary FucT2 mutant library, the gene coding for FucT2 was amplified with pSel2-FucT2 I FW and BW primers using a GeneMorph II Random Mutagenesis Kit (Agilent Technologies, USA) according to the manufacturer’s instructions. The resulting PCR products were ligated with the pSel2 plasmid to construct an intermediate plasmid, and additional mutations were introduced using a JBS DNA-Shuffling Kit (Jena Bioscience, Germany), as specified by the manufacturer. Briefly, the primary FucT2 mutant library present in the intermediate plasmid was amplified using Pfu polymerase (Elpis Biotech, Korea). The products were purified using a gel-prep kit (Elpis-Biotech) and digested with DNase I. The digested DNA fragments were reassembled using Taq polymerase (Elpis-Biotech) without primers, and reassembled
Selection of FucT2 Mutants with Improved Solubility
105–106
Preparation of Proteins
Analysis of Protein Expression
Protein samples were separated using 12% (w/v) sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then transferred to polyvinylidene difluoride membranes. In immunoblot assays, His6-fusion proteins were detected using an anti-polyhistidine antibody (Sigma-Aldrich), as specified by the manufacturer. Band intensities were quantified using densitometry software (GelAnalyzer 19.1, Hungary).
Culture Conditions and Analytical Methods
Lactose, glycerol, and 2'-FL concentrations were determined using high-performance liquid chromatography (Waters Corporation, USA). Metabolites were separated using a Rezex ROA-Organic Acid H+ column (Phenomenex, USA) in isocratic mode at a constant temperature (50°C) and a flow rate of 0.6 ml/min in 0.01 N H2SO4, and then passed through a refractive index detector (Fig. S1).
Statistical Analysis
Statistical methods were not used to determine sample size. Randomization and blind tests were not performed to evaluate the experimental procedures and results. Each experiment was performed in triplicate. Numerical analyses were performed using GraphPad Prism 5 (GraphPad Software Inc., San Diego, CA, USA). The Student’s
Results
Expression of an Insoluble FucT2-KanR Fusion Protein Comprising FucT2 and Kanamycin Resistance Protein
To construct an expression plasmid (pSel2-FucT2) for the fusion protein (FucT2-KanR) consisting of FucT2 and kanamycin resistance protein (KanR), the coding sequence of FucT2 was cloned into the pSel2 plasmid containing the
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Figure 2. The loss of Kan resistance owing to FucT2 insolubility.
(A) Western blot analysis was used to confirm the expression of FucT2-KanR. Cell lysates were prepared from recombinant
E. coli Top10 containing pSel2 and pSel2-FucT2 and fractionated into total (T) and soluble (S) fractions. (B, C) RecombinantE. coli Top10 containing pSel2 (B) and pSel2-FucT2 (C) were streaked on selection medium containing various concentrations of Kan.
To determine the minimum concentration of kanamycin that completely inhibits the growth of the
Construction of a FucT2 Mutant Library and Selection of FucT2 Mutants
In this study, a combination of error-prone PCR and DNA shuffling was used to obtain FucT2 variants with improved solubility. A primary FucT2 mutant library constructed via error-prone PCR (Fig. S3B) was re-amplified using Pfu polymerase (lane 2, Fig. S3C). After digesting the resulting PCR products with DNase I (lane 3, Fig. S3C), DNA fragments were reassembled into a full-length gene in the absence of primers (lane 4, Fig. S3C). The 903-bp DNA fragments containing FucT2 mutant libraries were amplified with pSel2-FucT2 I FW and BW primers and then ligated into the pSel2 plasmid to construct pSel2-FucT2mut (lane 5, Fig. S3C).
Fifteen large colonies of
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Table 2 . A list of FucT2 mutants isolated from five rounds of directed evolution process..
aDel: amino acid deletion.
Soluble Expression of FucT2 via KanR-Mediated Directed Evolution
F#1-5, F#1-13, and F#2-11 mutants were selected from the first and second rounds of directed evolution. Before measuring the expression of WT FucT2 and its mutants selected via directed evolution using KanR as a biosensor motif, colony-forming units (CFUs) of
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Figure 3. Validation of KanR-mediated directed evolution for improving the expression of soluble FucT2.
(A) Recombinant
E. coli Top10 expressing wild-type (WT) FucT2 and its mutants (F#1-5, F#1-13, and F#2-11) were grown on selection medium with and without 25 μg/ml Kan. (B) Western blot analysis was used to confirm FucT2-KanR expression. Cell lysates were prepared from recombinantE. coli Top10 expressing WT FucT2 and its mutants, and divided into total (T) and soluble (S) fractions. (C) Comparison of relative expression of soluble FucT2-KanR detected in Fig. 3B.
Next, we evaluated whether the expression of soluble FucT2 could be enhanced via KanR-mediated directed evolution. Although total expression of the F#2-11 mutant was slightly lower than that of the WT FucT2, and F#1-5 and F#1-13 mutants, the expression of soluble FucT2-KanR by the F#1-5, F#1-13, and F#2-11 mutants was significantly higher than that by the WT (Fig. 3B). The decrease in total expression level of the F#2-11 mutant is likely due to the dynamic transtriptional response of
Enhanced Production of 2'-FL by Engineered E. coli Expressing FucT2 Mutants with Improved Solubility
An engineered
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Figure 4. Comparison of 2'-FL production in engineered
E. coli strains expressing wild-type (WT) FucT2 (A) and F#1-5 (B), F#2-11 (C), and F#3-1 (D) mutants. At the mid-exponential growth phase, IPTG and lactose were added at final concentrations of 0.1 mM and 5 g/l, respectively. Results are the mean of duplicate experiments and error bars indicate standard deviation.
Discussion
α-1,2-Fucosyltransferase is the rate-limiting enzyme in
The overall process of directed evolution consists of generating a mutant library and high-throughput screening and/or selection (HTSS). Although mutant libraries with controllable numbers of mutations can be generated via modern mutagenesis techniques, such as error-prone PCR and DNA shuffling, the real bottleneck for solubility engineering lies in establishing HTSS for mutant isolation [25]. Using a biosensor of protein solubility may overcome such bottlenecks, thereby increasing the probability of selecting desired mutants. A typical biosensor of protein solubility consists of target and phenotypical reporter proteins [26]. Since these two are expressed as a fusion protein, the activity of the reporter is affected by the solubility of the target protein. Chloramphenicol acetyltransferase (CAT), which confers resistance to chloramphenicol, is a frequently used reporter protein owing to its easily detectable enzymatic activity [27]. Cells expressing insoluble and/or unstable proteins fused to CAT were unable to grow in the presence of chloramphenicol, whereas mutants with improved solubility and/or stability could be isolated from solid medium containing chloramphenicol. Examples of successful applications of CAT-based biosensors include isolation of mitochondrial Acytochrome P450 [28], imidazole glycerol phosphate synthase [29], and interleukin-15 [30] mutants with improved solubility and/or stability. In addition to CAT, green fluorescent protein (GFP) has been used as a phenotypical reporter protein. In recent studies, the solubility and/or stability of L-serine/L-threonine exchanger [31] and esterase [32] were significantly improved via the GFP-mediated directed evolution coupled with fluorescence size-exclusion chromatography analysis and fluorescence-activated cell sorting, respectively. In this system, variants with high levels of soluble protein expression can confer GFP with strong fluorescence, whereas low stability and/or solubility of target proteins results in improper folding of GFP which in turn lead to a decrease in the intensity of fluorescence.
For the biosensor with CAT to be viable, the activity of CAT should be solely dependent on FucT2 solubility. However, CAT activity in the fusion protein is dependent on its quaternary structure in addition to the solubility of target proteins because the homotrimeric CAT is catalytically active only as a trimer [33]. Therefore, KanR was employed in this study as an alternative phenotypic reporter. Although KanR thermodynamically favors dimers of identical subunits, dimerization does not affect its activity [34].
We noted that a single round of the overall directed evolution process enabled the expression of soluble FucT2, which resulted in a significant increase in 2'-FL production. However, the increase in FucT2 activity was not proportional to the extent of FucT2 solubility. Although the mechanism remains to be investigated, we hypothesize that one of the reasons for this might be due to the activity-solubility trade-offs, or rather, the negative correlation between activity and solubility [35, 36]. Since amino acids in enzymes have multiple roles, the adjustment of one physical parameter could influence other properties [37, 38]. Among seven FucT2 mutants with improved solubility, only three (F#1-5, F#1-13, and F# 2-11) exhibited higher activity than that of the WT FucT when expressed in ΔL M15 pBCGW strain (Fig. S5). In addition, the activity of KanR was not directly proportional to the expression level of soluble FucT2-KanR by the mutants. These results are consistent with those of previous studies that reported a decrease in enzyme activity of the mutants with improved solubility and/or stability [37-39]. In our ongoing research, we are striving to identify the key mutations that play crucial roles in solubility enhancement and/or mutations that enhance solubility without negatively affecting activity. The FucT2 structure predicted using AlphaFold [40], an artificial intelligence method for predicting protein structures, showed that the key mutation sites (V33, G84, D120, and I287) were present on the surface of FucT2 (Fig. S6). A previous study reported that hydrophobic amino acids on the surface of recombinant proteins played an important role in the formation of inclusion body [41]. Therefore, we speculated that the V33M, G84R, D120N, and I287M mutations enhanced expression level of soluble FucT2 by decreasing formation of inclusion body.
In conclusion, in this study, we aimed to enhance the expression of soluble FucT2 via directed evolution for the efficient production of 2'-FL. To this end, KanR was employed in this study as a phenotypic reporter, whose activity is affected by the solubility of FucT2. Three FucT2 mutants (F#1-5, #F2-11, and F#3-1) with improved solubility and activity were successfully isolated. Finally, ΔL M15 pBCGW strain expressing F#1-5, #F2-11, and F#3-1 produced 0.27–0.31 g/l 2'-FL, showing a 1.46–1.72 fold increase in 2'-FL titer, compared to those of the control strain. Therefore, our approach could be applied to other biotransformation processes that include highly unstable and insoluble enzymes.
Supplemental Materials
Acknowledgments
This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2017R1A6A1A03015642 and NRF-2020R1A2C2101964). This research was also supported by the Chung-Ang University Graduate Research Scholarship (Academic Scholarship for College of Biotechnology and Natural Resources) in 2022.
Conflict of Interest
The authors have no financial conflicts of interest to declare.
Fig 1.
Fig 2.
Fig 3.
Fig 4.
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Table 1 .
Escherichia coli strains and plasmids used in this study..Name Description Reference E. coli TOP10 F– mcrA Δ(mrr-hsdRMS-mcrBC ) Φ80lacZ ΔM15 ΔlacX74 recA1 ara D139 Δ(ara-leu )7697 galU galK rpsL (StrR)endA1 nupG Invitrogen (USA) ΔL M15 BL21 star (DE3) Δ lacZYA Tn7::lacZΔM15 [11] Plasmids pSel2 PBAD promoter-KanR expression system, ColEI origin, AmpR[42] pSel2-FucT2 pSel2 + wild type FucT2 This study pSel2-FucT2mut pSel2 + FucT2 mutants This study pColAduet-1 Two T7 promoters, ColA origin, KanRNovagen (Germany) pColAduet-FucT2 pColAduet + wild type FucT2 from H. pylori AP Technology (Republic of Korea) pColAduet-FucT2mut pColAduet + FucT2 mutants This study
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Table 2 . A list of FucT2 mutants isolated from five rounds of directed evolution process..
aDel: amino acid deletion.
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