Synthetic biology approaches for the production of chiral aminoalcohols in engineered E. coli strains

Transketolase catalyses asymmetric carbon-carbon bond formation and produces 1,3-dihydroxyketones, a functionality that is found in a vast number of natural and synthetic compounds. The wild-type transketolase enzymes from several species can accept a wide range of aldehydes, but industrially exploitable levels of activity tend to be limited to natural substrates and small aliphatic aldehydes. Several single mutants of the transketolase from E. coli were found to have enhanced activity towards non-phosphorylated substrates, non-hydroxylated aldehydes, and cyclic aldehydes. However, aromatic aldehydes still suffer from poor activities and yields while the key bottlenecks have not been identified. The strategy for creating new libraries from combining single mutations can have significant impact not only on the activity but also the stability of the enzyme due to the synergy between residues. On the other hand, the combination of two sites identified within a co-evolved network has created mutants with high towards propionaldehyde and decent stability. Kinetic studies of a small transkeloase library with 3-formylbenzoic acid (3-FBA) and 4-formylbenzoic acid (4-FBA) suggested that the affinity between the enzyme and the aromatic aldehyde, as well as their proximal orientations, was the key factor governing the reaction rate. This was also supported by computational modelling of substrate binding. Site-saturation mutagenesis at S385 and R358 was performed to further improve the activity of transketolase for 3-FBA, 4-FBA and also 3-hydroxybenzaldehyde (3-HBA). The new mutants were then assessed alongside transaminase for the ability to synthesise novel aromatic amino alcohols, which would provide building blocks for chloramphenicol and its derivatives. However, none of the available transaminases appeared to accept either of the compounds. The competitive reaction between 4-FBA and 4-DOPBA, the dihydroxy ketone product of 4-FBA, in an amination reaction suggested that 4-DOPBA was unable to access into the active site of CV2025 transaminase

Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes.

The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies

Second generation engineering of transketolase for polar aromatic aldehyde substrates

Transketolase has significant industrial potential for the asymmetric synthesis of carboncarbon bonds with new chiral centres. Variants evolved on propanal were found previously with nascent activity on polar aromatic aldehydes 3-formylbenzoic acid (3-FBA), 4-formylbenzoic acid (4-FBA), and 3-hydroxybenzaldehyde (3-HBA), suggesting a potential novel route to analogues of chloramphenicol. Here we evolved improved transketolase activities towards aromatic aldehydes, by saturation mutagenesis of two active-site residues (R358 and S385), predicted to interact with the aromatic substituents. S385 variants selectively controlled the aromatic substrate preference, with up to 13-fold enhanced activities, and KM values comparable to those of natural substrates with wild-type transketolase. S385E even completely removed the substrate inhibition for 3-FBA, observed in all previous variants. The mechanisms of catalytic improvement were both mutation type and substrate dependent. S385E improved 3-FBA activity via kcat, but reduced 4-FBA activity via KM. Conversely, S385Y/T improved 3-FBA activity via KM and 4-FBA activity via kcat. This suggested that both substrate proximity and active-site orientation are very sensitive to mutation. Comparison of all variant activities on each substrate indicated different binding modes for the three aromatic substrates, supported by computational docking. This highlights a potential divergence in the evolution of different substrate specificities, with implications for enzyme engineering

Rational substrate and enzyme engineering of transketolase for aromatics

The uses of 3-formylbenzoic acid and 4-formylbenzoic acid as molecular probes along with previous and new transketolase mutants revealed the factors governing the rate of reaction between transketolase and aromatic aldehydes. The novel α,α-dihydroxyketones were produced at 15 to 30-fold higher yields and up to 250-fold higher specific activities with D469T TK when compared to those obtained for benzaldehyde

Directed evolution to re-adapt a co-evolved network within an enzyme.

We have previously used targeted active-site saturation mutagenesis to identify a number of transketolase single mutants that improved activity towards either glycolaldehyde (GA), or the non-natural substrate propionaldehyde (PA). Here, all attempts to recombine the singles into double mutants led to unexpected losses of specific activity towards both substrates. A typical trade-off occurred between soluble expression levels and specific activity for all single mutants, but many double mutants decreased both properties more severely suggesting a critical loss of protein stability or native folding. Statistical coupling analysis (SCA) of a large multiple sequence alignment revealed a network of nine co-evolved residues that affected all but one double mutant. Such networks maintain important functional properties such as activity, specificity, folding, stability, and solubility and may be rapidly disrupted by introducing one or more non-naturally occurring mutations. To identify variants of this network that would accept and improve upon our best D469 mutants for activity towards PA, we created a library of random single, double and triple mutants across seven of the co-evolved residues, combining our D469 variants with only naturally occurring mutations at the remaining sites. A triple mutant cluster at D469, E498 and R520 was found to behave synergistically for the specific activity towards PA. Protein expression was severely reduced by E498D and improved by R520Q, yet variants containing both mutations led to improved specific activity and enzyme expression, but with loss of solubility and the formation of inclusion bodies. D469S and R520Q combined synergistically to improve k(cat) 20-fold for PA, more than for any previous transketolase mutant. R520Q also doubled the specific activity of the previously identified D469T to create our most active transketolase mutant to date. Our results show that recombining active-site mutants obtained by saturation mutagenesis can rapidly destabilise critical networks of co-evolved residues, whereas beneficial single mutants can be retained and improved upon by randomly recombining them with natural variants at other positions in the network

Transketolase catalysed upgrading of l-arabinose: the one-step stereoselective synthesis of l-gluco-heptulose

Conversion of biomass using biocatalysis is likely to become a technology that contributes significantly to the future production of chemical building blocks, materials and transport fuels. Here the synthesis of a value-added chemical from L-arabinose, a major component of the carbohydrates in sugar beet pulp (SBP), in a concise and sustainable manner has been investigated. Biocatalytic conversions using transketolase variants have been developed for the efficient, scalable synthesis of a rare naturally occurring ketoheptose, L-gluco-heptulose, from L-arabinose. New active E. coli TK mutants that readily accept L-arabinose were identified using a versatile colorimetric screening assay and the reaction was performed on a preparative scale

Influence of Degree of Polymerization of Low-Molecular-Weight Chitosan Oligosaccharides on the α-Glucosidase Inhibition

Chitosan oligosaccharide (COS) is a bioactive compound derived from marine by-products. COS consumption has been demonstrated to lower the risk of diabetes. However, there are limited data on the inhibitory effect of low-molecular-weight COSs with different degrees of polymerization (DP) on α-glucosidase. This study investigates the α-glucosidase inhibitory activity of two low-molecular-weight COSs, i.e., S-TU-COS with DP2–4 and L-TU-COS with DP2–5, both of which have different molecular weight distributions. The inhibition constants of the inhibitors binding to free enzymes (Ki) and an enzyme–substrate complex (Kii) were investigated to elucidate the inhibitory mechanism of COSs with different chain lengths. The kinetic inhibition model of S-TU-COS showed non-completive inhibition results which are close to the uncompetitive inhibition results with Ki and Kii values of 3.34 mM and 2.94 mM, respectively. In contrast, L-TU-COS showed uncompetitive inhibition with a Kii value of 5.84 mM. With this behavior, the IC50 values of S-TU-COS and L-TU-COS decreased from 12.54 to 11.84 mM and 20.42 to 17.75 mM, respectively, with an increasing substrate concentration from 0.075 to 0.3 mM. This suggests that S-TU-COS is a more potent inhibitor, and the different DP of COS may cause significantly different inhibition (p < 0.05) on the α-glucosidase activity. This research may provide new insights into the production of a COS with a suitable profile for antidiabetic activity

Circulating microtranscriptome profiles reveal distinct expression of microRNAs in severe leptospirosis.

Biomarkers to predict the severity of leptospirosis are still lacking. This study aimed to identify and validate microRNAs in patients with severe leptospirosis, that could potentially be used as biomarkers for predicting an unfavorable outcome. Serum samples were collected from participants with definite diagnosis of leptospirosis. The participants were divided into two groups, non-severe and severe leptospirosis, as defined by the Specific Organ Sequential Organ Failure (SOFA) Score of more than two in any organ. Microtranscriptome analysis was performed using the NanoString miRNA Expression Assay. The expression level of candidate miRNAs was then validated by quantitative RT-PCR. Based on the NanoString, the microtranscriptome profile of the severe group was significantly different from that of the non-severe group. Upregulation of miR155-5p, miR362-3p, miR502-5p, miR601, miR1323, and miR630 in the severe group were identified, and further investigated. A total of 119 participants were enrolled in the validation cohort. Serum miR155-5p and miR630 levels were significantly higher in the severe group compared to the non-severe group. The combined use of miR155-5p or miR-630 with serum bicarbonate levels had an AUC of 0.79 (95%CI; 0.69-0.89, p<0.001) in identifying the severity of the disease. This data provides the first evidence that the microtranscriptome profiles of patients with severe leptospirosis were different from the non-severe group. Serum miR155-5p and miR630 levels might be novel biomarkers for identifying severe leptospirosis

Towards a Mechanistic Understanding of Factors Controlling the Stereoselectivity of Transketolase

A structural model for thiamine‐diphosphate (ThDP)‐dependent transketolase (TK) was developed to analyse the effect of amino acid exchanges on the stereoselectivity of this synthetically important class of enzymes. In this study the carboligation of 3‐hydroxypyruvate as a donor and propanal, as well as pentanal, was studied. Based on literature data and additional mutagenesis studies using E. coli TK, a four‐state model was developed to explain the stereoselectivity of TKs by the relative orientation of donor and acceptor substrates in the active site prior to C−C‐bond formation. To enable a functional comparison of relevant amino acids of TKs from different species, a standard numbering scheme was developed. Using this concept, H26, H261, and F434 were identified as the key residues which mediate stereoselectivity, where two main factors influenced the arrangement of ThDP‐bound donor and acceptor prior to carboligation: the relative orientation of the substrate side chains and the orientation of the acceptor carbonyl group towards the donor hydroxy group. This model provides a first framework to understand the structure‐function relationships of TKs with respect to their stereoselectivity