NADH/NADPH bi-cofactor-utilizing and thermoactive ketol-acid reductoisomerase from Sulfolobus acidocaldarius

Characterization of a class II ketol-acid reductoisomerase from Mycobacterium tuberculosis

Mycobacterium tuberculosis ketol-acid reductoisomerases have been widely studied due to their metabolic importance towards development of drug-resistant bacteria treatment. We here report the biochemical characterization of a new KARI (MtKARI-II) from a Mycobacterium tuberculosis variant with a similar kinetic profile to class I KARIs. Phylogenetic analysis suggested that MtKARI-II is clustered into a class II KARI superfamily.

Biochemical characterization of an unusual class II KARI (MtKARI-II) from a Mycobacterium tuberculosis variant.

Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules

The functions of biological macromolecules are often associated with conformational malleability of the structures. This phenomenon of chemically identical molecules with different structures is coined structural polymorphism. Conventionally, structural polymorphism is observed directly by structural determination at the density map level from X-ray crystal diffraction. Although crystallography approach can report the conformation of a macromolecule with the position of each atom accurately defined in it, the exploration of structural polymorphism and interpreting biological function in terms of crystal structures is largely constrained by the crystal packing. An alternative approach to studying the macromolecule of interest in solution is thus desirable. With the advancement of instrumentation and computational methods for image analysis and reconstruction, cryo-electron microscope (cryo-EM) has been transformed to be able to produce “in solution” structures of macromolecules routinely with resolutions comparable to crystallography but without the need of crystals. Since the sample preparation of single-particle cryo-EM allows for all forms co-existing in solution to be simultaneously frozen, the image data contain rich information as to structural polymorphism. The ensemble of structure information can be subsequently disentangled through three-dimensional (3D) classification analyses. In this review, we highlight important examples of protein structural polymorphism in relation to allostery, subunit cooperativity and function plasticity recently revealed by cryo-EM analyses, and review recent developments in 3D classification algorithms including neural network/deep learning approaches that would enable cryo-EM analyese in this regard. Finally, we brief the frontier of cryo-EM structure determination of RNA molecules where resolving the structural polymorphism is at dawn.

Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen

Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg2+-site, the Mg2+-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs.

The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites

Background

Salting is a traditional procedure for producing pickled vegetables. Salting can be used as a pretreatment, for safe lactic acid fermentation and for salt stock preparation. This study aimed to provide valuable knowledge to improve pickle production by investigating the dynamics of microbiota and metabolites during the pretreatment and salt stock preparation processes, which have previously been overlooked. The differences in these process conditions would be expected to change the microbiota and consequently influence the content of metabolites in pickles.

Methods

Samples, collected from eight commercial pickle manufacturers in Japan, consisted of the initial raw materials, pickled vegetables and used brine. The microbiota were analyzed by 16S rRNA sequencing and the metabolites quantified by liquid chromatograph-mass spectrometry. Statistical analyses helped to identify any significant differences between samples from the initial raw materials, pretreatment process and salt stock preparation process groups.

Results

Under pretreatment conditions, aerobic and facultative anaerobic bacteria were predominant, including Vibrio, a potentially undesirable genus for pickle production. Under salt stock preparation conditions, the presence of halophilic bacteria, Halanaerobium, suggested their involvement in the increase in pyruvate derivatives such as branched-chain amino acids (BCAA). PICRUSt analysis indicated that the enhanced production of BCAA in salt stock was caused not by quantitative but by qualitative differences in the biosynthetic pathway of BCAA in the microbiota.

Conclusion

The differences in the microbiota between pretreatment and previously studied lactic acid fermentation processes emphasized the importance of anaerobic conditions and low pH under moderate salinity conditions for assuring safe pickle production. The results from the salt stock preparation process suggested that the Halanaerobium present may provide a key enzyme in the BCAA biosynthetic pathway which prefers NADH as a coenzyme. This feature can enhance BCAA production under anaerobic conditions where NADH is in excess. The effects shown in this study will be important for adjusting pickling conditions by changing the abundance of bacteria to improve the quality of pickled vegetables.

The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications

l-Valine, l-isoleucine, and l-leucine are three key proteinogenic amino acids, and they are also the essential amino acids required for mammalian growth, possessing important and to some extent, special physiological and biological functions. Because of the branched structures in their carbon chains, they are also named as branched-chain amino acids (BCAAs). This review will highlight the advance in studies of the enzymes involved in the biosynthetic pathway of BCAAs, concentrating on their chemical mechanisms and applications in screening herbicides and antibacterial agents. The uses of some of these enzymes in lab scale organic synthesis are also discussed.

Efficient production of an ezetimibe intermediate using carbonyl reductase coupled with glucose dehydrogenase

Ezetimibe is a top-selling hypolipidemic drug for the treatment of cardiovascular diseases. Biosynthesis of (4S)-3-[(5S)-5-(4-fluorophenyl)-5-hydroxypentanoyl]-4-phenyl-1,3-oxazolidin-2-one ((S)-ET-5) using carbonyl reductase has shown advantages including high catalytic efficiency, excellent stereoselectivity, mild reaction conditions, and environmental friendness, and was considered as the key step for ezetimibe production. The regeneration efficiency of the cofactor, nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) is one of the main restricted factor. Recombinant Escherichia coli strain (smCR125) coexpressing carbonyl reductase (CR125) and glucose dehydrogenase were successfully constructed and applied for the production of (S)-ET-5 for the first time. Without extra addition of the coenzyme NADPH, the yield of 99.8% and the enantiomeric excess (e.e.) of 99.9% were achieved under ET-4 concentration of 200 g/L. Using a substrate fed-batch strategy, under the optimal conditions, the substrate ET-4 concentration was increased to 250 g/L with the yield of 98.9% and the e.e. of 99.9% after 12 hr reaction. The space-time yield of 494.5 g L^-1 d^-1 and the space-time yield per gram biocatalyst of 24.7 g L^-1 d^-1 g^-1 DCW were achieved, which were higher than ever reported for the biosynthesis of the ezetimibe intermediate.

2-Methoxy-1,4-naphthoquinone Induces Metabolic Shifts in Penicillium Digitatum Revealed by High-Dimensional Biological Data

Penicillium digitatum is the primary pathogen causing the green mold of citrus. The need for the development of higher effective and lower toxic natural antifungal agents is urgent, owing to the lack of antifungal agents that can successfully combat P. digitatum. Herein, the effects and mechanisms of 2-methoxy-1,4-naphthoquinone (MNQ) as a potential inhibitor of P. digitatumwere studied. First, MNQ showed a significant anti-P. digitatum effect with a minimum inhibitory concentration value of 5.0 μg/mL. Then, transcriptome, proteome, and metabolome profiling were performed on the MNQ-treated P. digitatum. A total of 910 genes, 297 proteins, and 174 metabolites changed significantly. The omics analysis indicated that it could be seen that MNQ mainly inhibits the growth of P. digitatum by affecting the synthesis of branched-chain amino acids and cell walls. These findings will be a great contribution to the further understanding of the possible molecular action of MNQ.

Production of tert-butyl (3R,5S)-6-chloro-3,5-dihydroxyhexanoate using carbonyl reductase coupled with glucose dehydrogenase with high space-time yield

tert-Butyl (3R,5S)-6-chloro-3,5-dihydroxyhexanoate ((3R,5S)-CDHH) is an important chiral intermediate for the synthesis of rosuvastatin. The biotechnological production of (3R,5S)-CDHH is catalyzed from tert-butyl (S)-6-chloro-5-hydroxy-3-oxohexanoate ((S)-CHOH) by a carbonyl reductase, and this synthetic pathway is becoming a primary route for (3R,5S)-CDHH production due to its high enantioselectivity, mild reaction conditions, low cost, process safety, and environmental friendship. However, the requirement of the pyridine nucleotide cofactors, reduced nicotinamide adenine dinucleotide (NADH) or reduced nicotinamide adenine dinucleotide phosphate (NADPH) limits its economic flexibility. In the present study, a recombinant Escherichia coli strain harboring carbonyl reductase R9M and glucose dehydrogenase (GDH) was constructed with high carbonyl reduction activity and cofactor regeneration efficiency. The recombinant E. coli cells were applied for the efficient production of (3R,5S)-CDHH with a substrate conversion of 98.8%, a yield of 95.6% and an enantiomeric excess (e.e.) of >99.0% under 350 g/L of (S)-CHOH after 12 hr reaction. A substrate fed-batch strategy was further employed to increase the substrate concentration to 400 g/L resulting in an enhanced product yield to 98.5% after 12 hr reaction in a 1 L bioreactor. Meanwhile, the space-time yield was 1,182.3 g L^-1 day^-1 , which was the highest value ever reported by a coupled system of carbonyl reductase and glucose dehydrogenase.

Crystal Structure and Biochemical Characterization of Ketol-Acid Reductoisomerase from Corynebacterium glutamicum

l-Valine belongs to the branched-chain amino acids (BCAAs) and is an essential amino acid that is crucial for all living organisms. l-Valine is industrially produced by the nonpathogenic bacterium Corynebacterium glutamicum and is synthesized by the BCAA biosynthetic pathway. Ketol-acid reductoisomerase (KARI) is the second enzyme in the BCAA pathway and catalyzes the conversion of (S)-2-acetolactate into (R)-2,3-dihydroxy-isovalerate, or the conversion of (S)-2-aceto-2-hydroxybutyrate into (R)-2,3-dihydroxy-3-methylvalerate. To elucidate the enzymatic properties of KARI from C. glutamicum (CgKARI), we successfully produced CgKARI protein and determined its crystal structure in complex with NADP⁺ and two Mg²⁺ ions. Based on the complex structure, docking simulations, and site-directed mutagenesis experiments, we revealed that CgKARI belongs to Class I KARI and identified key residues involved in stabilization of the substrate, metal ions, and cofactor. Furthermore, we confirmed the difference in the binding of metal ions that depended on the conformational change.