Structural and enzymatic characterization of acetolactate decarboxylase from Bacillus subtilis

Genomic analysis reveals genes that encode the synthesis of volatile compounds by a Bacillus velezensis-based biofungicide used in the treatment of grapes to control Aspergillus carbonarius

Fungal control strategies based on the use of Bacillus have emerged in agriculture as eco-friendly alternatives to replace/reduce the use of synthetic pesticides. Bacillus sp. P1 was reported as a new promising strain for control of Aspergillus carbonarius, a known producer of ochratoxin A, categorized as possible human carcinogen with high nephrotoxic potential. Grape quality can be influenced by vineyard management practices, including the use of fungal control agents. The aim of this study was to evaluate, for the first time, the quality parameters of Chardonnay grapes exposed to an antifungal Bacillus-based strategy for control of A. carbonarius, supporting findings by genomic investigations. Furthermore, genomic tools were used to confirm that the strain P1 belongs to the non-pathogenic species Bacillus velezensis and also to certify its biosafety. The genome of B. velezensis P1 harbors genes that are putatively involved in the production of volatiles and hydrolytic enzymes, which are responsible for releasing the free form of aroma compounds. In addition to promote biocontrol of phytopathogenic fungi and ochratoxins, the treatment with B. velezensis P1 did not change the texture (hardness and firmness), color and pH of the grapes. Heat map and hierarchical clustering analysis (HCA) of volatiles evaluated by GC/MS revealed that Bacillus-treated grapes showed higher levels of compounds with a pleasant odor descriptions such as 3-hydroxy-2-butanone, 2,3-butanediol, 3-methyl-1-butanol, 3,4-dihydro-β-ionone, β-ionone, dihydroactinidiolide, linalool oxide, and β-terpineol. The results of this study indicate that B. velezensis P1 presents desirable properties to be used as a biocontrol agent.

Structural and enzymatic characterization of Bacillus subtilis R,R-2,3-butanediol dehydrogenase

2,3-butanediol dehydrogenase (BDH, EC 1.1.1.76) also known as acetoin reductase (AR, EC 1.1.1.4) is the key enzyme converting acetoin (AC) into 2,3-butanediol (BD) and undertaking the irreversible conversion of diacetyl to acetoin in various microorganisms. The existence of three BDHs (R,R-, meso-, and S,S-BDH) product different BD isomers. Catalyzing mechanisms of meso- and S,S-BDH have been understood with the assistance of their X-ray crystal structures. However, the lack of structural data for R,R-BDH restricts the integral understanding of the catalytic mechanism of BDHs. In this study, we successfully crystallized and solved the X-ray crystal structure of Bacillus subtilis R,R-BDH. A zinc ion was found locating in the catalytic center and coordinated by Cys37, His70 and Glu152, helping to stabilize the chiral substrates observed in the predicted molecular docking model. The interaction patterns of different chiral substrates in the molecular docking model explained the react priority measured by the enzyme activity assay of R,R-BDH. Site-directed mutation experiments determined that the amino acids Cys37, Thr244, Ile268 and Lys340 are important in the catalytically active center. The structural information of R,R-BDH presented in this study accomplished the understanding of BDHs catalytic mechanism and more importantly provides useful guidance for the directional engineering of R,R-BDH to obtain high-purity monochiral BD and AC.

Production of the Food Enzyme Acetolactate Decarboxylase (ALDC) from Bacillus subtilis ICA 56 Using Agro-Industrial Residues as Feedstock

During the beer brewing process, some compounds are formed in the primary fermentation step and may affect the final quality of beer. These compounds, called off flavors, such as diacetyl, are produced during fermentation and are related to a buttery taste. The use of acetolactate decarboxylase (ALDC) in the traditional beer brewing process may significantly increase productivity since it allows for a faster decrease in the adverse flavor caused by diacetyl. However, production costs directly impact its application. For this reason, we analyzed the effect of different cultivation media on ALDC production by Bacillus subtilis ICA 56 and process economics. Different carbon and nitrogen sources, including agro-industrial residues, were evaluated. The best result was obtained using sugarcane molasses and corn steep solids (CSS), allowing a 74% reduction in ALDC production cost and an enzyme activity of 4.43 ± 0.12 U·mL−1. The enzymatic extract was then characterized, showing an optimum temperature at 40 °C and stability at different pH levels, being able to maintain more than 80% of its catalytic capacity between pH values of 3.6 and 7.0, with higher enzymatic activity at pH 6.0 (50 mM MES Buffer), reaching an ALDC activity of 5.30 ± 0.06 U·mL−1.

Advances in biological production of acetoin: a comprehensive overview

Acetoin, a high-value-added bio-based platform chemical, is widely used in foods, cosmetics, agriculture, and the chemical industry. It is an important precursor for the synthesis of: 2,3-butanediol, liquid hydrocarbon fuels and heterocyclic compounds. Since the fossil resources are becoming increasingly scarce, biological production of acetoin has received increasing attention as an alternative to chemical synthesis. Although there are excellent reviews on the: application, catabolism and fermentative production of acetoin, little attention has been paid to acetoin production via: electrode-assisted fermentation, whole-cell biocatalysis, and in vitro/cell-free biocatalysis. In this review, acetoin biosynthesis pathways and relevant key enzymes are firstly reviewed. In addition, various strategies for biological acetoin production are summarized including: cell-free biocatalysis, whole-cell biocatalysis, microbial fermentation, and electrode-assisted fermentation. The advantages and disadvantages of the different approaches are discussed and weighed, illustrating the increasing progress toward economical, green and efficient production of acetoin. Additionally, recent advances in acetoin extraction and recovery in downstream processing are also briefly reviewed. Moreover, the current issues and future prospects of diverse strategies for biological acetoin production are discussed, with the hope of realizing the promises of industrial acetoin biomanufacturing in the near future.

One-pot efficient biosynthesis of (3R)-acetoin from pyruvate by a two-enzyme cascade

Opening the possibility of sustainable industrial (3R)-acetoin biomanufacturing in vitro.

Biosynthesis of Diverse Antimicrobial and Antiproliferative Acyloins in Anaerobic Bacteria

Metabolic profiling and genome mining revealed that anaerobic bacteria have the potential to produce acyloin natural products. In addition to sattazolin A and B, three new sattazolin congeners and a novel acyloin named clostrocyloin were isolated from three strains of Clostridium beijerinckii, a bacterium used for industrial solvent production. Bioactivity profiling showed that the sattazolin derivatives possess antimicrobial activities against mycobacteria and pseudomonads with only low cytotoxicity. Clostrocyloin was found to be mainly active against fungi. The thiamine diphosphate (ThDP)-dependent sattazolin-producing synthase was identified in silico and characterized both in vivo and in in vitro enzyme assays. A related acyloin synthase from the clostrocyloin producer was shown to be responsible for the production of the acyloin core of clostrocyloin. The biotransformation experiments provided first insights into the substrate scope of the clostrocyloin synthase and revealed biosynthetic intermediates.

Structural characterization of an acetolactate decarboxylase from Klebsiella pneumoniae

Acetolactate decarboxylase (ALDC) is a well-characterized anabolic enzyme involved with 3-hydroxy butanone (acetoin), an important physiological metabolite excreted by microbes. Although the enzyme is widely present in microorganisms, few atomic structures and functions of ALDC have been reported to date. Here we report the crystal structure of ALDC from Klebsiella pneumoniae KP (KpALDC). KpALDC crystallizes in space group P3₁21 with one monomer per asymmetric unit. Analytical ultracentrifugation data shows that KpALDC forms a stable dimer but can exist as a tetramer in solution. A Zn²⁺ ion is coordinated by three strictly-conserved histidines (His198, His200 and His211) and a conserved glutamate (Glu69), but the C-terminal tail that forms part of the active site in ALDC enzymes is disordered. A complex structure with ethane-1,2-diol shows a unusual mode of binding, whereby the ligand does not coordinate the Zn²⁺ ion. MicroScale Thermophoresis analysis shows that KpALDC binds Zn²⁺ ions, but no binding of Mg²⁺, Ca²⁺ and Mn²⁺ ions was detected.

Studies on structure-function relationships of acetolactate decarboxylase from Enterobacter cloacae

Acetoin is an important bio-based platform chemical with wide applications. Among all bacterial strains, Enterobacter cloacae is a well-known acetoin producer via α-acetolactate decarboxylase (ALDC), which converts α-acetolactate into acetoin and is identified as the key enzyme in the biosynthetic pathway of acetoin. In this work, the enzyme properties of Enterobacter cloacae ALDC (E.c.-ALDC) were characterized, revealing a K_m value of 12.19 mM and a k_cat value of 0.96 s⁻¹. Meanwhile, the optimum pH of E.c.-ALDC was 6.5, and the activity of E.c.-ALDC was activated by Mn²⁺, Ba²⁺, Mg²⁺, Zn²⁺ and Ca²⁺, while Cu²⁺ and Fe²⁺ significantly inhibited ALDC activity. More importantly, we solved and reported the first crystal structure of E.c.-ALDC at 2.4 Å resolution. The active centre consists of a zinc ion coordinated by highly conserved histidines (199, 201 and 212) and glutamates (70 and 259). However, the conserved Arg150 in E.c.-ALDC orients away from the zinc ion in the active centre of the molecule, losing contact with the zinc ion. Molecular docking of the two enantiomers of α-acetolactate, (R)-acetolactate and (S)-acetolactate allows us to further investigate the interaction networks of E.c.-ALDC with the unique conformation of Arg150. In the models, no direct contacts are observed between Arg150 and the substrates, which is unlikely to maintain the stabilization function of Arg150 in the catalytic reaction. The structure of E.c.-ALDC provides valuable information about its function, allowing a deeper understanding of the catalytic mechanism of ALDCs.

Arg150 in E.c.-ALDC exhibited a unique tilted conformation implying the lower activities of E.c.-ALDC comparing to other bacterial ALDCs. Sequence conservation of E.c.-ALDC is represented by ribbons and lines (conserved, magenta to variable, cyan).