Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus

A comparative study of two aldehyde dehydrogenases from Sphingobium sp.: the substrate spectrum and catalytic mechanism

Biocatalytic oxidation is one of the most important and indispensable organic reactions for the development of green and sustainable biomanufacturing processes. NAD(P)+-dependent aldehyde dehydrogenase (ALDH) catalyzes the oxidation of aldehydes to carboxylic acids. Here, two ALDHs, SpALDH1 and SpALDH2, were identified from Sphingobium sp. SYK-6. They belong to different ALDH families and share only 32.30% amino acid identity. Interestingly, SpALDH1 and SpALDH2 exhibit significantly different enzymatic properties and substrate profiles. SpALDH2 has better thermostability than SpALDH1. SpALDH1 is a metalloenzyme and is activated by potassium ions, while SpALDH2 is not metallic-dependent. Compared with SpALDH1, SpALDH2 has a relatively broad substrate spectrum toward aromatic aldehydes. Based on homology modeling and molecular docking analysis, mechanisms underlying the substrate specificity of ALDHs were elucidated. For both ALDHs, hydrophobicity of substrate binding pockets is important for the catalytic properties, especially substrate specificity. Notably, optimization of the flexible loop 444-457 reforms a hydrogen bond between pyridine substrates and SpALDH1, contributing to the high catalytic activity. Finally, a coupling reaction catalyzed by ALDHs and NOX was constructed for efficient production of aromatic carboxylic acids.

Structural Insight into the Catalytic Mechanisms of an L-Sorbosone Dehydrogenase

L-Sorbosone dehydrogenase (SNDH) is a key enzyme involved in the biosynthesis of 2-keto-L-gulonic acid , which is a direct precursor for the industrial scale production of vitamin C. Elucidating the structure and the catalytic mechanism is essential for improving SNDH performance. By solving the crystal structures of SNDH from Gluconobacter oxydans WSH-004, a reversible disulfide bond between Cys295 and the catalytic Cys296 residues is discovered. It allowed SNDH to switch between oxidation and reduction states, resulting in opening or closing the substrate pocket. Moreover, the Cys296 is found to affect the NADP+ binding pose with SNDH. Combining the in vitro biochemical and site-directed mutagenesis studies, the redox-based dynamic regulation and the catalytic mechanisms of SNDH are proposed. Moreover, the mutants with enhanced activity are obtained by extending substrate channels. This study not only elucidates the physiological control mechanism of the dehydrogenase, but also provides a theoretical basis for engineering similar enzymes.

Heterocyclic Diaryliodonium-Based Inhibitors of Carbapenem-Resistant Acinetobacter baumannii

Finding new therapeutic strategies against Gram-negative pathogens such as Acinetobacter baumannii is challenging. Starting from diphenyleneiodonium (dPI) salts, which are moderate Gram-positive antibacterials, we synthesized a focused heterocyclic library and found a potent inhibitor of patient-derived multidrug-resistant Acinetobacter baumannii strains that significantly reduced bacterial burden in an animal model of infection caused by carbapenem-resistant Acinetobacter baumannii (CRAB), listed as a priority 1 critical pathogen by the World Health Organization. Next, using advanced chemoproteomics platforms and activity-based protein profiling (ABPP), we identified and biochemically validated betaine aldehyde dehydrogenase (BetB), an enzyme that is involved in the metabolism and maintenance of osmolarity, as a potential target for this compound. Together, using a new class of heterocyclic iodonium salts, a potent CRAB inhibitor was identified, and our study lays the foundation for the identification of new druggable targets against this critical pathogen. IMPORTANCE Discovery of novel antibiotics targeting multidrug-resistant (MDR) pathogens such as A. baumannii is an urgent, unmet medical need. Our work has highlighted the potential of this unique scaffold to annihilate MDR A. baumannii alone and in combination with amikacin both in vitro and in animals, that too without inducing resistance. Further in depth analysis identified central metabolism to be a putative target. Taken together, these experiments lay down the foundation for effective management of infections caused due to highly MDR pathogens.

Antarctic aldehyde dehydrogenase from Flavobacterium PL002 as a potent catalyst for acetaldehyde determination in wine

Latest solutions in biotechnologies and biosensing targeted cold-active extremozymes. Analysis of acetaldehyde as a relevant quality indicator of wine is one example of application that could benefit from using low-temperatures operating catalysts. In search of novel aldehyde dehydrogenases (ALDH) with high stability and activity at low temperatures, the recombinant S2-ALDH from the Antarctic Flavobacterium PL002 was obtained by cloning and expression in Escherichia coli BL21(DE3). Structural and phylogenetic analyses revealed strong protein similarities (95%) with psychrophilic homologs, conserved active residues and structural elements conferring enzyme flexibility. Arrhenius plot revealed a conformational shift at 30 °C, favoring catalysis (low activation energy) at lower temperatures. In addition to a broad substrate specificity with preference for acetaldehyde (Km = 1.88 mM), this enzyme showed a high tolerance for ethanol (15%) and several salts and chelators (an advantage for wine analysis), while being sensitive to mercury (I₅₀ = 1.21 µM). The neutral optimal pH (7.5) and the stability up to 40 °C and after lyophilization represent major assets for developing S2-ALDH-based sensors. An enzymatic electrochemical assay was developed for acetaldehyde detection in wines with proven accuracy in comparison with the reference spectrophotometric method, thus evidencing the potential of S2-ALDH as effective biocatalyst for industry and biosensing.

Highly Stable, Cold-Active Aldehyde Dehydrogenase from the Marine Antarctic Flavobacterium sp. PL002

Stable aldehyde dehydrogenases (ALDH) from extremophilic microorganisms constitute efficient catalysts in biotechnologies. In search of active ALDHs at low temperatures and of these enzymes from cold-adapted microorganisms, we cloned and characterized a novel recombinant ALDH from the psychrotrophic Flavobacterium PL002 isolated from Antarctic seawater. The recombinant enzyme (F-ALDH) from this cold-adapted strain was obtained by cloning and expressing of the PL002 aldH gene (1506 bp) in Escherichia coli BL21(DE3). Phylogeny and structural analyses showed a high amino acid sequence identity (89%) with Flavobacterium frigidimaris ALDH and conservation of all active site residues. The purified F-ALDH by affinity chromatography was homotetrameric, preserving 80% activity at 4 °C for 18 days. F-ALDH used both NAD+ and NADP+ and a broad range of aliphatic and aromatic substrates, showing cofactor-dependent compensatory KM and kcat values and the highest catalytic efficiency (0.50 µM−1 s−1) for isovaleraldehyde. The enzyme was active in the 4–60 °C-temperature interval, with an optimal pH of 9.5, and a preference for NAD+-dependent reactions. Arrhenius plots of both NAD(P)+-dependent reactions indicated conformational changes occurring at 30 °C, with four(five)-fold lower activation energy at high temperatures. The high thermal stability and substrate-specific catalytic efficiency of this novel cold-active ALDH favoring aliphatic catalysis provided a promising catalyst for biotechnological and biosensing applications.

Spectroscopic analysis of coenzyme binding to betaine aldehyde dehydrogenase dependent on potassium

Glycine betaine is the main osmolyte synthesized and accumulated in mammalian renal cells. Glycine betaine synthesis is catalyzed by the enzyme betaine aldehyde dehydrogenase (BADH) using NAD⁺ as the coenzyme. Previous studies have shown that porcine kidney betaine aldehyde dehydrogenase (pkBADH) binds NAD⁺ with different affinities at each active site and that the binding is K⁺ dependent. The objective of this work was to analyze the changes in the pkBADH secondary and tertiary structure resulting from variable concentrations of NAD⁺ and the role played by K⁺ . Intrinsic fluorescence studies were carried out at fixed-variable concentrations of K⁺ and titrating the enzyme with varying concentrations of NAD⁺ . Fluorescence analysis showed a shift of the maximum emission towards red as the concentration of K⁺ was increased. Changes in the exposure of tryptophan located near the NAD⁺ binding site were found when the enzyme was titrated with NAD⁺ in the presence of potassium. Fluorescence data analysis showed that the K⁺ presence promoted static quenching that facilitated the pkBADH-NAD⁺ complex formation. DC data analysis showed that binding of K⁺ to the enzyme caused changes in the α-helix content of 4% and 12% in the presence of 25 mM and 100 mM K⁺ , respectively. The presence of K⁺ during NAD⁺ binding to pkBADH increased the thermal stability of the complex. These results indicated that K⁺ facilitated the pkBADH-NAD⁺ complex formation and suggested that K⁺ caused small changes in secondary and tertiary structures that could influence the active site conformation.

Role of potassium levels in pkBADH heterogeneity of NAD+ binding site

Betaine aldehyde dehydrogenase (BADH) catalyzes the oxidation of betaine aldehyde to glycine betaine using NAD⁺ as a coenzyme. Studies in porcine kidney BADH (pkBADH) suggested that the enzyme exhibits heterogeneity of active sites and undergoes potassium-induced conformational changes. This study aimed to analyze if potassium concentration plays a role in the heterogeneity of pkBADH active sites through changes in NAD⁺ affinity constants, in its secondary structure content and stability. The enzyme was titrated with NAD⁺ 1 mM at fixed-variable KCl concentration, and the interaction measured by Isothermal Titration Calorimetry (ITC) and Circular Dichroism (CD). ITC data showed that K⁺ increased the first active site affinity in a manner dependent on its concentration; K_D values to the first site were 14.4, 13.1, and 10.4 μM, at 25, 50, and 75 mM KCl. ΔG values showed that the coenzyme binding is a spontaneous reaction without changes between active sites or depending on KCl concentration. ΔH and TΔS_b values showed that NAD⁺ binding to the active site is an endothermic process and is carried out at the expense of changes in entropy. α-Helix content increased as KCl increased, enzyme (T_m)_app values were 2.6 °C and 3.3 °C higher at 20 mM and 200 mM K⁺. PkBADH molecular model showed three different interaction K⁺ sites. Results suggested K⁺ can interact with pkBADH and cause changes in the secondary structure, it provokes changes in the enzyme affinity by the coenzyme, and in the thermostability.

3,6-Anhydro-L-Galactose Dehydrogenase VvAHGD is a Member of a New Aldehyde Dehydrogenase Family and Catalyzes by a Novel Mechanism with Conformational Switch of Two Catalytic Residues Cysteine 282 and Glutamate 248

3,6-anhydro-α-L-galactose (L-AHG) is one of the main monosaccharide constituents of red macroalgae. In the recently discovered bacterial L-AHG catabolic pathway, L-AHG is first oxidized by a NAD(P)⁺-dependent dehydrogenase (AHGD), which is a key step of this pathway. However, the catalytic mechanism(s) of AHGDs is still unclear. Here, we identified and characterized an AHGD from marine bacterium Vibrio variabilis JCM 19239 (VvAHGD). The NADP⁺-dependent VvAHGD could efficiently oxidize L-AHG. Phylogenetic analysis suggested that VvAHGD and its homologs represent a new aldehyde dehydrogenase (ALDH) family with different substrate preferences from reported ALDH families, named the L-AHGDH family. To explain the catalytic mechanism of VvAHGD, we solved the structures of VvAHGD in the apo form and complex with NADP⁺ and modeled its structure with L-AHG. Based on structural, mutational, and biochemical analyses, the cofactor channel and the substrate channel of VvAHGD are identified, and the key residues involved in the binding of NADP⁺ and L-AHG and the catalysis are revealed. VvAHGD performs catalysis by controlling the consecutive connection and interruption of the cofactor channel and the substrate channel via the conformational changes of its two catalytic residues Cys282 and Glu248. Comparative analyses of structures and enzyme kinetics revealed that differences in the substrate channels (in shape, size, electrostatic surface, and residue composition) lead to the different substrate preferences of VvAHGD from other ALDHs. This study on VvAHGD sheds light on the diversified catalytic mechanisms and evolution of NAD(P)⁺-dependent ALDHs.

An expansin-like protein expands forage cell walls and synergistically increases hydrolysis, digestibility and fermentation of livestock feeds by fibrolytic enzymes

Bacterial expansin-like proteins have synergistically increased cellulose hydrolysis by cellulolytic enzymes during the initial stages of biofuel production, but they have not been tested on livestock feeds. The objectives of this study were to: isolate and express an expansin-like protein (BsEXLX1), to verify its disruptive activity (expansion) on cotton fibers by immunodetection (Experiment 1), and to determine the effect of dose, pH and temperature for BsEXLX1 and cellulase to synergistically hydrolyze filter paper (FP) and carboxymethyl cellulose (CMC) under laboratory (Experiment 2) and simulated ruminal (Experiment 3) conditions. In addition, we determined the ability of BsEXLX1 to synergistically increase hydrolysis of corn and bermudagrass silages by an exogenous fibrolytic enzyme (EFE) (Experiment 4) and how different doses of BsEXLX1 and EFE affect the gas production (GP), in vitro digestibility and fermentation of a diet for dairy cows (Experiment 5). In Experiment 1, immunofluorescence-based examination of cotton microfiber treated without or with recombinant expansin-like protein expressed from Bacillus subtilis (BsEXLX1) increased the surface area by > 100% compared to the untreated control. In Experiment 2, adding BsEXLX1 (100 μg/g FP) to cellulase (0.0148 FPU) increased release of reducing sugars compared to cellulase alone by more than 40% (P < 0.01) at optimal pH (4.0) and temperature (50°C) after 24 h. In Experiment 3 and 4, adding BsEXLX1 to cellulase or EFE, synergistically increased release of reducing sugars from FP, corn and bermudagrass silages under simulated ruminal conditions (pH 6.0, 39°C). In Experiment 5, increasing the concentration of BsEXLX1 linearly increased (P < 0.01) GP from fermentation of a diet for dairy cows by up to 17.8%. Synergistic effects between BsEXLX1 and EFE increased in vitro NDF digestibility of the diet by 23.3% compared to the control. In vitro digestibility of hemicellulose and butyrate concentration were linearly increased by BsEXLX1 compared to the control. This study demonstrated that BsEXLX1 can improve the efficacy of cellulase and EFE at hydrolyzing pure substrates and dairy cow feeds, respectively.

Studying NAD(P)H cofactor-binding to alcohol dehydrogenases through global analysis of circular dichroism spectra

The initial step in reactions catalyzed by NAD(P)H-dependent alcohol dehydrogenases (ADHs) is the binding of the cofactor to the active site. To study this process, we measured NAD(P)H concentration-dependent circular dichroism (CD) in the presence of purified enzymes (ADH from horse liver, HLADH; ADH-A from Rhodococcus ruber; YGL157w from Saccharomyces cerevisiae) or enzyme-containing whole cell extract (ADH from Lactobacillus brevis, LbADH). We determined the proportions of binding and non-binding NAD(P)H and the associated dissociation constants (Kd) from matrix least-squares global fitting of law of mass action-derived model. Furthermore, the fitting allowed the back calculation of CD spectra corresponding to the cofactor in its bound conformation. With increasing pH and/or increasing ionic strength, we detected an increase in Kd for the NADH·HLADH complex with the shape of the bound cofactor conformation spectrum remaining unaffected. While the bound cofactor spectrum for the ADH-A·NADH complex was similar to that for HLADH, the corresponding spectra obtained for the NADPH-dependent enzymes YGL157w and LbADH exhibited opposite signs of the most prominent band. In comparison to CD spectra calculated on cofactor geometries from the crystal structures at the sTD-DFT level, we found that the sign of the bound cofactor spectrum correlates with the orientation of the nicotinamide ring of the cofactor in the active site. These results demonstrate the usefulness of the global analysis of cofactor titration CD spectra to study the role of cofactor binding and its geometry in ADH catalysis.

Structural insights into betaine aldehyde dehydrogenase (BADH2) from Oryza sativa explored by modeling and simulations

Betaine aldehyde dehydrogenase 2 (BADH2) plays a key role in the accumulation of 2-acetyl-1-pyrroline (2AP), a fragrant compound in rice (Oryza sativa). BADH2 catalyses the oxidation of aminoaldehydes to carboxylic acids. An inactive BADH2 is known to promote fragrance in rice. The 3D structure and atomic level protein-ligand interactions are currently unknown. Here, the 3D dimeric structure of BADH2 was modeled using homology modeling. Furthermore, two 0.5 µs simulations were performed to explore the nature of BADH2 dimer structurally and dynamically. Each monomer comprises of 3 domains (substrate-binding, NAD⁺-binding, and oligomerization domains). The NAD⁺-binding domain is the most mobile. A scissor-like motion was observed between the monomers. Inside the binding pocket, N162 and E260 are tethered by strong hydrogen bonds to residues in close proximity. In contrast, the catalytic C294 is very mobile and interacts occasionally with N162. The flexibility of the nucleophilic C294 could facilitate the attack of free carbonyl on an aldehyde substrate. Key inter-subunit salt bridges contributing to dimerization were also identified. E487, D491, E492, K498, and K502 were found to form strong salt bridges with charged residues on the adjacent monomer. Specifically, the nearly permanent R430-E487 hydrogen bond (>90%) highlights its key role in dimer association. Structural and dynamic insights of BADH2 obtained here could play a role in the improvement of rice fragrance, which could lead to an enhancement in rice quality and market price.

Redox regulation by reversible protein S-thiolation in Gram-positive bacteria

Low molecular weight (LMW) thiols play an important role as thiol-cofactors for many enzymes and are crucial to maintain the reduced state of the cytoplasm. Most Gram-negative bacteria utilize glutathione (GSH) as major LMW thiol. However, in Gram-positive Actinomycetes and Firmicutes alternative LMW thiols, such as mycothiol (MSH) and bacillithiol (BSH) play related roles as GSH surrogates, respectively. Under conditions of hypochlorite stress, MSH and BSH are known to form mixed disulfides with protein thiols, termed as S-mycothiolation or S-bacillithiolation that function in thiol-protection and redox regulation. Protein S-thiolations are widespread redox-modifications discovered in different Gram-positive bacteria, such as Bacillus and Staphylococcus species, Mycobacterium smegmatis, Corynebacterium glutamicum and Corynebacterium diphtheriae. S-thiolated proteins are mainly involved in cellular metabolism, protein translation, redox regulation and antioxidant functions with some conserved targets across bacteria. The reduction of protein S-mycothiolations and S-bacillithiolations requires glutaredoxin-related mycoredoxin and bacilliredoxin pathways to regenerate protein functions.

In this review, we present an overview of the functions of mycothiol and bacillithiol and their physiological roles in protein S-bacillithiolations and S-mycothiolations in Gram-positive bacteria. Significant progress has been made to characterize the role of protein S-thiolation in redox-regulation and thiol protection of main metabolic and antioxidant enzymes. However, the physiological roles of the pathways for regeneration are only beginning to emerge as well as their interactions with other cellular redox systems. Future studies should be also directed to explore the roles of protein S-thiolations and their redox pathways in pathogenic bacteria under infection conditions to discover new drug targets and treatment options against multiple antibiotic resistant bacteria.

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Bacillithiol and mycothiol are major LMW thiols in many Gram-positive bacteria.

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HOCl leads to widespread protein S-mycothiolation and S-bacillithiolation which function in thiol-protection and redox regulation.

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Redox-sensitive metabolic and antioxidant enzymes are main targets for S-mycothiolation or S-bacillithiolation.

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Mycoredoxin and bacilliredoxin pathways mediate reduction of S-thiolations.

The aldehyde dehydrogenase AldA contributes to the hypochlorite defense and is redox-controlled by protein S-bacillithiolation in Staphylococcus aureus

Staphylococcus aureus produces bacillithiol (BSH) as major low molecular weight (LMW) thiol which functions in thiol-protection and redox-regulation by protein S-bacillithiolation under hypochlorite stress. The aldehyde dehydrogenase AldA was identified as S-bacillithiolated at its active site Cys279 under NaOCl stress in S. aureus. Here, we have studied the expression, function, redox regulation and structural changes of AldA of S. aureus. Transcription of aldA was previously shown to be regulated by the alternative sigma factor SigmaB. Northern blot analysis revealed SigmaB-independent induction of aldA transcription under formaldehyde, methylglyoxal, diamide and NaOCl stress. Deletion of aldA resulted in a NaOCl-sensitive phenotype in survival assays, suggesting an important role of AldA in the NaOCl stress defense. Purified AldA showed broad substrate specificity for oxidation of several aldehydes, including formaldehyde, methylglyoxal, acetaldehyde and glycol aldehyde. Thus, AldA could be involved in detoxification of aldehyde substrates that are elevated under NaOCl stress. Kinetic activity assays revealed that AldA is irreversibly inhibited under H2O2 treatment in vitro due to overoxidation of Cys279 in the absence of BSH. Pre-treatment of AldA with BSH prior to H2O2 exposure resulted in reversible AldA inactivation due to S-bacillithiolation as revealed by activity assays and BSH-specific Western blot analysis. Using molecular docking and molecular dynamic simulation, we further show that BSH occupies two different positions in the AldA active site depending on the AldA activation state. In conclusion, we show here that AldA is an important target for S-bacillithiolation in S. aureus that is up-regulated under NaOCl stress and functions in protection under hypochlorite stress.

Cloning and molecular characterization of the betaine aldehyde dehydrogenase involved in the biosynthesis of glycine betaine in white shrimp (Litopenaeus vannamei)

The enzyme betaine aldehyde dehydrogenase (BADH) catalyzes the irreversible oxidation of betaine aldehyde to glycine betaine (GB), a very efficient osmolyte accumulated during osmotic stress. In this study, we determined the nucleotide sequence of the cDNA for the BADH from the white shrimp Litopenaeus vannamei (LvBADH). The cDNA was 1882 bp long, with a complete open reading frame of 1524 bp, encoding 507 amino acids with a predicted molecular mass of 54.15 kDa and a pI of 5.4. The predicted LvBADH amino acid sequence shares a high degree of identity with marine invertebrate BADHs. Catalytic residues (C-298, E-264 and N-167) and the decapeptide VTLELGGKSP involved in nucleotide binding and highly conserved in BADHs were identified in the amino acid sequence. Phylogenetic analyses classified LvBADH in a clade that includes ALDH9 sequences from marine invertebrates. Molecular modeling of LvBADH revealed that the protein has amino acid residues and sequence motifs essential for the function of the ALDH9 family of enzymes. LvBADH modeling showed three potential monovalent cation binding sites, one site is located in an intra-subunit cavity; other in an inter-subunit cavity and a third in a central-cavity of the protein. The results show that LvBADH shares a high degree of identity with BADH sequences from marine invertebrates and enzymes that belong to the ALDH9 family. Our findings suggest that the LvBADH has molecular mechanisms of regulation similar to those of other BADHs belonging to the ALDH9 family, and that BADH might be playing a role in the osmoregulation capacity of L. vannamei.