Data-Driven Protein Engineering for Improving Catalytic Activity and Selectivity.

Protein engineering is essential for altering the substrate scope, catalytic activity and selectivity of enzymes for applications in biocatalysis. However, traditional approaches, such as directed evolution and rational design, encounter the challenge in dealing with the experimental screening process of a large protein mutation space. Machine learning methods allow the approximation of protein fitness landscapes and the identification of catalytic patterns using limited experimental data, thus providing a new avenue to guide protein engineering campaigns. In this concept article, we review machine learning models that have been developed to assess enzyme-substrate-catalysis performance relationships aiming to improve enzymes through data-driven protein engineering. Furthermore, we prospect the future development of this field to provide additional strategies and tools for achieving desired activities and selectivities.

High-Throughput Quantitative Screening of Glucose-Stimulated Insulin Secretion and Insulin Content Using Automated MALDI-TOF Mass Spectrometry.

Type 2 diabetes (T2D) is a metabolic disorder characterized by loss of pancreatic ß-cell function, decreased insulin secretion and increased insulin resistance, that affects more than 537 million people worldwide. Although several treatments are proposed to patients suffering from T2D, long-term control of glycemia remains a challenge. Therefore, identifying new potential drugs and targets that positively affect ß-cell function and insulin secretion remains crucial. Here, we developed an automated approach to allow the identification of new compounds or genes potentially involved in ß-cell function in a 384-well plate format, using the murine ß-cell model Min6. By using MALDI-TOF mass spectrometry, we implemented a high-throughput screening (HTS) strategy based on the automation of a cellular assay allowing the detection of insulin secretion in response to glucose, i.e., the quantitative detection of insulin, in a miniaturized system. As a proof of concept, we screened siRNA targeting well-know ß-cell genes and 1600 chemical compounds and identified several molecules as potential regulators of insulin secretion and/or synthesis, demonstrating that our approach allows HTS of insulin secretion in vitro.

Strengthening the Connection between Science, Society and Environment to Develop Future French and European Bioeconomies: Cutting-Edge Research of VAALBIO Team at UCCS.

The development of the future French and European bioeconomies will involve developing new green chemical processes in which catalytic transformations are key. The VAALBIO team (valorization of alkanes and biomass) of the UCCS laboratory (Unité de Catalyse et Chimie du Solide) are working on various catalytic processes, either developing new catalysts and/or designing the whole catalytic processes. Our research is focused on both the fundamental and applied aspects of the processes. Through this review paper, we demonstrate the main topics developed by our team focusing mostly on oxygen- and hydrogen-related processes as well as on green hydrogen production and hybrid catalysis. The social impacts of the bioeconomy are also discussed applying the concept of the institutional compass.

Screening of Antimicrobial Activities and Lipopeptide Production of Endophytic Bacteria Isolated from Vetiver Roots.

The exploration of certain microbial resources such as beneficial endophytic microorganisms is considered a promising strategy for the discovery of new antimicrobial compounds for the pharmaceutical industries and agriculture. Thirty-one endophytic bacterial strains affiliated with Bacillus, Janthinobacterium, Yokenella, Enterobacter, Pseudomonas, Serratia, and Microbacterium were previously isolated from vetiver (Chrysopogon zizanioides (L.) Roberty) roots. These endophytes showed antifungal activity against Fusarium graminearum and could be a source of antimicrobial metabolites. In this study, in particular, using high-throughput screening, we analyzed their antagonistic activities and those of their cell-free culture supernatants against three species of Fusarium plant pathogens, a bacterial strain of Escherichia coli, and a yeast strain of Saccharomyces cerevisiae, as well as their capacity to produce lipopeptides. The results showed that the culture supernatants of four strains close to B. subtilis species exhibited antimicrobial activities against Fusarium species and E. coli. Using mass spectrometry analyses, we identified two groups of lipopeptides (surfactins and plipastatins) in their culture supernatants. Whole-genome sequencing confirmed that these bacteria possess NRPS gene clusters for surfactin and plipastatin. In vitro tests confirmed the inhibitory effect of plipastatin alone or in combination with surfactin against the three Fusarium species.

Combining analytical approaches for better lignocellulosic biomass degradation: a way of improving fungal enzymatic cocktails?

PURPOSE: In this study, a combinatory approach was undertaken to assay the efficiency of fungal enzymatic cocktails from different fermentation conditions to degrade different lignocellulosic biomasses with the aim of finely characterizing fungal enzymatic cocktails. METHODS: Enzymatic assays (AZO and pNP-linked substrates and ABTS) were used to assess the composition of the fungal enzymatic cocktails for cellulase, xylanase and laccase activities. Comparisons were made with a new range of chromogenic substrates based on complex biomass (CBS substrates). The saccharification efficiency of the cocktails was evaluated as a quantification of the sugar monomers released from the different biomasses after incubation with the enzymatic cocktails. RESULTS: The results obtained showed striking differences between the AZO and pNP-linked substrates and the CBS substrates for the same enzymatic cocktails. On AZO and pNP-linked substrates, different hydrolysis profiles were observed between the different fungi species with Aspergillus oryzae being the most efficient. However, the results on CBS substrates were more contrasted depending on the biomass tested. Altogether, the results highlighted that assessing laccase activities and taking into account the complexity of the biomass to degrade were key in order to provide the best enzymatic cocktails. CONCLUSION: The complementary experiments performed in this study showed that different approaches needed to be taken in order to accurately assess the ability of an enzymatic cocktail to be efficient when it comes to lignocellulosic biomass degradation. The saccharification assay proved to be essential to validate the data obtained from both simple and complex substrates.

Plasmon-Driven Electrochemical Methanol Oxidation on Gold Nanohole Electrodes.

Direct methanol oxidation is expected to play a central role in low-polluting future power sources. However, the sluggish and complex electro-oxidation of methanol is one of the limiting factors for any practical application. To solve this issue, the use of plasmonic is considered as a promising way to accelerate the methanol oxidation reaction. In this study, we report on a novel approach for achieving enhanced methanol oxidation currents. Perforated gold thin film anodes were decorated with Pt/Ru via electrochemical deposition and investigated for their ability for plasmon-enhanced electrocatalytic methanol oxidation in alkaline media. The novel methanol oxidation anode (AuNHs/PtRu), combining the strong light absorption properties of a gold nanoholes array-based electrode (AuNHs) with surface-anchored bimetallic Pt/Ru nanostructures, known for their high activity toward methanol oxidation, proved to be highly efficient in converting methanol via the hot holes generated in the plasmonic electrode. Without light illumination, AuNHs/PtRu displayed a maximal current density of 13.7 mA/cm2 at -0.11 V vs Ag/AgCl. Enhancement to 17.2 mA/cm2 was achieved under 980 nm laser light illumination at a power density of 2 W/cm2. The thermal effect was negligible in this system, underlining a dominant plasmon process. Fast generation and injection of charge carriers were also evidenced by the abrupt change in the current density upon laser irradiation. The good stability of the interface over several cycles makes this system interesting for methanol electro-oxidation.

Innovative microscale workflow from fungi cultures to Cell Wall-Degrading Enzyme screening.

This study aimed at developing a complete miniaturized high-throughput screening workflow for the evaluation of the Cell Wall-Degrading Enzyme (CWDE) activities produced by any fungal strain directly cultivated on raw feedstock in a submerged manner. In this study, wheat straw was selected as model substrate as it represents an important carbon source but yet poorly valorised to yield high added value products. Fungi were grown in a microbioreactor in a high-throughput (HT) way to replace the fastidious shaking flask cultivations. Both approaches were compared in order to validate our new methodology. The range of CWDE activities produced from the cultures was assayed using AZO-died and pNP-linked substrates in an SBS plate format using a Biomek FXp pipetting platform. As highlighted in this study, it was shown that the CWDE activities gathered from the microbioreactor cultivations were similar or higher to those obtained from shake flasks cultures, with a lower standard deviation on the measured values, making this new method much faster than the traditional one and suitable for HT CWDE production thanks to its pipetting platform compatibility. Also, the results showed that the enzymatic activities measured were the same when doing the assay manually or using the automated method.

Screening of Lipopeptide-Producing Strains of Bacillus sp. Using a New Automated and Sensitive Fluorescence Detection Method.

Lipopeptides, such as surfactins are important biosurfactants produced by Bacillus sp. that find applications in many areas (environment, medicine, and food industries). Giving their importance, the use of simple detection methods will facilitate screening and quantification. In the present work, the authors describe a completely automated workflow for the screening of lipopeptide-producing strains, including quantification. First, isolated colonies from environmental samples are automatically picked and inoculated in 96 wells growth plate. After overnight incubation, surfactin produced in the broth is quantified, using a new sensitive fluorescent method. The method uses fluorescein (FL), which is an anionic dye at neutral to alkaline pH and forms a stable complex with the cationic surfactant cetylpiridinium chloride (CPC), quenching fluorescence. Upon addition of surfactin or other lipopeptides, fluorescein is released from the CPC-FL complex and quantified. The robustness of this method is assessed by comparing the quantification results to those conventionally measured by RP-UPLC and the results of strain screening are confirmed by MALDI-ToF analysis. The authors report for the first time the successful application of this analytical method for high-throughput screening of novel lipopeptide-producing strains.

Continuous High-Throughput Colorimetric Assays for α-Transaminases.

Transaminases are efficient tools for the stereoselective conversion of prochiral ketones into valuable chiral amines. Notably, the diversity of naturally occurring α-transaminases offers access to a wide range of L- and D-α-amino acids. We describe here two continuous colorimetric assays for the quantification of transamination activities between a keto acid and a standard donor substrate (L- or D-Glutamic acid or cysteine sulfinic acid). These assays are helpful for kinetic studies as well as for high-throughput screening of enzyme collections.

Stereoselective synthesis of γ-hydroxy-α-amino acids through aldolase-transaminase recycling cascades.

Efficient bi-enzymatic cascades combining aldolases and α-transaminases were designed for the synthesis of γ-hydroxy-α-amino acids. These recycling cascades provide high stereoselectivity, atom economy, and an equilibrium shift of the transamination. l-syn or anti-4-hydroxyglutamic acid and d-anti-4,5-dihydroxynorvaline were thus prepared in 83-95% yield in one step from simple substrates.

High-throughput strategies for the discovery and engineering of enzymes for biocatalysis.

Innovations in novel enzyme discoveries impact upon a wide range of industries for which biocatalysis and biotransformations represent a great challenge, i.e., food industry, polymers and chemical industry. Key tools and technologies, such as bioinformatics tools to guide mutant library design, molecular biology tools to create mutants library, microfluidics/microplates, parallel miniscale bioreactors and mass spectrometry technologies to create high-throughput screening methods and experimental design tools for screening and optimization, allow to evolve the discovery, development and implementation of enzymes and whole cells in (bio)processes. These technological innovations are also accompanied by the development and implementation of clean and sustainable integrated processes to meet the growing needs of chemical, pharmaceutical, environmental and biorefinery industries. This review gives an overview of the benefits of high-throughput screening approach from the discovery and engineering of biocatalysts to cell culture for optimizing their production in integrated processes and their extraction/purification.

Continuous colorimetric screening assays for the detection of specific L- or D-α-amino acid transaminases in enzyme libraries.

In the course of a project devoted to the stereoselective synthesis of non-proteinogenic α-amino acids using α-transaminases (α-TA), we report the design and optimization of generic high-throughput continuous assays for the screening of α-TA libraries. These assays are based on the use of L- or D-cysteine sulfinic acid (CSA) as irreversible amino donor and subsequent sulfite titration by colorimetry. The assays' quality was assessed under screening conditions. Hit selection thresholds were accurately determined for every couple of substrates and a library of 232 putative transaminases expressed in Escherichia coli host cells was screened. The reported high throughput screening assays proved very sensitive allowing the detection with high confidence of activities as low as 10 µU (i.e., 0.01 nmol substrate converted per min). The assays were also evidenced to be stereochemically discriminant since L-CSA and D-CSA allowed the exclusive detection of L-TA and D-TA, respectively. These generic assays thus allow testing the stereoselective conversion of a wide range of α-keto acids into α-amino acids of interest. As a proof of principle, the use of 2-oxo-4-phenylbutyric acid as acceptor substrate led to the identification of 54 new α-TA offering an access to valuable L- or D-homophenylalanine.

Profiling substrate specificity of two series of phenethylamine analogs at monoamine oxidase A and B.

The membrane bound enzyme monoamine oxidase exist in two splice variants designated A and B (MAO-A and MAO-B) and are key players in the oxidative metabolism of monoamines in mammalians. Despite their importance and being a prevalent target for the development of inhibitors as drugs, no systematic study of substrate specificity has been reported. In this study we present a systematic study of the MAO-A and MAO-B substrate specificity profile by probing two series of phenethylamine analogs. Km and kcat values were determined for four N-alkyl analogs 2-5 and four aryl halide analogs 6-9 at MAO-A and MAO-B. A following in silico study disclosed a new adjacent compartment to the MAO-B substrate pocket defined by amino acids Tyr188, Tyr435, Tyr398, Thr399, Cys172 and Gly434. This new insight is important for the understanding of the substrate specificity of the MAO-B enzyme and will be relevant for future drug design within the field of monoamines.