Integrating continuous hypermutation with high-throughput screening for optimization of cis,cis-muconic acid production in yeast

SummaryDirected evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection, and amplification. While powerful, systematic searches through large sequence-spaces is a labor-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generates enzyme variants using the recently developed orthogonal replication system, OrthoRep, and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a ratelimiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers >13-fold compared to reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study, is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.

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Directed Evolution of P450 Fatty Acid Decarboxylases via High-Throughput Screening Towards Improved Catalytic Activity

10.26434/chemrxiv.9791162 ◽

2019 ◽

Author(s):

Huifang Xu ◽

Weinan Liang ◽

Linlin Ning ◽

Yuanyuan Jiang ◽

Wenxia Yang ◽

...

Keyword(s):

Catalytic Activity ◽

Fatty Acid ◽

Directed Evolution ◽

High Throughput ◽

High Throughput Screening ◽

Colorimetric Detection ◽

Screening Method ◽

Random Mutagenesis ◽

Direct Production ◽

Consumption Activity

P450 fatty acid decarboxylases (FADCs) have recently been attracting considerable attention owing to their one-step direct production of industrially important 1-alkenes from biologically abundant feedstock free fatty acids under mild conditions. However, attempts to improve the catalytic activity of FADCs have met with little success. Protein engineering has been limited to selected residues and small mutant libraries due to lack of an effective high-throughput screening (HTS) method. Here, we devise a catalase-deficient Escherichia coli host strain and report an HTS approach based on colorimetric detection of H2O2-consumption activity of FADCs. Directed evolution enabled by this method has led to effective identification for the first time of improved FADC variants for medium-chain 1-alkene production from both DNA shuffling and random mutagenesis libraries. Advantageously, this screening method can be extended to other enzymes that stoichiometrically utilize H2O2 as co-substrate.

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A High-Throughput Screening System Based on Fluorescence-Activated Cell Sorting for the Directed Evolution of Chitinase A

International Journal of Molecular Sciences ◽

10.3390/ijms22063041 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3041

Author(s):

Gheorghita Menghiu ◽

Vasile Ostafe ◽

Radivoje Prodanović ◽

Rainer Fischer ◽

Raluca Ostafe

Keyword(s):

High Throughput ◽

Cell Sorting ◽

High Throughput Screening ◽

Screening Method ◽

Enzymatic Reaction ◽

Hydrolytic Enzymes ◽

Screening System ◽

Fluorescence Activated Cell Sorting ◽

Fungal Cell ◽

Chitinase A

Chitinases catalyze the degradation of chitin, a polymer of N-acetylglucosamine found in crustacean shells, insect cuticles, and fungal cell walls. There is great interest in the development of improved chitinases to address the environmental burden of chitin waste from the food processing industry as well as the potential medical, agricultural, and industrial uses of partially deacetylated chitin (chitosan) and its products (chito-oligosaccharides). The depolymerization of chitin can be achieved using chemical and physical treatments, but an enzymatic process would be more environmentally friendly and more sustainable. However, chitinases are slow-acting enzymes, limiting their biotechnological exploitation, although this can be overcome by molecular evolution approaches to enhance the features required for specific applications. The two main goals of this study were the development of a high-throughput screening system for chitinase activity (which could be extrapolated to other hydrolytic enzymes), and the deployment of this new method to select improved chitinase variants. We therefore cloned and expressed the Bacillus licheniformis DSM8785 chitinase A (chiA) gene in Escherichia coli BL21 (DE3) cells and generated a mutant library by error-prone PCR. We then developed a screening method based on fluorescence-activated cell sorting (FACS) using the model substrate 4-methylumbelliferyl β-d-N,N′,N″-triacetyl chitotrioside to identify improved enzymes. We prevented cross-talk between emulsion compartments caused by the hydrophobicity of 4-methylumbelliferone, the fluorescent product of the enzymatic reaction, by incorporating cyclodextrins into the aqueous phases. We also addressed the toxicity of long-term chiA expression in E. coli by limiting the reaction time. We identified 12 mutants containing 2–8 mutations per gene resulting in up to twofold higher activity than wild-type ChiA.

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Searching novel complex solid solution electrocatalysts in unconventional element combinations

Nano Research ◽

10.1007/s12274-021-3637-z ◽

2021 ◽

Author(s):

Olga A. Krysiak ◽

Simon Schumacher ◽

Alan Savan ◽

Wolfgang Schuhmann ◽

Alfred Ludwig ◽

...

Keyword(s):

High Throughput ◽

High Throughput Screening ◽

Active Sites ◽

Search Space ◽

Reduction Reaction ◽

Film Material ◽

X Ray ◽

High Entropy ◽

Catalyst Composition ◽

Scanning Transmission

AbstractDespite outstanding accomplishments in catalyst discovery, finding new, more efficient, environmentally neutral, and noble metal-free catalysts remains challenging and unsolved. Recently, complex solid solutions consisting of at least five different elements and often named as high-entropy alloys have emerged as a new class of electrocatalysts for a variety of reactions. The multicomponent combinations of elements facilitate tuning of active sites and catalytic properties. Predicting optimal catalyst composition remains difficult, making testing of a very high number of them indispensable. We present the high-throughput screening of the electrochemical activity of thin film material libraries prepared by combinatorial co-sputtering of metals which are commonly used in catalysis (Pd, Cu, Ni) combined with metals which are not commonly used in catalysis (Ti, Hf, Zr). Introducing unusual elements in the search space allows discovery of catalytic activity for hitherto unknown compositions. Material libraries with very similar composition spreads can show different activities vs. composition trends for different reactions. In order to address the inherent challenge of the huge combinatorial material space and the inability to predict active electrocatalyst compositions, we developed a high-throughput process based on co-sputtered material libraries, and performed high-throughput characterization using energy dispersive X-ray spectroscopy (EDS), scanning transmission electron microscopy (SEM), X-ray diffraction (XRD) and conductivity measurements followed by electrochemical screening by means of a scanning droplet cell. The results show surprising material compositions with increased activity for the oxygen reduction reaction and the hydrogen evolution reaction. Such data are important input data for future data-driven materials prediction.

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