Frontiers in Biocatalysis: Profiling Function across Sequence Space

Benitez, A. Rodriguez; Narayan, Alison R. H.

doi:10.1021/acscentsci.9b01112

Cited by 15 publications

(10 citation statements)

References 8 publications

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“…Despite their utility and newfound ease-of-use, phylogenetic trees can still prove overwhelming when examining extensive protein families or groups of sequences. , Tools like sequence similarity networks (SSNs) have emerged to help overcome these challenges. SSNs have gained much attention since its introduction to the bioinformatics community in 2003 .…”

Section: Accessibility Of Biocatalysis To Synthetic Chemistsmentioning

confidence: 99%

“…SSNs have gained much attention since its introduction to the bioinformatics community in 2003 . It provides a way to visualize family wide relationships and patterns in large groups of protein sequences by ranking sequences in “clusters” based on their alignment scores. − These networks comprise groups of “nodes,” representing a protein sequence or group of sequences. These nodes are then connected by lines called “edges”, representing a threshold for sequence similarity that can be set by the user (Figure B).…”

Section: Accessibility Of Biocatalysis To Synthetic Chemistsmentioning

confidence: 99%

“…Our group has also demonstrated the applicability of SSNs to examine previously uncharacterized enzymes with useful chemical functions. , We sought to identify homologous flavin-dependent monooxygenase (FDMO) proteins to investigate the factors that control their site and facial selectivity in an oxidative dearomatization reaction and to identify enzymes suitable to enable a stereodivergent chemoenzymatic natural product synthesis campaign . Analysis of an SSN comprised of over 45 000 sequences from the flavin adenine dinucleotide (FAD) binding domain protein family (pfam01494) identified several FDMOs that are highly similar to those our group had investigated previously .…”

Section: Accessibility Of Biocatalysis To Synthetic Chemistsmentioning

confidence: 99%

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State-of-the-Art Biocatalysis

et al. 2021

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The use of enzyme-mediated reactions has transcended ancient food production to the laboratory synthesis of complex molecules. This evolution has been accelerated by developments in sequencing and DNA synthesis technology, bioinformatic and protein engineering tools, and the increasingly interdisciplinary nature of scientific research. Biocatalysis has become an indispensable tool applied in academic and industrial spheres, enabling synthetic strategies that leverage the exquisite selectivity of enzymes to access target molecules. In this Outlook, we outline the technological advances that have led to the field’s current state. Integration of biocatalysis into mainstream synthetic chemistry hinges on increased access to well-characterized enzymes and the permeation of biocatalysis into retrosynthetic logic. Ultimately, we anticipate that biocatalysis is poised to enable the synthesis of increasingly complex molecules at new levels of efficiency and throughput.

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Section: Accessibility Of Biocatalysis To Synthetic Chemistsmentioning

confidence: 99%

Section: Accessibility Of Biocatalysis To Synthetic Chemistsmentioning

confidence: 99%

Section: Accessibility Of Biocatalysis To Synthetic Chemistsmentioning

confidence: 99%

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State-of-the-Art Biocatalysis

et al. 2021

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“…The goal of the presented work was to access unexplored members of the recently identified natural AmDH family, and their abundance in the biosphere by an unprecedented metagenomics screen which includes eukaryotic members. This approach aims to rapidly enrich the sequence space and known properties of AmDHs for wider green chemical applications . After identification and selection of candidates among the three metagenomics databases IGC, OM‐RGC and MATOUv1, eighteen potential AmDHs homologs were successfully cloned and overexpressed in Escherichia coli ( E. coli ).…”

Section: Introductionmentioning

confidence: 99%

“…This approach aims to rapidly enrich the sequence space and known properties of AmDHs for wider green chemical applications. [19] After identification and selection of candidates among the three metagenomics databases IGC, OM-RGC and MATOUv1, eighteen potential AmDHs homologs were successfully cloned and overexpressed in Escherichia coli (E. coli). Their activity and sequence similarity were compared to the template nat-AmDHs.…”

Section: Introductionmentioning

confidence: 99%

Metagenomic Mining for Amine Dehydrogenase Discovery

et al. 2020

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Amine dehydrogenases (AmDHs) catalyze the enzymatic reduction of ketones to amines, serving as a suitable biocatalytic route for amine synthesis. A limited number of experimentally validated native AmDHs (nat‐AmDHs) have been reported recently, expanding the sequences with this function to complement the small set of engineered enzymes. Since researchers can now probe into the vast diversity of enzymes within niche environments by a metagenomics approach, a tandem metagenomic and bioinformatic approach is a powerful tool to identify new members of limited enzyme families to access new features in an iterative fashion. The previously untapped biocatalytic reservoirs of the ocean environment and human microbiome were screened for potential AmDHs using a hidden Markov model. Among the hundreds of hits, a subset of 18 enzymes was selected for further characterization and were confirmed to display AmDH activity. Additional analysis on six enzymes confirmed altered cofactor specificities and variation in substrate scopes, catalytic efficiencies, and active site residues compared to the reference nat‐AmDHs previously described. Particularly, MATOUAmDH2 from an eukaryotic organism demonstrated specific activity of 11.07 and 0.88 U mg−1 toward isobutyraldehyde and 1,2‐cyclohexadione respectively. Their abundance among the screened environments was also described. The protein sequence diversity of validated AmDHs reached by this metagenomics mining strategy highlights the success of such an approach. Metagenomically mined proteins, including eukaryotic ones, stand to increase the reach of biocatalysis towards enviromentally benign processes.

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Versatile Biocatalytic C(sp³)−H Oxyfunctionalization for the Site‐ Selective and Stereodivergent Synthesis of α‐ and β‐Hydroxy Acids

Mao,

Zhang,

et al. 2023

Angewandte Chemie

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C(sp 3 )À H oxyfunctionalization, the insertion of an O-atom into C(sp 3 )À H bonds, streamlines the synthesis of complex molecules from easily accessible precursors and represents one of the most challenging tasks in organic chemistry with regard to site and stereoselectivity. Biocatalytic C(sp 3 )À H oxyfunctionalization has the potential to overcome limitations inherent to small-molecule-mediated approaches by delivering catalyst-controlled selectivity. Through enzyme repurposing and activity profiling of natural variants, we have developed a subfamily of α-ketoglutarate-dependent iron dioxygenases that catalyze the site-and stereodivergent oxyfunctionalization of secondary and tertiary C(sp 3 )À H bonds, providing concise synthetic routes towards four types of 92 α-and β-hydroxy acids with high efficiency and selectivity. This method provides a biocatalytic approach for the production of valuable but synthetically challenging chiral hydroxy acid building blocks.

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Frontiers in Biocatalysis: Profiling Function across Sequence Space

Abstract: High-throughput screening accelerates identification of biocatalysts for selective halogenation.

Cited by 15 publications

References 8 publications

State-of-the-Art Biocatalysis

State-of-the-Art Biocatalysis

Metagenomic Mining for Amine Dehydrogenase Discovery

Versatile Biocatalytic C(sp³)−H Oxyfunctionalization for the Site‐ Selective and Stereodivergent Synthesis of α‐ and β‐Hydroxy Acids

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Frontiers in Biocatalysis: Profiling Function across Sequence Space

Abstract: High-throughput screening accelerates identification of biocatalysts for selective halogenation.

Cited by 15 publications

References 8 publications

State-of-the-Art Biocatalysis

State-of-the-Art Biocatalysis

Metagenomic Mining for Amine Dehydrogenase Discovery

Versatile Biocatalytic C(sp3)−H Oxyfunctionalization for the Site‐ Selective and Stereodivergent Synthesis of α‐ and β‐Hydroxy Acids

Contact Info

Product

Resources

About

Versatile Biocatalytic C(sp³)−H Oxyfunctionalization for the Site‐ Selective and Stereodivergent Synthesis of α‐ and β‐Hydroxy Acids