Genome Mining for New Enzyme Chemistry

ACS Catalysis, Journal Year: 2024, Volume and Issue: 14(7), P. 4536 - 4553

Published: March 12, 2024

A revolution in the field of biocatalysis has enabled scalable access to compounds high societal values using enzymes. The construction biocatalytic routes relies on reservoir available enzymatic transformations. review uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove enzyme chemistry awaits be uncovered. This Review highlights transformations discovered through various genome mining methods and showcases their potential future applications biocatalysis.

Language: Английский

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Aromatic side-chain crosslinking in RiPP biosynthesis

Nature Chemical Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 15, 2025

Language: Английский

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Genome mining for natural products made by multinuclear iron-dependent oxidation enzymes (MNIOs)

Methods in enzymology on CD-ROM/Methods in enzymology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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A widespread family of ribosomal peptide metallophores involved in bacterial adaptation to metal stress

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(49)

Published: Nov. 27, 2024

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a structurally diverse group of natural products that bacteria employ in their survival strategies. Herein, we characterized the structure, biosynthetic pathway, mode action RiPP family called bufferins. With thousands homologous gene clusters throughout bacterial phylogenetic tree, bufferins form by far largest RiPPs multinuclear nonheme iron-dependent oxidases (MNIO, DUF692 family). Using Caulobacter vibrioides as model, showed conserved Cys residues precursors transformed into 5-thiooxazoles, further expanding reaction range MNIO enzymes. This rare modification is installed conjunction with partner protein DUF2063 family. Bufferin examples found to feature an N-terminal Sec signal peptide allowing them be exported ubiquitous pathway. We reveal involved copper homeostasis, metal-binding propensity requires thiooxazole heterocycles. Bufferins enhance growth under stress complexing excess metal ions. Our study thus describes large metallophores unveils widespread but overlooked homeostasis mechanism bacteria.

Language: Английский

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A multi-iron enzyme installs copper-binding oxazolone/thioamide pairs on a nontypeable Haemophilus influenzae virulence factor

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(28)

Published: July 5, 2024

The multinuclear nonheme iron-dependent oxidases (MNIOs) are a rapidly growing family of enzymes involved in the biosynthesis ribosomally synthesized, posttranslationally modified peptide natural products (RiPPs). Recently, secreted virulence factor from nontypeable Haemophilus influenzae (NTHi) was found to be expressed an operon, which we designate hvf that also encodes MNIO. Here, show by Mössbauer spectroscopy MNIO HvfB contains triiron cofactor. We demonstrate works together with HvfC [a RiPP recognition element (RRE)-containing partner protein] perform six posttranslational modifications cysteine residues on precursor HvfA. Structural characterization tandem mass spectrometry and NMR shows these converted oxazolone thioamide pairs, similar those methanobactin. Like methanobactin, mature factor, name oxazolin, uses coordinate Cu(I) ions. Considering necessity oxazolin for host cell invasion NTHi, findings point key role copper during NTHi infection. Furthermore, its biosynthetic pathway represent potential therapeutic target NTHi.

Language: Английский

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Multinuclear non-heme iron dependent oxidative enzymes (MNIOs) involved in unusual peptide modifications

Current Opinion in Chemical Biology, Journal Year: 2024, Volume and Issue: 80, P. 102467 - 102467

Published: May 20, 2024

Multinuclear non-heme iron dependent oxidative enzymes (MNIOs), formerly known as domain of unknown function 692 (DUF692), are involved in the post-translational modification peptides during biosynthesis peptide-based natural products. These catalyze highly unusual and diverse chemical modifications. Several class-defining features this large family (>14 000 members) beginning to emerge. Structurally, characterized by a TIM-barrel fold set conserved residues for di- or tri-iron binding site. They use molecular oxygen modify peptide substrates, often four-electron oxidation taking place at cysteine residue. This review summarizes current understanding MNIOs. Four modifications discussed detail: oxazolone-thioamide formation, β-carbon excision, hydantoin-macrocycle 5-thiooxazole formation. Briefly two other reactions that do not take on Cys residues.

Language: Английский

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Decarboxylation in Natural Products Biosynthesis

JACS Au, Journal Year: 2024, Volume and Issue: 4(8), P. 2715 - 2745

Published: July 25, 2024

Decarboxylation reactions are frequently found in the biosynthesis of primary and secondary metabolites. Decarboxylase enzymes responsible for these transformations operate via diverse mechanisms act on a large variety substrates, making them appealing terms biotechnological applications. This Perspective focuses occurrence decarboxylation natural product provides perspective their applications biocatalysis fine chemicals pharmaceuticals.

Language: Английский

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Peptide Backbone Editing via Post-Translational O to C Acyl Shift

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 11, 2025

Despite tremendous efforts to engineer translational machinery, replacing the encoded peptide backbone with new-to-nature structures remains a significant challenge. C, H, O, and N are elements of life, yet ribosomes capable forming only C–N bonds as amides, C–O esters, C–S thioesters. There is no current strategy site-selectively form C–C ketones embedded in backbones ribosomal products. As an alternative direct bond formation, here we report that peptides containing dehydrolactic acid motif rapidly isomerize generate backbone-embedded α,γ-diketoamides via spontaneous formal O C acyl shift rearrangement. The can be introduced into ribosomally or solid-phase synthesis using α-hydroxyphenylselenocysteine followed by oxidation. Subsequent incubation at physiological pH produces α,γ-diketoamide diversified variety nucleophiles, including hydrazines hydroxylamines, pyrazoles oximes, respectively. All these groups remain directly within polypeptide backbone. This general for editing, predicated on intricate cascade rearrangements, provides first nonenzymatic example reaction take place products so-produced easily protein-like materials heterocycles. Application this editing should accelerate discovery genetically molecules whose properties more closely resemble those bioactive natural

Language: Английский

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Synthetic Biology in Natural Product Biosynthesis

Chemical Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Synthetic biology has played an important role in the renaissance of natural products research during post-genomics era. The development and integration new tools have transformed workflow product discovery engineering, generating multidisciplinary interest field. In this review, we summarize recent developments biosynthesis from three different aspects. First, advances bioinformatics, experimental, analytical to identify associated with predicted biosynthetic gene clusters (BGCs) will be covered. This followed by extensive review on heterologous expression bacterial, fungal plant organisms. native host-independent paradigm identification, pathway characterization, enzyme is where synthetic most prominent role. Lastly, strategies engineer pathways for structural diversification complexity generation discussed, including assembly-line megasynthase precursor-directed modification, combinatorial biosynthesis.

Language: Английский

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Multinuclear Non-Heme Iron-Dependent Oxidative Enzymes: Landscape of Their Substrates, Partner Proteins

Published: April 10, 2025

Proteins of the multinuclear non-heme iron-dependent oxidative (MNIO) enzyme superfamily catalyze various modification reactions on precursors ribosomally synthesized, post-translationally modified peptides (RiPPs). We recently identified two large families MNIO-modified RiPPs called bufferins, which enhance bacterial growth under copper stress by chelating excess metal ions. Here, we explored diversity potential MNIO substrates performing extensive _in silico_ studies. Analyses MNIO-coding biosynthetic gene clusters (BGCs) groups putative most are characterized specific Cys-containing motifs, throughout eubacterial phylogenetic tree. The harbor N-terminal Sec-dependent signal peptides, a rare feature among RiPPs. Some very long relative to those typical RiPPs, indicating that enzymes could modify both peptide and protein substrates. also distinct family integral membrane proteins with predicted extra-cytoplasmic domains mostly found in Actinomycetota, frequently but not systematically associated MNIOs. Most BGCs genes coding for DUF2063 domain-containing or structurally related proteins, serving as partners precursor modification. uncovered correlation between presence absence Sec types partner enzymes. This study depicts global landscape MNIO-dependent natural products unveiling genetically It reveals treasure trove new RiPP likely represent widespread strategy deal stress, other stresses, environments. IMPACT STATEMENT. belong an emerging oxidation synthesized (RiPP) precursors. largest involved homeostasis. In this work performed analyses explore major families. much larger than precursors, may proteins. defined subtypes enzymes’ dedicated Our unveiled functions beyond homeostasis, response stresses. will be basis investigations into undoubtedly lead discovery modifications functions.

Language: Английский

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