Biosynthesis articles within Nature Communications

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  • Article
    | Open Access

    The chemical diversity of peptides from ribosomal origin is a growing field of research. Here, the authors report the discovery, genomic and biosynthetic investigations of kintamdin, a ribosomally synthesized and post-translationally modified peptides featuring a beta-enamino acid and a bis-thioether macrocyclic motif.

    • Shan Wang
    • , Sixing Lin
    •  & Hai Deng

  • Article
    | Open Access

    Epoxide ring opening reactions are important in both biological processes and synthetic applications. Here, the authors show that flavin cofactors can catalyze reductive and oxidative epoxide ring opening reactions and propose the underlying mechanisms.

    • Bidhan Chandra De
    • , Wenjun Zhang
    •  & Changsheng Zhang

  • Article
    | Open Access

    The genomes of filamentous fungi, such as Aspergillus, include many biosynthetic gene clusters of unknown function. Here, the authors show that copper starvation induces expression of an enzyme that generates a valine-derived isocyanide participating in two different pathways, for biosynthesis of acylated sugar alcohols and modified ergot alkaloids.

    • Tae Hyung Won
    • , Jin Woo Bok
    •  & Frank C. Schroeder

  • Article
    | Open Access

    Macrocyclization is an important process in bioactive natural product synthesis. Here, the authors report on the study of a macrocyclic ring constructing enzyme in the biosynthesis of alchivemycin A and using gene deletion, biochemical assays and isotope labelling show the enzyme catalyses tandem dehydration and Michael-type addition.

    • Hong Jie Zhu
    • , Bo Zhang
    •  & Hui Ming Ge

  • Article
    | Open Access

    Haloacid dehalogenase-like phosphatases are widespread across all domains of life and play a crucial role in the regulation of levels of sugar phosphate metabolites in cells. The authors report on the structure-guided engineering of phosphatases for dedicated substrate specificity for the conversion of sucrose and starch into fructose and mannose.

    • Chaoyu Tian
    • , Jiangang Yang
    •  & Yanhe Ma

  • Article
    | Open Access

    Reprogramming biosynthetic assembly-lines is a topic of interest for antibiotics. Here, the authors explore the evolutionary biosynthesis of anti-tubercular wollamides, show gene duplication and neo-functionalisation results in bifurcation allowing for testing of new structures with the ability to recover old structures by gene loss.

    • Thomas J. Booth
    • , Kenan A. J. Bozhüyük
    •  & Barrie Wilkinson

  • Article
    | Open Access

    The market demand for acarbose, a drug used for treatment of patients affected by type-2 diabetes, has increased. In this article, the authors report the acarbose complete biosynthetic pathway, clarifying previously unknown steps and identifying a pseudoglycosyltransferase enzyme, AcbS, a homologue of AcbI that catalyzes the formation of a non-glycosidic C-N bond.

    • Takeshi Tsunoda
    • , Arash Samadi
    •  & Taifo Mahmud

  • Article
    | Open Access

    Whole-cell biocatalysis is of interest for the efficient production of a range of products but cell stability can be an issue. Here, the authors turn recombinant enzyme-producing E. coli into artificial spores to add protection from UV radiation, heating, and organic solvents by coating the cells with polydopamine to create robust cell factories.

    • Zhiyong Sun
    • , René Hübner
    •  & Changzhu Wu

  • Article
    | Open Access

    Bio-inspired materials are an intense area of study as researchers try to adapt biomaterials for other applications. Here, the authors report on the processing of protein materials derived from the byssal thread of scallops to create high-extensibility materials with self-recovery under wet conditions.

    • Xiaokang Zhang
    • , Mengkui Cui
    •  & Weizhi Liu

  • Article
    | Open Access

    Pericyclase enzymes are an expanding family of enzymes. Here, the authors identify the norbornene synthase SdnG, a pericyclase for the intramolecular Diels-Alder reaction between a cyclopentadiene and an olefinic dienophile to form the sordaricin norbornene structure, and reconstitute the sordaricin biosynthesis.

    • Zuodong Sun
    • , Cooper S. Jamieson
    •  & Yi Tang

  • Article
    | Open Access

    Benzaldehyde is a simple aromatic aldehyde that attracts pollinators, has antifungal properties and contributes to flavor in many plants. Here the authors show that benzaldehyde is synthesized in petunia via the benzoic acid β-oxidative pathway by a peroxisomal heterodimeric enzyme consisting of α and β subunits.

    • Xing-Qi Huang
    • , Renqiuguo Li
    •  & Natalia Dudareva

  • Article
    | Open Access

    The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments. Here the authors report on the production of the ergot (fungus)-derived therapeutic precursor, D-lysergic acid (DLA), in baker’s yeast.

    • Garrett Wong
    • , Li Rong Lim
    •  & Wen Shan Yew

  • Article
    | Open Access

    Cytochalasans are a large family of fungal polyketide-nonribosomal peptide hybrid natural products that exhibit important pharmaceutical activities, but the mechanism of conversion of the monocytochalasans to the polycyclic, fused analogues is unclear. Here the authors reconstitute the core backbone of the cytochalasin family and describe an oxidase that catalyzes an unusual double-bond isomerization reaction.

    • Jin-Mei Zhang
    • , Xuan Liu
    •  & Yi Zou

  • Article
    | Open Access

    Non-heme iron and α-ketoglutarate-dependent (Fe/αKG) oxygenases have attracted attention for their application as biocatalysts due to their flexibility and high efficiency. Here, the authors show the biochemical and structural characterizations of the versatile Fe/αKG oxygenase SptF, involved in the biosynthesis of fungal meroterpenoid emervaridones.

    • Hui Tao
    • , Takahiro Mori
    •  & Ikuro Abe

  • Article
    | Open Access

    Antibiotic-producing organisms need to co-evolve self-protection mechanisms to avoid any damage to themselves caused by the antibiotic pharmacophore (the reactive part of the compound). In this study, the authors report a self-defense strategy in naphthyridinomycin (NDM)-producing Streptomyces lusitanus, that comprises reductive inactivation of the hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and HomW.

    • Wan-Hong Wen
    • , Yue Zhang
    •  & Gong-Li Tang

  • Article
    | Open Access

    Engineering biosynthetic assembly lines is a powerful path to new natural products but is challenging with current methods. Here the authors use CRISPR-Cas9 to exchange subdomains within NRPS to alter substrate selectivity.

    • Wei Li Thong
    • , Yingxin Zhang
    •  & Jason Micklefield

  • Article
    | Open Access

    Borosins are ribosomally encoded and posttranslationally modified peptide (RiPP) natural products featuring amide-backbone α-N-methylation. Here, the authors report the discovery and characterization of type IV borosin ‘split’ pathways encoding distinct, separate α-N-methyltransferases and precursor peptide substrates.

    • Fredarla S. Miller
    • , Kathryn K. Crone
    •  & Michael F. Freeman

  • Article
    | Open Access

    Glycomics can uncover important molecular changes but measured glycans are highly interconnected and incompatible with common statistical methods, introducing pitfalls during analysis. Here, the authors develop an approach to identify glycan dependencies across samples to facilitate comparative glycomics.

    • Bokan Bao
    • , Benjamin P. Kellman
    •  & Nathan E. Lewis

  • Article
    | Open Access

    The only known animal polyketide-nonribosomal peptides, the nemamides, are biosynthesized by two megasynthetases in the canal-associated neurons (CANs) of C. elegans. Here, the authors map the biosynthetic roles of individual megasynthetase domains and identify additional enzymes in the CANs required for nemamide biosynthesis.

    • Likui Feng
    • , Matthew T. Gordon
    •  & Rebecca A. Butcher

  • Article
    | Open Access

    Aurantinins are polyketides with unusual connectivities and broad antibacterial activity. Here the authors show the biosynthesis of aurantinins, which proceeds via an on-line methyl esterification at the terminus that enables the iterative chain elongations prior to condensation and cyclization.

    • Pengwei Li
    • , Meng Chen
    •  & Yihua Chen

  • Review Article
    | Open Access

    Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.

    • Kirstin Scherlach
    •  & Christian Hertweck

  • Article
    | Open Access

    Substrate channeling can improve biosynthetic efficiency and has been implicated in the reactions of fusicoccadiene synthase. Here, the authors analyze this bifunctional enzyme complex by cryoEM, cross-linking MS and integrative modeling, providing structural insights into how substrate channeling is achieved.

    • Jacque L. Faylo
    • , Trevor van Eeuwen
    •  & David W. Christianson

  • Article
    | Open Access

    Caerulomycins and collismycins are two types of 2,2’-bipyridine natural products that are biosynthesized via a hybrid NRPS-PKS pathway, but the details of their biosynthesis were unknown. Here, the authors elucidate their biosynthetic pathways, validate the generality of 2,2’-bipyridine formation, and clarify the process for 2,2’-bipyridine furcation.

    • Bo Pang
    • , Rijing Liao
    •  & Wen Liu

  • Article
    | Open Access

    Non-ribosomal peptide synthetases (NRPSs) are multi-modular enzymes assembling complex natural products. Here, the structures of a Thermobifida fusca NRPS condensation domain bound to the substrate-bearing peptidyl carrier protein (PCP) domain provide insight into the mechanisms of substrate selectivity and engagement within the catalytic pocket.

    • Thierry Izoré
    • , Y. T. Candace Ho
    •  & Max J. Cryle

  • Article
    | Open Access

    Streptoseomycin is a potent antibiotic that contains a pentacyclic 5/14/10/6/6 ring system. Here, the authors report the enzymatic and non-enzymatic steps of the downstream modification of streptoseomycin biosynthesis and show a [6 + 4]-cycloaddition adduct as an unexpected biosynthetic intermediate.

    • Kai Biao Wang
    • , Wen Wang
    •  & Hui Ming Ge

  • Article
    | Open Access

    Rubromycin family of natural products belongs to aromatic polyketides with diverse bioactivities, but details of their biosynthesis are limited. Here, the authors report the complete in vitro reconstitution of enzymatic formation of the spiroketal moiety of rubromycin polyketides, driven by flavin-dependent enzymes, and characterize reaction intermediates.

    • Britta Frensch
    • , Thorsten Lechtenberg
    •  & Robin Teufel

  • Article
    | Open Access

    Trans-acyltransferase polyketide synthases are multimodular enzymes that synthesise diverse polyketides. Here, the authors present an algorithm for the global study of their diversity, showing exchange of conserved consecutive modules as a driver of diversification, and guiding the discovery of polyketides.

    • Eric J. N. Helfrich
    • , Reiko Ueoka
    •  & Marnix H. Medema

  • Article
    | Open Access

    Microbial symbionts can help their hosts metabolise diverse diets. A study on herbivorous turtle ants identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution.

    • Christophe Duplais
    • , Vincent Sarou-Kanian
    •  & Corrie S. Moreau

  • Article
    | Open Access

    Azoles are five-membered heterocycles found in peptidic natural products and synthetic peptiodomimetics. Here the authors demonstrate a posttranslational chemical modification method for in vitro ribosomal synthesis of peptides with exotic azole groups at specific positions.

    • Haruka Tsutsumi
    • , Tomohiro Kuroda
    •  & Hiroaki Suga

  • Article
    | Open Access

    Nonribosomal lipopeptides contain an acyl chain important for bioactivity, but its incorporation into the peptidyl backbone, mediated by the starter condensation (Cs) domain of nonribosomal peptide synthases, is not fully understood. Here, the authors show that acyl chains of different lengths can be obtained by engineering Cs domains and identify residues that determine the selectivity for acyl chains.

    • Lin Zhong
    • , Xiaotong Diao
    •  & Xiaoying Bian

  • Article
    | Open Access

    FR900359 (FR) is a Gq protein inhibitor depsipeptide isolated from an uncultivable plant endosymbiont and synthesized by non-ribosomal peptide synthetases. Here, the authors discover a cultivable bacterial FR producer and show that FrsA thioesterase domain catalyses intermolecular transesterification of the FR side chain to the depsipeptide core during biosynthesis, improving Gq inhibition properties.

    • Cornelia Hermes
    • , René Richarz
    •  & Max Crüsemann

  • Article
    | Open Access

    Short-chain primary amines (SCPAs) are industrially important compounds that are commonly produced under harsh synthetic conditions. Here, the authors report a combination of retrobiosynthesis and precursor selection step for design of biosynthetic pathways leading to production of SCPAs, using valine decarboxylase-expressing Escherichia coli strains.

    • Dong In Kim
    • , Tong Un Chae
    •  & Sang Yup Lee

  • Article
    | Open Access

    A fundamental function of living systems is regenerating essential components. Here the authors design an artificial cell using a minimal transcription-translation system in microfluidic reactors for sustained regeneration of multiple essential proteins.

    • Barbora Lavickova
    • , Nadanai Laohakunakorn
    •  & Sebastian J. Maerkl

  • Article
    | Open Access

    Heme biosynthesis depends on iron-sulfur (Fe-S) cluster biogenesis but the molecular connection between these pathways is not fully understood. Here, the authors show that the heme biosynthesis enzyme ALAD contains an Fe-S cluster, disruption of which reduces ALAD activity and heme production in human cells.

    • Gang Liu
    • , Debangsu Sil
    •  & Tracey Ann Rouault

  • Article
    | Open Access

    Bacterial heterodimeric tryptophan-containing diketopiperazines (HTDKPs) are bioactive natural products that are difficult to access chemically. Here, the authors identify a family of three related HTDKP-forming cytochrome P450s and engineer key amino acid residues to produce distinct diketopiperazines frameworks.

    • Chenghai Sun
    • , Zhenyao Luo
    •  & Xudong Qu

  • Article
    | Open Access

    Large-scale sequencing efforts have uncovered a large number of secondary metabolic pathways, but the chemicals they synthesise remain unknown. Here the authors present PRISM 4, which predicts the chemical structures encoded by microbial genome sequences, including all classes of bacterial antibiotics in clinical use.

    • Michael A. Skinnider
    • , Chad W. Johnston
    •  & Nathan A. Magarvey

  • Article
    | Open Access

    Biosynthesis of biotin precursor, pimelate moiety, is elucidated in Escherichia coli and Bacillus subtilis, but not understood in alphaproteobacteria. Here, the authors show that BioZ, a 3-ketoacyl-ACP synthase, catalayses pimeloyl-thioester synthesis in alphaproteobacteria using malonyl-ACP and glutaryl-CoA that is derived from lysine degradation.

    • Yuanyuan Hu
    •  & John E. Cronan

  • Article
    | Open Access

    The extreme oxygen sensitive character of hydrogenases is a longstanding issue for hydrogen production in bacteria. Here, the authors build carboxysome shells in E. coli and incorporate catalytically active hydrogenases and functional partners within the empty shell for the production of hydrogen.

    • Tianpei Li
    • , Qiuyao Jiang
    •  & Lu-Ning Liu

  • Article
    | Open Access

    Aliphatic α,ω-dicarboxylic acids (DCAs) are widely used chemicals that are synthesised by multistage chemical oxidations. Here, the authors report an artificially designed biocatalytic cascade for the oxidation of cycloalkanes or cycloalkanols to DCAs in the form of microbial consortia, composed of three Escherichia coli cell modules.

    • Fei Wang
    • , Jing Zhao
    •  & Aitao Li

  • Article
    | Open Access

    Oxepinamides are a class of fungal oxepins with biological activities. Here, the authors elucidate the biosynthetic pathway of oxepinamide F from Aspergillus ustus and show that it involves enyme-catalysed oxepin ring formation, hydroxylation-induced double bond migration, epimerization and methylation.

    • Liujuan Zheng
    • , Haowen Wang
    •  & Shu-Ming Li

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