Journal ArticleDOI
The confluence of big data and evolutionary genome mining for the discovery of natural products.
Marc G. Chevrette,Athina Gavrilidou,Shrikant Mantri,Nelly Selem-Mojica,Nadine Ziemert,Francisco Barona-Gómez +5 more
TLDR
This review covers literature between 2003-2021 and highlights examples where Big Data and evolutionary analyses have been combined to provide bioinformatic resources and tools for the discovery of novel natural products and their biosynthetic enzymes.About:
This article is published in Natural Product Reports.The article was published on 2021-11-17. It has received 21 citations till now.read more
Citations
More filters
A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis - eScholarship
Andrej Sali,Michael A. Fischbach,Marnix H. Medema,Peter Cimermancic,Eriko Takano,MA Fischbach +5 more
TL;DR: By performing a systematic computational analysis of BGC evolution, this work derives evidence for three findings that shed light on the ways in which, despite these constraints, nature successfully invents new molecules.
Journal ArticleDOI
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes
Athina Gavriilidou,Satria A. Kautsar,Nestor Zaburannyi,Daniel Krug,Rolf Müller,Marnix H. Medema,Nadine Ziemert +6 more
TL;DR: The authors analyzed ~170,000 bacterial genomes and ~47,000 metagenome assembled genomes using a modified BiG-SLiCE and the new clust-o-matic algorithm.
Journal ArticleDOI
Microbiome composition modulates secondary metabolism in a multispecies bacterial community
Marc G. Chevrette,Chris S. Thomas,Amanda Hurley,Natalia Rosario-Meléndez,Krishnan P. Sankaran,Yixing Tu,Austin W. Hall,S.B. Magesh,Jo Handelsman +8 more
TL;DR: Results from this model community show that bacterial BGC expression and chemical output depend on the identity and biosynthetic capacity of coculture partners, suggesting community composition and microbiome interactions may shape the regulation of secondary metabolism in nature.
Journal ArticleDOI
Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery
TL;DR: Genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data are discussed, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities.
Journal ArticleDOI
Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery
TL;DR: This work considers innovative approaches which have led to prioritization of strain targets and have mitigated rediscovery rates, and discusses integration of principles of comparative evolutionary studies and retrobiosynthetic predictions to better understand biosynthetic mechanistic details and link genome sequence to structure.
References
More filters
Journal ArticleDOI
Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae
Zhenhua Liu,Hernando G. Suarez Duran,Yosapol Harnvanichvech,Michael J. Stephenson,M. Eric Schranz,David R. Nelson,Marnix H. Medema,Anne Osbourn +7 more
TL;DR: The results indicate that plant genomes are remarkably plastic, and that dynamic GNs generate new biosynthetic pathways in different Brassicaceae lineages by shuffling the genes encoding a core palette of triterpene‐diversifying enzymes, presumably in response to strong environmental selection pressure.
Journal ArticleDOI
Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale
Christophe Lemetre,Jeffrey Maniko,Zachary Charlop-Powers,Ben Sparrow,Andrew J. Lowe,Sean F. Brady +5 more
TL;DR: Of the factors assessed, changes in latitude were found to correlate most consistently with changes in biosynthetic domain composition on a continent-wide scale, and the identification of a latitudinal basis for differences in soil metagenome biosynthesis domain compositions should help guide future natural product discovery efforts.
Journal ArticleDOI
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow.
Alexander Crits-Christoph,Matthew R. Olm,Spencer Diamond,Keith Bouma-Gregson,Jillian F. Banfield +4 more
TL;DR: The results indicate that recombination and gene-specific selection commonly shape genetic variation in several understudied soil bacterial lineages.
Journal ArticleDOI
EvoMining reveals the origin and fate of natural product biosynthetic enzymes
Nelly Selem-Mojica,César Aguilar,Karina Gutiérrez-García,Christian E. Martínez-Guerrero,Francisco Barona-Gómez +4 more
TL;DR: By defining the origin and fate of enzymes, EvoMining complements traditional genome-mining approaches as an unbiased strategy and opens the door to gaining insights into the evolution of NP biosynthesis.
Journal ArticleDOI
Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity.
Pengxiang Fan,Peipei Wang,Yann-Ru Lou,Bryan J. Leong,Bethany M. Moore,Bethany M. Moore,Craig A. Schenck,Rachel Combs,Pengfei Cao,Federica Brandizzi,Shin-Han Shiu +10 more
TL;DR: A tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl- CoA synthetase and enoyl-CoA hydratase genes is described and insights into the dynamics behind gene cluster evolution and cell-type specific metabolite diversity are revealed.
Related Papers (5)
Identifying key questions in the ecology and evolution of cancer.
Antoine M. Dujon,Antoine M. Dujon,Athena Aktipis,Catherine Alix-Panabières,Sarah R. Amend,Amy M. Boddy,Joel S. Brown,Jean Pascal Capp,James DeGregori,Paul W. Ewald,Robert A. Gatenby,Marco Gerlinger,Mathieu Giraudeau,Mathieu Giraudeau,Rodrigo Hamede,Elsa Hansen,Irina Kareva,Carlo C. Maley,Andriy Marusyk,Nicholas McGranahan,Nicholas McGranahan,Michael J. Metzger,Aurora M. Nedelcu,Robert Noble,Robert Noble,Leonard Nunney,Kenneth J. Pienta,Kornelia Polyak,Pascal Pujol,Andrew F. Read,Benjamin Roche,Benjamin Roche,Susanne Sebens,Eric Solary,Eric Solary,Kateřina Staňková,Kateřina Staňková,Holly A. Swain Ewald,Frédéric Thomas,Beata Ujvari +39 more