Literature DB >> 31475269

Applied evolution: phylogeny-based approaches in natural products research.

Martina Adamek1, Mohammad Alanjary2, Nadine Ziemert1.   

Abstract

Covering: up to 2019Phylogenetic methods become increasingly important in natural product research. The growing amount of genetic data available today is enabling us to infer the evolutionary history of secondary metabolite gene clusters and their encoded compounds. We are starting to understand patterns and mechanisms of how the enormous diversity of chemical compounds produced by nature has evolved and are able to use phylogenetic inference to facilitate functional predictions of involved enzymes. In this review, we highlight how phylogenetic methods can aid natural product discovery and predictions and demonstrate several examples how these have been used in the past. We are featuring a number of easy to use tools that aid tree building and analysis and are providing a short overview how to create and interpret a phylogenetic tree.

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Year:  2019        PMID: 31475269     DOI: 10.1039/c9np00027e

Source DB:  PubMed          Journal:  Nat Prod Rep        ISSN: 0265-0568            Impact factor:   13.423


  14 in total

Review 1.  Deep learning approaches for natural product discovery from plant endophytic microbiomes.

Authors:  Shiva Abdollahi Aghdam; Amanda May Vivian Brown
Journal:  Environ Microbiome       Date:  2021-03-18

2.  ActDES - a curated Actinobacterial Database for Evolutionary Studies.

Authors:  Jana K Schniete; Nelly Selem-Mojica; Anna S Birke; Pablo Cruz-Morales; Iain S Hunter; Francisco Barona-Gomez; Paul A Hoskisson
Journal:  Microb Genom       Date:  2021-01

3.  Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis.

Authors:  Marc G Chevrette; Nelly Selem-Mojica; César Aguilar; Kristin Labby; Edder D Bustos-Diaz; Jo Handelsman; Francisco Barona-Gómez
Journal:  Methods Mol Biol       Date:  2022

4.  Evolution-Informed Discovery of the Naphthalenone Biosynthetic Pathway in Fungi.

Authors:  Olga V Mosunova; Jorge C Navarro-Muñoz; Diksha Haksar; Jacq van Neer; Jelmer Hoeksma; Jeroen den Hertog; Jérôme Collemare
Journal:  mBio       Date:  2022-05-26       Impact factor: 7.786

5.  Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes.

Authors:  Athina Gavriilidou; Satria A Kautsar; Nestor Zaburannyi; Daniel Krug; Rolf Müller; Marnix H Medema; Nadine Ziemert
Journal:  Nat Microbiol       Date:  2022-05-02       Impact factor: 30.964

6.  Evaluating the Distribution of Bacterial Natural Product Biosynthetic Genes across Lake Huron Sediment.

Authors:  Maryam Elfeki; Shrikant Mantri; Chase M Clark; Stefan J Green; Nadine Ziemert; Brian T Murphy
Journal:  ACS Chem Biol       Date:  2021-10-04       Impact factor: 5.100

Review 7.  Deep learning approaches for natural product discovery from plant endophytic microbiomes.

Authors:  Shiva Abdollahi Aghdam; Amanda May Vivian Brown
Journal:  Environ Microbiome       Date:  2021-03-18

8.  Thioesterase-mediated side chain transesterification generates potent Gq signaling inhibitor FR900359.

Authors:  Cornelia Hermes; René Richarz; Daniel A Wirtz; Julian Patt; Wiebke Hanke; Stefan Kehraus; Jan Hendrik Voß; Jim Küppers; Tsubasa Ohbayashi; Vigneshwaran Namasivayam; Judith Alenfelder; Asuka Inoue; Peter Mergaert; Michael Gütschow; Christa E Müller; Evi Kostenis; Gabriele M König; Max Crüsemann
Journal:  Nat Commun       Date:  2021-01-08       Impact factor: 17.694

9.  Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite.

Authors:  Agustina Undabarrena; Ricardo Valencia; Andrés Cumsille; Leonardo Zamora-Leiva; Eduardo Castro-Nallar; Francisco Barona-Gomez; Beatriz Cámara
Journal:  Microb Genom       Date:  2021-07

Review 10.  Mining and unearthing hidden biosynthetic potential.

Authors:  Kirstin Scherlach; Christian Hertweck
Journal:  Nat Commun       Date:  2021-06-23       Impact factor: 14.919

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