Literature DB >> 34083778

Mining genomes to illuminate the specialized chemistry of life.

Marnix H Medema1, Tristan de Rond2, Bradley S Moore3,4.   

Abstract

All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.
© 2021. Springer Nature Limited.

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Year:  2021        PMID: 34083778      PMCID: PMC8364890          DOI: 10.1038/s41576-021-00363-7

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  222 in total

1.  Revealing the macromolecular targets of complex natural products.

Authors:  Daniel Reker; Anna M Perna; Tiago Rodrigues; Petra Schneider; Michael Reutlinger; Bettina Mönch; Andreas Koeberle; Christina Lamers; Matthias Gabler; Heinrich Steinmetz; Rolf Müller; Manfred Schubert-Zsilavecz; Oliver Werz; Gisbert Schneider
Journal:  Nat Chem       Date:  2014-11-02       Impact factor: 24.427

2.  Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom.

Authors:  John K Brunson; Shaun M K McKinnie; Jonathan R Chekan; John P McCrow; Zachary D Miles; Erin M Bertrand; Vincent A Bielinski; Hanna Luhavaya; Miroslav Oborník; G Jason Smith; David A Hutchins; Andrew E Allen; Bradley S Moore
Journal:  Science       Date:  2018-09-28       Impact factor: 47.728

3.  A machine learning-based method for prediction of macrocyclization patterns of polyketides and non-ribosomal peptides.

Authors:  Priyesh Agrawal; Debasisa Mohanty
Journal:  Bioinformatics       Date:  2021-05-05       Impact factor: 6.937

4.  Molecular cloning of the whole biosynthetic pathway of a Streptomyces antibiotic and its expression in a heterologous host.

Authors:  F Malpartida; D A Hopwood
Journal:  Nature       Date:  1984 May 31-Jun 6       Impact factor: 49.962

5.  Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes.

Authors:  Kou-San Ju; Jiangtao Gao; James R Doroghazi; Kwo-Kwang A Wang; Christopher J Thibodeaux; Steven Li; Emily Metzger; John Fudala; Joleen Su; Jun Kai Zhang; Jaeheon Lee; Joel P Cioni; Bradley S Evans; Ryuichi Hirota; David P Labeda; Wilfred A van der Donk; William W Metcalf
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-31       Impact factor: 11.205

6.  Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Authors:  Grímur Hjörleifsson Eldjárn; Andrew Ramsay; Justin J J van der Hooft; Katherine R Duncan; Sylvia Soldatou; Juho Rousu; Rónán Daly; Joe Wandy; Simon Rogers
Journal:  PLoS Comput Biol       Date:  2021-05-04       Impact factor: 4.475

7.  A new cyanogenic metabolite in Arabidopsis required for inducible pathogen defence.

Authors:  Jakub Rajniak; Brenden Barco; Nicole K Clay; Elizabeth S Sattely
Journal:  Nature       Date:  2015-09-09       Impact factor: 49.962

8.  A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis.

Authors:  Marnix H Medema; Peter Cimermancic; Andrej Sali; Eriko Takano; Michael A Fischbach
Journal:  PLoS Comput Biol       Date:  2014-12-04       Impact factor: 4.475

9.  Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes.

Authors:  Tao Zhao; M Eric Schranz
Journal:  Proc Natl Acad Sci U S A       Date:  2019-01-23       Impact factor: 11.205

10.  Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping.

Authors:  Rakesh Santhanam; Van Thi Luu; Arne Weinhold; Jay Goldberg; Youngjoo Oh; Ian T Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-25       Impact factor: 11.205

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  31 in total

1.  A wealth of new biosynthetic pathways from the global ocean microbiome.

Authors: 
Journal:  Nature       Date:  2022-06-22       Impact factor: 49.962

2.  Biosynthetic potential of the global ocean microbiome.

Authors:  Hans-Joachim Ruscheweyh; Clarissa C Forneris; Florian Hubrich; Lucas Paoli; Satria Kautsar; Agneya Bhushan; Alessandro Lotti; Quentin Clayssen; Guillem Salazar; Alessio Milanese; Charlotte I Carlström; Chrysa Papadopoulou; Daniel Gehrig; Mikhail Karasikov; Harun Mustafa; Martin Larralde; Laura M Carroll; Pablo Sánchez; Ahmed A Zayed; Dylan R Cronin; Silvia G Acinas; Peer Bork; Chris Bowler; Tom O Delmont; Josep M Gasol; Alvar D Gossert; André Kahles; Matthew B Sullivan; Patrick Wincker; Georg Zeller; Serina L Robinson; Jörn Piel; Shinichi Sunagawa
Journal:  Nature       Date:  2022-06-22       Impact factor: 69.504

3.  The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function.

Authors:  Leesa J Klau; Sheila Podell; Kaitlin E Creamer; Alyssa M Demko; Hans W Singh; Eric E Allen; Bradley S Moore; Nadine Ziemert; Anne Catrin Letzel; Paul R Jensen
Journal:  J Biol Chem       Date:  2022-09-12       Impact factor: 5.486

4.  Genome mining of Fusarium reveals structural and functional diversity of pectin lyases: a bioinformatics approach.

Authors:  Kanchan Yadav; Shruti Dwivedi; Supriya Gupta; Amit K Dubey; Vinay K Singh; Aiman Tanveer; Sangeeta Yadav; Dinesh Yadav
Journal:  3 Biotech       Date:  2022-09-06       Impact factor: 2.893

5.  Ancient plant-like terpene biosynthesis in corals.

Authors:  Immo Burkhardt; Tristan de Rond; Percival Yang-Ting Chen; Bradley S Moore
Journal:  Nat Chem Biol       Date:  2022-05-23       Impact factor: 16.174

6.  Biosynthesis of Xylariolide D in Penicillium crustosum Implies a Chain Branching Reaction Catalyzed by a Highly Reducing Polyketide Synthase.

Authors:  Sina A Stierle; Shu-Ming Li
Journal:  J Fungi (Basel)       Date:  2022-05-09

7.  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

Review 8.  Harnessing ortho-Quinone Methides in Natural Product Biosynthesis and Biocatalysis.

Authors:  Trevor N Purdy; Bradley S Moore; April L Lukowski
Journal:  J Nat Prod       Date:  2022-02-02       Impact factor: 4.803

Review 9.  The Studies in Constructing Yeast Cell Factories for the Production of Fatty Acid Alkyl Esters.

Authors:  Yang Zhang; Xiao Guo; Huaiyi Yang; Shuobo Shi
Journal:  Front Bioeng Biotechnol       Date:  2022-01-11

10.  In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology.

Authors:  Antoine Danchin
Journal:  Microb Biotechnol       Date:  2021-09-27       Impact factor: 5.813

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