Literature DB >> 33807702

Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows.

Max Crüsemann1.   

Abstract

Bacterial natural products possess potent bioactivities and high structural diversity and are typically encoded in biosynthetic gene clusters. Traditional natural product discovery approaches rely on UV- and bioassay-guided fractionation and are limited in terms of dereplication. Recent advances in mass spectrometry, sequencing and bioinformatics have led to large-scale accumulation of genomic and mass spectral data that is increasingly used for signature-based or correlation-based mass spectrometry genome mining approaches that enable rapid linking of metabolomic and genomic information to accelerate and rationalize natural product discovery. In this mini-review, these approaches are presented, and discovery examples provided. Finally, future opportunities and challenges for paired omics-based natural products discovery workflows are discussed.

Entities:  

Keywords:  bacterial natural products; genome mining; mass spectrometry; paired omics

Year:  2021        PMID: 33807702      PMCID: PMC7998270          DOI: 10.3390/md19030142

Source DB:  PubMed          Journal:  Mar Drugs        ISSN: 1660-3397            Impact factor:   5.118


  56 in total

1.  Salinipyrone and Pacificanone Are Biosynthetic By-products of the Rosamicin Polyketide Synthase.

Authors:  Takayoshi Awakawa; Max Crüsemann; Jason Munguia; Nadine Ziemert; Victor Nizet; William Fenical; Bradley S Moore
Journal:  Chembiochem       Date:  2015-05-15       Impact factor: 3.164

Review 2.  CRISPR/Cas-based genome engineering in natural product discovery.

Authors:  Yaojun Tong; Tilmann Weber; Sang Yup Lee
Journal:  Nat Prod Rep       Date:  2019-09-18       Impact factor: 13.423

3.  Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019.

Authors:  David J Newman; Gordon M Cragg
Journal:  J Nat Prod       Date:  2020-03-12       Impact factor: 4.050

4.  Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations.

Authors:  Ryan A McClure; Anthony W Goering; Kou-San Ju; Joshua A Baccile; Frank C Schroeder; William W Metcalf; Regan J Thomson; Neil L Kelleher
Journal:  ACS Chem Biol       Date:  2016-11-15       Impact factor: 5.100

5.  Mass spectrometry searches using MASST.

Authors:  Mingxun Wang; Alan K Jarmusch; Fernando Vargas; Alexander A Aksenov; Julia M Gauglitz; Kelly Weldon; Daniel Petras; Ricardo da Silva; Robert Quinn; Alexey V Melnik; Justin J J van der Hooft; Andrés Mauricio Caraballo-Rodríguez; Louis Felix Nothias; Christine M Aceves; Morgan Panitchpakdi; Elizabeth Brown; Francesca Di Ottavio; Nicole Sikora; Emmanuel O Elijah; Lara Labarta-Bajo; Emily C Gentry; Shabnam Shalapour; Kathleen E Kyle; Sara P Puckett; Jeramie D Watrous; Carolina S Carpenter; Amina Bouslimani; Madeleine Ernst; Austin D Swafford; Elina I Zúñiga; Marcy J Balunas; Jonathan L Klassen; Rohit Loomba; Rob Knight; Nuno Bandeira; Pieter C Dorrestein
Journal:  Nat Biotechnol       Date:  2020-01       Impact factor: 54.908

6.  MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.

Authors:  Liu Cao; Alexey Gurevich; Kelsey L Alexander; C Benjamin Naman; Tiago Leão; Evgenia Glukhov; Tal Luzzatto-Knaan; Fernando Vargas; Robby Quinn; Amina Bouslimani; Louis Felix Nothias; Nitin K Singh; Jon G Sanders; Rodolfo A S Benitez; Luke R Thompson; Md-Nafiz Hamid; James T Morton; Alla Mikheenko; Alexander Shlemov; Anton Korobeynikov; Iddo Friedberg; Rob Knight; Kasthuri Venkateswaran; William H Gerwick; Lena Gerwick; Pieter C Dorrestein; Pavel A Pevzner; Hosein Mohimani
Journal:  Cell Syst       Date:  2019-10-16       Impact factor: 10.304

7.  Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.

Authors:  Kai Dührkop; Louis-Félix Nothias; Markus Fleischauer; Raphael Reher; Marcus Ludwig; Martin A Hoffmann; Daniel Petras; William H Gerwick; Juho Rousu; Pieter C Dorrestein; Sebastian Böcker
Journal:  Nat Biotechnol       Date:  2020-11-23       Impact factor: 54.908

8.  A community resource for paired genomic and metabolomic data mining.

Authors:  Michelle A Schorn; Stefan Verhoeven; Lars Ridder; Florian Huber; Deepa D Acharya; Alexander A Aksenov; Gajender Aleti; Jamshid Amiri Moghaddam; Allegra T Aron; Saefuddin Aziz; Anelize Bauermeister; Katherine D Bauman; Martin Baunach; Christine Beemelmanns; J Michael Beman; María Victoria Berlanga-Clavero; Alex A Blacutt; Helge B Bode; Anne Boullie; Asker Brejnrod; Tim S Bugni; Alexandra Calteau; Liu Cao; Víctor J Carrión; Raquel Castelo-Branco; Shaurya Chanana; Alexander B Chase; Marc G Chevrette; Leticia V Costa-Lotufo; Jason M Crawford; Cameron R Currie; Bart Cuypers; Tam Dang; Tristan de Rond; Alyssa M Demko; Elke Dittmann; Chao Du; Christopher Drozd; Jean-Claude Dujardin; Rachel J Dutton; Anna Edlund; David P Fewer; Neha Garg; Julia M Gauglitz; Emily C Gentry; Lena Gerwick; Evgenia Glukhov; Harald Gross; Muriel Gugger; Dulce G Guillén Matus; Eric J N Helfrich; Benjamin-Florian Hempel; Jae-Seoun Hur; Marianna Iorio; Paul R Jensen; Kyo Bin Kang; Leonard Kaysser; Neil L Kelleher; Chung Sub Kim; Ki Hyun Kim; Irina Koester; Gabriele M König; Tiago Leao; Seoung Rak Lee; Yi-Yuan Lee; Xuanji Li; Jessica C Little; Katherine N Maloney; Daniel Männle; Christian Martin H; Andrew C McAvoy; Willam W Metcalf; Hosein Mohimani; Carlos Molina-Santiago; Bradley S Moore; Michael W Mullowney; Mitchell Muskat; Louis-Félix Nothias; Ellis C O'Neill; Elizabeth I Parkinson; Daniel Petras; Jörn Piel; Emily C Pierce; Karine Pires; Raphael Reher; Diego Romero; M Caroline Roper; Michael Rust; Hamada Saad; Carmen Saenz; Laura M Sanchez; Søren Johannes Sørensen; Margherita Sosio; Roderich D Süssmuth; Douglas Sweeney; Kapil Tahlan; Regan J Thomson; Nicholas J Tobias; Amaro E Trindade-Silva; Gilles P van Wezel; Mingxun Wang; Kelly C Weldon; Fan Zhang; Nadine Ziemert; Katherine R Duncan; Max Crüsemann; Simon Rogers; Pieter C Dorrestein; Marnix H Medema; Justin J J van der Hooft
Journal:  Nat Chem Biol       Date:  2021-04       Impact factor: 15.040

9.  Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics.

Authors:  Justin J J van der Hooft; Joe Wandy; Francesca Young; Sandosh Padmanabhan; Konstantinos Gerasimidis; Karl E V Burgess; Michael P Barrett; Simon Rogers
Journal:  Anal Chem       Date:  2017-07-05       Impact factor: 6.986

10.  Comparative Genomics and Metabolomics in the Genus Nocardia.

Authors:  Daniel Männle; Shaun M K McKinnie; Shrikant S Mantri; Katharina Steinke; Zeyin Lu; Bradley S Moore; Nadine Ziemert; Leonard Kaysser
Journal:  mSystems       Date:  2020-06-02       Impact factor: 6.496

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  3 in total

Review 1.  Recent Advances in Discovery of Lead Structures from Microbial Natural Products: Genomics- and Metabolomics-Guided Acceleration.

Authors:  Linda Sukmarini
Journal:  Molecules       Date:  2021-04-27       Impact factor: 4.411

2.  Ion Mobility-Derived Collision Cross-Sections Add Extra Capability in Distinguishing Isomers and Compounds with Similar Retention Times: The Case of Aphidicolanes.

Authors:  Jinmei Xia; Wenhai Xiao; Xihuang Lin; Yiduo Zhou; Peng Qiu; Hongkun Si; Xiaorong Wu; Siwen Niu; Zhuhua Luo; Xianwen Yang
Journal:  Mar Drugs       Date:  2022-08-23       Impact factor: 6.085

Review 3.  Novel Alkaloids from Marine Actinobacteria: Discovery and Characterization.

Authors:  Anne-Sofie De Rop; Jeltien Rombaut; Thomas Willems; Marilyn De Graeve; Lynn Vanhaecke; Paco Hulpiau; Sofie L De Maeseneire; Maarten L De Mol; Wim K Soetaert
Journal:  Mar Drugs       Date:  2021-12-22       Impact factor: 5.118

  3 in total

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