Literature DB >> 32232178

The hidden enzymology of bacterial natural product biosynthesis.

Thomas A Scott1, Jörn Piel1.   

Abstract

Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similarity-based bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed.

Entities:  

Year:  2019        PMID: 32232178      PMCID: PMC7104373          DOI: 10.1038/s41570-019-0107-1

Source DB:  PubMed          Journal:  Nat Rev Chem        ISSN: 2397-3358            Impact factor:   34.035


  227 in total

1.  Cloning and heterologous expression of the thioviridamide biosynthesis gene cluster from Streptomyces olivoviridis.

Authors:  Masumi Izawa; Takashi Kawasaki; Yoichi Hayakawa
Journal:  Appl Environ Microbiol       Date:  2013-08-30       Impact factor: 4.792

Review 2.  Expansion of chemical space for natural products by uncommon P450 reactions.

Authors:  Xingwang Zhang; Shengying Li
Journal:  Nat Prod Rep       Date:  2017-08-30       Impact factor: 13.423

3.  Human immunodeficiency virus type 1 Nef-induced CD4 cell surface downregulation is inhibited by ikarugamycin.

Authors:  T Luo; B L Fredericksen; K Hasumi; A Endo; J V Garcia
Journal:  J Virol       Date:  2001-03       Impact factor: 5.103

4.  In situ cultivation of previously uncultivable microorganisms using the ichip.

Authors:  Brittany Berdy; Amy L Spoering; Losee L Ling; Slava S Epstein
Journal:  Nat Protoc       Date:  2017-09-29       Impact factor: 13.491

5.  Biocatalytic Total Synthesis of Ikarugamycin.

Authors:  Christian Greunke; Anna Glöckle; Janine Antosch; Tobias A M Gulder
Journal:  Angew Chem Int Ed Engl       Date:  2017-01-27       Impact factor: 15.336

6.  Bioactive Polycyclic Tetramate Macrolactams from Lysobacter enzymogenes and Their Absolute Configurations by Theoretical ECD Calculations.

Authors:  Liangxiong Xu; Ping Wu; Stephen J Wright; Liangcheng Du; Xiaoyi Wei
Journal:  J Nat Prod       Date:  2015-07-22       Impact factor: 4.050

7.  Ikarugamycin induces DNA damage, intracellular calcium increase, p38 MAP kinase activation and apoptosis in HL-60 human promyelocytic leukemia cells.

Authors:  Ruxandra Popescu; Elke Hannelore Heiss; Franziska Ferk; Andrea Peschel; Siegfried Knasmueller; Verena Maria Dirsch; Georg Krupitza; Brigitte Kopp
Journal:  Mutat Res       Date:  2011-03-12       Impact factor: 2.433

8.  Natural Product Discovery through Improved Functional Metagenomics in Streptomyces.

Authors:  Hala A Iqbal; Lila Low-Beinart; Joseph U Obiajulu; Sean F Brady
Journal:  J Am Chem Soc       Date:  2016-07-22       Impact factor: 15.419

9.  Thioholgamides: Thioamide-Containing Cytotoxic RiPP Natural Products.

Authors:  Louise Kjaerulff; Asfandyar Sikandar; Nestor Zaburannyi; Sebastian Adam; Jennifer Herrmann; Jesko Koehnke; Rolf Müller
Journal:  ACS Chem Biol       Date:  2017-10-17       Impact factor: 5.100

10.  Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks.

Authors:  Suwen Zhao; Ayano Sakai; Xinshuai Zhang; Matthew W Vetting; Ritesh Kumar; Brandan Hillerich; Brian San Francisco; Jose Solbiati; Adam Steves; Shoshana Brown; Eyal Akiva; Alan Barber; Ronald D Seidel; Patricia C Babbitt; Steven C Almo; John A Gerlt; Matthew P Jacobson
Journal:  Elife       Date:  2014-06-30       Impact factor: 8.140

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  15 in total

1.  Precursor-Guided Mining of Marine Sponge Metabolomes Lends Insight into Biosynthesis of Pyrrole-Imidazole Alkaloids.

Authors:  Ipsita Mohanty; Samuel G Moore; Dongqi Yi; Jason S Biggs; David A Gaul; Neha Garg; Vinayak Agarwal
Journal:  ACS Chem Biol       Date:  2020-07-29       Impact factor: 5.100

Review 2.  Cell-Free Exploration of the Natural Product Chemical Space.

Authors:  Jonathan W Bogart; Maria D Cabezas; Bastian Vögeli; Derek A Wong; Ashty S Karim; Michael C Jewett
Journal:  Chembiochem       Date:  2020-09-22       Impact factor: 3.164

Review 3.  Strategies for Natural Products Discovery from Uncultured Microorganisms.

Authors:  Khorshed Alam; Muhammad Nazeer Abbasi; Jinfang Hao; Youming Zhang; Aiying Li
Journal:  Molecules       Date:  2021-05-17       Impact factor: 4.411

Review 4.  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

5.  Co-occurrence of enzyme domains guides the discovery of an oxazolone synthetase.

Authors:  Tristan de Rond; Julia E Asay; Bradley S Moore
Journal:  Nat Chem Biol       Date:  2021-06-07       Impact factor: 15.040

Review 6.  Diversity and Distribution of Volatile Secondary Metabolites Throughout Bacillus subtilis Isolates.

Authors:  Marco Kai
Journal:  Front Microbiol       Date:  2020-04-08       Impact factor: 5.640

7.  Computationally-guided exchange of substrate selectivity motifs in a modular polyketide synthase acyltransferase.

Authors:  Edward Kalkreuter; Kyle S Bingham; Aaron M Keeler; Andrew N Lowell; Jennifer J Schmidt; David H Sherman; Gavin J Williams
Journal:  Nat Commun       Date:  2021-04-13       Impact factor: 14.919

8.  Ribosomally derived lipopeptides containing distinct fatty acyl moieties.

Authors:  Florian Hubrich; Nina M Bösch; Clara Chepkirui; Brandon I Morinaka; Michael Rust; Muriel Gugger; Serina L Robinson; Anna L Vagstad; Jörn Piel
Journal:  Proc Natl Acad Sci U S A       Date:  2022-01-18       Impact factor: 11.205

Review 9.  A roadmap for metagenomic enzyme discovery.

Authors:  Serina L Robinson; Jörn Piel; Shinichi Sunagawa
Journal:  Nat Prod Rep       Date:  2021-11-17       Impact factor: 13.423

10.  Post-translational formation of strained cyclophanes in bacteria.

Authors:  Thi Quynh Ngoc Nguyen; Yi Wei Tooh; Ryosuke Sugiyama; Thi Phuong Diep Nguyen; Mugilarasi Purushothaman; Li Chuan Leow; Karyna Hanif; Rubin How Sheng Yong; Irene Agatha; Fernaldo R Winnerdy; Muriel Gugger; Anh Tuân Phan; Brandon I Morinaka
Journal:  Nat Chem       Date:  2020-08-17       Impact factor: 24.427

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