Literature DB >> 27491886

Natural Products and the Gene Cluster Revolution.

Paul R Jensen1.   

Abstract

Genome sequencing has created unprecedented opportunities for natural-product discovery and new insight into the diversity and distributions of natural-product biosynthetic gene clusters (BGCs). These gene collectives are highly evolved for horizontal exchange, thus providing immediate opportunities to test the effects of small molecules on fitness. The marine actinomycete genus Salinispora maintains extraordinary levels of BGC diversity and has become a useful model for studies of secondary metabolism. Most Salinispora BGCs are observed infrequently, resulting in high population-level diversity while conforming to constraints associated with maximum genome size. Comparative genomics is providing a mechanism to assess secondary metabolism in the context of evolution and evidence that some products represent ecotype-defining traits while others appear selectively neutral.
Copyright © 2016 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Salinispora; bioinformatics; biosynthetic gene clusters; genomics; natural products; secondary metabolites

Mesh:

Substances:

Year:  2016        PMID: 27491886      PMCID: PMC5123934          DOI: 10.1016/j.tim.2016.07.006

Source DB:  PubMed          Journal:  Trends Microbiol        ISSN: 0966-842X            Impact factor:   17.079


  81 in total

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Review 2.  Computational tools for the synthetic design of biochemical pathways.

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Review 3.  Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation.

Authors:  Anne Osbourn
Journal:  Trends Genet       Date:  2010-08-24       Impact factor: 11.639

Review 4.  Regulation of secondary metabolism in streptomycetes.

Authors:  Mervyn J Bibb
Journal:  Curr Opin Microbiol       Date:  2005-04       Impact factor: 7.934

Review 5.  Actinomycetes as agents of biodegradation in the environment--a review.

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Journal:  Gene       Date:  1992-06-15       Impact factor: 3.688

Review 6.  In silico tools for the analysis of antibiotic biosynthetic pathways.

Authors:  Tilmann Weber
Journal:  Int J Med Microbiol       Date:  2014-02-19       Impact factor: 3.473

Review 7.  Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms.

Authors:  Ben Shen
Journal:  Curr Opin Chem Biol       Date:  2003-04       Impact factor: 8.822

8.  Giant linear plasmids in Streptomyces which code for antibiotic biosynthesis genes.

Authors:  H Kinashi; M Shimaji; A Sakai
Journal:  Nature       Date:  1987 Jul 30-Aug 5       Impact factor: 49.962

9.  Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms.

Authors:  Reiko Ueoka; Agustinus R Uria; Silke Reiter; Tetsushi Mori; Petra Karbaum; Eike E Peters; Eric J N Helfrich; Brandon I Morinaka; Muriel Gugger; Haruko Takeyama; Shigeki Matsunaga; Jörn Piel
Journal:  Nat Chem Biol       Date:  2015-08-03       Impact factor: 15.040

10.  antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Authors:  Marnix H Medema; Kai Blin; Peter Cimermancic; Victor de Jager; Piotr Zakrzewski; Michael A Fischbach; Tilmann Weber; Eriko Takano; Rainer Breitling
Journal:  Nucleic Acids Res       Date:  2011-06-14       Impact factor: 16.971

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  43 in total

1.  Genomic insights into specialized metabolism in the marine actinomycete Salinispora.

Authors:  Anne-Catrin Letzel; Jing Li; Gregory C A Amos; Natalie Millán-Aguiñaga; Joape Ginigini; Usama R Abdelmohsen; Susana P Gaudêncio; Nadine Ziemert; Bradley S Moore; Paul R Jensen
Journal:  Environ Microbiol       Date:  2017-08-14       Impact factor: 5.491

2.  Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities.

Authors:  Nastassia V Patin; Michelle Schorn; Kristen Aguinaldo; Tommie Lincecum; Bradley S Moore; Paul R Jensen
Journal:  Appl Environ Microbiol       Date:  2017-02-01       Impact factor: 4.792

3.  Genome-guided investigation of secondary metabolites produced by a potential new strain Streptomyces BA2 isolated from an endemic plant rhizosphere in Turkey.

Authors:  Ekrem Kum; Ebru İnce
Journal:  Arch Microbiol       Date:  2021-03-05       Impact factor: 2.552

4.  Synthetic-Bioinformatic Natural Product Antibiotics with Diverse Modes of Action.

Authors:  John Chu; Bimal Koirala; Nicholas Forelli; Xavier Vila-Farres; Melinda A Ternei; Thahmina Ali; Dominic A Colosimo; Sean F Brady
Journal:  J Am Chem Soc       Date:  2020-08-11       Impact factor: 15.419

5.  15N Stable Isotope Labeling and Comparative Metabolomics Facilitates Genome Mining in Cultured Cyanobacteria.

Authors:  Daniel S May; Camila M Crnkovic; Aleksej Krunic; Tyler A Wilson; James R Fuchs; Jimmy E Orjala
Journal:  ACS Chem Biol       Date:  2020-03-04       Impact factor: 5.100

6.  IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase.

Authors:  Krishnaveni Palaniappan; I-Min A Chen; Ken Chu; Anna Ratner; Rekha Seshadri; Nikos C Kyrpides; Natalia N Ivanova; Nigel J Mouncey
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

7.  CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria.

Authors:  Gaoyan Wang; Zhiying Zhao; Jing Ke; Yvonne Engel; Yi-Ming Shi; David Robinson; Kerem Bingol; Zheyun Zhang; Benjamin Bowen; Katherine Louie; Bing Wang; Robert Evans; Yu Miyamoto; Kelly Cheng; Suzanne Kosina; Markus De Raad; Leslie Silva; Alicia Luhrs; Andrea Lubbe; David W Hoyt; Charles Francavilla; Hiroshi Otani; Samuel Deutsch; Nancy M Washton; Edward M Rubin; Nigel J Mouncey; Axel Visel; Trent Northen; Jan-Fang Cheng; Helge B Bode; Yasuo Yoshikuni
Journal:  Nat Microbiol       Date:  2019-10-14       Impact factor: 17.745

Review 8.  Ecology and genomics of Actinobacteria: new concepts for natural product discovery.

Authors:  Doris A van Bergeijk; Barbara R Terlouw; Marnix H Medema; Gilles P van Wezel
Journal:  Nat Rev Microbiol       Date:  2020-06-01       Impact factor: 60.633

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.  Nanotechnological Applications Based on Bacterial Encapsulins.

Authors:  Javier M Rodríguez; Carolina Allende-Ballestero; Jeroen J L M Cornelissen; José R Castón
Journal:  Nanomaterials (Basel)       Date:  2021-06-01       Impact factor: 5.076

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