Literature DB >> 32483324

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

Doris A van Bergeijk1, Barbara R Terlouw2, Marnix H Medema3, Gilles P van Wezel4,5.   

Abstract

Actinobacteria constitute a highly diverse bacterial phylum with an unrivalled metabolic versatility. They produce most of the clinically used antibiotics and a plethora of other natural products with medical or agricultural applications. Modern 'omics'-based technologies have revealed that the genomic potential of Actinobacteria greatly outmatches the known chemical space. In this Review, we argue that combining insights into actinobacterial ecology with state-of-the-art computational approaches holds great promise to unlock this unexplored reservoir of actinobacterial metabolism. This enables the identification of small molecules and other stimuli that elicit the induction of poorly expressed biosynthetic gene clusters, which should help reinvigorate screening efforts for their precious bioactive natural products.

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Year:  2020        PMID: 32483324     DOI: 10.1038/s41579-020-0379-y

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  141 in total

Review 1.  Origins and evolution of antibiotic resistance.

Authors:  Julian Davies; Dorothy Davies
Journal:  Microbiol Mol Biol Rev       Date:  2010-09       Impact factor: 11.056

Review 2.  Taxonomy, Physiology, and Natural Products of Actinobacteria.

Authors:  Essaid Ait Barka; Parul Vatsa; Lisa Sanchez; Nathalie Gaveau-Vaillant; Cedric Jacquard; Jan P Meier-Kolthoff; Hans-Peter Klenk; Christophe Clément; Yder Ouhdouch; Gilles P van Wezel
Journal:  Microbiol Mol Biol Rev       Date:  2015-11-25       Impact factor: 11.056

Review 3.  Drugs for bad bugs: confronting the challenges of antibacterial discovery.

Authors:  David J Payne; Michael N Gwynn; David J Holmes; David L Pompliano
Journal:  Nat Rev Drug Discov       Date:  2006-12-08       Impact factor: 84.694

Review 4.  Natural products as sources of new drugs over the last 25 years.

Authors:  David J Newman; Gordon M Cragg
Journal:  J Nat Prod       Date:  2007-02-20       Impact factor: 4.050

Review 5.  Secretory production of recombinant proteins by Streptomyces.

Authors:  Kristof Vrancken; Jozef Anné
Journal:  Future Microbiol       Date:  2009-03       Impact factor: 3.165

Review 6.  Renaissance in antibacterial discovery from actinomycetes.

Authors:  Richard H Baltz
Journal:  Curr Opin Pharmacol       Date:  2008-06-03       Impact factor: 5.547

7.  Fix the antibiotics pipeline.

Authors:  Matthew A Cooper; David Shlaes
Journal:  Nature       Date:  2011-04-07       Impact factor: 49.962

Review 8.  Chemical ecology of antibiotic production by actinomycetes.

Authors:  Anne van der Meij; Sarah F Worsley; Matthew I Hutchings; Gilles P van Wezel
Journal:  FEMS Microbiol Rev       Date:  2017-05-01       Impact factor: 16.408

9.  Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

Authors:  S D Bentley; K F Chater; A-M Cerdeño-Tárraga; G L Challis; N R Thomson; K D James; D E Harris; M A Quail; H Kieser; D Harper; A Bateman; S Brown; G Chandra; C W Chen; M Collins; A Cronin; A Fraser; A Goble; J Hidalgo; T Hornsby; S Howarth; C-H Huang; T Kieser; L Larke; L Murphy; K Oliver; S O'Neil; E Rabbinowitsch; M-A Rajandream; K Rutherford; S Rutter; K Seeger; D Saunders; S Sharp; R Squares; S Squares; K Taylor; T Warren; A Wietzorrek; J Woodward; B G Barrell; J Parkhill; D A Hopwood
Journal:  Nature       Date:  2002-05-09       Impact factor: 49.962

10.  Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.

Authors:  Haruo Ikeda; Jun Ishikawa; Akiharu Hanamoto; Mayumi Shinose; Hisashi Kikuchi; Tadayoshi Shiba; Yoshiyuki Sakaki; Masahira Hattori; Satoshi Omura
Journal:  Nat Biotechnol       Date:  2003-04-14       Impact factor: 54.908

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  48 in total

1.  Unconventional Antibacterials and Adjuvants.

Authors:  Mayland Chang; Kiran V Mahasenan; Juan A Hermoso; Shahriar Mobashery
Journal:  Acc Chem Res       Date:  2021-01-29       Impact factor: 22.384

2.  Complex microbial communities inhabiting natural Cordyceps militaris and the habitat soil and their predicted functions.

Authors:  Xiao-Mei Zhang; De-Xiang Tang; Qing-Qing Li; Yuan-Bing Wang; Zhi-Hong Xu; Wen-Jun Li; Hong Yu
Journal:  Antonie Van Leeuwenhoek       Date:  2021-02-27       Impact factor: 2.271

3.  Streptomyces spinosus sp. nov. and Streptomyces shenzhenensis subsp. oryzicola subsp. nov. endophytic actinobacteria isolated from Jasmine rice and their genome mining for potential as antibiotic producers and plant growth promoters.

Authors:  Onuma Kaewkla; Sudarat Sukpanoa; Chanwit Suriyachadkun; Nitcha Chamroensaksi; Theeraphan Chumroenphat; Christopher Milton Mathew Franco
Journal:  Antonie Van Leeuwenhoek       Date:  2022-05-21       Impact factor: 2.271

4.  Nutrient Availability Shifts the Biosynthetic Potential of Soil-Derived Microbial Communities.

Authors:  Marc G Chevrette; Bradley W Himes; Camila Carlos-Shanley
Journal:  Curr Microbiol       Date:  2022-01-12       Impact factor: 2.188

5.  Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters.

Authors:  Zhen-Yu Zan; Xian-Feng Ge; Rui-Rui Huang; Wen-Zheng Liu
Journal:  Curr Microbiol       Date:  2022-02-07       Impact factor: 2.188

6.  Gene editing enables rapid engineering of complex antibiotic assembly lines.

Authors:  Wei Li Thong; Yingxin Zhang; Ying Zhuo; Katherine J Robins; Joanna K Fyans; Abigail J Herbert; Brian J C Law; Jason Micklefield
Journal:  Nat Commun       Date:  2021-11-25       Impact factor: 14.919

7.  ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria.

Authors:  Morgan Anne Feeney; Jake Terry Newitt; Emily Addington; Lis Algora-Gallardo; Craig Allan; Lucas Balis; Anna S Birke; Laia Castaño-Espriu; Louise K Charkoudian; Rebecca Devine; Damien Gayrard; Jacob Hamilton; Oliver Hennrich; Paul A Hoskisson; Molly Keith-Baker; Joshua G Klein; Worarat Kruasuwan; David R Mark; Yvonne Mast; Rebecca E McHugh; Thomas C McLean; Elmira Mohit; John T Munnoch; Jordan Murray; Katie Noble; Hiroshi Otani; Jonathan Parra; Camila F Pereira; Louisa Perry; Linamaria Pintor-Escobar; Leighton Pritchard; Samuel M M Prudence; Alicia H Russell; Jana K Schniete; Ryan F Seipke; Nelly Sélem-Mojica; Agustina Undabarrena; Kristiina Vind; Gilles P van Wezel; Barrie Wilkinson; Sarah F Worsley; Katherine R Duncan; Lorena T Fernández-Martínez; Matthew I Hutchings
Journal:  Microb Genom       Date:  2022-07

8.  Linear paths to genome reduction in a defensive symbiont.

Authors:  Suegene Noh
Journal:  Proc Natl Acad Sci U S A       Date:  2021-06-01       Impact factor: 11.205

9.  Genetic Network Architecture and Environmental Cues Drive Spatial Organization of Phenotypic Division of Labor in Streptomyces coelicolor.

Authors:  Vineetha M Zacharia; Yein Ra; Catherine Sue; Elizabeth Alcala; Jewel N Reaso; Steven E Ruzin; Matthew F Traxler
Journal:  mBio       Date:  2021-05-18       Impact factor: 7.867

Review 10.  Natural products that target the cell envelope.

Authors:  Julia E Page; Suzanne Walker
Journal:  Curr Opin Microbiol       Date:  2021-03-01       Impact factor: 7.584

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