Literature DB >> 32283638

Genome Mining as New Challenge in Natural Products Discovery.

Luisa Albarano1,2, Roberta Esposito1,2, Nadia Ruocco1, Maria Costantini1.   

Abstract

Drug discovery is based on bioactivity screening of natural sources, traditionally represented by bacteria fungi and plants. Bioactive natural products and their secondary metabolites have represented the main source for new therapeutic agents, used as drug leads for new antibiotics and anticancer agents. After the discovery of the first biosynthetic genes in the last decades, the researchers had in their hands the tool to understand the biosynthetic logic and genetic basis leading to the production of these compounds. Furthermore, in the genomic era, in which the number of available genomes is increasing, genome mining joined to synthetic biology are offering a significant help in drug discovery. In the present review we discuss the importance of genome mining and synthetic biology approaches to identify new natural products, also underlining considering the possible advantages and disadvantages of this technique. Moreover, we debate the associated techniques that can be applied following to genome mining for validation of data. Finally, we review on the literature describing all novel natural drugs isolated from bacteria, fungi, and other living organisms, not only from the marine environment, by a genome-mining approach, focusing on the literature available in the last ten years.

Entities:  

Keywords:  bacteria; fungi; genome mining; natural products; synthetic biology

Mesh:

Substances:

Year:  2020        PMID: 32283638      PMCID: PMC7230286          DOI: 10.3390/md18040199

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


  74 in total

Review 1.  Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms.

Authors:  Marnix H Medema; Rainer Breitling; Roel Bovenberg; Eriko Takano
Journal:  Nat Rev Microbiol       Date:  2010-12-29       Impact factor: 60.633

2.  Strategies for the discovery of new natural products by genome mining.

Authors:  Malek Zerikly; Gregory L Challis
Journal:  Chembiochem       Date:  2009-03-02       Impact factor: 3.164

Review 3.  Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides.

Authors:  Christopher N Boddy
Journal:  J Ind Microbiol Biotechnol       Date:  2013-10-31       Impact factor: 3.346

4.  Identification of nickel response genes in abnormal early developments of sea urchin by differential display polymerase chain reaction.

Authors:  Tae Kwon Ryu; Gunsup Lee; Yong Rhee; Heung-Sik Park; Man Chang; Sukchan Lee; Jaean Lee; Taek-Kyun Lee
Journal:  Ecotoxicol Environ Saf       Date:  2012-07-17       Impact factor: 6.291

5.  Perspective: Synthetic biology revives antibiotics.

Authors:  Gerard Wright
Journal:  Nature       Date:  2014-05-01       Impact factor: 49.962

Review 6.  The evolution of genome mining in microbes - a review.

Authors:  Nadine Ziemert; Mohammad Alanjary; Tilmann Weber
Journal:  Nat Prod Rep       Date:  2016-06-08       Impact factor: 13.423

Review 7.  Global cyclotide adventure: a journey dedicated to the discovery of circular peptides from flowering plants.

Authors:  Christian W Gruber
Journal:  Biopolymers       Date:  2010       Impact factor: 2.505

8.  Genome mining in Streptomyces. Elucidation of the role of Baeyer-Villiger monooxygenases and non-heme iron-dependent dehydrogenase/oxygenases in the final steps of the biosynthesis of pentalenolactone and neopentalenolactone.

Authors:  Myung-Ji Seo; Dongqing Zhu; Saori Endo; Haruo Ikeda; David E Cane
Journal:  Biochemistry       Date:  2011-02-08       Impact factor: 3.162

Review 9.  Chasing the treasures of the sea - bacterial marine natural products.

Authors:  Tobias A M Gulder; Bradley S Moore
Journal:  Curr Opin Microbiol       Date:  2009-05-28       Impact factor: 7.934

10.  Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting.

Authors:  Kevin Purves; Lynsey Macintyre; Debra Brennan; Guðmundur Ó Hreggviðsson; Eva Kuttner; Margrét E Ásgeirsdóttir; Louise C Young; David H Green; Ruangelie Edrada-Ebel; Katherine R Duncan
Journal:  Metabolites       Date:  2016-01-08
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  16 in total

1.  Whole-genome sequence and broad-spectrum antibacterial activity of Chryseobacterium cucumeris strain MW-6 isolated from the Arabian Sea.

Authors:  Sajid Iqbal; Muhammad Sufyan Vohra; Hussnain Ahmed Janjua
Journal:  3 Biotech       Date:  2021-11-07       Impact factor: 2.406

2.  Characterization of siderophores from Escherichia coli strains through genome mining tools: an antiSMASH study.

Authors:  Levent Cavas; Ibrahim Kirkiz
Journal:  AMB Express       Date:  2022-06-15       Impact factor: 4.126

Review 3.  Deep learning approaches for natural product discovery from plant endophytic microbiomes.

Authors:  Shiva Abdollahi Aghdam; Amanda May Vivian Brown
Journal:  Environ Microbiome       Date:  2021-03-18

4.  Genome Mining and Synthetic Biology in Marine Natural Product Discovery.

Authors:  Maria Costantini
Journal:  Mar Drugs       Date:  2020-12-03       Impact factor: 5.118

5.  Draft Genome Sequence of Aestuariibacter halophilus Type Strain JC2043.

Authors:  Sarah A Emsley; Kaysa M Pfannmuller; Blake Ushijima; Jimmy H Saw; Michael O Gaylor; Patrick Videau
Journal:  Microbiol Resour Announc       Date:  2021-12-16

Review 6.  Genome mining methods to discover bioactive natural products.

Authors:  Katherine D Bauman; Keelie S Butler; Bradley S Moore; Jonathan R Chekan
Journal:  Nat Prod Rep       Date:  2021-11-17       Impact factor: 13.423

Review 7.  Antibiotic Discovery and Resistance: The Chase and the Race.

Authors:  Katia Iskandar; Jayaseelan Murugaiyan; Dalal Hammoudi Halat; Said El Hage; Vindana Chibabhai; Saranya Adukkadukkam; Christine Roques; Laurent Molinier; Pascale Salameh; Maarten Van Dongen
Journal:  Antibiotics (Basel)       Date:  2022-01-30

8.  Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach.

Authors:  Ira Handayani; Hamada Saad; Shanti Ratnakomala; Puspita Lisdiyanti; Wien Kusharyoto; Janina Krause; Andreas Kulik; Wolfgang Wohlleben; Saefuddin Aziz; Harald Gross; Athina Gavriilidou; Nadine Ziemert; Yvonne Mast
Journal:  Mar Drugs       Date:  2021-05-28       Impact factor: 5.118

Review 9.  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

Review 10.  Advances in Biosynthesis of Natural Products from Marine Microorganisms.

Authors:  Quan Zhou; Kinya Hotta; Yaming Deng; Rui Yuan; Shu Quan; Xi Chen
Journal:  Microorganisms       Date:  2021-12-10
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