Abstract
Secondary metabolites offer a wide variety of biologically active compounds with great potential in medicine, agriculture, or livestock. With the advance of computational techniques and genome sequencing availability, laborious screening of microbial products can be replaced by more efficient genome mining using extensive genome databases available online. Rapidly developing bioinformatic tools, such as antiSMASH, enable researches to effectively explore the genome of many organisms including plants, fungi, and bacteria and identify biosynthetic gene clusters potentially encoding novel bioactive compounds. In this chapter, we provide a step-by-step guide of using the antiSMASH online tool to identify gene clusters potentially encoding for secondary metabolites in the genome of the model strain Streptomyces griseus NBRC 13350.
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References
Saha S et al (2020) Discovery of unusual cyanobacterial tryptophan-containing anabaenopeptins by MS/MS-based molecular networking. Molecules 25(17):3786
Lee N et al (2020) Mini review: genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces. Comput Struct Biotechnol J 18:1548–1556
Lee N et al (2020) Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters. Sci Data 7(1):55
Ventola CL (2015) The antibiotic resistance crisis: part 1: causes and threats. P T 40(4):277–283
Fair RJ, Tor Y (2014) Antibiotics and bacterial resistance in the 21st century. Perspect Medicin Chem 6:25–64
Pham JV et al (2019) A review of the microbial production of bioactive natural products and biologics. Front Microbiol 10:1404
Belknap KC et al (2020) Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria. Sci Rep 10(1):2003
Aigle B et al (2014) Genome mining of Streptomyces ambofaciens. J Ind Microbiol Biotechnol 41(2):251–263
Ikeda H et al (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21(5):526–531
Ishaque NM et al (2020) Isolation, genomic and metabolomic characterization of Streptomyces tendae VITAKN with quorum sensing inhibitory activity from Southern India. Microorganisms 8(1):121
Saha S et al (2021) Draft genome sequence of terrestrial Streptomyces sp. strain VITNK9, isolated from Vellore, Tamil Nadu, India, exhibiting antagonistic activity against fish pathogens. Microbiol Resource Announcements 10(1):e01282–e01220
Weber T, Kim HU (2016) The secondary metabolite bioinformatics portal: computational tools to facilitate synthetic biology of secondary metabolite production. Synth Syst Biotechnol 1(2):69–79
Blin K et al (2019) Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. Brief Bioinform 20(4):1103–1113
Blin K et al (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47(W1):W81–W87
Hyatt D et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119
Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20(16):2878–2879
Medema MH et al (2015) Minimum information about a biosynthetic gene cluster. Nat Chem Biol 11(9):625–631
Finn RD et al (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44(D1):D279–D285
Medema MH, Takano E, Breitling R (2013) Detecting sequence homology at the gene cluster level with MultiGeneBlast. Mol Biol Evol 30(5):1218–1223
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Macho, M. et al. (2022). Biosynthetic Gene Cluster Analysis in Actinobacterial Genus Streptomyces. In: Dharumadurai, D. (eds) Methods in Actinobacteriology. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1728-1_33
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DOI: https://doi.org/10.1007/978-1-0716-1728-1_33
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