Genome Mining for Biosynthetic and Biodegradation Applications

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (20 November 2021) | Viewed by 3013

Special Issue Editor


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Guest Editor
Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 305-764, Korea
Interests: actinobacteria; prokaryotic taxonomy; biodiversity; prokaryotic genomics; bioactive compounds

Special Issue Information

Dear Colleagues,

Microorganisms play essential and irreplaceable roles in the ecosystem as decomposers, which includes the removal of xenobiotic substances and pollutants from the environment. Microbes have also been a major source of various secondary metabolites such as antibacterial, antifungal, antiviral, antiparasitic, antitumor, herbicidal, and immunomodulating compounds.

Traditional approaches to excavate such activities or compounds are primarily cultivation-based, while identification of the corresponding genes and gene clusters for biosynthesis or biodegradation is an independent subject of study, both of which have taken much time and effort. However, with the sharp increase in microbial genome data thanks to rapid advances in DNA sequencing technology in combination with bioinformatic tools for genome analysis, the potential of in silico mining has begun to attract attention.

For this Special Issue, original research or review articles on the following topics are invited: genome mining for discovery of novel natural products, genome-based in silico analysis of biodegradation, methodology for in silico analysis of genomes in relation to biosynthesis or biodegradation potential, identification of genes and gene clusters responsible for biosynthesis or biodegradation based on the in silico analysis of genome data, and evolutionary aspects of biosynthesis and biodegradation potential.

Prof. Dr. Seung Bum Kim
Guest Editor

Manuscript Submission Information

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Keywords

  • microorganism
  • genome mining
  • in silico analysis
  • biosynthesis
  • secondary metabolites
  • biodegradation
  • natural product
  • xenobiotic compound

Published Papers (1 paper)

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Research

11 pages, 4951 KiB  
Article
Identification of an Oxidosqualene Cyclase Gene Involved in Steroidal Triterpenoid Biosynthesis in Cordyceps farinosa
by Gi-Hong An, Jae-Gu Han, Hye-Sung Park, Gi-Ho Sung and Ok-Tae Kim
Genes 2021, 12(6), 848; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12060848 - 31 May 2021
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Abstract
Various fungi including Cordyceps farinosa, an entomopathogenic fungus, can produce steroidal triterpenoids. Protostadienol (protosta-17(20)Z,24-dien-3β-ol) is a precursor of steroidal triterpenoid compounds. To identify oxidosqualene cyclase (OSC) gene candidates involved in triterpenoid biosynthesis, genome mining was performed using Illumina sequencing platform. In the [...] Read more.
Various fungi including Cordyceps farinosa, an entomopathogenic fungus, can produce steroidal triterpenoids. Protostadienol (protosta-17(20)Z,24-dien-3β-ol) is a precursor of steroidal triterpenoid compounds. To identify oxidosqualene cyclase (OSC) gene candidates involved in triterpenoid biosynthesis, genome mining was performed using Illumina sequencing platform. In the sequence database, two OSC genes, CfaOSC1 and CfaOSC2, in the genome of C. farinosa were identified. Predicted amino-acid sequences of CfaOSC2 shared 66% similarities with protostadienol synthase (OSPC) of Aspergillus fumigatus. Phylogenetic analysis showed a clear grouping of CfaOSC2 in the OSPC clade. Function of CfaOSC2 was examined using a yeast INVSc1 heterologous expression system to endogenously synthesize 2,3-oxidosqualene. GC–MS analysis indicated that CfaOSC2 produced protosta-13(17),24-dien-3β-ol and protostadienol at a 5:95 ratio. Our results demonstrate that CfaOSC2 is a multifunctional triterpene synthase yielding a predominant protostadienol together with a minor triterpenoid. These results will facilitate a greater understanding of biosynthetic mechanisms underlying steroidal triterpenoid biosynthesis in C. farinosa and other fungi. Full article
(This article belongs to the Special Issue Genome Mining for Biosynthetic and Biodegradation Applications)
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