Natural product biosynthesis and discovery in actinomycetes

Natural products remain a valuable source of drug leads in the 21st Century. Revival of actinomycete natural product discovery in the Post Genomics Era is driven by realization of largely concealed biosynthetic potential revealed through genome mining efforts. Implementation of bioinformatics also p...

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Main Author: Low, Zhen Jie
Other Authors: Liang Zhao-Xun
Format: Theses and Dissertations
Language:English
Published: 2019
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Online Access:https://hdl.handle.net/10356/90198
http://hdl.handle.net/10220/47317
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-901982023-02-28T18:32:15Z Natural product biosynthesis and discovery in actinomycetes Low, Zhen Jie Liang Zhao-Xun School of Biological Sciences DRNTU::Science::Chemistry::Biochemistry Natural products remain a valuable source of drug leads in the 21st Century. Revival of actinomycete natural product discovery in the Post Genomics Era is driven by realization of largely concealed biosynthetic potential revealed through genome mining efforts. Implementation of bioinformatics also prompted a paradigm shift in natural product discovery as a bottom up approach guided by genomics directs investigative efforts at specific biosynthetic gene clusters (BGCs). In this work, a genomics guided approach was adopted to study natural product discovery and biosynthesis in three actinomycete strains – 2 Streptomyces strains and 1 Micromonospora strain. Effectiveness of this approach was underlined by successful dereplication of known clusters and prioritization of novel gene clusters. Genome mining was combined with CRISPR/Cas9, a powerful tool for genetic engineering, to identify four novel BGCs through gene knockout studies in vivo. Development of other synthetic biology tools also facilitated the upregulation of cryptic BGCs, through constitutive overexpression of positive regulators, for compound discovery. Whilst one of the four identified BGCs encoded a known polyene macrolactam (sceliphrolactam), it piqued the possible involvement of an iterative, partially reducing polyketide synthase module, which is unprecedented. One of the three novel compounds discovered was meijiemycin, a novel linear polyene that exhibited antifungal properties. The prospect of bioengineering its BGC holds promise in generating other structural analogs with improved therapeutic properties. The other two novel compounds were discovered from the Micromonospora strain, reflecting the promise of unlocking the immense biosynthetic potential displayed by rare actinomycetes using modern synthetic biology approaches. Discovery of lumpurmycin, the largest ansamycin natural product identified till date, adds onto a growing family of benzoquinone ansamycin natural products that are antagonistic against heat shock protein 90. The final compound, sungeidine, was derived from a novel 10-membered enediyne BGC, whose biosynthetic pathway is currently under investigation. Overall, this work demonstrated the potential of actinomycetes as a continued source of novel natural products and more importantly, established a methodical approach to uncover novel natural products in other actinomycete strains. Doctor of Philosophy 2019-01-02T07:44:26Z 2019-12-06T17:42:55Z 2019-01-02T07:44:26Z 2019-12-06T17:42:55Z 2018 Thesis Low, Z. J. (2018). Natural product biosynthesis and discovery in actinomycetes. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/90198 http://hdl.handle.net/10220/47317 10.32657/10220/47317 en 242 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Science::Chemistry::Biochemistry
spellingShingle DRNTU::Science::Chemistry::Biochemistry
Low, Zhen Jie
Natural product biosynthesis and discovery in actinomycetes
description Natural products remain a valuable source of drug leads in the 21st Century. Revival of actinomycete natural product discovery in the Post Genomics Era is driven by realization of largely concealed biosynthetic potential revealed through genome mining efforts. Implementation of bioinformatics also prompted a paradigm shift in natural product discovery as a bottom up approach guided by genomics directs investigative efforts at specific biosynthetic gene clusters (BGCs). In this work, a genomics guided approach was adopted to study natural product discovery and biosynthesis in three actinomycete strains – 2 Streptomyces strains and 1 Micromonospora strain. Effectiveness of this approach was underlined by successful dereplication of known clusters and prioritization of novel gene clusters. Genome mining was combined with CRISPR/Cas9, a powerful tool for genetic engineering, to identify four novel BGCs through gene knockout studies in vivo. Development of other synthetic biology tools also facilitated the upregulation of cryptic BGCs, through constitutive overexpression of positive regulators, for compound discovery. Whilst one of the four identified BGCs encoded a known polyene macrolactam (sceliphrolactam), it piqued the possible involvement of an iterative, partially reducing polyketide synthase module, which is unprecedented. One of the three novel compounds discovered was meijiemycin, a novel linear polyene that exhibited antifungal properties. The prospect of bioengineering its BGC holds promise in generating other structural analogs with improved therapeutic properties. The other two novel compounds were discovered from the Micromonospora strain, reflecting the promise of unlocking the immense biosynthetic potential displayed by rare actinomycetes using modern synthetic biology approaches. Discovery of lumpurmycin, the largest ansamycin natural product identified till date, adds onto a growing family of benzoquinone ansamycin natural products that are antagonistic against heat shock protein 90. The final compound, sungeidine, was derived from a novel 10-membered enediyne BGC, whose biosynthetic pathway is currently under investigation. Overall, this work demonstrated the potential of actinomycetes as a continued source of novel natural products and more importantly, established a methodical approach to uncover novel natural products in other actinomycete strains.
author2 Liang Zhao-Xun
author_facet Liang Zhao-Xun
Low, Zhen Jie
format Theses and Dissertations
author Low, Zhen Jie
author_sort Low, Zhen Jie
title Natural product biosynthesis and discovery in actinomycetes
title_short Natural product biosynthesis and discovery in actinomycetes
title_full Natural product biosynthesis and discovery in actinomycetes
title_fullStr Natural product biosynthesis and discovery in actinomycetes
title_full_unstemmed Natural product biosynthesis and discovery in actinomycetes
title_sort natural product biosynthesis and discovery in actinomycetes
publishDate 2019
url https://hdl.handle.net/10356/90198
http://hdl.handle.net/10220/47317
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