Cargando…

Functional mining of novel terpene synthases from metagenomes

BACKGROUND: Terpenes are one of the most diverse and abundant classes of natural biomolecules, collectively enabling a variety of therapeutic, energy, and cosmetic applications. Recent genomics investigations have predicted a large untapped reservoir of bacterial terpene synthases residing in the ge...

Descripción completa

Detalles Bibliográficos
Autores principales: Kwak, Suryang, Crook, Nathan, Yoneda, Aki, Ahn, Naomi, Ning, Jie, Cheng, Jiye, Dantas, Gautam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9548185/
https://www.ncbi.nlm.nih.gov/pubmed/36209178
http://dx.doi.org/10.1186/s13068-022-02189-9
_version_ 1784805390447280128
author Kwak, Suryang
Crook, Nathan
Yoneda, Aki
Ahn, Naomi
Ning, Jie
Cheng, Jiye
Dantas, Gautam
author_facet Kwak, Suryang
Crook, Nathan
Yoneda, Aki
Ahn, Naomi
Ning, Jie
Cheng, Jiye
Dantas, Gautam
author_sort Kwak, Suryang
collection PubMed
description BACKGROUND: Terpenes are one of the most diverse and abundant classes of natural biomolecules, collectively enabling a variety of therapeutic, energy, and cosmetic applications. Recent genomics investigations have predicted a large untapped reservoir of bacterial terpene synthases residing in the genomes of uncultivated organisms living in the soil, indicating a vast array of putative terpenoids waiting to be discovered. RESULTS: We aimed to develop a high-throughput functional metagenomic screening system for identifying novel terpene synthases from bacterial metagenomes by relieving the toxicity of terpene biosynthesis precursors to the Escherichia coli host. The precursor toxicity was achieved using an inducible operon encoding the prenyl pyrophosphate synthetic pathway and supplementation of the mevalonate precursor. Host strain and screening procedures were finely optimized to minimize false positives arising from spontaneous mutations, which avoid the precursor toxicity. Our functional metagenomic screening of human fecal metagenomes yielded a novel β-farnesene synthase, which does not show amino acid sequence similarity to known β-farnesene synthases. Engineered S. cerevisiae expressing the screened β-farnesene synthase produced 120 mg/L β-farnesene from glucose (2.86 mg/g glucose) with a productivity of 0.721 g/L∙h. CONCLUSIONS: A unique functional metagenomic screening procedure was established for screening terpene synthases from metagenomic libraries. This research proves the potential of functional metagenomics as a sequence-independent avenue for isolating targeted enzymes from uncultivated organisms in various environmental habitats. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-022-02189-9.
format Online
Article
Text
id pubmed-9548185
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-95481852022-10-10 Functional mining of novel terpene synthases from metagenomes Kwak, Suryang Crook, Nathan Yoneda, Aki Ahn, Naomi Ning, Jie Cheng, Jiye Dantas, Gautam Biotechnol Biofuels Bioprod Research BACKGROUND: Terpenes are one of the most diverse and abundant classes of natural biomolecules, collectively enabling a variety of therapeutic, energy, and cosmetic applications. Recent genomics investigations have predicted a large untapped reservoir of bacterial terpene synthases residing in the genomes of uncultivated organisms living in the soil, indicating a vast array of putative terpenoids waiting to be discovered. RESULTS: We aimed to develop a high-throughput functional metagenomic screening system for identifying novel terpene synthases from bacterial metagenomes by relieving the toxicity of terpene biosynthesis precursors to the Escherichia coli host. The precursor toxicity was achieved using an inducible operon encoding the prenyl pyrophosphate synthetic pathway and supplementation of the mevalonate precursor. Host strain and screening procedures were finely optimized to minimize false positives arising from spontaneous mutations, which avoid the precursor toxicity. Our functional metagenomic screening of human fecal metagenomes yielded a novel β-farnesene synthase, which does not show amino acid sequence similarity to known β-farnesene synthases. Engineered S. cerevisiae expressing the screened β-farnesene synthase produced 120 mg/L β-farnesene from glucose (2.86 mg/g glucose) with a productivity of 0.721 g/L∙h. CONCLUSIONS: A unique functional metagenomic screening procedure was established for screening terpene synthases from metagenomic libraries. This research proves the potential of functional metagenomics as a sequence-independent avenue for isolating targeted enzymes from uncultivated organisms in various environmental habitats. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13068-022-02189-9. BioMed Central 2022-10-08 /pmc/articles/PMC9548185/ /pubmed/36209178 http://dx.doi.org/10.1186/s13068-022-02189-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Kwak, Suryang
Crook, Nathan
Yoneda, Aki
Ahn, Naomi
Ning, Jie
Cheng, Jiye
Dantas, Gautam
Functional mining of novel terpene synthases from metagenomes
title Functional mining of novel terpene synthases from metagenomes
title_full Functional mining of novel terpene synthases from metagenomes
title_fullStr Functional mining of novel terpene synthases from metagenomes
title_full_unstemmed Functional mining of novel terpene synthases from metagenomes
title_short Functional mining of novel terpene synthases from metagenomes
title_sort functional mining of novel terpene synthases from metagenomes
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9548185/
https://www.ncbi.nlm.nih.gov/pubmed/36209178
http://dx.doi.org/10.1186/s13068-022-02189-9
work_keys_str_mv AT kwaksuryang functionalminingofnovelterpenesynthasesfrommetagenomes
AT crooknathan functionalminingofnovelterpenesynthasesfrommetagenomes
AT yonedaaki functionalminingofnovelterpenesynthasesfrommetagenomes
AT ahnnaomi functionalminingofnovelterpenesynthasesfrommetagenomes
AT ningjie functionalminingofnovelterpenesynthasesfrommetagenomes
AT chengjiye functionalminingofnovelterpenesynthasesfrommetagenomes
AT dantasgautam functionalminingofnovelterpenesynthasesfrommetagenomes