Mouncey, Nigel J

Otani, Hiroshi

Udwary, Daniel W

eScholarship - University of California

Lawrence Berkeley National LaboratoryLBL PublicationsTitleNew keys to unlock the treasure trove of microbial natural productsPermalinkhttps://escholarship.org/uc/item/79s3p5b6JournalNature Reviews Microbiology, 19(11)ISSN1740-1526AuthorsUdwary, Daniel WOtani, HiroshiMouncey, Nigel JPublication Date2021-11-01DOI10.1038/s41579-021-00631-7 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaNew keys to unlock the treasure trove ofmicrobial natural productsDaniel W. Udwary , Hiroshi Otani and Nigel J. MounceyThis month’s Genome Watch highlightshow recent advances in computationalidentification of biosynthetic geneclusters (BGCs), and in their experimentalmanipulation, are opening new avenuesto access novel secondary metabolites.Secondary metabolism- based compound discoveryhas produced invaluable medical andagricultural treatments, but the discovery processhas been beset with technical complications,from genomic identification to physicalisolation.As genome- scale sequencing has becomeroutine, computational tools have been crucialas a first- pass approach for identifyingsecondary metabolism pathways. For manyyears, antiSMASH has been the most comprehensiveand accurate tool for predictingsecondary metabolite biosynthetic geneclusters (BGCs), and the BiG- FAM databasewill further advance BGC identification1.Constructed by clustering more than amillion antiSMASH- identified BGCs frompublic sequence data into ‘gene cluster families’(GCFs), the database allows users toquickly identify groups of closely relatedBGCs. BiG- FAM is closely tied with the antiSMASHecosystem, and users can connectantiSMASH webtool result IDs directly withBiG- FAM’s data, easily identifying BGC relationshipsin their own data. Having a system to assist in such comparisons is expected toprove invaluable for advancing secondarymetabolism knowledge.The expression of BGCs is governed by amyriad of tight regulatory systems so that specializednatural products are only producedwhen required by the host. This presentschallenges to researchers attempting to coaxhost organisms to synthesize these products.To understand the mechanism of regulation,comparative metabologenomic analysis ofthe polycyclic tetramate macrolactam (PTM)BGC was conducted. The researchers gathereda panel of Streptomyces griseus strains,including poor and robust PTM producers2,and by comparing PTM BGC and genomicsequences with PTM production, regulatorymechanisms were revealed, including thetranscriptional regulator controlling expression,and variations in the promoter that differentiateproduction. These results highlightthe importance of studying closely relatedorganisms to discover regulators of BGCexpression and should be broadly applicableto highly sequenced bacterial clades.Rewiring regulatory systems offers approachesto express BGCs and synthesize theirproducts. Park et al. employed a massivelyparallel reporter assay to explore a library of>3,000 natural BGC regulatory sequencesin Streptomyces albidoflavus J1074 (ref.3).Through this approach, the authors foundtranscription levels spanning a 1,000- foldrange and identified key features associatedwith expression. By expressing global regulatoryproteins, the authors could differentiallymodulate BGC regulatory sequences.Heterologous expression of transcriptionalregulators can lead to BGC expression, providingfoundational knowledge to overcomecontrol mechanisms, and allowing novelmetabolites to be produced on demand.Cloning and heterologous expression ofBGCs is an alternative strategy. However, thelarge and repetitive sequence of many BGCclasses makes their cloning via traditionalmethods inefficient. ‘CAPTURE’ is a rapidand highly efficient direct cloning methodconsisting of DNA digestion by Cas12a,DNA assembly and Cre–lox in vivo DNAcircularization. The technique was successfullyused to clone 47 BGCs with varyingsizes up to 113 kb (ref.4). Characterizing theseBGCs resulted in the discovery of 15 newsecondary metabolites, including bipentaromycin,which showed strong antimicrobialactivity against multiple bacteria, includingmethicillin- resistant Staphylococcus aureus.Although there are a tremendous numberof natural products remaining to be discovered,continuous advancement in genomictechnologies, using a multi- faceted combinationof computational and laboratory techniques,will be essential for unlocking themetabolic potential of microorganisms.1. Kautsar, S. A. et al. BiG- FAM: the biosynthetic genecluster families database. Nucleic Acids Res. 49,D490–D497 (2021).2. Qi, Y., Nepal, K. K. & Blodgett, J. A. V. A comparativemetabologenomic approach reveals mechanisticinsights into Streptomyces antibiotic crypticity.Proc. Natl Acad. Sci. USA 118, e2103515118(2021).3. Park, J., Yim, S. S. & Wang, H. H. High- throughputtranscriptional characterization of regulatorysequences from bacterial biosynthetic gene clusters.ACS Synth. Biol. 10, 1859–1873 (2021).4. Enghiad, B. et al. Cas12a- assisted precise targetedcloning using in vivo Cre- lox recombination.Nat. Commun. 12, 1171 (2021).

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New keys to unlock the treasure trove of microbial natural products

https://escholarship.org/uc/item/79s3p5b6

New keys to unlock the treasure trove of microbial natural products.

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