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Metagenomic Natural Product Discovery in Lichen Provides Metagenomic natural product discovery in lichen PNAS PLUS provides evidence for a family of biosynthetic pathways in diverse symbioses Annette Kampaa,1, Andrey N. Gagunashvilib,1, Tobias A. M. Guldera, Brandon I. Morinakaa, Cristina Daolioc, Markus Godejohannc, Vivian P. W. Miaod, Jörn Piela,e,2, and Ólafur S. Andréssonb,2 aKekule Institute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany; bFaculty of Life and Environmental Sciences, University of Iceland, 101 Reykjavik, Iceland; cBruker BioSpin GmbH, 76287 Rheinstetten, Germany; dDepartment of Microbiology and Immunology, University of British Columbia, V6T 1Z3 Vancouver, Canada; and eInstitute of Microbiology, Eidgenössische Technische Hochschule Zurich, 8093 Zurich, Switzerland Edited by Nancy A. Moran, Yale University, West Haven, CT, and approved June 18, 2013 (received for review March 27, 2013) Bacteria are a major source of natural products that provide rich of mycobiont lectin genes (6), and PCR-based phylogenetics in opportunities for both chemical and biological investigation. Al- investigation of intrathalline bacterial diversity (7). though the vast majority of known bacterial metabolites derive In a number of bacterial–eukaryote symbioses, bacterial from free-living organisms, increasing evidence supports the wide- partners have been implicated in the production of complex spread existence of chemically prolific bacteria living in symbioses. A molecules derived from polyketide synthase (PKS) and nonri- strategy based on bioinformatic prediction, symbiont cultivation, bosomal peptide synthetase (NRPS) pathways (3, 8, 9). Exam- isotopic enrichment, and advanced analytics was used to character- ples include pederin, made by bacteria that live in rove beetles of ize a unique polyketide, nosperin, from a lichen-associated Nostoc the genus Paederus, and structurally related metabolites, the sp. cyanobacterium. The biosynthetic gene cluster and the structure onnamides and psymberin, produced by bacteria that live in of nosperin, determined from 30 μg of compound, are related to marine sponges (Fig. 2). In general, metabolites known or sus- those of the pederin group previously known only from nonphoto- pected to be of symbiont origin show remarkably low structural synthetic bacteria associated with beetles and marine sponges. The overlap with natural products discovered in screening programs presence of this natural product family in such highly dissimilar from free-living bacteria (10). This phenomenon raises the in- associations suggests that some bacterial metabolites may be spe- triguing question of whether symbiont chemistry might encom- fi ci c to symbioses with eukaryotes and encourages exploration pass structural scaffolds covering distinctive regions of chem- of other symbioses for drug discovery and better understand- ical space. ing of ecological interactions mediated by complex bacterial In this study, we applied a combination of metagenomic and metabolites. natural product discovery methods to identify nosperin, the first biosynthesis | Peltigera membranacea | trans-acyltransferase polyketide Significance synthase | 13C nuclear magnetic resonance fi “ Remarkable chemical families are being recognized by studying ymbiosis, de ned by de Bary (1) as the living together of two fi ” diverse symbioses. We identi ed, through metagenomics, the Sorganisms, includes a broad range of partnerships, from fi – rst cyanobacterial trans-AT polyketide biosynthetic pathway loose associations to obligate interdependencies and host para- in the Nostoc symbiont of the lichen Peltigera membranacea site interactions. Many involve microbes, with perhaps the most and showed its expression in natural thalli. An isotope-based — successful between bacteria and early nucleated cells in the technique designed for characterizing minute amounts of ma- Precambrian—leading to mitochondria and chloroplasts in mod- terial confirmed predictions that its product, nosperin, is a dis- ern eukaryotes (2). Symbiotic interactions are being examined tinct member of the pederin family of compounds that was with increasing molecular detail, focusing not only on attributes previously thought exclusive to animal–bacteria associations. that may be beneficial for each organism individually but also on The unexpected discovery of nosperin in lichen expands the what might be important for the association. It is increasingly structural range and known distribution of this family of nat- being recognized that biosynthetic pathways leading to synthesis ural products and suggests a role associated with symbiosis. of specialized metabolites may play key roles in the biology of symbiosis (3). Author contributions: A.N.G. and Ó.S.A. initiated project; A.K., A.N.G., V.P.W.M., J.P., and Ó.S.A. designed research; A.K., A.N.G., B.I.M., V.P.W.M., J.P., and Ó.S.A. performed re- Lichens are ancient and physiologically highly integrated search; A.N.G. carried out bioinformatic analyses of WGS, isolated Nostoc strains and symbioses between heterotrophic filamentous fungi (mycobionts) conducted gene expression studies; A.K. performed feeding studies and compound iso- and cyanobacteria or coccoidal green algae (photobionts) that lations; A.K., T.A.M.G., B.I.M., C.D., and M.G. performed metabolic analyses and elucidated may date as far back as 600 Mya (4). The morphology of the structure; J.P. analyzed the trans-AT PKS genes and performed metabolic prediction; C.D. and M.G. contributed new reagents/analytic tools; A.N.G. and V.P.W.M. examined distri- characteristic and stable macroscopic body of a lichen, the bution of gene cluster; A.K., A.N.G., T.A.M.G., B.I.M., C.D., M.G., V.P.W.M., J.P., and Ó.S.A. thallus, typically bears little resemblance to the individual analyzed data; A.K., A.N.G., T.A.M.G., V.P.W.M., J.P., and Ó.S.A. wrote the paper. organisms that form it and, in many cases, can be highly orga- The authors declare no conflict of interest. nized: fungal cells on the periphery for physical support and This article is a PNAS Direct Submission. MICROBIOLOGY protection and photobiont cells inside, providing photosynthate Data deposition: The sequences reported in this paper have been deposited in the Gen- or fixed nitrogen or both (5) (Fig. 1 A–C). Although the pho- Bank database [accession nos. GQ979609 (nsp gene cluster), JQ975876 (second trans-AT gene cluster), GU591312 (nostopeptolide-like gene cluster), JX181775 (P. membranacea tobionts can often be isolated in pure culture (Fig. 1D), most WGS Nostoc rRNA genes), KC489223 (heterocyst glycolipid gene cluster), KC291407 mycobionts (almost exclusively from the Ascomycota) are re- (rbcLXS operon), and JX975209 (Nostoc sp. N6 rRNA genes)]. fractory to propagation in vitro by standard methods, and intact 1A.K. and A.N.G. contributed equally to this work. fi lichens cannot be maintained arti cially for long. Nevertheless, 2To whom correspondence should be addressed. E-mail: [email protected] or [email protected]. such limitations are gradually being overcome using advanced This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. analytical platforms, e.g., metagenomics in the characterization 1073/pnas.1305867110/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1305867110 PNAS | Published online July 29, 2013 | E3129–E3137 Downloaded by guest on September 25, 2021 A B C D Fig. 1. The foliose lichen Peltigera membranacea and Nostoc symbiont. (A) Lichen in situ. (Scale bar, 5 cm.) (B) Rhizines (Rhi) on lower surface and apothecia (Apo) protruding from thallus edge. (C) Thallus cross section illustrating stratified internal structure including photosynthetic cyanobiont layer (shown with arrows) between cortical and medullary mycobiont layers (above and below, respectively). (Scale bar, 100 μm.) (D) Nostoc sp. N6 in culture. (Scale bar, 100 μm.) (photograph for Fig. 1C, courtesy of Martin Grube). member of the pederin family from a lichenized cyanobacterium of the Nostoc genome, such as hgl (involvedinheterocystgly- and a further example toward the emerging concept of symbio- colipid biosynthesis; SI Appendix,TableS1). The longer of the sis-associated natural product pathways (10). two gene clusters in P. membranacea, designated “nsp” (Fig. 3) had significant homology to the gene clusters for the biosynthesis Results of pederin family compounds and therefore was selected for Discovery of Trans-AT PKS Genes in the Lichen Metagenome. Peltigera further investigation. membranacea is a widely distributed terrestrial lichen carrying The nsp gene cluster consists of a 59-kb region with 3 large Nostoc sp. as its photobiont (Fig. 1 A–D). Total lichen DNA genes (nspA, nspC, and nspD) that encode multidomain PKS or extracted from field samples collected in Iceland processed for PKS/NRPS proteins and a suite of 10 smaller genes that encode whole genome sequencing (WGS) (11) revealed approximately accessory enzymes (Fig. 3; Table 1). The multidomain proteins equal contributions from the mycobiont, the photobiont, and the together comprise a “starter” module 0, followed by nine PKS or community of intrathalline microbes. Bioinformatic mining of PKS/NRPS elongating modules (modules 1–9). The 5′ end of the the initial metagenome assembly yielded 18 candidate clusters gene cluster, i.e., nspA (modules 0–3), nspB, and the beginning of containing genes that encode PKS enzymes (SI Appendix, Table nspC (module 4 and the KS region of module 5), as well as ac- S1). Among the putative bacterial gene clusters, two were cessory genes at the 3′ end of the
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