Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in penicillium species

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ABSTRACT Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However,


less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we sequenced the genomes of 9 _Penicillium_ species and, together with 15


published genomes, we investigated the secondary metabolism of _Penicillium_ and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of


1,317 putative biosynthetic gene clusters (BGCs) were identified, and polyketide synthase and non-ribosomal peptide synthetase based BGCs were grouped into gene cluster families and mapped


to known pathways. The grouping of BGCs allowed us to study the evolutionary trajectory of pathways based on 6-methylsalicylic acid (6-MSA) synthases. Finally, we cross-referenced the


predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a


previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic diversity of Penicillia and highlights the potential of these species


as a source of new antibiotics and other pharmaceuticals. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS


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Food Microbiol._ 189, 51–60 (2014). CAS  PubMed  Google Scholar  Download references ACKNOWLEDGEMENTS This work was supported by the European Commission Marie Curie Initial Training Network


Quantfung (FP7-People-2013-ITN, grant no. 607332), the Novo Nordisk Foundation and the Knut and Alice Wallenberg Foundation. The computations were performed using resources at the Chalmers


Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). Sequencing support was provided by the Science for Life


Laboratory (SciLifeLab), National Genomics Infrastructure (NGI) and UPPMAX (UPPNEX project ID no. b2014081). Support on genome annotation by the National Bioinformatics Infrastructure Sweden


(NBIS) is acknowledged. Agilent Technologies is acknowledged for the Thought Leader Donation of the 6545 UHPLC-QTOF. The authors thank H. Wang for comments on the manuscript. AUTHOR


INFORMATION AUTHORS AND AFFILIATIONS * Department of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden Jens Christian Nielsen, Sylvain


Prigent, Boyang Ji & Jens Nielsen * Department of Biotechnology and Biomedicine, Technical University of Denmark, DK2800 Kgs. Lyngby, Denmark Sietske Grijseels, Kristian Fog Nielsen, 


Jens Christian Frisvad & Mhairi Workman * Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden Jacques Dainat * National Bioinformatics


Infrastructure Sweden (NBIS), SciLifeLab, Uppsala University, 752 37 Uppsala, Sweden Jacques Dainat * Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark,


DK2800 Kgs. Lyngby, Denmark Jens Nielsen Authors * Jens Christian Nielsen View author publications You can also search for this author inPubMed Google Scholar * Sietske Grijseels View author


publications You can also search for this author inPubMed Google Scholar * Sylvain Prigent View author publications You can also search for this author inPubMed Google Scholar * Boyang Ji


View author publications You can also search for this author inPubMed Google Scholar * Jacques Dainat View author publications You can also search for this author inPubMed Google Scholar *


Kristian Fog Nielsen View author publications You can also search for this author inPubMed Google Scholar * Jens Christian Frisvad View author publications You can also search for this


author inPubMed Google Scholar * Mhairi Workman View author publications You can also search for this author inPubMed Google Scholar * Jens Nielsen View author publications You can also


search for this author inPubMed Google Scholar CONTRIBUTIONS J.C.N., J.C.F., M.W. and J.N. conceived the study. J.C.N. designed and performed the bioinformatics computations, and analysed


and interpreted the data. S.P. and B.J. assisted with bioinformatics design and interpretation. J.D. carried out the annotation of the genomes. S.G. and K.F.N. generated culture extracts and


performed LC–MS analysis. J.C.N., S.G. and J.N. wrote the manuscript. All authors read and approved the final version of the manuscript. CORRESPONDING AUTHOR Correspondence to Jens Nielsen.


ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary Figures 1–12, Supplementary


Table 1, Supplementary References. (PDF 13841 kb) SUPPLEMENTARY DATA 1 AND 2 Supplementary Data 1: Detected PKS containing BGCs mapped to BGCs in the MIBiG database. Supplementary Data 2:


Detected NRPS containing BGCs mapped to BGCs in the MIBiG database. (XLSX 51 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Nielsen, J., Grijseels,


S., Prigent, S. _et al._ Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in _Penicillium_ species. _Nat Microbiol_ 2, 17044 (2017).


https://doi.org/10.1038/nmicrobiol.2017.44 Download citation * Received: 03 December 2016 * Accepted: 02 March 2017 * Published: 03 April 2017 * DOI:


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