Iron-meditated fungal starvation by lupine rhizosphere-associated and extremotolerant Streptomyces sp. S29 desferrioxamine production

Open Access via the RSC Open Access Agreement. Acknowledgements SAJ would like to thank the University of Aberdeen for funding doctoral studies through and Elphinstone Scholarship. DL would like to thank the Agencia Nacional de Investigación y Desarrollo (ANID) for funding doctoral studies through ‘Beca nacional de doctorado’ Scholarship. ED would like to thank the Ministry of Higher Education and Scientific Research – Sudan, together with the University of Khartoum, for joint funding of master's studies. We would like to thank to Valeria Razmilic and Jean Franco Castro for their valuable advice and work in the setup of Lupine Streptomyces culture collection. We would also like to thank the support team at GNPS and Justin J. J. van der Hooft at MS2LDA for help with data deposition and for help at any stage of running the relevant workflows.Peer reviewedPublisher PD

Cutting the Gordian knot : early and complete amino acid sequence confirmation of class II lasso peptides by HCD fragmentation

SAJ would like to thank the University of Aberdeen for an Elphinstone Scholarship. CC-A thanks CONICYT PFCHA/DOCTORADO BECAS CHILE/2016 (#21160585) fellowship and CONICYT Basal Centre Grant for the Centre for Biotechnology and Bioengineering, CeBiB (FB0001). JFC also thanks CONICYT for a National PhD Scholarship (#21110356) and a Visiting Student Scholarship.Peer reviewedPostprin

Heterologous expression of a cryptic gene cluster from Streptomyces leeuwenhoekii C34T yields a novel lasso peptide, leepeptin

ACKNOWLEDGEMENTS. We are grateful to Michael Goodfellow and Alan Bull for providing S. leeuwenhoekii C34T , and to Michael Fischbach and Jan Claesen for S. viridochromogenes and S. pristinaspiralis, Matthias Mach for S. davawensis, and Kristian Apel on October 31, 2019 at University of Aberdeen http://aem.asm.org/ Downloaded from 17 for S. roseochromogenes. We thank Govind Chandra for advice on blastP analyses of the lasso peptide data sets, Solène Rollet for technical support in the isolation of leepeptin and Andrew Truman for his comments on the manuscript. J.F.C. and V.R. received National PhD Scholarships (#21110356 and #21110384, respectively) and Visiting Student Scholarships (Becas Chile, 2013–2014) from the National Commission for Scientific and Technological Research (CONICYT). S.A.J. thanks the University of Aberdeen for an Elphinstone Scholarship. This work was supported financially by the Biotechnological and Biological Sciences Research Council (BBSRC, United Kingdom) Institute Strategic Programme Grant “Understanding and Exploiting Plant and Microbial Secondary Metabolism” (BB/J004561/1), the Basal Programme of CONICYT (Chile) for funding of the Centre for Biotechnology and Bioengineering, CeBiB (project FB0001) and the UK Newton Project for UK–Chile collaboration (grant JIC CA586).Peer reviewedPublisher PD

N-Prenylation of Tryptophan by an Aromatic Prenyltransferase from the Cyanobactin Biosynthetic Pathway

Funding This work was supported by grants from the Academy of Finland (259505, D.P.F.), Helsinki University Research grant (490085, D.P.F.) ESCMID grant (4720572, D.P.F.), the Industrial Biotechnology Innovation Centre (IBioIC) studentship (L. D.), the Jane and Aatos Erkko Foundation (K.S.), the BBSRC FoF grant (no BB/M013669/1, W. E. H.), IBCatalyst grant (no. BB/M028526/1, W. E. H.), the Sarcoma UK grant (W. E. H.) and the SULSA Leaders and SULSA PECRE awards (W. E. H.). W. E. H. acknowledges the fund from the ERC grant no. 339367. ACKNOWLEDGEMENTS D.P.F. and K.S. are grateful to Lyudmila Saari, Department of Microbiology, University of Helsinki, for her valuable help in handling the Anabaena sp. UHCC-0232 culture. W. E. H. thanks the Aberdeen Proteomics Facility and the Marine Biodiscovery Centre Mass Spectrometry Facility for extensive MS analysis. W. E. H. is grateful to Mr. Russell Gray (Marine Biodiscovery Centre, University of Aberdeen) for the NMR analysis of our samples.Peer reviewedPostprin

American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18

Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems

Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free‐living Pseudonocardia remains understudied. This study applies a multi‐omics approach to investigate the chemical ecology of free‐living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry‐based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix‐assisted laser desorption/ionisation‐mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free‐living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions

Advancements in capturing and mining mass spectrometry data are transforming natural products research

Covering: 2016 up to 2021 Mass spectrometry (MS) is an essential technology in natural products research with MS fragmentation (MS/MS) approaches becoming a key tool. Recent advancements in MS yield dense metabolomics datasets which have been, conventionally, used by individual labs for individual projects; however, a shift is brewing. The movement towards open MS data (and other structural characterization data) and accessible data mining tools is emerging in natural products research. Over the past 5 years, this movement has rapidly expanded and evolved with no slowdown in sight; the capabilities of today vastly exceed those of 5 years ago. Herein, we address the analysis of individual datasets, a situation we are calling the '2021 status quo', and the emergent framework to systematically capture sample information (metadata) and perform repository-scale analyses. We evaluate public data deposition, discuss the challenges of working in the repository scale, highlight the challenges of metadata capture and provide illustrative examples of the power of utilizing repository data and the tools that enable it. We conclude that the advancements in MS data collection must be met with advancements in how we utilize data; therefore, we argue that open data and data mining is the next evolution in obtaining the maximum potential in natural products research

Current status of secondary metabolite pathways linked to their related biosynthetic gene clusters in <i>Aspergillus</i> section <i>Nigri</i>

Covering: up to the end of 2021Aspergilli are biosynthetically 'talented' micro-organisms and therefore the natural products community has continually been interested in the wealth of biosynthetic gene clusters (BGCs) encoding numerous secondary metabolites related to these fungi. With the rapid increase in sequenced fungal genomes combined with the continuous development of bioinformatics tools such as antiSMASH, linking new structures to unknown BGCs has become much easier when taking retro-biosynthetic considerations into account. On the other hand, in most cases it is not as straightforward to prove proposed biosynthetic pathways due to the lack of implemented genetic tools in a given fungal species. As a result, very few secondary metabolite biosynthetic pathways have been characterized even amongst some of the most well studied Aspergillus spp., section Nigri (black aspergilli). This review will cover all known biosynthetic compound families and their structural diversity known from black aspergilli. We have logically divided this into sub-sections describing major biosynthetic classes (polyketides, non-ribosomal peptides, terpenoids, meroterpenoids and hybrid biosynthesis). Importantly, we will focus the review on metabolites which have been firmly linked to their corresponding BGCs