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      Draft Genome Sequences of Six Type Strains of the Genus Massilia

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          Abstract

          High-quality draft genome sequences were determined for 6 Massilia sp. type strains. The genomes of these strains show considerable biosynthetic potential for producing secondary metabolites.

          ABSTRACT

          High-quality draft genome sequences were determined for 6 Massilia sp. type strains. The genomes of these strains show considerable biosynthetic potential for producing secondary metabolites.

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          Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters.

          Peter Cimermancic, Marnix H Medema, Jan Claesen … (2014)
          Although biosynthetic gene clusters (BGCs) have been discovered for hundreds of bacterial metabolites, our knowledge of their diversity remains limited. Here, we used a novel algorithm to systematically identify BGCs in the extensive extant microbial sequencing data. Network analysis of the predicted BGCs revealed large gene cluster families, the vast majority uncharacterized. We experimentally characterized the most prominent family, consisting of two subfamilies of hundreds of BGCs distributed throughout the Proteobacteria; their products are aryl polyenes, lipids with an aryl head group conjugated to a polyene tail. We identified a distant relationship to a third subfamily of aryl polyene BGCs, and together the three subfamilies represent the largest known family of biosynthetic gene clusters, with more than 1,000 members. Although these clusters are widely divergent in sequence, their small molecule products are remarkably conserved, indicating for the first time the important roles these compounds play in Gram-negative cell biology. Copyright © 2014 Elsevier Inc. All rights reserved.
          Article 0 comments Cited 359 times – based on 0 reviews     Review now
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            Mass spectral molecular networking of living microbial colonies.

            J. Watrous, P. Roach, T Alexandrov … (2012)
            Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a "holy grail" in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of live microbial colonies directly from a Petri dish without any sample preparation. Nanospray desorption electrospray ionization mass spectrometry (MS), combined with alignment of MS data and molecular networking, enabled monitoring of metabolite production from live microbial colonies from diverse bacterial genera, including Bacillus subtilis, Streptomyces coelicolor, Mycobacterium smegmatis, and Pseudomonas aeruginosa. This work demonstrates that, by using these tools to visualize small molecular changes within bacterial interactions, insights can be gained into bacterial developmental processes as a result of the improved organization of MS/MS data. To validate this experimental platform, metabolic profiling was performed on Pseudomonas sp. SH-C52, which protects sugar beet plants from infections by specific soil-borne fungi [R. Mendes et al. (2011) Science 332:1097-1100]. The antifungal effect of strain SH-C52 was attributed to thanamycin, a predicted lipopeptide encoded by a nonribosomal peptide synthetase gene cluster. Our technology, in combination with our recently developed peptidogenomics strategy, enabled the detection and partial characterization of thanamycin and showed that it is a monochlorinated lipopeptide that belongs to the syringomycin family of antifungal agents. In conclusion, the platform presented here provides a significant advancement in our ability to understand the spatiotemporal dynamics of metabolite production in live microbial colonies and communities.
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              The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters.

              Harald Gross, Virginia O. Stockwell, Marcella D. Henkels … (2007)
              With the increasing number of genomes sequenced and available in the public domain, a large number of orphan gene clusters, for which the encoded natural product is unknown, have been identified. These orphan gene clusters represent a tremendous source of novel and possibly bioactive compounds. Here, we describe a "genomisotopic approach," which employs a combination of genomic sequence analysis and isotope-guided fractionation to identify unknown compounds synthesized from orphan gene clusters containing nonribosomal peptide synthetases. Analysis of the Pseudomonas fluorescens Pf-5 genome led to the identification of an orphan gene cluster predicted to code for the biosynthesis of a lipopeptide natural product. Application of the genomisotopic approach to isolate the product of this gene cluster resulted in the discovery of orfamide A, founder of a group of bioactive cyclic lipopeptides.
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                Author and article information

                Contributors
                J. Cameron Thrash: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                Journal ID (publisher-id): MRA
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic): 30 April 2020
                Publication date Collection: April 2020
                Volume: 9
                Issue: 18
                Electronic Location Identifier: e00226-20
                Affiliations
                [a ]Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
                [b ]Research Division for Natural Product Technology (BPTBA), Indonesian Institute of Sciences (LIPI), Wonosari, Indonesia
                [c ]Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
                [d ]German Center for Infection Research (DZIF), Tübingen Partner Site, Tübingen, Germany
                University of Southern California
                Author notes
                Address correspondence to Harald Gross, harald.gross@ 123456uni-tuebingen.de .

                Citation Miess H, Frediansyah A, Göker M, Gross H. 2020. Draft genome sequences of six type strains of the genus Massilia. Microbiol Resour Announc 9:e00226-20. https://doi.org/10.1128/MRA.00226-20.

                Author information
                https://orcid.org/0000-0002-0731-821X
                Article
                Publisher ID: MRA00226-20
                DOI: 10.1128/MRA.00226-20
                PMC ID: 7193931
                PubMed ID: 32354976
                SO-VID: 298b9d38-4129-4ef7-83a5-b187c2da23b0
                Copyright © Copyright © 2020 Miess et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 3 March 2020
                Date accepted : 15 April 2020
                Page count
                Figures: 0, Tables: 1, Equations: 0, References: 38, Pages: 3, Words: 2492
                Funding
                Funded by: Deutsche Forschungsgemeinschaft (DFG), https://doi.org/10.13039/501100001659;
                Award ID: GR2673/2-1
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date April 2020

                Data availability:

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