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secondary metabolism

  • Open Access
    Twists and Turns in the Salicylate Catabolism of <em>Aspergillus terreus</em>, Revealing New Roles of the 3-Hydroxyanthranilate Pathway
    Research Article | Molecular Biology and Physiology
    Twists and Turns in the Salicylate Catabolism of Aspergillus terreus, Revealing New Roles of the 3-Hydroxyanthranilate Pathway

    Aspergilli are versatile cell factories used in industry for the production of organic acids, enzymes, and pharmaceutical drugs. To date, bio-based production of organic acids relies on food substrates.

    Tiago M. Martins, Celso Martins, Paula Guedes, Cristina Silva Pereira
  • Open Access
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
    Editor's Pick Research Article | Applied and Environmental Science
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses

    Nongrowth states are common for bacteria that live in environments that are densely populated and predominantly nutrient exhausted, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary-phase exometabolites and RNA transcripts for each of three environmental bacterial strains.

    John L. Chodkowski, Ashley Shade
  • Open Access
    Elucidating the Diversity and Potential Function of Nonribosomal Peptide and Polyketide Biosynthetic Gene Clusters in the Root Microbiome
    Research Article | Host-Microbe Biology
    Elucidating the Diversity and Potential Function of Nonribosomal Peptide and Polyketide Biosynthetic Gene Clusters in the Root Microbiome

    We identified distinct secondary-metabolite-encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode novel metabolites and may have unique...

    Barak Dror, Zongqiang Wang, Sean F. Brady, Edouard Jurkevitch, Eddie Cytryn
  • Open Access
    RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery
    Research Article | Novel Systems Biology Techniques
    RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

    Bioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary...

    Alexander M. Kloosterman, Kyle E. Shelton, Gilles P. van Wezel, Marnix H. Medema, Douglas A. Mitchell
  • Open Access
    Resistance Gene-Directed Genome Mining of 50 <em>Aspergillus</em> Species
    Research Article | Novel Systems Biology Techniques
    Resistance Gene-Directed Genome Mining of 50 Aspergillus Species

    Species belonging to the Aspergillus genus are known to produce a large number of secondary metabolites; some of these compounds are used as pharmaceuticals, such as penicillin, cyclosporine, and statin. With whole-genome sequencing, it became apparent that the genetic potential for secondary metabolite production is much larger than expected. As an increasing number of species are whole-genome sequenced, thousands of secondary...

    Inge Kjærbølling, Tammi Vesth, Mikael R. Andersen
  • Open Access
    Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi
    Research Article | Molecular Biology and Physiology
    Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi

    Secondary metabolites are a major source of pharmaceuticals, especially antibiotics. However, the development of efficient processes of production of secondary metabolites has proved troublesome due to a limited understanding of the metabolic regulations governing secondary metabolism. By analyzing the conservation in gene expression across secondary metabolite-producing fungal species, we identified a metabolic signature that links...

    Jens Christian Nielsen, Sylvain Prigent, Sietske Grijseels, Mhairi Workman, Boyang Ji, Jens Nielsen
  • Open Access
    Considering the Lives of Microbes in Microbial Communities
    Special Issue Perspective | Molecular Biology and Physiology
    Considering the Lives of Microbes in Microbial Communities

    Over the last decades, sequencing technologies have transformed our ability to investigate the composition and functional capacity of microbial communities. Even so, critical questions remain about these complex systems that cannot be addressed by the bulk, community-averaged data typically provided by sequencing methods.

    Elizabeth A. Shank
  • Open Access
    <em>luxR</em> Homolog-Linked Biosynthetic Gene Clusters in <em>Proteobacteria</em>
    Research Article | Ecological and Evolutionary Science
    luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria

    Bacteria biosynthesize specialized metabolites with a variety of ecological functions, including defense against other microbes. Genes that code for specialized metabolite biosynthetic enzymes are frequently clustered together. These BGCs are often regulated by a transcription factor encoded within the cluster itself. These pathway-specific regulators respond to a signal or indirectly through other means of environmental sensing. Many...

    Carolyn A. Brotherton, Marnix H. Medema, E. Peter Greenberg
  • Open Access
    Large-Scale Bioinformatics Analysis of <em>Bacillus</em> Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology
    Research Article | Molecular Biology and Physiology
    Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology

    Bacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus’s metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial...

    Kirk J. Grubbs, Rachel M. Bleich, Kevin C. Santa Maria, Scott E. Allen, Sherif Farag, AgBiome Team, Elizabeth A. Shank, Albert A. Bowers
  • Open Access
    Growth on Chitin Impacts the Transcriptome and Metabolite Profiles of Antibiotic-Producing <span class="named-content genus-species" id="named-content-1">Vibrio coralliilyticus</span> S2052 and <span class="named-content genus-species" id="named-content-2">Photobacterium galatheae</span> S2753
    Editor's Pick Research Article | Applied and Environmental Science
    Growth on Chitin Impacts the Transcriptome and Metabolite Profiles of Antibiotic-Producing Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753

    The bacterial family Vibrionaceae (vibrios) is considered a major player in the degradation of chitin, the most abundant polymer in the marine environment; however, the majority of studies on the topic have focused on a small number of Vibrio species. In this study, we analyzed the genomes of two vibrios to assess their genetic potential for the degradation of chitin. We then used transcriptomics and metabolomics to...

    Sonia Giubergia, Christopher Phippen, Kristian Fog Nielsen, Lone Gram
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