41 results on '"Mouncey, Nigel J"'
Search Results
2. Phylogenomics and genetic analysis of solvent-producing Clostridium species
- Author
-
Jensen, Rasmus O., Schulz, Frederik, Roux, Simon, Klingeman, Dawn M., Mitchell, Wayne P., Udwary, Daniel, Moraïs, Sarah, Reynoso, Vinicio, Winkler, James, Nagaraju, Shilpa, De Tissera, Sashini, Shapiro, Nicole, Ivanova, Natalia, Reddy, T. B. K., Mizrahi, Itzhak, Utturkar, Sagar M., Bayer, Edward A., Woyke, Tanja, Mouncey, Nigel J., Jewett, Michael C., Simpson, Séan D., Köpke, Michael, Jones, David T., and Brown, Steven D.
- Published
- 2024
- Full Text
- View/download PDF
3. Cytochromes P450 involved in bacterial RiPP biosyntheses
- Author
-
Kunakom, Sylvia, Otani, Hiroshi, Udwary, Daniel W, Doering, Drew T, and Mouncey, Nigel J
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Biotechnology ,Ribosomes ,Protein Processing ,Post-Translational ,Bacteria ,Peptides ,Cytochrome P-450 Enzyme System ,Biological Products ,Cytochrome P450 ,Natural products ,RiPP ,Secondary metabolites ,Food Sciences ,Industrial Biotechnology ,Biochemistry and cell biology ,Industrial biotechnology ,Microbiology - Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally synthesized proteins and additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 (P450s) are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of P450s distributed across all domains of life. While the number of characterized P450s involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C-C or C-N bond formation. Formation of some RiPPs is catalyzed by more than one P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered.SummaryThe presence of genes encoding P450s in gene clusters for ribosomally synthesized and post-translationally modified peptides expand structural and functional diversity of these secondary metabolites, and here, we review the current state of this knowledge.
- Published
- 2023
4. Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.
- Author
-
Seshadri, Rekha, Roux, Simon, Huber, Katharina J, Wu, Dongying, Yu, Sora, Udwary, Dan, Call, Lee, Nayfach, Stephen, Hahnke, Richard L, Pukall, Rüdiger, White, James R, Varghese, Neha J, Webb, Cody, Palaniappan, Krishnaveni, Reimer, Lorenz C, Sardà, Joaquim, Bertsch, Jonathon, Mukherjee, Supratim, Reddy, TBK, Hajek, Patrick P, Huntemann, Marcel, Chen, I-Min A, Spunde, Alex, Clum, Alicia, Shapiro, Nicole, Wu, Zong-Yen, Zhao, Zhiying, Zhou, Yuguang, Evtushenko, Lyudmila, Thijs, Sofie, Stevens, Vincent, Eloe-Fadrosh, Emiley A, Mouncey, Nigel J, Yoshikuni, Yasuo, Whitman, William B, Klenk, Hans-Peter, Woyke, Tanja, Göker, Markus, Kyrpides, Nikos C, and Ivanova, Natalia N
- Subjects
actinobacteria ,comparative genomics ,ecology ,evolution ,metagenomics ,microbiology ,mycobacteria ,secondary metabolites ,Infectious Diseases ,Genetics ,Biotechnology ,Vaccine Related ,Rare Diseases ,Human Genome ,Infection ,Good Health and Well Being - Abstract
The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.
- Published
- 2022
5. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles
- Author
-
Volland, Jean-Marie, Gonzalez-Rizzo, Silvina, Gros, Olivier, Tyml, Tomáš, Ivanova, Natalia, Schulz, Frederik, Goudeau, Danielle, Elisabeth, Nathalie H, Nath, Nandita, Udwary, Daniel, Malmstrom, Rex R, Guidi-Rontani, Chantal, Bolte-Kluge, Susanne, Davies, Karen M, Jean, Maïtena R, Mansot, Jean-Louis, Mouncey, Nigel J, Angert, Esther R, Woyke, Tanja, and Date, Shailesh V
- Subjects
Microbiology ,Biological Sciences ,Biotechnology ,Human Genome ,Genetics ,DNA Copy Number Variations ,DNA ,Bacterial ,Life Cycle Stages ,Organelles ,Polyploidy ,Thiotrichaceae ,General Science & Technology - Abstract
Cells of most bacterial species are around 2 micrometers in length, with some of the largest specimens reaching 750 micrometers. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Candidatus (Ca.) Thiomargarita magnifica, a bacterium that has an average cell length greater than 9000 micrometers and is visible to the naked eye. These cells grow orders of magnitude over theoretical limits for bacterial cell size, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes into daughter cells. These features, along with compartmentalization of genomic material and ribosomes in translationally active organelles bound by bioenergetic membranes, indicate gain of complexity in the Thiomargarita lineage and challenge traditional concepts of bacterial cells.
- Published
- 2022
6. Compendium of Metabolomic and Genomic Datasets for Cyanobacteria: Mined the Gap
- Author
-
Ferrinho, Scarlet, Connaris, Helen, Mouncey, Nigel J., and Goss, Rebecca J.M.
- Published
- 2024
- Full Text
- View/download PDF
7. Comparative and pangenomic analysis of the genus Streptomyces
- Author
-
Otani, Hiroshi, Udwary, Daniel W, and Mouncey, Nigel J
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Industrial Biotechnology ,Human Genome ,Streptomyces ,Biosynthetic Pathways ,Secondary Metabolism ,Sequence Analysis ,DNA ,Polyketides ,Multigene Family - Abstract
Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.
- Published
- 2022
8. RIViT-seq enables systematic identification of regulons of transcriptional machineries
- Author
-
Otani, Hiroshi and Mouncey, Nigel J
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Human Genome ,Biotechnology ,Genetics ,1.1 Normal biological development and functioning ,Underpinning research ,Generic health relevance ,Gene Expression Regulation ,Bacterial ,Gene Regulatory Networks ,Regulon ,Sigma Factor ,Streptomyces coelicolor ,Transcription Factors - Abstract
Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcription factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is laborious and not scalable. Here, we demonstrate regulon identification by in vitro transcription-sequencing (RIViT-seq) that enables systematic identification of regulons of transcription factors by combining an in vitro transcription assay and RNA-sequencing. Using this technology, target genes of 11 sigma factors were identified in Streptomyces coelicolor A3(2). The RIViT-seq data expands the transcriptional regulatory network in this bacterium, discovering regulatory cascades and crosstalk between sigma factors. Implementation of RIViT-seq with other transcription factors and in other organisms will improve our understanding of transcriptional regulatory networks across biology.
- Published
- 2022
9. The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource
- Author
-
Eloe-Fadrosh, Emiley A, Ahmed, Faiza, Anubhav, Babinski, Michal, Baumes, Jeffrey, Borkum, Mark, Bramer, Lisa, Canon, Shane, Christianson, Danielle S, Corilo, Yuri E, Davenport, Karen W, Davis, Brandon, Drake, Meghan, Duncan, William D, Flynn, Mark C, Hays, David, Hu, Bin, Huntemann, Marcel, Kelliher, Julia, Lebedeva, Sofya, Li, Po-E, Lipton, Mary, Lo, Chien-Chi, Martin, Stanton, Millard, David, Miller, Kayd, Miller, Mark A, Piehowski, Paul, Jackson, Elais Player, Purvine, Samuel, Reddy, TBK, Richardson, Rachel, Rudolph, Marisa, Sarrafan, Setareh, Shakya, Migun, Smith, Montana, Stratton, Kelly, Sundaramurthi, Jagadish Chandrabose, Vangay, Pajau, Winston, Donald, Wood-Charlson, Elisha M, Xu, Yan, Chain, Patrick SG, McCue, Lee Ann, Mans, Douglas, Mungall, Christopher J, Mouncey, Nigel J, and Fagnan, Kjiersten
- Subjects
Microbiology ,Biological Sciences ,Human Genome ,Genetics ,Data Science ,Microbiome ,Good Health and Well Being ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
The National Microbiome Data Collaborative (NMDC) Data Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles (1). The NMDC Data Portal currently hosts 10.2 terabytes of multi-omics microbiome data, spanning five data types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, and natural organic matter characterizations), generated at two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Systems Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). A flexible data schema (https://github.com/microbiomedata/nmdc-schema) leveraging community-driven standards underpins how data is managed and integrated. Annotated multi-omic data products are produced by the NMDC workflows and linked through common biosamples to enable search capabilities based on environmental context, instrumentation, and functional attributes. As a pilot system, the NMDC Data Portal offers download capabilities and several search components, including interactive geographic visualization of samples; environmental classification distribution visualized through an interactive Sankey diagram; time-series slider to select longitudinal samples of interest; and an upset plot displaying the number of multi-omics data generated from the same biosample within a study.
- Published
- 2022
10. Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE
- Author
-
Ke, Jing, Zhao, Zhiying, Coates, Cameron R, Hadjithomas, Michalis, Kuftin, Andrea, Louie, Katherine, Weller, David, Thomashow, Linda, Mouncey, Nigel J, Northen, Trent R, and Yoshikuni, Yasuo
- Subjects
Biological Sciences ,Industrial Biotechnology ,Infectious Diseases ,Biotechnology ,Emerging Infectious Diseases ,Biodefense ,Multigene Family ,Phenazines ,Recombinases ,CRAGE ,Chassis-Independent Recombinase-Assisted ,Genome Engineering ,Natural Products ,Secondary metabolites ,Multi-Chassis Engineering ,Chassis-Independent Recombinase-Assisted Genome Engineering ,Biochemistry and cell biology ,Industrial biotechnology - Abstract
Phenazines (Phzs), a family of chemicals with a phenazine backbone, are secondary metabolites with diverse properties such as antibacterial, anti-fungal, or anticancer activity. The core derivatives of phenazine, phenazine-1-carboxylic acid (PCA) and phenazine-1,6-dicarboxylic acid (PDC), are themselves precursors for various other derivatives. Recent advances in genome mining tools have enabled researchers to identify many biosynthetic gene clusters (BGCs) that might produce novel Phzs. To characterize the function of these BGCs efficiently, we performed modular construct assembly and subsequent multi-chassis heterologous expression using chassis-independent recombinase-assisted genome engineering (CRAGE). CRAGE allowed rapid integration of a PCA BGC into 23 diverse γ-proteobacteria species and allowed us to identify top PCA producers. We then used the top five chassis hosts to express four partially refactored PDC BGCs. A few of these platforms produced high levels of PDC. Specifically, Xenorhabdus doucetiae and Pseudomonas simiae produced PDC at a titer of 293 mg/L and 373 mg/L, respectively, in minimal media. These titers are significantly higher than those previously reported. Furthermore, selectivity toward PDC production over PCA production was improved by up to 9-fold. The results show that these strains are promising chassis for production of PCA, PDC, and their derivatives, as well as for function characterization of Phz BGCs identified via bioinformatics mining.
- Published
- 2022
11. New keys to unlock the treasure trove of microbial natural products
- Author
-
Udwary, Daniel W, Otani, Hiroshi, and Mouncey, Nigel J
- Subjects
Microbiology ,Biological Sciences ,Bacteria ,Biological Products ,Cloning ,Molecular ,DNA ,Bacterial ,Genome ,Bacterial ,Multigene Family ,Medical Microbiology - Published
- 2021
12. A genomic catalog of Earth’s microbiomes
- Author
-
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, TBK, Nielsen, Torben, Kirton, Edward, Faria, José P, Edirisinghe, Janaka N, Henry, Christopher S, Jungbluth, Sean P, Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M, Arkin, Adam P, Tringe, Susannah G, Visel, Axel, Woyke, Tanja, Mouncey, Nigel J, Ivanova, Natalia N, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A
- Subjects
Climate Change Impacts and Adaptation ,Biological Sciences ,Ecology ,Microbiology ,Environmental Sciences ,Genetics ,Human Genome ,Air Microbiology ,Animals ,Archaea ,Bacteria ,Catalogs as Topic ,Ecosystem ,Humans ,Metabolomics ,Metagenome ,Metagenomics ,Phylogeny ,Soil Microbiology ,Viruses ,Water Microbiology ,IMG/M Data Consortium - Abstract
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
- Published
- 2021
13. Author Correction: A genomic catalog of Earth’s microbiomes
- Author
-
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, TBK, Nielsen, Torben, Kirton, Edward, Faria, José P, Edirisinghe, Janaka N, Henry, Christopher S, Jungbluth, Sean P, Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M, Arkin, Adam P, Tringe, Susannah G, Visel, Axel, Woyke, Tanja, Mouncey, Nigel J, Ivanova, Natalia N, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Human Genome ,IMG/M Data Consortium - Abstract
In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria; Jeffrey L. Blanchard of the Biology Department, University of Massachusetts Amherst, Amherst, MA, USA; Kristen M. DeAngelis of the Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA; and William Rodriguez-Reillo of the Research Computing Division, Harvard Medical School, Boston, MA, USA. The error has been corrected in the PDF and HTML versions of the article.
- Published
- 2021
14. Publisher Correction: A genomic catalog of Earth’s microbiomes
- Author
-
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, TBK, Nielsen, Torben, Kirton, Edward, Faria, José P, Edirisinghe, Janaka N, Henry, Christopher S, Jungbluth, Sean P, Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M, Arkin, Adam P, Tringe, Susannah G, Visel, Axel, Woyke, Tanja, Mouncey, Nigel J, Ivanova, Natalia N, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A
- Subjects
Historical Studies ,Engineering ,History ,Heritage and Archaeology ,Biotechnology ,Human Genome ,Genetics ,IMG/M Data Consortium - Abstract
This paper was originally published under standard Springer Nature copyright (© The Author(s), under exclusive licence to Springer Nature America, Inc.). It is now available as an open-access paper under a Creative Commons Attribution 4.0 International license. The error has been corrected in the print, HTML and PDF versions of the article.
- Published
- 2021
15. Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery
- Author
-
Hurley, Amanda, Chevrette, Marc G, Acharya, Deepa D, Lozano, Gabriel L, Garavito, Manuel, Heinritz, Jen, Balderrama, Luis, Beebe, Mara, DenHartog, Martel L, Corinaldi, Kamiyah, Engels, Renee, Gutierrez, Alyssa, Jona, Orli, Putnam, Josephine HI, Rhodes, Brody, Tsang, Tiffany, Hernandez, Simon, Bascom-Slack, Carol, Blum, Jessamina E, Price, Paul A, Davis, Debra, Klein, Joanna, Pultorak, Joshua, Sullivan, Nora L, Mouncey, Nigel J, Dorrestein, Pieter C, Miller, Sarah, Broderick, Nichole A, and Handelsman, Jo
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Biodefense ,Antimicrobial Resistance ,Infectious Diseases ,Emerging Infectious Diseases ,Infection ,Anti-Bacterial Agents ,Bacteria ,Drug Discovery ,Humans ,Science ,Students ,antimicrobial activity ,crowdsourcing ,multiomics ,Microbiology ,Biochemistry and cell biology ,Medical microbiology - Abstract
The world faces two seemingly unrelated challenges-a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.
- Published
- 2021
16. The National Microbiome Data Collaborative: enabling microbiome science
- Author
-
Wood-Charlson, Elisha M, Anubhav, Auberry, Deanna, Blanco, Hannah, Borkum, Mark I, Corilo, Yuri E, Davenport, Karen W, Deshpande, Shweta, Devarakonda, Ranjeet, Drake, Meghan, Duncan, William D, Flynn, Mark C, Hays, David, Hu, Bin, Huntemann, Marcel, Li, Po-E, Lipton, Mary, Lo, Chien-Chi, Millard, David, Miller, Kayd, Piehowski, Paul D, Purvine, Samuel, Reddy, TBK, Shakya, Migun, Sundaramurthi, Jagadish Chandrabose, Vangay, Pajau, Wei, Yaxing, Wilson, Bruce E, Canon, Shane, Chain, Patrick SG, Fagnan, Kjiersten, Martin, Stanton, McCue, Lee Ann, Mungall, Christopher J, Mouncey, Nigel J, Maxon, Mary E, and Eloe-Fadrosh, Emiley A
- Subjects
Microbiology ,Biological Sciences ,Microbiome ,Data Science ,Humans ,Intersectoral Collaboration ,Microbiota ,Medical Microbiology - Published
- 2020
17. IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase
- Author
-
Palaniappan, Krishnaveni, Chen, I-Min A, Chu, Ken, Ratner, Anna, Seshadri, Rekha, Kyrpides, Nikos C, Ivanova, Natalia N, and Mouncey, Nigel J
- Subjects
Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Human Genome ,Genetics ,Infection ,Bacteriocins ,Biosynthetic Pathways ,Databases ,Genetic ,Genome ,Microbial ,Knowledge Bases ,Metadata ,Metagenome ,Multigene Family ,Secondary Metabolism ,User-Computer Interface ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
Microbial secondary metabolism is a reservoir of bioactive compounds of immense biotechnological and biomedical potential. The biosynthetic machinery responsible for the production of these secondary metabolites (SMs) (also called natural products) is often encoded by collocated groups of genes called biosynthetic gene clusters (BGCs). High-throughput genome sequencing of both isolates and metagenomic samples combined with the development of specialized computational workflows is enabling systematic identification of BGCs and the discovery of novel SMs. In order to advance exploration of microbial secondary metabolism and its diversity, we developed the largest publicly available database of predicted BGCs combined with experimentally verified BGCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc-public). Here we describe the first major content update of the IMG-ABC knowledgebase, since its initial release in 2015, refreshing the BGC prediction pipeline with the latest version of antiSMASH (v5) as well as presenting the data in the context of underlying environmental metadata sourced from GOLD (https://gold.jgi.doe.gov/). This update has greatly improved the quality and expanded the types of predicted BGCs compared to the previous version.
- Published
- 2020
18. The emergence of microbiome centres
- Author
-
Martiny, Jennifer BH, Whiteson, Katrine L, Bohannan, Brendan JM, David, Lawrence A, Hynson, Nicole A, McFall-Ngai, Margaret, Rawls, John F, Schmidt, Thomas M, Abdo, Zaid, Blaser, Martin J, Bordenstein, Seth, Bréchot, Christian, Bull, Carolee T, Dorrestein, Pieter, Eisen, Jonathan A, Garcia-Pichel, Ferran, Gilbert, Jack, Hofmockel, Kirsten S, Holtz, Mary L, Knight, Rob, Mark Welch, David B, McDonald, Daniel, Methé, Barbara, Mouncey, Nigel J, Mueller, Noel T, Pfister, Catherine A, Proctor, Lita, and Sachs, Joel L
- Subjects
Microbiology ,Biological Sciences ,Animals ,Capital Financing ,Communication ,Humans ,Interdisciplinary Research ,Microbiota ,Medical Microbiology - Published
- 2020
19. CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria.
- Author
-
Wang, Gaoyan, Zhao, Zhiying, Ke, Jing, Engel, Yvonne, Shi, Yi-Ming, Robinson, David, Bingol, Kerem, Zhang, Zheyun, Bowen, Benjamin, Louie, Katherine, Wang, Bing, Evans, Robert, Miyamoto, Yu, Cheng, Kelly, Kosina, Suzanne, De Raad, Markus, Silva, Leslie, Luhrs, Alicia, Lubbe, Andrea, Hoyt, David W, Francavilla, Charles, Otani, Hiroshi, Deutsch, Samuel, Washton, Nancy M, Rubin, Edward M, Mouncey, Nigel J, Visel, Axel, Northen, Trent, Cheng, Jan-Fang, Bode, Helge B, and Yoshikuni, Yasuo
- Subjects
Bacteria ,Photorhabdus ,Polyketide Synthases ,Peptide Synthases ,Recombinases ,Genetic Engineering ,Gene Expression Regulation ,Bacterial ,Genes ,Bacterial ,Genome ,Bacterial ,Multigene Family ,Biosynthetic Pathways ,Secondary Metabolism ,Gene Expression Regulation ,Bacterial ,Genes ,Genome ,Microbiology ,Medical Microbiology - Abstract
It is generally believed that exchange of secondary metabolite biosynthetic gene clusters (BGCs) among closely related bacteria is an important driver of BGC evolution and diversification. Applying this idea may help researchers efficiently connect many BGCs to their products and characterize the products' roles in various environments. However, existing genetic tools support only a small fraction of these efforts. Here, we present the development of chassis-independent recombinase-assisted genome engineering (CRAGE), which enables single-step integration of large, complex BGC constructs directly into the chromosomes of diverse bacteria with high accuracy and efficiency. To demonstrate the efficacy of CRAGE, we expressed three known and six previously identified but experimentally elusive non-ribosomal peptide synthetase (NRPS) and NRPS-polyketide synthase (PKS) hybrid BGCs from Photorhabdus luminescens in 25 diverse γ-Proteobacteria species. Successful activation of six BGCs identified 22 products for which diversity and yield were greater when the BGCs were expressed in strains closely related to the native strain than when they were expressed in either native or more distantly related strains. Activation of these BGCs demonstrates the feasibility of exploiting their underlying catalytic activity and plasticity, and provides evidence that systematic approaches based on CRAGE will be useful for discovering and identifying previously uncharacterized metabolites.
- Published
- 2019
20. New voyages to explore the natural product galaxy.
- Author
-
Mouncey, Nigel J, Otani, Hiroshi, Udwary, Daniel, and Yoshikuni, Yasuo
- Subjects
Bacteria ,Biological Products ,Anti-Bacterial Agents ,Genome ,Bacterial ,Multigene Family ,Biosynthetic Pathways ,High-Throughput Nucleotide Sequencing ,Secondary Metabolism ,Biosynthetic gene clusters ,Genome mining ,Integrated platform ,Natural products ,Secondary metabolites ,Streptomyces ,Genetics ,Antimicrobial Resistance ,Human Genome ,Biochemistry and Cell Biology ,Food Sciences ,Industrial Biotechnology ,Biotechnology - Abstract
Natural products are a large family of diverse and complex chemical molecules that have roles in both primary and secondary metabolism, and over 210,000 natural products have been described. Secondary metabolite natural products are of high commercial and societal value with therapeutic uses as antibiotics, antifungals, antitumor and antiparasitic products and in agriculture as products for crop protection and animal health. There is a resurgence of activity in exploring natural products for a wide range of applications, due to not only increasing antibiotic resistance, but the advent of next-generation genome sequencing and new technologies to interrogate and investigate natural product biosynthesis. Genome mining has revealed a previously undiscovered richness of biosynthetic potential in novel biosynthetic gene clusters for natural products. Complementing these computational processes are new experimental platforms that are being developed and deployed to access new natural products.
- Published
- 2019
21. An integrated workflow for phenazine-modifying enzyme characterization
- Author
-
Coates, R Cameron, Bowen, Benjamin P, Oberortner, Ernst, Thomashow, Linda, Hadjithomas, Michalis, Zhao, Zhiying, Ke, Jing, Silva, Leslie, Louie, Katherine, Wang, Gaoyan, Robinson, David, Tarver, Angela, Hamilton, Matthew, Lubbe, Andrea, Feltcher, Meghan, Dangl, Jeffery L, Pati, Amrita, Weller, David, Northen, Trent R, Cheng, Jan-Fang, Mouncey, Nigel J, Deutsch, Samuel, and Yoshikuni, Yasuo
- Subjects
Biological Sciences ,Industrial Biotechnology ,Genetics ,Bacterial Proteins ,Biosynthetic Pathways ,Escherichia coli ,Multigene Family ,Phenazines ,Synthetic biology ,Biosynthesis ,Phenazine ,Pathway ,Refactored ,Pathway design ,Biochemistry and Cell Biology ,Food Sciences ,Biotechnology ,Biochemistry and cell biology ,Industrial biotechnology ,Microbiology - Abstract
Increasing availability of new genomes and putative biosynthetic gene clusters (BGCs) has extended the opportunity to access novel chemical diversity for agriculture, medicine, environmental and industrial purposes. However, functional characterization of BGCs through heterologous expression is limited because expression may require complex regulatory mechanisms, specific folding or activation. We developed an integrated workflow for BGC characterization that integrates pathway identification, modular design, DNA synthesis, assembly and characterization. This workflow was applied to characterize multiple phenazine-modifying enzymes. Phenazine pathways are useful for this workflow because all phenazines are derived from a core scaffold for modification by diverse modifying enzymes (PhzM, PhzS, PhzH, and PhzO) that produce characterized compounds. We expressed refactored synthetic modules of previously uncharacterized phenazine BGCs heterologously in Escherichia coli and were able to identify metabolic intermediates they produced, including a previously unidentified metabolite. These results demonstrate how this approach can accelerate functional characterization of BGCs.
- Published
- 2018
22. Mass Spectrometry for Natural Product Discovery
- Author
-
Louie, Katherine B., primary, Kosina, Suzanne M., additional, Hu, Yuntao, additional, Otani, Hiroshi, additional, de Raad, Markus, additional, Kuftin, Andrea N., additional, Mouncey, Nigel J., additional, Bowen, Benjamin P., additional, and Northen, Trent R., additional
- Published
- 2020
- Full Text
- View/download PDF
23. Characterisation of molybdenum transport and processing in Azotobacter vinelandii
- Author
-
Mouncey, Nigel J.
- Subjects
572 ,Molybdate - Published
- 1995
24. Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE
- Author
-
Ke, Jing, primary, Zhao, Zhiying, additional, Coates, Cameron R., additional, Hadjithomas, Michalis, additional, Kuftin, Andrea, additional, Louie, Katherine, additional, Weller, David, additional, Thomashow, Linda, additional, Mouncey, Nigel J., additional, Northen, Trent R., additional, and Yoshikuni, Yasuo, additional
- Published
- 2022
- Full Text
- View/download PDF
25. Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery
- Author
-
Hurley, Amanda, primary, Chevrette, Marc G., additional, Acharya, Deepa D., additional, Lozano, Gabriel L., additional, Garavito, Manuel, additional, Heinritz, Jen, additional, Balderrama, Luis, additional, Beebe, Mara, additional, DenHartog, Martel L., additional, Corinaldi, Kamiyah, additional, Engels, Renee, additional, Gutierrez, Alyssa, additional, Jona, Orli, additional, Putnam, Josephine H. I., additional, Rhodes, Brody, additional, Tsang, Tiffany, additional, Hernandez, Simon, additional, Bascom-Slack, Carol, additional, Blum, Jessamina E., additional, Price, Paul A., additional, Davis, Debra, additional, Klein, Joanna, additional, Pultorak, Joshua, additional, Sullivan, Nora L., additional, Mouncey, Nigel J., additional, Dorrestein, Pieter C., additional, Miller, Sarah, additional, Broderick, Nichole A., additional, and Handelsman, Jo, additional
- Published
- 2020
- Full Text
- View/download PDF
26. The emergence of microbiome centres
- Author
-
Martiny, Jennifer B. H., primary, Whiteson, Katrine L., additional, Bohannan, Brendan J. M., additional, David, Lawrence A., additional, Hynson, Nicole A., additional, McFall-Ngai, Margaret, additional, Rawls, John F., additional, Schmidt, Thomas M., additional, Abdo, Zaid, additional, Blaser, Martin J., additional, Bordenstein, Seth, additional, Bréchot, Christian, additional, Bull, Carolee T., additional, Dorrestein, Pieter, additional, Eisen, Jonathan A., additional, Garcia-Pichel, Ferran, additional, Gilbert, Jack, additional, Hofmockel, Kirsten S., additional, Holtz, Mary L., additional, Knight, Rob, additional, Mark Welch, David B., additional, McDonald, Daniel, additional, Methé, Barbara, additional, Mouncey, Nigel J., additional, Mueller, Noel T., additional, Pfister, Catherine A., additional, Proctor, Lita, additional, and Sachs, Joel L., additional
- Published
- 2019
- Full Text
- View/download PDF
27. IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase
- Author
-
Palaniappan, Krishnaveni, primary, Chen, I-Min A, additional, Chu, Ken, additional, Ratner, Anna, additional, Seshadri, Rekha, additional, Kyrpides, Nikos C, additional, Ivanova, Natalia N, additional, and Mouncey, Nigel J, additional
- Published
- 2019
- Full Text
- View/download PDF
28. Cascade regulation of dimethyl sulfoxide reductase (dor) gene expression in the facultative phototroph Rhodobacter sphaeroides 2.4.1(super T)
- Author
-
Mouncey, Nigel J. and Kaplan, Samuel
- Subjects
Phototropism -- Analysis ,Genetic regulation -- Research ,Dimethyl sulfoxide -- Physiological aspects ,Gene expression -- Analysis ,Genetic transcription -- Analysis ,Bacteria, Photosynthetic -- Genetic aspects ,Biological sciences - Abstract
The mechanism behind the regulation of dimethyl sulfoxide (DMSO) reductase genes of the phototroph Rhodobacter sphaeroides by both DMSO and oxygen was studied by investigating the transcriptional regulation of the dorC, dorR and dorS promoters. The dorC::lacZ expression was minimized by up to one-third when the cells were grown photosynthetically with DMSO and with medium to high lighting. The induction also depends on the DorR and DorS proteins.
- Published
- 1998
29. Oxygen regulation of the ccoN gene encoding a component of the cbb3 oxidase in Rhodobacter sphaeroides 2.4.1T: involvement of the FnrL protein
- Author
-
Mouncey, Nigel J. and Kaplan, Samuel
- Subjects
Bacteria -- Physiological aspects ,Cytochrome oxidase -- Genetic aspects ,Genetic regulation -- Environmental aspects ,Oxygen -- Physiological aspects ,Biological sciences - Abstract
Rhodobacter sphaeroides expresses different cytochrome oxidases depending on the availability of oxygen. Cytochrome oxidase aa3 is expressed with high oxygen tension while cbb3 is expressed under microaerophilic conditions. The genetic control of cbb3 expression is investigated in a fused transcriptional system using the promoter of cbb3, ccoN and the lacZ gene. Results indicate that oxygen concentration influences cbb3 expression and the protein FnrL is a positive regulator of cbb3 expression.
- Published
- 1998
30. Characterization of genes encoding dimethyl sulfoxide reductase of Rhodobacter sphaeroides 2.4.1T: an essential metabolic gene function encoded on chromosome II
- Author
-
Mouncey, Nigel J., Choudhary, Madhu, and Kaplan, Samuel
- Subjects
Dimethyl sulfoxide -- Genetic aspects ,Bacterial genetics -- Research ,DNA sequencers -- Research ,Biological sciences - Abstract
Research was conducted to describe the genes encoding the dimethyl sulfoxide reductase of Rhodobacter sphaeroides 2.4.1T. Recombinant DNA methods were utilized for the construction of mutants while automated DNA sequencing was carried out with an ABI 373A automatic DNA sequencer. Results indicated that the level of DorA protein expressed from the plasmids was sufficient to restore growth to the mutants. They also showed that dorS and dorR gene products are important for the production of DorA protein expression.
- Published
- 1997
31. Analysis of the fnrL gene and its function in Rhodobacter capsulatus
- Author
-
Zeilstra-Ryalls, Jill H., Gabbert, Karen, Mouncey, Nigel J., Kaplan, Samuel, and Kranz, Robert G.
- Subjects
Bacterial genetics -- Research ,Amino acids -- Research ,Biological sciences - Abstract
Research was conducted to study the functions of the fnrL gene in Rhodobacter capsulatus. R. capsulatus was prepared in a Sistrom's succinate minimal medium while DNA manipulations and enyzymatic treatments were determined according to standard protocols. Based on the identity of the amino acid sequences of the gene products, it is suggested that the fnrL gene identified in the study was the R. capsulatus homology of R. sphaeroides fnrL.
- Published
- 1997
32. The modE gene product mediates molybdenum-dependent expression of genes for the high-affinity molybdate transporter and modG in Azotobacter vinelandii
- Author
-
Mouncey, Nigel J., Mitchenall, Lesley A., and Pau, Richard N.
- Subjects
Molybdenum -- Genetic aspects ,Gene expression -- Research ,Genetic regulation -- Research ,Biological sciences - Abstract
The molybdenum-dependent regulation of transcription of the operons of Azotobacter vinelandii, modEABC and modG, is mediated by the modE, the first gene in the modEABC operon. However, modE was not observed to have any control on the Mo-dependent expression of alternative nitrogenase structural genes. Mo accumulation of cells in the presence of molybdate were substantially reduced in a modE mutant, contrary to expectations of maximal rates of Mo transport with the constitutive expression of the high-affinity Mo-transport system.
- Published
- 1996
33. Mutational analysis of genes of the mod locus involved in molybdenum transport, homeostasis, and processing in Azotobacter vinelandii
- Author
-
Mouncey, Nigel J., Mitchenall, Lesley A., and Pau, Richard N.
- Subjects
Mutation (Biology) -- Genetic aspects ,Biological transport -- Research ,Molybdenum -- Physiological aspects ,Homeostasis -- Research ,Biological sciences - Abstract
An open reading frame, modG, that may encode a protein with a tandem repeat sequence similar to the molybdopterin-binding protein Mop was found upstream of the modEABC operon in Azotobacter vinelandii. Mutations in these mod genes, involved in the molybdenum transport system, appeared to reveal separate high and low affinity molybdenum transport systems. The modE and modG genes may have a role in molybdate processing, which may be important for nitrogenase cofactor biosynthesis.
- Published
- 1995
34. Metabolic engineering of Gluconobacter oxydans for improved growth rate and growth yield on glucose by elimination of gluconate formation
- Author
-
Krajewski, Vera, Simic, Petra, Mouncey, Nigel J., Bringer, Stephanie, Sahm, Hermann, and Bott, Michael
- Subjects
Gene mutations -- Analysis ,Glucose metabolism -- Analysis ,Gram-negative bacteria -- Physiological aspects ,Gram-negative bacteria -- Genetic aspects ,Oxidoreductases -- Chemical properties ,Biological sciences - Abstract
The mutants of strain N44-1 in which the gene encoding the membrane-bound glucose dehydrogenase was inactivated either alone or together with the gene encoding the cytoplasmic glucose dehydrogenase to understand the low growth yield of glucose metabolism in the cytoplasm. The conversion of glucose to gluconate and ketogluconates in the cytoplasm was found to have strong negative impact on the growth of Gluconobacter oxydans N44-1.
- Published
- 2010
35. Redox-dependent gene regulation in Rhodobacter sphaeroides 2.4.1(super T): effects on dimethyl sulfoxide reductase (dor) gene expression
- Author
-
Mouncey, Nigel J. and Kaplan, Samuel
- Subjects
Genetic regulation -- Research ,Oxidation-reduction reaction -- Research ,Gene expression -- Research ,Bacterial genetics -- Research ,Biological sciences - Abstract
Research was conducted to examine the effects of redox-dependent gene regulation in Rhodobacter sphaeroides 2.4.1(super T) on dimethyl sulfoxide (DMSO) reductase (dor) gene expression. Expression of dor::lacZ transcriptional fusions in the CcoP mutant provided evidence that the effects of the ccoP mutation occurred at the transcriptional level. Results demonstrate a role for redox-generated responses in the expression of genes encoding DMSO reductase in R sphaeroides.
- Published
- 1998
36. Respiratory pathways ofRhodobacter sphaeroides2.4.1T: identification and characterization of genes encoding quinol oxidases
- Author
-
Mouncey, Nigel J, primary, Gak, Evgueni, additional, Choudhary, Madhu, additional, Oh, Jeong-Il, additional, and Kaplan, Samuel, additional
- Published
- 2000
- Full Text
- View/download PDF
37. Oxygen Regulation of the ccoN Gene Encoding a Component of the cbb 3 Oxidase in Rhodobacter sphaeroides 2.4.1 T : Involvement of the FnrL Protein
- Author
-
Mouncey, Nigel J., primary and Kaplan, Samuel, additional
- Published
- 1998
- Full Text
- View/download PDF
38. Redox-Dependent Gene Regulation in Rhodobacter sphaeroides 2.4.1...: Effects on Dimethyl...
- Author
-
Mouncey, Nigel J. and Kaplan, Samuel
- Subjects
- *
GENETIC regulation , *DIMETHYL sulfoxide - Abstract
Provides information on a study which examined the role of redox potentiation in the regulation of dimethyl sulfoxide reductase (DOR) expression. Materials and methods; Results of the study; Conclusion.
- Published
- 1998
- Full Text
- View/download PDF
39. Respiratory pathways of Rhodobacter sphaeroides2.4.1T: identification and characterization of genes encoding quinol oxidases
- Author
-
Mouncey, Nigel J, Gak, Evgueni, Choudhary, Madhu, Oh, Jeong‐Il, and Kaplan, Samuel
- Abstract
Rhodobacter sphaeroides2.4.1Trespires aerobically via a branched respiratory chain consisting of both cytochrome coxidases and quinol oxidases. Here, genes from chromosome II encoding two distinct quinol oxidases have been characterized. The qoxBAgenes encode a putative heme‐copper quinol oxidase, whereas the qxtABgenes encode a quinol oxidase homologous to the cyanide‐insensitive oxidase of Pseudomonas aeruginosa. No phenotype was observed for mutations in either oxidase in the wild‐type background. A strain containing a qxtAmutation in a cytochrome bc1complex mutant background was unable to grow aerobically. No role was found for the Qox oxidase, nor was a qoxB::lacZtranscriptional fusion expressed under a variety of conditions. These are the first molecular studies to characterize the quinol oxidases of R. sphaeroides2.4.1T.
- Published
- 2000
- Full Text
- View/download PDF
40. Respiratory pathways of Rhodobacter sphaeroides 2.4.1T: identification and characterization of genes encoding quinol oxidases
- Author
-
Mouncey, Nigel J, Gak, Evgueni, Choudhary, Madhu, Oh, Jeong-Il, and Kaplan, Samuel
- Abstract
Rhodobacter sphaeroides 2.4.1T respires aerobically via a branched respiratory chain consisting of both cytochrome c oxidases and quinol oxidases. Here, genes from chromosome II encoding two distinct quinol oxidases have been characterized. The qoxBA genes encode a putative heme-copper quinol oxidase, whereas the qxtAB genes encode a quinol oxidase homologous to the cyanide-insensitive oxidase of Pseudomonas aeruginosa. No phenotype was observed for mutations in either oxidase in the wild-type background. A strain containing a qxtA mutation in a cytochrome bc
1 complex mutant background was unable to grow aerobically. No role was found for the Qox oxidase, nor was a qoxB::lacZ transcriptional fusion expressed under a variety of conditions. These are the first molecular studies to characterize the quinol oxidases of R. sphaeroides 2.4.1T.- Published
- 2000
- Full Text
- View/download PDF
41. Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes
- Author
-
Rekha Seshadri, Simon Roux, Katharina J. Huber, Dongying Wu, Sora Yu, Dan Udwary, Lee Call, Stephen Nayfach, Richard L. Hahnke, Rüdiger Pukall, James R. White, Neha J. Varghese, Cody Webb, Krishnaveni Palaniappan, Lorenz C. Reimer, Joaquim Sardà, Jonathon Bertsch, Supratim Mukherjee, T.B.K. Reddy, Patrick P. Hajek, Marcel Huntemann, I-Min A. Chen, Alex Spunde, Alicia Clum, Nicole Shapiro, Zong-Yen Wu, Zhiying Zhao, Yuguang Zhou, Lyudmila Evtushenko, Sofie Thijs, Vincent Stevens, Emiley A. Eloe-Fadrosh, Nigel J. Mouncey, Yasuo Yoshikuni, William B. Whitman, Hans-Peter Klenk, Tanja Woyke, Markus Göker, Nikos C. Kyrpides, Natalia N. Ivanova, Seshadri, Rekha, Roux, Simon, Huber, Katharina J., Wu, Dongying, Yu, Sora, Udwary, Dan, Call, Lee, Nayfach, Stephen, Hahnke, Richard L., Pukall, Rüdiger, White, James R., Varghese, Neha J., Webb, Cody, Palaniappan, Krishnaveni, Reimer, Lorenz C., Sardà, Joaquim, Bertsch, Jonathon, Mukherjee, Supratim, Reddy, T.B.K., Hajek, Patrick P., Huntemann, Marcel, Chen, I-Min A., Spunde, Alex, Clum, Alicia, Shapiro, Nicole, Wu, Zong-Yen, Zhao, Zhiying, Zhou, Yuguang, Evtushenko, Lyudmila, THIJS, Sofie, STEVENS, Vincent, Eloe-Fadrosh, Emiley A., Mouncey, Nigel J., Yoshikuni, Yasuo, Whitman, William B., Klenk, Hans-Peter, Woyke, Tanja, Göker, Markus, Kyrpides, Nikos C., and Ivanova, Natalia N.
- Subjects
Genetics ,Biochemistry, Genetics and Molecular Biology (miscellaneous) - Abstract
The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences. The work (proposal DOI[s]: https://doi.org/10.46936/10.25585/60001024; https://doi.org/10.46936/10.25585/60000886; https://doi.org/10.46936/10. 25585/60001401; https://doi.org/10.46936/10.25585/60001087; https:// doi.org/10.46936/10.25585/60001079; https://doi.org/10.46936/10.25585/ 60001044) conducted by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy operated under contract no. DE-AC02-05CH11231. Design and synthesis of peptide constructs were supported by the Biosystems Design program (DOE Office of Science contract DE-SC0018260) and the US Department of Energy Joint Genome Institute (DOE Office of Science contract DEAC02-05CH1123), respectively. Characterization of the peptide was supported by the Secured Biosystem Design project entitled ‘‘Rapid Design and Engineering of Smart and Secure Microbiological Systems’’ (DOE Office of Science contract DE-AC02-05CH1123). We thank the following researchers for their support of this study by providing free use of their public genome data: Kristen De-Angelis, Grace Pold, Mallory Choudoir, Camila Carlos-Shanley, Paul Carini, H. Corby C. Kistler, James Elkins, Javier A. Izquierdo, Dimitris Hatzinikolaou, Daniel Schachtman, Paul R. Jensen, Aindrila Mukhopadhyay, John Vogel, Carolin Frank, Paul M. D’Agostino, Ann M. Hirsch, Satoshi Yuzawa, Regina Lamendella, Bernhard Fuchs, Dale Pelletier, Laila P. Partida-Martinez, Cameron Currie, Seth De-Bolt, Jeff Dangl, David Mead, Susannah Tringe, David A. Baltrus, Seung Bum Kim, Linda Kinkel, Kelly Wrighton, William Mohn, Ludmila Christoserdova, Sarah Lebeis, Janet Janssen, Sandra Baena Garzon, and Nicholas Coleman. Special thanks to Marie Louise Ballon at the JGI Communications and Outreach office for all her help with the graphical abstract and many other details.
- Published
- 2022
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.