1
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Yılmaz TM, Mungan MD, Berasategui A, Ziemert N. FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi. Nucleic Acids Res 2023:7173779. [PMID: 37207330 DOI: 10.1093/nar/gkad386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
There is an urgent need to diversify the pipeline for discovering novel natural products due to the increase in multi-drug resistant infections. Like bacteria, fungi also produce secondary metabolites that have potent bioactivity and rich chemical diversity. To avoid self-toxicity, fungi encode resistance genes which are often present within the biosynthetic gene clusters (BGCs) of the corresponding bioactive compounds. Recent advances in genome mining tools have enabled the detection and prediction of BGCs responsible for the biosynthesis of secondary metabolites. The main challenge now is to prioritize the most promising BGCs that produce bioactive compounds with novel modes of action. With target-directed genome mining methods, it is possible to predict the mode of action of a compound encoded in an uncharacterized BGC based on the presence of resistant target genes. Here, we introduce the 'fungal bioactive compound resistant target seeker' (FunARTS) available at https://funarts.ziemertlab.com. This is a specific and efficient mining tool for the identification of fungal bioactive compounds with interesting and novel targets. FunARTS rapidly links housekeeping and known resistance genes to BGC proximity and duplication events, allowing for automated, target-directed mining of fungal genomes. Additionally, FunARTS generates gene cluster networking by comparing the similarity of BGCs from multi-genomes.
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Affiliation(s)
- Turgut Mesut Yılmaz
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Mehmet Direnç Mungan
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Aileen Berasategui
- University of Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Nadine Ziemert
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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2
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Contreras-Castro L, MartÍnez-GarcÍa S, Cancino-Diaz JC, Maldonado LA, HernÁndez-Guerrero CJ, MartÍnez-DÍaz SF, GonzÁlez-Acosta BÁ, Quintana ET. Marine Sediment Recovered Salinispora sp. Inhibits the Growth of Emerging Bacterial Pathogens and other Multi-Drug-Resistant Bacteria. Pol J Microbiol 2021; 69:321-330. [PMID: 33574861 PMCID: PMC7810121 DOI: 10.33073/pjm-2020-035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/22/2020] [Accepted: 07/25/2020] [Indexed: 11/05/2022] Open
Abstract
Marine obligate actinobacteria produce a wide variety of secondary metabolites with biological activity, notably those with antibiotic activity urgently needed against multi-drug-resistant bacteria. Seventy-five marine actinobacteria were isolated from a marine sediment sample collected in Punta Arena de La Ventana, Baja California Sur, Mexico. The 16S rRNA gene identification, Multi Locus Sequence Analysis, and the marine salt requirement for growth assigned seventy-one isolates as members of the genus Salinispora, grouped apart but related to the main Salinispora arenicola species clade. The ability of salinisporae to inhibit bacterial growth of Staphylococcus epidermidis, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacer baumannii, Pseudomonas aeruginosa, and Enterobacter spp. was evaluated by cross-streaking plate and supernatant inhibition tests. Ten supernatants inhibited the growth of eight strains of S. epidermidis from patients suffering from ocular infections, two out of the eight showed growth inhibition on ten S. epidermidis strains from prosthetic joint infections. Also, it inhibited the growth of the remaining six multi-drug-resistant bacteria tested. These results showed that some Salinispora strains could produce antibacterial compounds to combat bacteria of clinical importance and prove that studying different geographical sites uncovers untapped microorganisms with metabolic potential.
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Affiliation(s)
- Luis Contreras-Castro
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Ciudad de México, México
| | - Sergio MartÍnez-GarcÍa
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Ciudad de México, México
| | - Juan C Cancino-Diaz
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Ciudad de México, México
| | - Luis A Maldonado
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Claudia J HernÁndez-Guerrero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, 23096, La Paz, Baja California Sur, México
| | - Sergio F MartÍnez-DÍaz
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, 23096, La Paz, Baja California Sur, México
| | - BÁrbara GonzÁlez-Acosta
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, 23096, La Paz, Baja California Sur, México
| | - Erika T Quintana
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Ciudad de México, México
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3
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Stahlecker J, Mingyar E, Ziemert N, Mungan MD. SYN-View: A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance. Molecules 2020; 26:molecules26010144. [PMID: 33396183 PMCID: PMC7795190 DOI: 10.3390/molecules26010144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 01/05/2023] Open
Abstract
The development of new antibacterial drugs has become one of the most important tasks of the century in order to overcome the posing threat of drug resistance in pathogenic bacteria. Many antibiotics originate from natural products produced by various microorganisms. Over the last decades, bioinformatical approaches have facilitated the discovery and characterization of these small compounds using genome mining methodologies. A key part of this process is the identification of the most promising biosynthetic gene clusters (BGCs), which encode novel natural products. In 2017, the Antibiotic Resistant Target Seeker (ARTS) was developed in order to enable an automated target-directed genome mining approach. ARTS identifies possible resistant target genes within antibiotic gene clusters, in order to detect promising BGCs encoding antibiotics with novel modes of action. Although ARTS can predict promising targets based on multiple criteria, it provides little information about the cluster structures of possible resistant genes. Here, we present SYN-view. Based on a phylogenetic approach, SYN-view allows for easy comparison of gene clusters of interest and distinguishing genes with regular housekeeping functions from genes functioning as antibiotic resistant targets. Our aim is to implement our proposed method into the ARTS web-server, further improving the target-directed genome mining strategy of the ARTS pipeline.
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Affiliation(s)
- Jason Stahlecker
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (J.S.); (E.M.); (N.Z.)
| | - Erik Mingyar
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (J.S.); (E.M.); (N.Z.)
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (J.S.); (E.M.); (N.Z.)
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 38124 Tübingen, Germany
| | - Mehmet Direnç Mungan
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (J.S.); (E.M.); (N.Z.)
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 38124 Tübingen, Germany
- Correspondence:
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4
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Mungan MD, Alanjary M, Blin K, Weber T, Medema MH, Ziemert N. ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Res 2020; 48:W546-W552. [PMID: 32427317 PMCID: PMC7319560 DOI: 10.1093/nar/gkaa374] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/19/2020] [Accepted: 04/29/2020] [Indexed: 01/21/2023] Open
Abstract
Multi-drug resistant pathogens have become a major threat to human health and new antibiotics are urgently needed. Most antibiotics are derived from secondary metabolites produced by bacteria. In order to avoid suicide, these bacteria usually encode resistance genes, in some cases within the biosynthetic gene cluster (BGC) of the respective antibiotic compound. Modern genome mining tools enable researchers to computationally detect and predict BGCs that encode the biosynthesis of secondary metabolites. The major challenge now is the prioritization of the most promising BGCs encoding antibiotics with novel modes of action. A recently developed target-directed genome mining approach allows researchers to predict the mode of action of the encoded compound of an uncharacterized BGC based on the presence of resistant target genes. In 2017, we introduced the ‘Antibiotic Resistant Target Seeker’ (ARTS). ARTS allows for specific and efficient genome mining for antibiotics with interesting and novel targets by rapidly linking housekeeping and known resistance genes to BGC proximity, duplication and horizontal gene transfer (HGT) events. Here, we present ARTS 2.0 available at http://arts.ziemertlab.com. ARTS 2.0 now includes options for automated target directed genome mining in all bacterial taxa as well as metagenomic data. Furthermore, it enables comparison of similar BGCs from different genomes and their putative resistance genes.
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Affiliation(s)
- Mehmet Direnç Mungan
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, Germany
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5
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Chevrette MG, Gutiérrez-García K, Selem-Mojica N, Aguilar-Martínez C, Yañez-Olvera A, Ramos-Aboites HE, Hoskisson PA, Barona-Gómez F. Evolutionary dynamics of natural product biosynthesis in bacteria. Nat Prod Rep 2019; 37:566-599. [PMID: 31822877 DOI: 10.1039/c9np00048h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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6
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Potnis N, Kandel PP, Merfa MV, Retchless AC, Parker JK, Stenger DC, Almeida RPP, Bergsma-Vlami M, Westenberg M, Cobine PA, De La Fuente L. Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa. THE ISME JOURNAL 2019; 13:2319-2333. [PMID: 31110262 PMCID: PMC6776109 DOI: 10.1038/s41396-019-0423-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/09/2022]
Abstract
High rates of homologous recombination (HR) in the bacterial plant pathogen Xylella fastidiosa have been previously detected. This study aimed to determine the extent and explore the ecological significance of HR in the genomes of recombinants experimentally generated by natural transformation and wild-type isolates. Both sets of strains displayed widespread HR and similar average size of recombined fragments consisting of random events (2-10 kb) of inter- and intrasubspecific recombination. A significantly higher proportion and greater lengths (>10 kb, maximum 31.5 kb) of recombined fragments were observed in subsp. morus and in strains isolated in Europe from intercepted coffee plants shipped from the Americas. Such highly recombinant strains pose a serious risk of emergence of novel variants, as genetically distinct and formerly geographically isolated genotypes are brought in close proximity by global trade. Recently recombined regions in wild-type strains included genes involved in regulation and signaling, host colonization, nutrient acquisition, and host evasion, all fundamental traits for X. fastidiosa ecology. Identification of four recombinant loci shared between wild-type and experimentally generated recombinants suggests potential hotspots of recombination in this naturally competent pathogen. These findings provide insights into evolutionary forces possibly affecting the adaptive potential to colonize the host environments of X. fastidiosa.
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Affiliation(s)
- Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
| | - Prem P Kandel
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Marcus V Merfa
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
| | - Adam C Retchless
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
- Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer K Parker
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Drake C Stenger
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Maria Bergsma-Vlami
- Dutch National Plant Protection Organization (NPPO-NL), P.O. Box. 9102, Wageningen, 6700 HC, The Netherlands
| | - Marcel Westenberg
- Dutch National Plant Protection Organization (NPPO-NL), P.O. Box. 9102, Wageningen, 6700 HC, The Netherlands
| | - Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, 209 Rouse Life Sciences Bldg, Auburn, AL, USA.
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7
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Alanjary M, Kronmiller B, Adamek M, Blin K, Weber T, Huson D, Philmus B, Ziemert N. The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Res 2019; 45:W42-W48. [PMID: 28472505 PMCID: PMC5570205 DOI: 10.1093/nar/gkx360] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/20/2017] [Indexed: 11/12/2022] Open
Abstract
With the rise of multi-drug resistant pathogens and the decline in number of potential new antibiotics in development there is a fervent need to reinvigorate the natural products discovery pipeline. Most antibiotics are derived from secondary metabolites produced by microorganisms and plants. To avoid suicide, an antibiotic producer harbors resistance genes often found within the same biosynthetic gene cluster (BGC) responsible for manufacturing the antibiotic. Existing mining tools are excellent at detecting BGCs or resistant genes in general, but provide little help in prioritizing and identifying gene clusters for compounds active against specific and novel targets. Here we introduce the 'Antibiotic Resistant Target Seeker' (ARTS) available at https://arts.ziemertlab.com. ARTS allows for specific and efficient genome mining for antibiotics with interesting and novel targets. The aim of this web server is to automate the screening of large amounts of sequence data and to focus on the most promising strains that produce antibiotics with new modes of action. ARTS integrates target directed genome mining methods, antibiotic gene cluster predictions and 'essential gene screening' to provide an interactive page for rapid identification of known and putative targets in BGCs.
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Affiliation(s)
- Mohammad Alanjary
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology, University of Tübingen, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, 97331 OR, USA
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology, University of Tübingen, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Daniel Huson
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, 97331 OR, USA
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology, University of Tübingen, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
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8
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O'Neill EC, Schorn M, Larson CB, Millán-Aguiñaga N. Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining. Crit Rev Microbiol 2019; 45:255-277. [PMID: 30985219 DOI: 10.1080/1040841x.2019.1590307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Intense competition between microbes in the environment has directed the evolution of antibiotic production in bacteria. Humans have harnessed these natural molecules for medicinal purposes, magnifying them from environmental concentrations to industrial scale. This increased exposure to antibiotics has amplified antibiotic resistance across bacteria, spurring a global antimicrobial crisis and a search for antibiotics with new modes of action. Genetic insights into these antibiotic-producing microbes reveal that they have evolved several resistance strategies to avoid self-toxicity, including product modification, substrate transport and binding, and target duplication or modification. Of these mechanisms, target duplication or modification will be highlighted in this review, as it uniquely links an antibiotic to its mode of action. We will further discuss and propose a strategy to mine microbial genomes for these genes and their associated biosynthetic gene clusters to discover novel antibiotics using target directed genome mining.
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Affiliation(s)
- Ellis C O'Neill
- a Department of Plant Sciences, University of Oxford , Oxford , Oxfordshire , UK
| | - Michelle Schorn
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Charles B Larson
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Natalie Millán-Aguiñaga
- c Universidad Autónoma de Baja California, Facultad de Ciencias Marinas , Ensenada , Baja California , México
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9
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Tran PN, Yen MR, Chiang CY, Lin HC, Chen PY. Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi. Appl Microbiol Biotechnol 2019; 103:3277-3287. [PMID: 30859257 PMCID: PMC6449301 DOI: 10.1007/s00253-019-09708-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/17/2019] [Accepted: 02/18/2019] [Indexed: 11/23/2022]
Abstract
Secondary metabolites (SM) produced by fungi and bacteria have long been of exceptional interest owing to their unique biomedical ramifications. The traditional discovery of new natural products that was mainly driven by bioactivity screening has now experienced a fresh new approach in the form of genome mining. Several bioinformatics tools have been continuously developed to detect potential biosynthetic gene clusters (BGCs) that are responsible for the production of SM. Although the principles underlying the computation of these tools have been discussed, the biological background is left underrated and ambiguous. In this review, we emphasize the biological hypotheses in BGC formation driven from the observations across genomes in bacteria and fungi, and provide a comprehensive list of updated algorithms/tools exclusively for BGC detection. Our review points to a direction that the biological hypotheses should be systematically incorporated into the BGC prediction and assist the prioritization of candidate BGC.
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Affiliation(s)
- Phuong Nguyen Tran
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan
| | - Chen-Yu Chiang
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan.
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan.
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10
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Adamek M, Alanjary M, Ziemert N. Applied evolution: phylogeny-based approaches in natural products research. Nat Prod Rep 2019; 36:1295-1312. [DOI: 10.1039/c9np00027e] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we highlight how phylogenetic analyses can be used to facilitate natural product discovery and structure elucidation.
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Affiliation(s)
- Martina Adamek
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
| | | | - Nadine Ziemert
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
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11
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Almabruk KH, Dinh LK, Philmus B. Self-Resistance of Natural Product Producers: Past, Present, and Future Focusing on Self-Resistant Protein Variants. ACS Chem Biol 2018; 13:1426-1437. [PMID: 29763292 DOI: 10.1021/acschembio.8b00173] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nature is a prolific producers of bioactive natural products with an array of biological activities and impact on human and animal health. But with great power comes great responsibility, and the organisms that produce a bioactive compound must be resistant to its biological effects to survive during production/accumulation. Microorganisms, particularly bacteria, have developed different strategies to prevent self-toxicity. Here, we review a few of the major mechanisms including the mechanism of resistance with a focus on self-resistant protein variants, target proteins that contain amino acid substitutions to reduce the binding of the bioactive natural product, and therefore its inhibitory effects are highlighted in depth. We also try to identify some future avenues of research and challenges that need to be addressed.
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Affiliation(s)
- Khaled H. Almabruk
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Linh K. Dinh
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
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12
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Hoetzinger M, Hahn MW. Genomic divergence and cohesion in a species of pelagic freshwater bacteria. BMC Genomics 2017; 18:794. [PMID: 29037158 PMCID: PMC5644125 DOI: 10.1186/s12864-017-4199-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 10/08/2017] [Indexed: 11/15/2022] Open
Abstract
Background In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity – i.e. elevated geographic barriers to gene flow – is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P. asymbioticus. Results Comparisons among 20 PnecC genomes revealed a clearly discontinuous distribution of nucleotide sequence similarities. Among the nine conspecific individuals (P. asymbioticus) all average nucleotide identity (ANI) values were greater than 97%, whereas all other comparisons exhibited ANI values lower than 85%. The reconstruction of recombination and mutation events for the P. asymbioticus core genomes yielded an r/m ratio of 7.4, which is clearly above estimated thresholds for recombination to act as a cohesive force. Hotspots of recombination were found to be located in the flanking regions of genomic islands. Even between geographically separated habitats a high flux of recombination was evident. While a biogeographic population structure was suggested from MLST data targeting rather conserved loci, such a structure was barely visible when whole genome data was considered. However, both MLST and whole genome data showed evidence of differentiation between two lineages of P. asymbioticus. The ratios of non-synonymous to synonymous substitution rates as well as growth rates in transplantation experiments suggested that this divergence was not selectively neutral. Conclusions The high extent of homologous recombination among P. asymbioticus bacteria can act as a cohesive force that effectively counteracts genetic divergence. At least on a regional scale, homologous recombination can act across geographically separated ecosystems and therefore plays an important role in the evolution and consistency of bacterial freshwater species. A species model akin to the biological species concept may be applicable for P. asymbioticus. Nonetheless, two genetically distinct lineages have emerged and further research may clarify if their divergence has been initiated by reinforced geographical barriers or has been evolving in sympatry. Electronic supplementary material The online version of this article (10.1186/s12864-017-4199-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Hoetzinger
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310, Mondsee, Austria.
| | - Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310, Mondsee, Austria
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13
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Millán-Aguiñaga N, Chavarria KL, Ugalde JA, Letzel AC, Rouse GW, Jensen PR. Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations. Sci Rep 2017; 7:3564. [PMID: 28620214 PMCID: PMC5472633 DOI: 10.1038/s41598-017-02845-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/18/2017] [Indexed: 11/12/2022] Open
Abstract
Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.
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Affiliation(s)
- Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Universidad Autónoma de Baja California. Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - Krystle L Chavarria
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Juan A Ugalde
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bella, Santiago, Chile
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Greg W Rouse
- Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States. .,Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.
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14
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Crüsemann M, O’Neill EC, Larson CB, Melnik AV, Floros DJ, da Silva RR, Jensen PR, Dorrestein PC, Moore BS. Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols. JOURNAL OF NATURAL PRODUCTS 2017; 80:588-597. [PMID: 28335604 PMCID: PMC5367486 DOI: 10.1021/acs.jnatprod.6b00722] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, while minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with high-throughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions.
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Affiliation(s)
- Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ellis C. O’Neill
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Charles B. Larson
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexey V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dimitrios J Floros
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R. da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Research Support Center in Natural and Synthetic Products, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Paul R. Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bradley S. Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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15
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Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities. Appl Environ Microbiol 2017; 83:AEM.02676-16. [PMID: 27986719 DOI: 10.1128/aem.02676-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023] Open
Abstract
Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.
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16
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Planet PJ, Narechania A, Chen L, Mathema B, Boundy S, Archer G, Kreiswirth B. Architecture of a Species: Phylogenomics of Staphylococcus aureus. Trends Microbiol 2016; 25:153-166. [PMID: 27751626 DOI: 10.1016/j.tim.2016.09.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/07/2016] [Accepted: 09/22/2016] [Indexed: 12/11/2022]
Abstract
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.
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Affiliation(s)
- Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia & University of Pennsylvania, Philadelphia, PA, USA.
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Liang Chen
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
| | - Barun Mathema
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sam Boundy
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Gordon Archer
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Barry Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
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17
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Widespread interspecies homologous recombination reveals reticulate evolution within the genus Streptomyces. Mol Phylogenet Evol 2016; 102:246-54. [DOI: 10.1016/j.ympev.2016.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 06/07/2016] [Accepted: 06/17/2016] [Indexed: 01/14/2023]
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18
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Jensen PR. Natural Products and the Gene Cluster Revolution. Trends Microbiol 2016; 24:968-977. [PMID: 27491886 DOI: 10.1016/j.tim.2016.07.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/29/2016] [Accepted: 07/19/2016] [Indexed: 11/24/2022]
Abstract
Genome sequencing has created unprecedented opportunities for natural-product discovery and new insight into the diversity and distributions of natural-product biosynthetic gene clusters (BGCs). These gene collectives are highly evolved for horizontal exchange, thus providing immediate opportunities to test the effects of small molecules on fitness. The marine actinomycete genus Salinispora maintains extraordinary levels of BGC diversity and has become a useful model for studies of secondary metabolism. Most Salinispora BGCs are observed infrequently, resulting in high population-level diversity while conforming to constraints associated with maximum genome size. Comparative genomics is providing a mechanism to assess secondary metabolism in the context of evolution and evidence that some products represent ecotype-defining traits while others appear selectively neutral.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Center for Microbiome Innovation, Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA.
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19
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Lai HC, Ng TH, Ando M, Lee CT, Chen IT, Chuang JC, Mavichak R, Chang SH, Yeh MD, Chiang YA, Takeyama H, Hamaguchi HO, Lo CF, Aoki T, Wang HC. Pathogenesis of acute hepatopancreatic necrosis disease (AHPND) in shrimp. FISH & SHELLFISH IMMUNOLOGY 2015; 47:1006-14. [PMID: 26549178 DOI: 10.1016/j.fsi.2015.11.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/26/2015] [Accepted: 11/02/2015] [Indexed: 05/21/2023]
Abstract
Acute hepatopancreatic necrosis disease (AHPND), also called early mortality syndrome (EMS), is a recently emergent shrimp bacterial disease that has resulted in substantial economic losses since 2009. AHPND is known to be caused by strains of Vibrio parahaemolyticus that contain a unique virulence plasmid, but the pathology of the disease is still unclear. In this study, we show that AHPND-causing strains of V. parahaemolyticus secrete the plasmid-encoded binary toxin PirAB(vp) into the culture medium. We further determined that, after shrimp were challenged with AHPND-causing bacteria, the bacteria initially colonized the stomach, where they started to produce PirAB(vp) toxin. At the same early time point (6 hpi), PirB(vp) toxin, but not PirA(vp) toxin, was detected in the hepatopancreas, and the characteristic histopathological signs of AHPND, including sloughing of the epithelial cells of the hepatopancreatic tubules, were also seen. Although some previous studies have found that both components of the binary PirAB(vp) toxin are necessary to induce a toxic effect, our present results are consistent with other studies which have suggested that PirB(vp) alone may be sufficient to cause cellular damage. At later time points, the bacteria and PirA(vp) and PirB(vp) toxins were all detected in the hepatopancreas. We also show that Raman spectroscopy "Whole organism fingerprints" were unable to distinguish between AHPND-causing and non-AHPND causing strains. Lastly, by using minimum inhibitory concentrations, we found that both virulent and non-virulent V. parahaemolyticus strains were resistant to several antibiotics, suggesting that the use of antibiotics in shrimp culture should be more strictly regulated.
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Affiliation(s)
- Hung-Chiao Lai
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Tze Hann Ng
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Masahiro Ando
- Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Tokyo 162-0041, Japan
| | - Chung-Te Lee
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - I-Tung Chen
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | | | - Rapeepat Mavichak
- Aquatic Animal Health Research Center, Charoen Pokphand Foods, Bangkok, Thailand
| | - Sheng-Hsiung Chang
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Mi-De Yeh
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Yi-An Chiang
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Hiro-o Hamaguchi
- College of Science, National Ciao Tung University, 300, Taiwan, ROC
| | - Chu-Fang Lo
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan, ROC
| | - Takashi Aoki
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC.
| | - Han-Ching Wang
- Institute of Biotechnology, National Cheng Kung University, 701, Taiwan, ROC.
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20
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Patin NV, Duncan KR, Dorrestein PC, Jensen PR. Competitive strategies differentiate closely related species of marine actinobacteria. ISME JOURNAL 2015; 10:478-90. [PMID: 26241505 DOI: 10.1038/ismej.2015.128] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/26/2015] [Accepted: 06/18/2015] [Indexed: 01/12/2023]
Abstract
Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.
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Affiliation(s)
- Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Katherine R Duncan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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21
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Woegerbauer M, Kuffner M, Domingues S, Nielsen KM. Involvement of aph(3')-IIa in the formation of mosaic aminoglycoside resistance genes in natural environments. Front Microbiol 2015; 6:442. [PMID: 26042098 PMCID: PMC4437187 DOI: 10.3389/fmicb.2015.00442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/24/2015] [Indexed: 11/13/2022] Open
Abstract
Intragenic recombination leading to mosaic gene formation is known to alter resistance profiles for particular genes and bacterial species. Few studies have examined to what extent aminoglycoside resistance genes undergo intragenic recombination. We screened the GenBank database for mosaic gene formation in homologs of the aph(3')-IIa (nptII) gene. APH(3')-IIa inactivates important aminoglycoside antibiotics. The gene is widely used as a selectable marker in biotechnology and enters the environment via laboratory discharges and the release of transgenic organisms. Such releases may provide opportunities for recombination in competent environmental bacteria. The retrieved GenBank sequences were grouped in three datasets comprising river water samples, duck pathogens and full-length variants from various bacterial genomes and plasmids. Analysis for recombination in these datasets was performed with the Recombination Detection Program (RDP4), and the Genetic Algorithm for Recombination Detection (GARD). From a total of 89 homologous sequences, 83% showed 99-100% sequence identity with aph(3')-IIa originally described as part of transposon Tn5. Fifty one were unique sequence variants eligible for recombination analysis. Only a single recombination event was identified with high confidence and indicated the involvement of aph(3')-IIa in the formation of a mosaic gene located on a plasmid of environmental origin in the multi-resistant isolate Pseudomonas aeruginosa PA96. The available data suggest that aph(3')-IIa is not an archetypical mosaic gene as the divergence between the described sequence variants and the number of detectable recombination events is low. This is in contrast to the numerous mosaic alleles reported for certain penicillin or tetracycline resistance determinants.
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Affiliation(s)
- Markus Woegerbauer
- Integrative Risk Assessment - Data - Statistics, GMO Risk Assessment, Austrian Agency for Health and Food Safety Vienna, Austria
| | - Melanie Kuffner
- Integrative Risk Assessment - Data - Statistics, GMO Risk Assessment, Austrian Agency for Health and Food Safety Vienna, Austria
| | - Sara Domingues
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology, University of Coimbra Coimbra, Portugal
| | - Kaare M Nielsen
- Department of Pharmacy, University of Tromsø Tromsø, Norway ; Genøk-Center for Biosafety Tromsø Tromsø, Norway
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22
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Jensen PR, Moore BS, Fenical W. The marine actinomycete genus Salinispora: a model organism for secondary metabolite discovery. Nat Prod Rep 2015; 32:738-51. [PMID: 25730728 PMCID: PMC4414829 DOI: 10.1039/c4np00167b] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review covers the initial discovery of the marine actinomycete genus Salinispora through its development as a model for natural product research. A focus is placed on the novel chemical structures reported with reference to their biological activities and the synthetic and biosynthetic studies they have inspired. The time line of discoveries progresses from more traditional bioassay-guided approaches through the application of genome mining and genetic engineering techniques that target the products of specific biosynthetic gene clusters. This overview exemplifies the extraordinary biosynthetic diversity that can emanate from a narrowly defined genus and supports future efforts to explore marine taxa in the search for novel natural products.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
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23
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Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. ACTA ACUST UNITED AC 2015; 22:460-471. [PMID: 25865308 DOI: 10.1016/j.chembiol.2015.03.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/26/2015] [Accepted: 03/10/2015] [Indexed: 12/12/2022]
Abstract
Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.
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Affiliation(s)
- Katherine R Duncan
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anna Lechner
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anindita Sarkar
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jie Li
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Nadine Ziemert
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Paul R Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA.
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Bonet B, Teufel R, Crüsemann M, Ziemert N, Moore BS. Direct capture and heterologous expression of Salinispora natural product genes for the biosynthesis of enterocin. JOURNAL OF NATURAL PRODUCTS 2015; 78:539-42. [PMID: 25382643 PMCID: PMC4380194 DOI: 10.1021/np500664q] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Heterologous expression of secondary metabolic pathways is a promising approach for the discovery and characterization of bioactive natural products. Herein we report the first heterologous expression of a natural product from the model marine actinomycete genus Salinispora. Using the recently developed method of yeast-mediated transformation-associated recombination for natural product gene clusters, we captured a type II polyketide synthase pathway from Salinispora pacifica with high homology to the enterocin pathway from Streptomyces maritimus and successfully produced enterocin in two different Streptomyces host strains. This result paves the way for the systematic interrogation of Salinispora's promising secondary metabolome.
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Affiliation(s)
- Bailey Bonet
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Robin Teufel
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Max Crüsemann
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Nadine Ziemert
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
- E-mail:
| | - Bradley S. Moore
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, La Jolla, California 92037, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
- E-mail:
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Population genetic analysis of Streptomyces albidoflavus reveals habitat barriers to homologous recombination in the diversification of streptomycetes. Appl Environ Microbiol 2014; 81:966-75. [PMID: 25416769 DOI: 10.1128/aem.02925-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes.
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Duncan KR, Haltli B, Gill KA, Correa H, Berrué F, Kerr RG. Exploring the diversity and metabolic potential of actinomycetes from temperate marine sediments from Newfoundland, Canada. J Ind Microbiol Biotechnol 2014; 42:57-72. [PMID: 25371290 DOI: 10.1007/s10295-014-1529-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
Marine sediments from Newfoundland, Canada were explored for biotechnologically promising Actinobacteria using culture-independent and culture-dependent approaches. Culture-independent pyrosequencing analyses uncovered significant actinobacterial diversity (H'-2.45 to 3.76), although the taxonomic diversity of biotechnologically important actinomycetes could not be fully elucidated due to limited sampling depth. Assessment of culturable actinomycete diversity resulted in the isolation of 360 actinomycetes representing 59 operational taxonomic units, the majority of which (94 %) were Streptomyces. The biotechnological potential of actinomycetes from NL sediments was assessed by bioactivity and metabolomics-based screening of 32 representative isolates. Bioactivity was exhibited by 41 % of isolates, while 11 % exhibited unique chemical signatures in metabolomics screening. Chemical analysis of two isolates resulted in the isolation of the cytotoxic metabolite 1-isopentadecanoyl-3β-D-glucopyranosyl-X-glycerol from Actinoalloteichus sp. 2L868 and sungsanpin from Streptomyces sp. 8LB7. These results demonstrate the potential for the discovery of novel bioactive metabolites from actinomycetes isolated from Atlantic Canadian marine sediments.
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Affiliation(s)
- K R Duncan
- Department of Biomedical Sciences, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE, C1A 4P3, Canada
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Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proc Natl Acad Sci U S A 2014; 111:E1130-9. [PMID: 24616526 DOI: 10.1073/pnas.1324161111] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Access to genome sequence data has challenged traditional natural product discovery paradigms by revealing that the products of most bacterial biosynthetic pathways have yet to be discovered. Despite the insight afforded by this technology, little is known about the diversity and distributions of natural product biosynthetic pathways among bacteria and how they evolve to generate structural diversity. Here we analyze genome sequence data derived from 75 strains of the marine actinomycete genus Salinispora for pathways associated with polyketide and nonribosomal peptide biosynthesis, the products of which account for some of today's most important medicines. The results reveal high levels of diversity, with a total of 124 pathways identified and 229 predicted with continued sequencing. Recent horizontal gene transfer accounts for the majority of pathways, which occur in only one or two strains. Acquired pathways are incorporated into genomic islands and are commonly exchanged within and between species. Acquisition and transfer events largely involve complete pathways, which subsequently evolve by gene gain, loss, and duplication followed by divergence. The exchange of similar pathway types at the precise chromosomal locations in different strains suggests that the mechanisms of integration include pathway-level homologous recombination. Despite extensive horizontal gene transfer there is clear evidence of species-level vertical inheritance, supporting the concept that secondary metabolites represent functional traits that help define Salinispora species. The plasticity of the Salinispora secondary metabolome provides an effective mechanism to maximize population-level secondary metabolite diversity while limiting the number of pathways maintained within any individual genome.
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