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Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 DOI: 10.1016/j.mib.2024.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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2
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Carpenter SCD, Bogdanove AJ, Abbot B, Stajich JE, Uehling JK, Lovett B, Kasson MT, Carter ME. Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp. Microb Genom 2024; 10. [PMID: 38860878 DOI: 10.1099/mgen.0.001261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024] Open
Abstract
Endofungal Mycetohabitans (formerly Burkholderia) spp. rely on a type III secretion system to deliver mostly unidentified effector proteins when colonizing their host fungus, Rhizopus microsporus. The one known secreted effector family from Mycetohabitans consists of homologues of transcription activator-like (TAL) effectors, which are used by plant pathogenic Xanthomonas and Ralstonia spp. to activate host genes that promote disease. These 'Burkholderia TAL-like (Btl)' proteins bind corresponding specific DNA sequences in a predictable manner, but their genomic target(s) and impact on transcription in the fungus are unknown. Recent phenotyping of Btl mutants of two Mycetohabitans strains revealed that the single Btl in one Mycetohabitans endofungorum strain enhances fungal membrane stress tolerance, while others in a Mycetohabitans rhizoxinica strain promote bacterial colonization of the fungus. The phenotypic diversity underscores the need to assess the sequence diversity and, given that sequence diversity translates to DNA targeting specificity, the functional diversity of Btl proteins. Using a dual approach to maximize capture of Btl protein sequences for our analysis, we sequenced and assembled nine Mycetohabitans spp. genomes using long-read PacBio technology and also mined available short-read Illumina fungal-bacterial metagenomes. We show that btl genes are present across diverse Mycetohabitans strains from Mucoromycota fungal hosts yet vary in sequences and predicted DNA binding specificity. Phylogenetic analysis revealed distinct clades of Btl proteins and suggested that Mycetohabitans might contain more species than previously recognized. Within our data set, Btl proteins were more conserved across M. rhizoxinica strains than across M. endofungorum, but there was also evidence of greater overall strain diversity within the latter clade. Overall, the results suggest that Btl proteins contribute to bacterial-fungal symbioses in myriad ways.
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Affiliation(s)
- Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | - Bhuwan Abbot
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARS, Ithaca, NY 14850, USA
| | - Matt T Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Morgan E Carter
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- CIPHER Center, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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3
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Lax C, Nicolás FE, Navarro E, Garre V. Molecular mechanisms that govern infection and antifungal resistance in Mucorales. Microbiol Mol Biol Rev 2024; 88:e0018822. [PMID: 38445820 PMCID: PMC10966947 DOI: 10.1128/mmbr.00188-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
SUMMARYThe World Health Organization has established a fungal priority pathogens list that includes species critical or highly important to human health. Among them is the order Mucorales, a fungal group comprising at least 39 species responsible for the life-threatening infection known as mucormycosis. Despite the continuous rise in cases and the poor prognosis due to innate resistance to most antifungal drugs used in the clinic, Mucorales has received limited attention, partly because of the difficulties in performing genetic manipulations. The COVID-19 pandemic has further escalated cases, with some patients experiencing the COVID-19-associated mucormycosis, highlighting the urgent need to increase knowledge about these fungi. This review addresses significant challenges in treating the disease, including delayed and poor diagnosis, the lack of accurate global incidence estimation, and the limited treatment options. Furthermore, it focuses on the most recent discoveries regarding the mechanisms and genes involved in the development of the disease, antifungal resistance, and the host defense response. Substantial advancements have been made in identifying key fungal genes responsible for invasion and tissue damage, host receptors exploited by the fungus to invade tissues, and mechanisms of antifungal resistance. This knowledge is expected to pave the way for the development of new antifungals to combat mucormycosis. In addition, we anticipate significant progress in characterizing Mucorales biology, particularly the mechanisms involved in pathogenesis and antifungal resistance, with the possibilities offered by CRISPR-Cas9 technology for genetic manipulation of the previously intractable Mucorales species.
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Affiliation(s)
- Carlos Lax
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Francisco E. Nicolás
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Eusebio Navarro
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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Zhang P, Huguet-Tapia J, Peng Z, Liu S, Obasa K, Block AK, White FF. Genome analysis and hyphal movement characterization of the hitchhiker endohyphal Enterobacter sp. from Rhizoctonia solani. Appl Environ Microbiol 2024; 90:e0224523. [PMID: 38319098 PMCID: PMC10952491 DOI: 10.1128/aem.02245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Bacterial-fungal interactions are pervasive in the rhizosphere. While an increasing number of endohyphal bacteria have been identified, little is known about their ecology and impact on the associated fungal hosts and the surrounding environment. In this study, we characterized the genome of an Enterobacter sp. Crenshaw (En-Cren), which was isolated from the generalist fungal pathogen Rhizoctonia solani, and examined the genetic potential of the bacterium with regard to the phenotypic traits associated with the fungus. Overall, the En-Cren genome size was typical for members of the genus and was capable of free-living growth. The genome was 4.6 MB in size, and no plasmids were detected. Several prophage regions and genomic islands were identified that harbor unique genes in comparison with phylogenetically closely related Enterobacter spp. Type VI secretion system and cyanate assimilation genes were identified from the bacterium, while some common heavy metal resistance genes were absent. En-Cren contains the key genes for indole-3-acetic acid (IAA) and phenylacetic acid (PAA) biosynthesis, and produces IAA and PAA in vitro, which may impact the ecology or pathogenicity of the fungal pathogen in vivo. En-Cren was observed to move along hyphae of R. solani and on other basidiomycetes and ascomycetes in culture. The bacterial flagellum is essential for hyphal movement, while other pathways and genes may also be involved.IMPORTANCEThe genome characterization and comparative genomics analysis of Enterobacter sp. Crenshaw provided the foundation and resources for a better understanding of the ecology and evolution of this endohyphal bacteria in the rhizosphere. The ability to produce indole-3-acetic acid and phenylacetic acid may provide new angles to study the impact of phytohormones during the plant-pathogen interactions. The hitchhiking behavior of the bacterium on a diverse group of fungi, while inhibiting the growth of some others, revealed new areas of bacterial-fungal signaling and interaction, which have yet to be explored.
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Affiliation(s)
- Peiqi Zhang
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Jose Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Ken Obasa
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- High Plains Plant Disease Diagnostic Lab, Texas A&M AgriLife Extension Service, Amarillo, Texas, USA
| | - Anna K. Block
- Chemistry Research Unit, US Department of Agriculture-Agricultural Research Service, Gainesville, Florida, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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Liu XL, Zhao H, Wang YX, Liu XY, Jiang Y, Tao MF, Liu XY. Detecting and characterizing new endofungal bacteria in new hosts: Pandoraea sputorum and Mycetohabitans endofungorum in Rhizopus arrhizus. Front Microbiol 2024; 15:1346252. [PMID: 38486702 PMCID: PMC10939042 DOI: 10.3389/fmicb.2024.1346252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
The fungus Rhizopus arrhizus (=R. oryzae) is commonly saprotrophic, exhibiting a nature of decomposing organic matter. Additionally, it serves as a crucial starter in food fermentation and can act as a pathogen causing mucormycosis in humans and animals. In this study, two distinct endofungal bacteria (EFBs), associated with individual strains of R. arrhizus, were identified using live/dead staining, fluorescence in situ hybridization, transmission electron microscopy, and 16S rDNA sequencing. The roles of these bacteria were elucidated through antibiotic treatment, pure cultivation, and comparative genomics. The bacterial endosymbionts, Pandoraea sputorum EFB03792 and Mycetohabitans endofungorum EFB03829, were purified from the host fungal strains R. arrhizus XY03792 and XY03829, respectively. Notably, this study marks the first report of Pandoraea as an EFB genus. Compared to its free-living counterparts, P. sputorum EFB03792 exhibited 28 specific virulence factor-related genes, six specific CE10 family genes, and 74 genes associated with type III secretion system (T3SS), emphasizing its pivotal role in invasion and colonization. Furthermore, this study introduces R. arrhizus as a new host for EFB M. endofungorum, with EFB contributing to host sporulation. Despite a visibly reduced genome, M. endofungorum EFB03829 displayed a substantial number of virulence factor-related genes, CE10 family genes, T3SS genes, mobile elements, and significant gene rearrangement. While EFBs have been previously identified in R. arrhizus, their toxin-producing potential in food fermentation has not been explored until this study. The discovery of these two new EFBs highlights their potential for toxin production within R. arrhizus, laying the groundwork for identifying suitable R. arrhizus strains for fermentation processes.
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Affiliation(s)
- Xiao-Ling Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Heng Zhao
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yi-Xin Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xin-Ye Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yang Jiang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Meng-Fei Tao
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Richter I, Hasan M, Kramer JW, Wein P, Krabbe J, Wojtas KP, Stinear TP, Pidot SJ, Kloss F, Hertweck C, Lackner G. Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction. THE ISME JOURNAL 2024; 18:wrae074. [PMID: 38691425 PMCID: PMC11104420 DOI: 10.1093/ismejo/wrae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
The endosymbiosis between the pathogenic fungus Rhizopus microsporus and the toxin-producing bacterium Mycetohabitans rhizoxinica represents a unique example of host control by an endosymbiont. Fungal sporulation strictly depends on the presence of endosymbionts as well as bacterially produced secondary metabolites. However, an influence of primary metabolites on host control remained unexplored. Recently, we discovered that M. rhizoxinica produces FO and 3PG-F420, a derivative of the specialized redox cofactor F420. Whether FO/3PG-F420 plays a role in the symbiosis has yet to be investigated. Here, we report that FO, the precursor of 3PG-F420, is essential to the establishment of a stable symbiosis. Bioinformatic analysis revealed that the genetic inventory to produce cofactor 3PG-F420 is conserved in the genomes of eight endofungal Mycetohabitans strains. By developing a CRISPR/Cas-assisted base editing strategy for M. rhizoxinica, we generated mutant strains deficient in 3PG-F420 (M. rhizoxinica ΔcofC) and in both FO and 3PG-F420 (M. rhizoxinica ΔfbiC). Co-culture experiments demonstrated that the sporulating phenotype of apo-symbiotic R. microsporus is maintained upon reinfection with wild-type M. rhizoxinica or M. rhizoxinica ΔcofC. In contrast, R. microsporus is unable to sporulate when co-cultivated with M. rhizoxinica ΔfbiC, even though the fungus was observed by super-resolution fluorescence microscopy to be successfully colonized. Genetic and chemical complementation of the FO deficiency of M. rhizoxinica ΔfbiC led to restoration of fungal sporulation, signifying that FO is indispensable for establishing a functional symbiosis. Even though FO is known for its light-harvesting properties, our data illustrate an important role of FO in inter-kingdom communication.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Mahmudul Hasan
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Johannes W Kramer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - K Philip Wojtas
- Transfer Group Anti-Infectives, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 3010 Melbourne, Victoria, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 3010 Melbourne, Victoria, Australia
| | - Florian Kloss
- Transfer Group Anti-Infectives, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Thuringia, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Thuringia, Germany
| | - Gerald Lackner
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Thuringia, Germany
- Chair of Biochemistry of Microorganisms, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, 95326 Kulmbach, Bavaria, Germany
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7
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Valadez-Cano C, Olivares-Hernández R, Espino-Vázquez AN, Partida-Martínez LP. Genome-Scale Model of Rhizopus microsporus: Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts. Environ Microbiol 2024; 26:e16551. [PMID: 38072824 DOI: 10.1111/1462-2920.16551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
Rhizopus microsporus often lives in association with bacterial and viral symbionts that alter its biology. This fungal model represents an example of the complex interactions established among diverse organisms in functional holobionts. We constructed a Genome-Scale Model (GSM) of the fungal-bacterial-viral holobiont (iHol). We employed a constraint-based method to calculate the metabolic fluxes to decipher the metabolic interactions of the symbionts with their host. Our computational analyses of iHol simulate the holobiont's growth and the production of the toxin rhizoxin. Analyses of the calculated fluxes between R. microsporus in symbiotic (iHol) versus asymbiotic conditions suggest that changes in the lipid and nucleotide metabolism of the host are necessary for the functionality of the holobiont. Glycerol plays a pivotal role in the fungal-bacterial metabolic interaction, as its production does not compromise fungal growth, and Mycetohabitans bacteria can efficiently consume it. Narnavirus RmNV-20S and RmNV-23S affected the nucleotide metabolism without impacting the fungal-bacterial symbiosis. Our analyses highlighted the metabolic stability of Mycetohabitans throughout its co-evolution with the fungal host. We also predicted changes in reactions of the bacterial metabolism required for the active production of rhizoxin. This iHol is the first GSM of a fungal holobiont.
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Affiliation(s)
- Cecilio Valadez-Cano
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Roberto Olivares-Hernández
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, Mexico
| | - Astrid N Espino-Vázquez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Laila P Partida-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
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8
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Takashima Y, Yamamoto K, Degawa Y, Guo Y, Nishizawa T, Ohta H, Narisawa K. Detection and isolation of a new member of Burkholderiaceae-related endofungal bacteria from Saksenaea boninensis sp. nov., a new thermotolerant fungus in Mucorales. IMA Fungus 2023; 14:24. [PMID: 37996922 PMCID: PMC10666400 DOI: 10.1186/s43008-023-00129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 11/05/2023] [Indexed: 11/25/2023] Open
Abstract
Thermotolerance in Mucorales (Mucoromycotina) is one of the factors to be opportunistic pathogens, causing mucormycosis. Among thermotolerant mucoralean fungi, Burkholderiaceae-related endobacteria (BRE) are rarely found and the known range of hosts is limited to Rhizopus spp. The phylogenetic divergence of BRE has recently expanded in other fungal groups such as Mortierellaceae spp. (Mortierellomycotina); however, it remains unexplored in Mucorales. Here, we found a thermotolerant mucoralean fungus obtained from a litter sample collected from Haha-jima Island in the Ogasawara (Bonin) Islands, Japan. The fungus was morphologically, phylogenetically, and physiologically characterized and proposed as a new species, Saksenaea boninensis sp. nov. Besides the fungal taxonomy, we also found the presence of BRE in isolates of this species by diagnostic PCR amplification of the 16S rRNA gene from mycelia, fluorescence microscopic observations, and isolation of the bacterium in pure culture. Phylogenetic analysis of the 16S rRNA gene of BRE revealed that it is distinct from all known BRE. The discovery of a culturable BRE lineage in the genus Saksenaea will add new insight into the evolutional origin of mucoralean fungus-BRE associations and emphasize the need to pay more attention to endofungal bacteria potentially associated with isolates of thermotolerant mucoralean fungi causing mucormycosis.
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Affiliation(s)
- Yusuke Takashima
- Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Mountain Science Center, Sugadaira Research Station, University of Tsukuba, Sugadaira-kogen 1278-294, Nagano, 386-2204, Japan.
- Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami-machi, Ibaraki, 300-0393, Japan.
| | - Kohei Yamamoto
- Tochigi Prefectural Museum, 2-2 Mutsumi-cho, Utsunomiya, Tochigi, 320-0865, Japan
| | - Yousuke Degawa
- Mountain Science Center, Sugadaira Research Station, University of Tsukuba, Sugadaira-kogen 1278-294, Nagano, 386-2204, Japan
| | - Yong Guo
- Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami-machi, Ibaraki, 300-0393, Japan
- Institute for Plant Protection, National Agriculture and Food Research Organization, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Tomoyasu Nishizawa
- Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami-machi, Ibaraki, 300-0393, Japan
| | - Hiroyuki Ohta
- Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki, 310-8512, Japan
| | - Kazuhiko Narisawa
- Ibaraki University College of Agriculture, 3-21-1 Chuo, Ami-machi, Ibaraki, 300-0393, Japan
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9
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Richter I, Uzum Z, Wein P, Molloy EM, Moebius N, Stinear TP, Pidot SJ, Hertweck C. Transcription activator-like effectors from endosymbiotic bacteria control the reproduction of their fungal host. mBio 2023; 14:e0182423. [PMID: 37971247 PMCID: PMC10746252 DOI: 10.1128/mbio.01824-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Interactions between fungi and bacteria are critically important in ecology, medicine, and biotechnology. In this study, we shed light on factors that promote the persistence of a toxin-producing, phytopathogenic Rhizopus-Mycetohabitans symbiosis that causes severe crop losses in Asia. We present an unprecedented case where bacterially produced transcription activator-like (TAL) effectors are key to maintaining a stable endosymbiosis. In their absence, fungal sporulation is abrogated, leading to collapse of the phytopathogenic alliance. The Mycetohabitans TAL (MTAL)-mediated mechanism of host control illustrates a unique role of bacterial effector molecules that has broader implications, potentially serving as a model to understand how prokaryotic symbionts interact with their eukaryotic hosts.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Evelyn M. Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, Melbourne, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
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10
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Longley R, Robinson A, Liber JA, Bryson AE, Morales DP, LaButti K, Riley R, Mondo SJ, Kuo A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Desirò A, Chain PSG, Bonito G. Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi. Commun Biol 2023; 6:948. [PMID: 37723238 PMCID: PMC10507103 DOI: 10.1038/s42003-023-05299-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/29/2023] [Indexed: 09/20/2023] Open
Abstract
Diverse members of early-diverging Mucoromycota, including mycorrhizal taxa and soil-associated Mortierellaceae, are known to harbor Mollicutes-related endobacteria (MRE). It has been hypothesized that MRE were acquired by a common ancestor and transmitted vertically. Alternatively, MRE endosymbionts could have invaded after the divergence of Mucoromycota lineages and subsequently spread to new hosts horizontally. To better understand the evolutionary history of MRE symbionts, we generated and analyzed four complete MRE genomes from two Mortierellaceae genera: Linnemannia (MRE-L) and Benniella (MRE-B). These genomes include the smallest known of fungal endosymbionts and showed signals of a tight relationship with hosts including a reduced functional capacity and genes transferred from fungal hosts to MRE. Phylogenetic reconstruction including nine MRE from mycorrhizal fungi revealed that MRE-B genomes are more closely related to MRE from Glomeromycotina than MRE-L from the same host family. We posit that reductions in genome size, GC content, pseudogene content, and repeat content in MRE-L may reflect a longer-term relationship with their fungal hosts. These data indicate Linnemannia and Benniella MRE were likely acquired independently after their fungal hosts diverged from a common ancestor. This work expands upon foundational knowledge on minimal genomes and provides insights into the evolution of bacterial endosymbionts.
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Affiliation(s)
- Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Julian A Liber
- Department of Biology, Duke University, Durham, NC, 27704, USA
| | - Abigail E Bryson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Kurt LaButti
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80521, USA
| | - Alan Kuo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
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11
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Wein P, Dornblut K, Herkersdorf S, Krüger T, Molloy EM, Brakhage AA, Hoffmeister D, Hertweck C. Bacterial secretion systems contribute to rapid tissue decay in button mushroom soft rot disease. mBio 2023; 14:e0078723. [PMID: 37486262 PMCID: PMC10470514 DOI: 10.1128/mbio.00787-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023] Open
Abstract
The soft rot pathogen Janthinobacterium agaricidamnosum causes devastating damage to button mushrooms (Agaricus bisporus), one of the most cultivated and commercially relevant mushrooms. We previously discovered that this pathogen releases the membrane-disrupting lipopeptide jagaricin. This bacterial toxin, however, could not solely explain the rapid decay of mushroom fruiting bodies, indicating that J. agaricidamnosum implements a more sophisticated infection strategy. In this study, we show that secretion systems play a crucial role in soft rot disease. By mining the genome of J. agaricidamnosum, we identified gene clusters encoding a type I (T1SS), a type II (T2SS), a type III (T3SS), and two type VI secretion systems (T6SSs). We targeted the T2SS and T3SS for gene inactivation studies, and subsequent bioassays implicated both in soft rot disease. Furthermore, through a combination of comparative secretome analysis and activity-guided fractionation, we identified a number of secreted lytic enzymes responsible for mushroom damage. Our findings regarding the contribution of secretion systems to the disease process expand the current knowledge of bacterial soft rot pathogens and represent a significant stride toward identifying targets for their disarmament with secretion system inhibitors. IMPORTANCE The button mushroom (Agaricus bisporus) is the most popular edible mushroom in the Western world. However, mushroom crops can fall victim to serious bacterial diseases that are a major threat to the mushroom industry, among them being soft rot disease caused by Janthinobacterium agaricidamnosum. Here, we show that the rapid dissolution of mushroom fruiting bodies after bacterial invasion is due to degradative enzymes and putative effector proteins secreted via the type II secretion system (T2SS) and the type III secretion system (T3SS), respectively. The ability to degrade mushroom tissue is significantly attenuated in secretion-deficient mutants, which establishes that secretion systems are key factors in mushroom soft rot disease. This insight is of both ecological and agricultural relevance by shedding light on the disease processes behind a pathogenic bacterial-fungal interaction which, in turn, serves as a starting point for the development of secretion system inhibitors to control disease progression.
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Affiliation(s)
- Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Katharina Dornblut
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Sebastian Herkersdorf
- Department of Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University Jena, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Evelyn M. Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Axel A. Brakhage
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University Jena, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
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12
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Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales DP, Cailleau G, Junier P, Bonito G, Chain PSG. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. MICROBIOME 2023; 11:192. [PMID: 37626434 PMCID: PMC10463477 DOI: 10.1186/s40168-023-01634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023]
Abstract
As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.
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Affiliation(s)
| | | | - Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
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13
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Tsumori C, Matsuo S, Murai Y, Kai K. Quorum Sensing-Dependent Invasion of Ralstonia solanacearum into Fusarium oxysporum Chlamydospores. Microbiol Spectr 2023; 11:e0003623. [PMID: 37367297 PMCID: PMC10433826 DOI: 10.1128/spectrum.00036-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Strains of the Ralstonia solanacearum species complex (RSSC), although known as the causative agent of bacterial wilt disease in plants, induce the chlamydospores of many fungal species and invade them through the spores. The lipopeptide ralstonins are the chlamydospore inducers produced by RSSC and are essential for this invasion. However, no mechanistic investigation of this interaction has been conducted. In this study, we report that quorum sensing (QS), which is a bacterial cell-cell communication, is important for RSSC to invade the fungus Fusarium oxysporum (Fo). ΔphcB, a deletion mutant of QS signal synthase, lost the ability to both produce ralstonins and invade Fo chlamydospores. The QS signal methyl 3-hydroxymyristate rescued these disabilities. In contrast, exogenous ralstonin A, while inducing Fo chlamydospores, failed to rescue the invasive ability. Gene-deletion and -complementation experiments revealed that the QS-dependent production of extracellular polysaccharide I (EPS I) is essential for this invasion. The RSSC cells adhered to Fo hyphae and formed biofilms there before inducing chlamydospores. This biofilm formation was not observed in the EPS I- or ralstonin-deficient mutant. Microscopic analysis showed that RSSC infection resulted in the death of Fo chlamydospores. Altogether, we report that the RSSC QS system is important for this lethal endoparasitism. Among the factors regulated by the QS system, ralstonins, EPS I, and biofilm are important parasitic factors. IMPORTANCE Ralstonia solanacearum species complex (RSSC) strains infect both plants and fungi. The phc quorum-sensing (QS) system of RSSC is important for parasitism on plants, because it allows them to invade and proliferate within the hosts by causing appropriate activation of the system at each infection step. In this study, we confirm that ralstonin A is important not only for Fusarium oxysporum (Fo) chlamydospore induction but also for RSSC biofilm formation on Fo hyphae. Extracellular polysaccharide I (EPS I) is also essential for biofilm formation, while the phc QS system controls these factors in terms of production. The present results advocate a new QS-dependent mechanism for the process by which a bacterium invades a fungus.
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Affiliation(s)
- Chiaki Tsumori
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan
| | - Shoma Matsuo
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan
| | - Yuta Murai
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan
| | - Kenji Kai
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan
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14
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Njovu IK, Nalumaga PP, Ampaire L, Nuwagira E, Mwesigye J, Musinguzi B, Kassaza K, Taseera K, Kiguli Mukasa J, Bazira J, Iramiot JS, Baguma A, Bongomin F, Kwizera R, Achan B, Cox MJ, King JS, May R, Ballou ER, Itabangi H. Investigating Metabolic and Molecular Ecological Evolution of Opportunistic Pulmonary Fungal Coinfections: Protocol for a Laboratory-Based Cross-Sectional Study. JMIR Res Protoc 2023; 12:e48014. [PMID: 37581914 PMCID: PMC10466149 DOI: 10.2196/48014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Fungal-bacterial cocolonization and coinfections pose an emerging challenge among patients suspected of having pulmonary tuberculosis (PTB); however, the underlying pathogenic mechanisms and microbiome interactions are poorly understood. Understanding how environmental microbes, such as fungi and bacteria, coevolve and develop traits to evade host immune responses and resist treatment is critical to controlling opportunistic pulmonary fungal coinfections. In this project, we propose to study the coexistence of fungal and bacterial microbial communities during chronic pulmonary diseases, with a keen interest in underpinning fungal etiological evolution and the predominating interactions that may exist between fungi and bacteria. OBJECTIVE This is a protocol for a study aimed at investigating the metabolic and molecular ecological evolution of opportunistic pulmonary fungal coinfections through determining and characterizing the burden, etiological profiles, microbial communities, and interactions established between fungi and bacteria as implicated among patients with presumptive PTB. METHODS This will be a laboratory-based cross-sectional study, with a sample size of 406 participants. From each participant, 2 sputa samples (one on-spot and one early morning) will be collected. These samples will then be analyzed for both fungal and bacterial etiology using conventional metabolic and molecular (intergenic transcribed spacer and 16S ribosomal DNA-based polymerase chain reaction) approaches. We will also attempt to design a genome-scale metabolic model for pulmonary microbial communities to analyze the composition of the entire microbiome (ie, fungi and bacteria) and investigate host-microbial interactions under different patient conditions. This analysis will be based on the interplays of genes (identified by metagenomics) and inferred from amplicon data and metabolites (identified by metabolomics) by analyzing the full data set and using specific computational tools. We will also collect baseline data, including demographic and clinical history, using a patient-reported questionnaire. Altogether, this approach will contribute to a diagnostic-based observational study. The primary outcome will be the overall fungal and bacterial diagnostic profile of the study participants. Other diagnostic factors associated with the etiological profile, such as incidence and prevalence, will also be analyzed using univariate and multivariate schemes. Odds ratios with 95% CIs will be presented with a statistical significance set at P<.05. RESULTS The study has been approved by the Mbarara University Research Ethic Committee (MUREC1/7-07/09/20) and the Uganda National Council of Science and Technology (HS1233ES). Following careful scrutiny, the protocol was designed to enable patient enrollment, which began in March 2022 at Mbarara University Teaching Hospital. Data collection is ongoing and is expected to be completed by August 2023, and manuscripts will be submitted for publication thereafter. CONCLUSIONS Through this protocol, we will explore the metabolic and molecular ecological evolution of opportunistic pulmonary fungal coinfections among patients with presumptive PTB. Establishing key fungal-bacterial cross-kingdom synergistic relationships is crucial for instituting fungal bacterial coinfecting etiology. TRIAL REGISTRATION ISRCTN Registry ISRCTN33572982; https://tinyurl.com/caa2nw69. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/48014.
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Affiliation(s)
- Israel Kiiza Njovu
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Pauline Petra Nalumaga
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Lucas Ampaire
- Department of Medical Laboratory Sciences, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Edwin Nuwagira
- Department of Internal Medicine, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - James Mwesigye
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Benson Musinguzi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Muni University, Arua, Uganda
| | - Kennedy Kassaza
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Kabanda Taseera
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - James Kiguli Mukasa
- Department of Microbiology and Immunology, School of Health Sciences, Soroti University, Soroti, Uganda
| | - Joel Bazira
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Jacob Stanley Iramiot
- Mycology Unit, Department of Microbiology and Immunology, Busitema University, Mbale, Uganda
| | - Andrew Baguma
- Department of Microbiology, School of Medicine, Kabale University, Kabale, Uganda
| | - Felix Bongomin
- Department of Microbiology and Immunology, Faculty of Medicine, Gulu University, Gulu, Uganda
| | - Richard Kwizera
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Beatrice Achan
- Department of Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Michael J Cox
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jason S King
- School of Biosciences, Sheffield University, Sheffield, United Kingdom
| | - Robin May
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Elizabeth R Ballou
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Herbert Itabangi
- Medical Mycology Unit, Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
- Mycology Unit, Department of Microbiology and Immunology, Busitema University, Mbale, Uganda
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15
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Uzum Z, Ershov D, Pavia MJ, Mallet A, Gorgette O, Plantard O, Sassera D, Stavru F. Three-dimensional images reveal the impact of the endosymbiont Midichloria mitochondrii on the host mitochondria. Nat Commun 2023; 14:4133. [PMID: 37438329 DOI: 10.1038/s41467-023-39758-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
The hard tick, Ixodes ricinus, a main Lyme disease vector, harbors an intracellular bacterial endosymbiont. Midichloria mitochondrii is maternally inherited and resides in the mitochondria of I. ricinus oocytes, but the consequences of this endosymbiosis are not well understood. Here, we provide 3D images of wild-type and aposymbiotic I. ricinus oocytes generated with focused ion beam-scanning electron microscopy. Quantitative image analyses of endosymbionts and oocyte mitochondria at different maturation stages show that the populations of both mitochondrion-associated bacteria and bacterium-hosting mitochondria increase upon vitellogenisation, and that mitochondria can host multiple bacteria in later stages. Three-dimensional reconstructions show symbiosis-dependent morphologies of mitochondria and demonstrate complete M. mitochondrii inclusion inside a mitochondrion. Cytoplasmic endosymbiont located close to mitochondria are not oriented towards the mitochondria, suggesting that bacterial recolonization is unlikely. We further demonstrate individual globular-shaped mitochondria in the wild type oocytes, while aposymbiotic oocytes only contain a mitochondrial network. In summary, our study suggests that M. mitochondrii modulates mitochondrial fragmentation in oogenesis possibly affecting organelle function and ensuring its presence over generations.
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Affiliation(s)
- Zerrin Uzum
- Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur; CNRS UMR2001, Paris, France.
| | - Dmitry Ershov
- Image Analysis Hub, Cell Biology and Infection Department, Institut Pasteur, Paris, France
- Bioinformatics and Biostatistics HUB, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Adeline Mallet
- Ultrastructural BioImaging Core Facility, Institut Pasteur, Paris, France
| | - Olivier Gorgette
- Ultrastructural BioImaging Core Facility, Institut Pasteur, Paris, France
| | | | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Fabrizia Stavru
- Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur; CNRS UMR2001, Paris, France
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16
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Richter I, Wein P, Uzum Z, Stanley CE, Krabbe J, Molloy EM, Moebius N, Ferling I, Hillmann F, Hertweck C. Transcription activator-like effector protects bacterial endosymbionts from entrapment within fungal hyphae. Curr Biol 2023:S0960-9822(23)00623-1. [PMID: 37301202 DOI: 10.1016/j.cub.2023.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/30/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
As an endosymbiont of the ecologically and medically relevant fungus Rhizopus microsporus, the toxin-producing bacterium Mycetohabitans rhizoxinica faces myriad challenges, such as evading the host's defense mechanisms. However, the bacterial effector(s) that facilitate the remarkable ability of M. rhizoxinica to freely migrate within fungal hyphae have thus far remained unknown. Here, we show that a transcription activator-like (TAL) effector released by endobacteria is an essential symbiosis factor. By combining microfluidics with fluorescence microscopy, we observed enrichment of TAL-deficient M. rhizoxinica in side hyphae. High-resolution live imaging showed the formation of septa at the base of infected hyphae, leading to the entrapment of endobacteria. Using a LIVE/DEAD stain, we demonstrate that the intracellular survival of trapped TAL-deficient bacteria is significantly reduced compared with wild-type M. rhizoxinica, indicative of a protective host response in the absence of TAL proteins. Subversion of host defense in TAL-competent endobacteria represents an unprecedented function of TAL effectors. Our data illustrate an unusual survival strategy of endosymbionts in the host and provide deeper insights into the dynamic interactions between bacteria and eukaryotes.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Claire E Stanley
- Department of Bioengineering, Imperial College, South Kensington, London SW7 2AZ, UK
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Evelyn M Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
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17
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Niehs SP, Scherlach K, Dose B, Uzum Z, Stinear TP, Pidot SJ, Hertweck C. A highly conserved gene locus in endofungal bacteria codes for the biosynthesis of symbiosis-specific cyclopeptides. PNAS NEXUS 2022; 1:pgac152. [PMID: 36714835 PMCID: PMC9802438 DOI: 10.1093/pnasnexus/pgac152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/30/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
The tight association of the pathogenic fungus Rhizopus microsporus and its toxin-producing, bacterial endosymbionts (Mycetohabitans spp.) is distributed worldwide and has significance for agriculture, food production, and human health. Intriguingly, the endofungal bacteria are essential for the propagation of the fungal host. Yet, little is known about chemical mediators fostering the symbiosis, and universal metabolites that support the mutualistic relationship have remained elusive. Here, we describe the discovery of a complex of specialized metabolites produced by endofungal bacteria under symbiotic conditions. Through full genome sequencing and comparative genomics of eight endofungal symbiont strains from geographically distant regions, we discovered a conserved gene locus (hab) for a nonribosomal peptide synthetase as a unifying trait. Bioinformatics analyses, targeted gene deletions, and chemical profiling uncovered unprecedented depsipeptides (habitasporins) whose structures were fully elucidated. Computational network analysis and labeling experiments granted insight into the biosynthesis of their nonproteinogenic building blocks (pipecolic acid and β-phenylalanine). Deletion of the hab gene locus was shown to impair the ability of the bacteria to enter their fungal host. Our study unveils a common principle of the endosymbiotic lifestyle of Mycetohabitans species and expands the repertoire of characterized chemical mediators of a globally occurring mutualistic association.
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Affiliation(s)
| | | | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (Leibniz-HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne, 3000, Australia
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18
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Cheng S, Jiang JW, Tan LT, Deng JX, Liang PY, Su H, Sun ZX, Zhou Y. Plant Growth-Promoting Ability of Mycorrhizal Fusarium Strain KB-3 Enhanced by Its IAA Producing Endohyphal Bacterium, Klebsiella aerogenes. Front Microbiol 2022; 13:855399. [PMID: 35495715 PMCID: PMC9051524 DOI: 10.3389/fmicb.2022.855399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022] Open
Abstract
Fusarium oxysporum KB-3 had been reported as a mycorrhizal fungus of Bletilla striata, which can promote the seed germination and vegetative growth. Endohyphal bacteria were demonstrated in the hyphae of the KB-3 by 16S rDNA PCR amplification and SYTO-9 fluorescent nucleic acid staining. A strain Klebsiella aerogenes KE-1 was isolated and identified based on the multilocus sequence analysis. The endohyphal bacterium was successfully removed from the wild strain KB-3 (KB-3−), and GFP-labeled KE-1 was also transferred to the cured strain KB-3− (KB-3+). The production of indole-3-acetic acid (IAA) in the culturing broths of strains of KE-1, KB-3, KB-3−, and KB-3+ was examined by HPLC. Their IAA productions were estimated using Salkowski colorimetric technique. The highest concentrations of IAA were 76.9 (at 48 h after inoculation), 31.4, 9.6, and 19.4 μg/ml (at 60 h after inoculation), respectively. Similarly, the three fungal cultural broths exhibited plant promoting abilities on the tomato root and stem growth. The results indicated that the ability of mycorrhizal Fusarium strain KB-3 to promote plant growth was enhanced because its endohyphal bacterium, Klebsiella aerogenes KE-1, produced a certain amount of IAA.
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19
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Transcriptional Profiles of a Foliar Fungal Endophyte ( Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont ( Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction. mSystems 2022; 7:e0009122. [PMID: 35293790 PMCID: PMC9040847 DOI: 10.1128/msystems.00091-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Symbiosis with bacteria is widespread among eukaryotes, including fungi. Bacteria that live within fungal mycelia (endohyphal bacteria) occur in many plant-associated fungi, including diverse Mucoromycota and Dikarya. Pestalotiopsis sp. strain 9143 is a filamentous ascomycete isolated originally as a foliar endophyte of Platycladus orientalis (Cupressaceae). It is infected naturally with the endohyphal bacterium Luteibacter sp. strain 9143, which influences auxin and enzyme production by its fungal host. Previous studies have used transcriptomics to examine similar symbioses between endohyphal bacteria and root-associated fungi such as arbuscular mycorrhizal fungi and plant pathogens. However, currently there are no gene expression studies of endohyphal bacteria of Ascomycota, the most species-rich fungal phylum. To begin to understand such symbioses, we developed methods for assessing gene expression by Pestalotiopsis sp. and Luteibacter sp. when grown in coculture and when each was grown axenically. Our assays showed that the density of Luteibacter sp. in coculture was greater than in axenic culture, but the opposite was true for Pestalotiopsis sp. Dual-transcriptome sequencing (RNA-seq) data demonstrate that growing in coculture modulates developmental and metabolic processes in both the fungus and bacterium, potentially through changes in the balance of organic sulfur via methionine acquisition. Our analyses also suggest an unexpected, potential role of the bacterial type VI secretion system in symbiosis establishment, expanding current understanding of the scope and dynamics of fungal-bacterial symbioses. IMPORTANCE Interactions between microbes and their hosts have important outcomes for host and environmental health. Foliar fungal endophytes that infect healthy plants can harbor facultative endosymbionts called endohyphal bacteria, which can influence the outcome of plant-fungus interactions. These bacterial-fungal interactions can be influential but are poorly understood, particularly from a transcriptome perspective. Here, we report on a comparative, dual-RNA-seq study examining the gene expression patterns of a foliar fungal endophyte and a facultative endohyphal bacterium when cultured together versus separately. Our findings support a role for the fungus in providing organic sulfur to the bacterium, potentially through methionine acquisition, and the potential involvement of a bacterial type VI secretion system in symbiosis establishment. This work adds to the growing body of literature characterizing endohyphal bacterial-fungal interactions, with a focus on a model facultative bacterial-fungal symbiosis in two species-rich lineages, the Ascomycota and Proteobacteria.
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Itabangi H, Sephton-Clark PCS, Tamayo DP, Zhou X, Starling GP, Mahamoud Z, Insua I, Probert M, Correia J, Moynihan PJ, Gebremariam T, Gu Y, Ibrahim AS, Brown GD, King JS, Ballou ER, Voelz K. A bacterial endosymbiont of the fungus Rhizopus microsporus drives phagocyte evasion and opportunistic virulence. Curr Biol 2022; 32:1115-1130.e6. [PMID: 35134329 PMCID: PMC8926845 DOI: 10.1016/j.cub.2022.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 11/04/2021] [Accepted: 01/11/2022] [Indexed: 02/07/2023]
Abstract
Opportunistic infections by environmental fungi are a growing clinical problem, driven by an increasing population of people with immunocompromising conditions. Spores of the Mucorales order are ubiquitous in the environment but can also cause acute invasive infections in humans through germination and evasion of the mammalian host immune system. How they achieve this and the evolutionary drivers underlying the acquisition of virulence mechanisms are poorly understood. Here, we show that a clinical isolate of Rhizopus microsporus contains a Ralstonia pickettii bacterial endosymbiont required for virulence in both zebrafish and mice and that this endosymbiosis enables the secretion of factors that potently suppress growth of the soil amoeba Dictyostelium discoideum, as well as their ability to engulf and kill other microbes. As amoebas are natural environmental predators of both bacteria and fungi, we propose that this tri-kingdom interaction contributes to establishing endosymbiosis and the acquisition of anti-phagocyte activity. Importantly, we show that this activity also protects fungal spores from phagocytosis and clearance by human macrophages, and endosymbiont removal renders the fungal spores avirulent in vivo. Together, these findings describe a new role for a bacterial endosymbiont in Rhizopus microsporus pathogenesis in animals and suggest a mechanism of virulence acquisition through environmental interactions with amoebas.
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Affiliation(s)
- Herbert Itabangi
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Poppy C S Sephton-Clark
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Diana P Tamayo
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Xin Zhou
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Georgina P Starling
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Zamzam Mahamoud
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ignacio Insua
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark Probert
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joao Correia
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Patrick J Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Teclegiorgis Gebremariam
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yiyou Gu
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ashraf S Ibrahim
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA; David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gordon D Brown
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Jason S King
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Elizabeth R Ballou
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Kerstin Voelz
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Galindo-Solís JM, Fernández FJ. Endophytic Fungal Terpenoids: Natural Role and Bioactivities. Microorganisms 2022; 10:microorganisms10020339. [PMID: 35208794 PMCID: PMC8875210 DOI: 10.3390/microorganisms10020339] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/01/2023] Open
Abstract
Endophytic fungi are a highly diverse group of fungi that intermittently colonize all plants without causing symptoms of the disease. They sense and respond to physiological and environmental changes of their host plant and microbiome. The inter-organism interactions are largely driven by chemical networks mediated by specialized metabolites. The balance of these complex interactions leads to healthy and strong host plants. Endophytic strains have particular machinery to produce a plethora of secondary metabolites with a variety of bioactivities and unknown functions in an ecological niche. Terpenoids play a key role in endophytism and represent an important source of bioactive molecules for human health and agriculture. In this review, we describe the role of endophytic fungi in plant health, fungal terpenoids in multiple interactions, and bioactive fungal terpenoids recently reported from endophytes, mainly from plants used in traditional medicine, as well as from algae and mangroves. Additionally, we highlight endophytic fungi as producers of important chemotherapeutic terpenoids, initially discovered in plants. Despite advances in understanding endophytism, we still have much to learn in this field. The study of the role, the evolution of interactions of endophytic fungi and their terpenoids provide an opportunity for better applications in human health and agriculture.
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Affiliation(s)
- Juan M. Galindo-Solís
- Posgrado en Biotecnología, Universidad Autonoma Metropolitana, Unidad Iztapalapa, Mexico City CP 09340, Mexico;
| | - Francisco J. Fernández
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, San Rafael Atlixco No. 186, Col. Vicentina, Mexico City CP 09340, Mexico
- Correspondence: ; Tel.: +52-(55)-5804-6453
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Szabó G, Schulz F, Manzano-Marín A, Toenshoff ER, Horn M. Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles. THE ISME JOURNAL 2022; 16:247-256. [PMID: 34294881 PMCID: PMC8692619 DOI: 10.1038/s41396-021-01056-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelges tardus species complex containing betaproteobacterial ("Candidatus Vallotia tarda") and gammaproteobacterial ("Candidatus Profftia tarda") symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other's role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.
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Affiliation(s)
- Gitta Szabó
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary.
| | - Frederik Schulz
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- US Department of Energy (DOE) Joint Genome Institute, Berkeley, CA, USA
| | - Alejandro Manzano-Marín
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Elena Rebecca Toenshoff
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Wallner A, Moulin L, Busset N, Rimbault I, Béna G. Genetic Diversity of Type 3 Secretion System in Burkholderia s.l. and Links With Plant Host Adaptation. Front Microbiol 2021; 12:761215. [PMID: 34745070 PMCID: PMC8565462 DOI: 10.3389/fmicb.2021.761215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
Burkholderia sensu lato species are prominent for their diversity of hosts. The type 3 secretion system (T3SS) is a major mechanism impacting the interactions between bacteria and eukaryotic hosts. Besides the human pathogenic species Burkholderia pseudomallei and closely affiliated species, the T3SS has received little attention in this genus as in taxonomically and evolutionary close genera Paraburkholderia, Caballeronia, Trinickia, and Mycetohabitans. We proceeded to identify and characterize the diversity of T3SS types using the genomic data from a subset of 145 strains representative of the species diversity found in the Burkholderia s.l. group. Through an analysis of their phylogenetic distribution, we identified two new T3SS types with an atypical chromosomal organization and which we propose to name BCI (Burkholderia cepacia complex Injectisome) and PSI (Paraburkholderia Short Injectisome). BCI is the dominant T3SS type found in Burkholderia sensu stricto (s.s.) species and PSI is mostly restricted to the Paraburkholderia genus. By correlating their distribution with the ecology of their strains of origin, we propose a role in plant interaction for these T3SS types. Experimentally, we demonstrated that a BCI deficient B. vietnamiensis LMG10929 mutant was strongly affected in its rice colonization capacity.
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Affiliation(s)
- Adrian Wallner
- PHIM Plant Health Institute, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Lionel Moulin
- PHIM Plant Health Institute, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nicolas Busset
- PHIM Plant Health Institute, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Isabelle Rimbault
- PHIM Plant Health Institute, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gilles Béna
- PHIM Plant Health Institute, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Bacterial endosymbionts protect beneficial soil fungus from nematode attack. Proc Natl Acad Sci U S A 2021; 118:2110669118. [PMID: 34504005 PMCID: PMC8449335 DOI: 10.1073/pnas.2110669118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 12/27/2022] Open
Abstract
Soil is a complex and competitive environment, forcing its inhabitants to develop strategies against competitors, predators, and pathogens. Identifying and understanding the molecular mechanisms has translational value for medicine, ecology, and agriculture. In this study, we show that a member of important soil-dwelling fungi (Mortierella) forms a tight alliance with toxin-producing bacteria (Mycoavidus) that live within the fungal hyphae and protect their host from nematode attack. This discovery is relevant since Mortierella species correlate with healthy soils and are used as plant growth–promoting fungi in agriculture. Unraveling an ecological role for fungal endosymbionts in Mortierella, our results contribute to the understanding of a mainspring in fungal–endobacterial symbioses and open the possibility for the development of new biocontrol agents. Fungi of the genus Mortierella occur ubiquitously in soils where they play pivotal roles in carbon cycling, xenobiont degradation, and promoting plant growth. These important fungi are, however, threatened by micropredators such as fungivorous nematodes, and yet little is known about their protective tactics. We report that Mortierella verticillata NRRL 6337 harbors a bacterial endosymbiont that efficiently shields its host from nematode attacks with anthelmintic metabolites. Microscopic investigation and 16S ribosomal DNA analysis revealed that a previously overlooked bacterial symbiont belonging to the genus Mycoavidus dwells in M. verticillata hyphae. Metabolic profiling of the wild-type fungus and a symbiont-free strain obtained by antibiotic treatment as well as genome analyses revealed that highly cytotoxic macrolactones (CJ-12,950 and CJ-13,357, syn. necroxime C and D), initially thought to be metabolites of the soil-inhabiting fungus, are actually biosynthesized by the endosymbiont. According to comparative genomics, the symbiont belongs to a new species (Candidatus Mycoavidus necroximicus) with 12% of its 2.2 Mb genome dedicated to natural product biosynthesis, including the modular polyketide-nonribosomal peptide synthetase for necroxime assembly. Using Caenorhabditis elegans and the fungivorous nematode Aphelenchus avenae as test strains, we show that necroximes exert highly potent anthelmintic activities. Effective host protection was demonstrated in cocultures of nematodes with symbiotic and chemically complemented aposymbiotic fungal strains. Image analysis and mathematical quantification of nematode movement enabled evaluation of the potency. Our work describes a relevant role for endofungal bacteria in protecting fungi against mycophagous nematodes.
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Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm. PLANTS 2021; 10:plants10010125. [PMID: 33435275 PMCID: PMC7827841 DOI: 10.3390/plants10010125] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/28/2022]
Abstract
Plants are functional macrobes living in a close association with diverse communities of microbes and viruses as complex systems that continuously interact with the surrounding environment. The microbiota within the plant holobiont serves various essential and beneficial roles, such as in plant growth at different stages, starting from seed germination. Meanwhile, pathogenic microbes—differentiated from the rest of the plant microbiome based on their ability to damage the plant tissues through transient blooming under specific conditions—are also a part of the plant microbiome. Recent advances in multi-omics have furthered our understanding of the structure and functions of plant-associated microbes, and a pathobiome paradigm has emerged as a set of organisms (i.e., complex eukaryotic, microbial, and viral communities) within the plant’s biotic environment which interact with the host to deteriorate its health status. Recent studies have demonstrated that the one pathogen–one disease hypothesis is insufficient to describe the disease process in many cases, particularly when complex organismic communities are involved. The present review discusses the plant holobiont and covers the steady transition of plant pathology from the one pathogen–one disease hypothesis to the pathobiome paradigm. Moreover, previous reports on model plant diseases, in which more than one pathogen or co-operative interaction amongst pathogenic microbes is implicated, are reviewed and discussed.
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Steffan BN, Venkatesh N, Keller NP. Let's Get Physical: Bacterial-Fungal Interactions and Their Consequences in Agriculture and Health. J Fungi (Basel) 2020; 6:E243. [PMID: 33114069 PMCID: PMC7712096 DOI: 10.3390/jof6040243] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/01/2023] Open
Abstract
Fungi serve as a biological scaffold for bacterial attachment. In some specialized interactions, the bacteria will invade the fungal host, which in turn provides protection and nutrients for the bacteria. Mechanisms of the physical interactions between fungi and bacteria have been studied in both clinical and agricultural settings, as discussed in this review. Fungi and bacteria that are a part of these dynamic interactions can have altered growth and development as well as changes in microbial fitness as it pertains to antibiotic resistance, nutrient acquisition, and microbial dispersal. Consequences of these interactions are not just limited to the respective microorganisms, but also have major impacts in the health of humans and plants alike. Examining the mechanisms behind the physical interactions of fungi and bacteria will provide us with an understanding of multi-kingdom community processes and allow for the development of therapeutic approaches for disease in both ecological settings.
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Affiliation(s)
- Breanne N. Steffan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; (B.N.S.); (N.V.)
| | - Nandhitha Venkatesh
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; (B.N.S.); (N.V.)
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; (B.N.S.); (N.V.)
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Abstract
Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter. Fungal-bacterial symbioses range from antagonisms to mutualisms and remain one of the least understood interdomain interactions despite their ubiquity as well as ecological and medical importance. To build a predictive conceptual framework for understanding interactions between fungi and bacteria in different types of symbioses, we surveyed fungal and bacterial transcriptional responses in the mutualism between Rhizopus microsporus (Rm) (ATCC 52813, host) and its Mycetohabitans (formerly Burkholderia) endobacteria versus the antagonism between a nonhost Rm (ATCC 11559) and Mycetohabitans isolated from the host, at two time points, before and after partner physical contact. We found that bacteria and fungi sensed each other before contact and altered gene expression patterns accordingly. Mycetohabitans did not discriminate between the host and nonhost and engaged a common set of genes encoding known as well as novel symbiosis factors. In contrast, responses of the host versus nonhost to endobacteria were dramatically different, converging on the altered expression of genes involved in cell wall biosynthesis and reactive oxygen species (ROS) metabolism. On the basis of the observed patterns, we formulated a set of hypotheses describing fungal-bacterial interactions and tested some of them. By conducting ROS measurements, we confirmed that nonhost fungi increased production of ROS in response to endobacteria, whereas host fungi quenched their ROS output, suggesting that ROS metabolism contributes to the nonhost resistance to bacterial infection and the host ability to form a mutualism. Overall, our study offers a testable framework of predictions describing interactions of early divergent Mucoromycotina fungi with bacteria.
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Abstract
Interactions among microbes are key drivers of evolutionary progress and constantly shape ecological niches. Microorganisms rely on chemical communication to interact with each other and surrounding organisms. They synthesize natural products as signaling molecules, antibiotics, or modulators of cellular processes that may be applied in agriculture and medicine. Whereas major insight has been gained into the principles of intraspecies interaction, much less is known about the molecular basis of interspecies interplay. In this review, we summarize recent progress in the understanding of chemically mediated bacterial-fungal interrelations. We discuss pairwise interactions among defined species and systems involving additional organisms as well as complex interactions among microbial communities encountered in the soil or defined as microbiota of higher organisms. Finally, we give examples of how the growing understanding of microbial interactions has contributed to drug discovery and hypothesize what may be future directions in studying and engineering microbiota for agricultural or medicinal purposes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07745 Jena, Germany
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Bastías DA, Johnson LJ, Card SD. Symbiotic bacteria of plant-associated fungi: friends or foes? CURRENT OPINION IN PLANT BIOLOGY 2020; 56:1-8. [PMID: 31786411 DOI: 10.1016/j.pbi.2019.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Many bacteria form symbiotic associations with plant-associated fungi. The effects of these symbionts on host fitness usually depend on symbiont or host genotypes and environmental conditions. However, bacterial endosymbionts, that is those living within fungal cells, may positively regulate host performance as their survival is often heavily dependent on host fitness. Contrary to this, bacteria that establish ectosymbiotic associations with fungi, that is those located on the hyphal surface or in close vicinity to fungal mycelia, may not have an apparent net effect on fungal performance due to the low level of fitness dependency on their host. Our analysis supports the hypothesis that endosymbiotic bacteria of fungi are beneficial symbionts, and that effects of ectosymbiotic bacteria on fungal performance depends on the bacterial type involved in the interaction (e.g. helper versus pathogen of fungi). Ecological scenarios, where the presence of beneficial bacterial endosymbionts of fungi could be compromised, are also discussed.
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Affiliation(s)
- Daniel A Bastías
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
| | - Linda J Johnson
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Stuart D Card
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Yadav SK, Das J, Kumar R, Jha G. Calcium regulates the mycophagous ability of Burkholderia gladioli strain NGJ1 in a type III secretion system-dependent manner. BMC Microbiol 2020; 20:216. [PMID: 32689944 PMCID: PMC7372643 DOI: 10.1186/s12866-020-01897-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 07/12/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND A rice associated bacterium Burkholderia gladioli strain NGJ1 demonstrates mycophagy, a phenomenon wherein bacteria feed on fungi. Previously, we have reported that NGJ1 utilizes type III secretion system (T3SS) to deliver a prophage tail-like protein (Bg_9562) into fungal cells to establish mycophagy. RESULTS In this study, we report that calcium ion concentration influences the mycophagous ability of NGJ1 on Rhizoctonia solani, an important fungal pathogen. The calcium limiting condition promotes mycophagy while high calcium environment prevents it. The expression of various T3SS apparatus encoding genes of NGJ1 was induced and secretion of several potential T3SS effector proteins (including Bg_9562) into extracellular milieu was triggered under calcium limiting condition. Using LC-MS/MS proteome analysis, we identified several calcium regulated T3SS effector proteins of NGJ1. The expression of genes encoding some of these effector proteins was upregulated during mycophagous interaction of NGJ1 with R. solani. Further, mutation of one of these genes (endo-β-1, 3- glucanase) rendered the mutant NGJ1 bacterium defective in mycophagy while complementation with full length copy of the gene restored its mycophagous activity. CONCLUSION Our study provides evidence that low calcium environment triggers secretion of various T3SS effectors proteins into the extracellular milieu and suggests the importance of cocktail of these proteins in promoting mycophagy.
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Affiliation(s)
- Sunil Kumar Yadav
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Joyati Das
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rahul Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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A TAL effector-like protein of an endofungal bacterium increases the stress tolerance and alters the transcriptome of the host. Proc Natl Acad Sci U S A 2020; 117:17122-17129. [PMID: 32632014 PMCID: PMC7382252 DOI: 10.1073/pnas.2003857117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Endosymbiotic bacteria are found in diverse fungi, but little is known about how they communicate with their hosts. Some plant pathogenic bacteria use type III-translocated TAL effectors to control host transcription, and TAL-like proteins are encoded in genomes of the fungal endosymbiotic bacterium Mycetohabitans rhizoxinica. In this paper, we present evidence that these proteins are, like TAL effectors, type III-secreted, nuclear-localizing effectors that perturb host transcription and show that one enhances tolerance of the fungal host to cell membrane stress. Our characterization of an effector in a bacterial–fungal symbiosis opens a new door to molecular understanding of these interkingdom partnerships. Our findings also provide insight into the functional diversity and evolution of the TAL effector protein family. Symbioses of bacteria with fungi have only recently been described and are poorly understood. In the symbiosis of Mycetohabitans (formerly Burkholderia) rhizoxinica with the fungus Rhizopus microsporus, bacterial type III (T3) secretion is known to be essential. Proteins resembling T3-secreted transcription activator-like (TAL) effectors of plant pathogenic bacteria are encoded in the three sequenced Mycetohabitans spp. genomes. TAL effectors nuclear-localize in plants, where they bind and activate genes important in disease. The Burkholderia TAL-like (Btl) proteins bind DNA but lack the N- and C-terminal regions, in which TAL effectors harbor their T3 and nuclear localization signals, and activation domain. We characterized a Btl protein, Btl19-13, and found that, despite the structural differences, it can be T3-secreted and can nuclear-localize. A btl19-13 gene knockout did not prevent the bacterium from infecting the fungus, but the fungus became less tolerant to cell membrane stress. Btl19-13 did not alter transcription in a plant-based reporter assay, but 15 R. microsporus genes were differentially expressed in comparisons both of the fungus infected with the wild-type bacterium vs. the mutant and with the mutant vs. a complemented strain. Southern blotting revealed btl genes in 14 diverse Mycetohabitans isolates. However, banding patterns and available sequences suggest variation, and the btl19-13 phenotype could not be rescued by a btl gene from a different strain. Our findings support the conclusion that Btl proteins are effectors that act on host DNA and play important but varied or possibly host genotype-specific roles in the M. rhizoxinica–R. microsporus symbiosis.
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Bratovanov EV, Ishida K, Heinze B, Pidot SJ, Stinear TP, Hegemann JD, Marahiel MA, Hertweck C. Genome Mining and Heterologous Expression Reveal Two Distinct Families of Lasso Peptides Highly Conserved in Endofungal Bacteria. ACS Chem Biol 2020; 15:1169-1176. [PMID: 31800204 DOI: 10.1021/acschembio.9b00805] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome mining identified the fungal-bacterial endosymbiosis Rhizopus microsporus-Mycetohabitans (previously Burkholderia) rhizoxinica as a rich source of novel natural products. However, most of the predicted compounds have remained cryptic. In this study, we employed heterologous expression to isolate and characterize three ribosomally synthesized and post-translationally modified peptides with lariat topology (lasso peptides) from the endosymbiont M. rhizoxinica: burhizin-23, mycetohabin-16, and mycetohabin-15. Through coexpression experiments, it was shown that an orphan gene product results in mature mycetohabin-15, albeit encoded remotely from the core biosynthetic gene cluster. Comparative genomics revealed that mycetohabins are highly conserved among M. rhizoxinica and related endosymbiotic bacteria. Gene knockout and reinfection experiments indicated that the lasso peptides are not crucial for establishing symbiosis; instead, the peptides are exported into the environment during endosymbiosis. This is the first report on lasso peptides from endosymbiotic bacteria.
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Affiliation(s)
- Evgeni V. Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Beatrix Heinze
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Julian D. Hegemann
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124/TC2, 10623 Berlin, Germany
- Department of Chemistry and Biochemistry, Philipps University Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry and Biochemistry, Philipps University Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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33
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Niehs SP, Dose B, Richter S, Pidot SJ, Dahse H, Stinear TP, Hertweck C. Mining Symbionts of a Spider‐Transmitted Fungus Illuminates Uncharted Biosynthetic Pathways to Cytotoxic Benzolactones. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Sophie Richter
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology Doherty Institute 792 Elizabeth Street Melbourne 3000 Australia
| | | | - Timothy P. Stinear
- Department of Microbiology and Immunology Doherty Institute 792 Elizabeth Street Melbourne 3000 Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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34
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Drivers of Foliar Fungal Endophytic Communities of Kudzu (Pueraria montana var. lobata) in the Southeast United States. DIVERSITY 2020. [DOI: 10.3390/d12050185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fungal endophytes play important roles in plant fitness and plant–microbe interactions. Kudzu (Pueraria montana var. lobata) is a dominant, abundant, and highly aggressive invasive plant in the Southeast United States. Kudzu serves as a pathogen reservoir that impacts economically important leguminous crops. We conducted the first investigations on kudzu fungal endophytes (Illumina MiSeq—ITS2) to elucidate drivers of endophytic communities across the heart of the invasive range in the Southeast United States (TN, MS, AL, GA). We tested the impacts of multiple environmental parameters (Chlorophyll, NO3−, K+, soil pH, leaf area, host genotype, traffic intensity, and geographic location) on foliar endophyte communities. Endophytic communities were diverse and structured by many factors in our PerMANOVA analyses, but location, genotype, and traffic (proxy for pollution) were the strongest drivers of community composition (R2 = 0.152, p < 0.001, R2 = 0.129, p < 0.001, and R2 = 0.126, p < 0.001, respectively). Further, we examined the putative ecological interactions between endophytic fungi and plant pathogens. We identify numerous OTUs that are positively and strongly associated with pathogen occurrence, largely within the families Montagnulaceae and Tremellales incertae sedis. Taken together, these data suggest location, host genetics and local pollution play instrumental roles in structuring communities, and integrative plant management must consider these factors when developing management strategies.
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Yan F, Huang C, Wang X, Tan J, Cheng S, Wan M, Wang Z, Wang S, Luo S, Li A, Guo X, Feng M, Liu X, Zhu Y, Zhou Y. Threonine ADP-Ribosylation of Ubiquitin by a Bacterial Effector Family Blocks Host Ubiquitination. Mol Cell 2020; 78:641-652.e9. [PMID: 32330457 DOI: 10.1016/j.molcel.2020.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/10/2020] [Accepted: 03/10/2020] [Indexed: 12/16/2022]
Abstract
Ubiquitination is essential for numerous eukaryotic cellular processes. Here, we show that the type III effector CteC from Chromobacterium violaceum functions as an adenosine diphosphate (ADP)-ribosyltransferase that specifically modifies ubiquitin via threonine ADP-ribosylation on residue T66. The covalent modification prevents the transfer of ubiquitin from ubiquitin-activating enzyme E1 to ubiquitin-conjugating enzyme E2, which inhibits subsequent ubiquitin activation by E2 and E3 enzymes in the ubiquitination cascade and leads to the shutdown of polyubiquitin synthesis in host cells. This unique modification also causes dysfunction of polyubiquitin chains in cells, thereby blocking host ubiquitin signaling. The disruption of host ubiquitination by CteC plays a crucial role in C. violaceum colonization in mice during infection. CteC represents a family of effector proteins in pathogens of hosts from different kingdoms. All the members of this family specifically ADP-ribosylate ubiquitin. The action of CteC reveals a new mechanism for interfering with host ubiquitination by pathogens.
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Affiliation(s)
- Fujie Yan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Chunfeng Huang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaofei Wang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiaxing Tan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sen Cheng
- Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Muyang Wan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhao Wang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuangyu Wang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuhui Luo
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Arong Li
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xing Guo
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mingguang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongqun Zhu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, China.
| | - Yan Zhou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Takashima Y, Degawa Y, Nishizawa T, Ohta H, Narisawa K. Aposymbiosis of a Burkholderiaceae-Related Endobacterium Impacts on Sexual Reproduction of Its Fungal Host. Microbes Environ 2020; 35. [PMID: 32295978 PMCID: PMC7308579 DOI: 10.1264/jsme2.me19167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacterial endosymbionts inhabit diverse fungal lineages. Although the number of studies on bacteria is increasing, the mechanisms by which bacteria affect their fungal hosts remain unclear. We herein examined the homothallic isolate, Mortierella sugadairana YTM39, harboring a Burkholderiaceae-related endobacterium, which did not produce sexual spores. We successfully eliminated the bacterium from fungal isolates using ciprofloxacin treatment and asexual spore isolation for germinated asexual spores. Sexual spore formation by the fungus was restored by eliminating the bacterium from isolates. These results indicate that sexual reproduction by the fungus was inhibited by the bacterium. This is the first study on the sexual spore infertility of fungal hosts by endofungal bacteria.
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Affiliation(s)
- Yusuke Takashima
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology.,Ibaraki University College of Agriculture
| | - Yousuke Degawa
- Sugadaira Research Station Mountain Science Center, University of Tsukuba
| | - Tomoyasu Nishizawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology.,Ibaraki University College of Agriculture
| | - Hiroyuki Ohta
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology.,Ibaraki University College of Agriculture
| | - Kazuhiko Narisawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology.,Ibaraki University College of Agriculture
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37
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Espino-Vázquez AN, Bermúdez-Barrientos JR, Cabrera-Rangel JF, Córdova-López G, Cardoso-Martínez F, Martínez-Vázquez A, Camarena-Pozos DA, Mondo SJ, Pawlowska TE, Abreu-Goodger C, Partida-Martínez LP. Narnaviruses: novel players in fungal-bacterial symbioses. ISME JOURNAL 2020; 14:1743-1754. [PMID: 32269378 DOI: 10.1038/s41396-020-0638-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 12/31/2022]
Abstract
Rhizopus microsporus is an early-diverging fungal species with importance in ecology, agriculture, food production, and public health. Pathogenic strains of R. microsporus harbor an intracellular bacterial symbiont, Mycetohabitans (formerly named Burkholderia). This vertically transmitted bacterial symbiont is responsible for the production of toxins crucial to the pathogenicity of Rhizopus and remarkably also for fungal reproduction. Here we show that R. microsporus can live not only in symbiosis with bacteria but also with two viral members of the genus Narnavirus. Our experiments revealed that both viruses replicated similarly in the growth conditions we tested. Viral copies were affected by the developmental stage of the fungus, the substrate, and the presence or absence of Mycetohabitans. Absolute quantification of narnaviruses in isolated asexual sporangiospores and sexual zygospores indicates their vertical transmission. By curing R. microsporus of its viral and bacterial symbionts and reinfecting bacteria to reestablish symbiosis, we demonstrate that these viruses affect fungal biology. Narnaviruses decrease asexual reproduction, but together with Mycetohabitans, are required for sexual reproductive success. This fungal-bacterial-viral system represents an outstanding model to investigate three-way microbial symbioses and their evolution.
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Affiliation(s)
- Astrid N Espino-Vázquez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico
| | - J Roberto Bermúdez-Barrientos
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico.,Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico
| | - J Francisco Cabrera-Rangel
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico
| | - Gonzalo Córdova-López
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico.,Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico
| | - Faviola Cardoso-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico
| | - Azul Martínez-Vázquez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico
| | - David A Camarena-Pozos
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Bioagricultural Science and Pest Management Department, Colorado State University, Fort Collins, CO, 80521, USA
| | - Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Cei Abreu-Goodger
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico
| | - Laila P Partida-Martínez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Irapuato, 36824, Mexico.
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38
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Niehs SP, Dose B, Richter S, Pidot SJ, Dahse HM, Stinear TP, Hertweck C. Mining Symbionts of a Spider-Transmitted Fungus Illuminates Uncharted Biosynthetic Pathways to Cytotoxic Benzolactones. Angew Chem Int Ed Engl 2020; 59:7766-7771. [PMID: 32040253 PMCID: PMC7318616 DOI: 10.1002/anie.201916007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Indexed: 11/17/2022]
Abstract
A spider‐transmitted fungus (Rhizopus microsporus) that was isolated from necrotic human tissue was found to harbor endofungal bacteria (Burkholderia sp.). Metabolic profiling of the symbionts revealed a complex of cytotoxic agents (necroximes). Their structures were characterized as oxime‐substituted benzolactone enamides with a peptidic side chain. The potently cytotoxic necroximes are also formed in symbiosis with the fungal host and could have contributed to the necrosis. Genome sequencing and computational analyses revealed a novel modular PKS/NRPS assembly line equipped with several non‐canonical domains. Based on gene‐deletion mutants, we propose a biosynthetic model for bacterial benzolactones. We identified specific traits that serve as genetic handles to find related salicylate macrolide pathways (lobatamide, oximidine, apicularen) in various other bacterial genera. Knowledge of the biosynthetic pathway enables biosynthetic engineering and genome‐mining approaches.
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Affiliation(s)
- Sarah P Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sophie Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | | | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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Perez-Quintero AL, Szurek B. A Decade Decoded: Spies and Hackers in the History of TAL Effectors Research. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:459-481. [PMID: 31387457 DOI: 10.1146/annurev-phyto-082718-100026] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transcription activator-like effectors (TALEs) from the genus Xanthomonas are proteins with the remarkable ability to directly bind the promoters of genes in the plant host to induce their expression, which often helps bacterial colonization. Metaphorically, TALEs act as spies that infiltrate the plant disguised as high-ranking civilians (transcription factors) to trick the plant into activating weak points that allow an invasion. Current knowledge of how TALEs operate allows researchers to predict their activity (counterespionage) and exploit their function, engineering them to do our bidding (a Manchurian agent). This has been possible thanks particularly to the discovery of their DNA binding mechanism, which obeys specific amino acid-DNA correspondences (the TALE code). Here, we review the history of how researchers discovered the way these proteins work and what has changed in the ten years since the discovery of the code. Recommended music for reading this review can be found in the Supplemental Material.
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Affiliation(s)
- Alvaro L Perez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523-1177, USA;
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
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40
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Niehs SP, Dose B, Scherlach K, Pidot SJ, Stinear TP, Hertweck C. Genome Mining Reveals Endopyrroles from a Nonribosomal Peptide Assembly Line Triggered in Fungal-Bacterial Symbiosis. ACS Chem Biol 2019; 14:1811-1818. [PMID: 31283172 DOI: 10.1021/acschembio.9b00406] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial endosymbiont (Burkholderia rhizoxinica) of the rice seedling blight fungus (Rhizopus microsporus) harbors a large number of cryptic biosynthesis gene clusters. Genome mining and sequence similarity networks based on an encoded nonribosomal peptide assembly line and the associated pyrrole-forming enzymes in the symbiont indicated that the encoded metabolites are unique among a large number of tentative pyrrole natural products in diverse and unrelated bacterial phyla. By performing comparative metabolic profiling using a mutant generated with an improved pheS Burkholderia counterselection marker, we found that the symbionts' biosynthetic pathway is mainly activated under salt stress and exclusively in symbiosis with the fungal host. The cryptic metabolites were fully characterized as novel pyrrole-substituted depsipeptides (endopyrroles). A broader survey showed that endopyrrole production is a hallmark of geographically distant endofungal bacteria, which produce the peptides solely under symbiotic conditions.
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Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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41
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Arora P, Riyaz-Ul-Hassan S. Endohyphal bacteria; the prokaryotic modulators of host fungal biology. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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42
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Mannaa M, Park I, Seo YS. Genomic Features and Insights into the Taxonomy, Virulence, and Benevolence of Plant-Associated Burkholderia Species. Int J Mol Sci 2018; 20:E121. [PMID: 30598000 PMCID: PMC6337347 DOI: 10.3390/ijms20010121] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/24/2018] [Accepted: 12/24/2018] [Indexed: 11/17/2022] Open
Abstract
The members of the Burkholderia genus are characterized by high versatility and adaptability to various ecological niches. With the availability of the genome sequences of numerous species of Burkholderia, many studies have been conducted to elucidate the unique features of this exceptional group of bacteria. Genomic and metabolic plasticity are common among Burkholderia species, as evidenced by their relatively large multi-replicon genomes that are rich in insertion sequences and genomic islands and contain a high proportion of coding regions. Such unique features could explain their adaptability to various habitats and their versatile lifestyles, which are reflected in a multiplicity of species including free-living rhizospheric bacteria, plant endosymbionts, legume nodulators, and plant pathogens. The phytopathogenic Burkholderia group encompasses several pathogens representing threats to important agriculture crops such as rice. Contrarily, plant-beneficial Burkholderia have also been reported, which have symbiotic and growth-promoting roles. In this review, the taxonomy of Burkholderia is discussed emphasizing the recent updates and the contributions of genomic studies to precise taxonomic positioning. Moreover, genomic and functional studies on Burkholderia are reviewed and insights are provided into the mechanisms underlying the virulence and benevolence of phytopathogenic and plant-beneficial Burkholderia, respectively, on the basis of cutting-edge knowledge.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
| | - Inmyoung Park
- Department of Oriental Food and Culinary Arts, Youngsan University, Busan 48015, Korea.
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea.
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43
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Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, van Elsas JD, Wick LY. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol Rev 2018; 42:335-352. [PMID: 29471481 DOI: 10.1093/femsre/fuy008] [Citation(s) in RCA: 318] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 02/16/2018] [Indexed: 12/14/2022] Open
Abstract
Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.
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Affiliation(s)
- Aurélie Deveau
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jessie Uehling
- Biology Department, Duke University, Box 90338, Durham, NC 27705, USA.,Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Mathieu Paoletti
- Institut de Biologie et Génétique Cellulaire, UMR 5095 CNRS et Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux cedex, France
| | - Matthias Becker
- IGZ, Leibniz-Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland.,Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Olga A Lastovetsky
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Sophie Mieszkin
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Larry J Millet
- Joint Institute for Biological Science, University of Tennessee, and the Biosciences Division of Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of Torino, 10125 Torino, Italy
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry, G. Mahlerlaan 3004, 1081 LA, Amsterdam, The Netherlands
| | - Stefan Olsson
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Jan Dirk van Elsas
- Microbial Ecology group, GELIFES, University of Groningen, 9747 Groningen, The Netherlands
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
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44
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Niehs SP, Dose B, Scherlach K, Roth M, Hertweck C. Genomics-Driven Discovery of a Symbiont-Specific Cyclopeptide from Bacteria Residing in the Rice Seedling Blight Fungus. Chembiochem 2018; 19:2167-2172. [PMID: 30113119 DOI: 10.1002/cbic.201800400] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 12/24/2022]
Abstract
The rice seedling blight fungus Rhizopus microsporus harbors endosymbiotic bacteria (Burkholderia rhizoxinica) that produce the virulence factor rhizoxin and control host development. Genome mining indicated a massive inventory of cryptic nonribosomal peptide synthetase (NRPS) genes, which have not yet been linked to any natural products. The discovery and full characterization of a novel cyclopeptide from endofungal bacteria is reported. In silico analysis of an orphan, symbiont-specific NRPS predicted the structure of a nonribosomal peptide, which was targeted by LC-MS/MS profiling of wild-type and engineered null mutants. NMR spectroscopy and chemical derivatization elucidated the structure of the bacterial cyclopeptide. Phylogenetic analyses revealed the relationship of starter C domains for rare N-acetyl-capped peptides. Heptarhizin is produced under symbiotic conditions in geographically constrained strains from the Pacific clade; this indicates a potential ecological role of the peptide.
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Affiliation(s)
- Sarah P Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Martin Roth
- BioPilotPlant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Friedrich Schiller University Jena, 07743, Jena, Germany
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45
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Pawlowska TE, Gaspar ML, Lastovetsky OA, Mondo SJ, Real-Ramirez I, Shakya E, Bonfante P. Biology of Fungi and Their Bacterial Endosymbionts. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:289-309. [PMID: 30149793 DOI: 10.1146/annurev-phyto-080417-045914] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Heritable symbioses, in which endosymbiotic bacteria (EB) are transmitted vertically between host generations, are an important source of evolutionary novelties. A primary example of such symbioses is the eukaryotic cell with its EB-derived organelles. Recent discoveries suggest that endosymbiosis-related innovations can be also found in associations formed by early divergent fungi in the phylum Mucoromycota with heritable EB from two classes, Betaproteobacteria and Mollicutes. These symbioses exemplify novel types of host-symbiont interactions. Studies of these partnerships fuel theoretical models describing mechanisms that stabilize heritable symbioses, control the rate of molecular evolution, and enable the establishment of mutualisms. Lastly, by altering host phenotypes and metabolism, these associations represent an important instrument for probing the basic biology of the Mucoromycota hosts, which remain one of the least explored filamentous fungi.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, New York 14853, USA;
| | - Maria L Gaspar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Olga A Lastovetsky
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Evaniya Shakya
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, New York 14853, USA;
| | - Paola Bonfante
- Department of Life Sciences & Systems Biology, University of Torino, 10125 Torino, Italy
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46
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 485] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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47
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Sharmin D, Guo Y, Nishizawa T, Ohshima S, Sato Y, Takashima Y, Narisawa K, Ohta H. Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica. Microbes Environ 2018. [PMID: 29540638 PMCID: PMC5877345 DOI: 10.1264/jsme2.me17138] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Endohyphal bacteria (EHB), dwelling within fungal hyphae, markedly affect the growth and metabolic potential of their hosts. To date, two EHB belonging to the family Burkholderiaceae have been isolated and characterized as new taxa, Burkholderia rhizoxinica (HKI 454T) and Mycoavidus cysteinexigens (B1-EBT), in Japan. Metagenome sequencing was recently reported for Mortierella elongata AG77 together with its endosymbiont M. cysteinexigens (Mc-AG77) from a soil/litter sample in the USA. In the present study, we elucidated the complete genome sequence of B1-EBT and compared it with those of Mc-AG77 and HKI 454T. The genomes of B1-EBT and Mc-AG77 contained a higher level of prophage sequences and were markedly smaller than that of HKI 454T. Although the B1-EBT and Mc-AG77 genomes lacked the chitinolytic enzyme genes responsible for invasion into fungal cells, they contained several predicted toxin-antitoxin systems including an insecticidal toxin complex and PIN domain imposing an addiction-like mechanism essential for endohyphal growth control during host colonization. Despite the different host fungi, the alignment of amino acid sequences showed that the HKI 454T genome consisted of 1,265 (32.6%) and 1,221 (31.5%) orthologous coding sequences (CDSs) with those of B1-EBT and Mc-AG77, respectively. This comparative study of three phylogenetically associated endosymbionts has provided insights into their origin and evolution, and suggests the later bacterial invasion and adaptation of B1-EBT to its host metabolism.
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Affiliation(s)
- Dilruba Sharmin
- Ibaraki University College of Agriculture, Department of Bioresource Science
| | - Yong Guo
- Ibaraki University College of Agriculture, Department of Bioresource Science
| | - Tomoyasu Nishizawa
- Ibaraki University College of Agriculture, Department of Bioresource Science.,United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
| | - Shoko Ohshima
- Ibaraki University College of Agriculture, Department of Bioresource Science
| | - Yoshinori Sato
- Center for Conservation and Restoration Techniques, Tokyo National Research Institute for Cultural Properties
| | - Yusuke Takashima
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
| | - Kazuhiko Narisawa
- Ibaraki University College of Agriculture, Department of Bioresource Science.,United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
| | - Hiroyuki Ohta
- Ibaraki University College of Agriculture, Department of Bioresource Science.,United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
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48
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Scherlach K, Hertweck C. Mediators of mutualistic microbe–microbe interactions. Nat Prod Rep 2018; 35:303-308. [DOI: 10.1039/c7np00035a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This viewpoint summarizes recent advances in understanding the role of natural products as regulators of mutualistic microbial interactions.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Chemistry
- Infection Biology (HKI)
- 07745 Jena
- Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Chemistry
- Infection Biology (HKI)
- 07745 Jena
- Germany
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49
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Niehs SP, Scherlach K, Hertweck C. Genomics-driven discovery of a linear lipopeptide promoting host colonization by endofungal bacteria. Org Biomol Chem 2018; 16:8345-8352. [DOI: 10.1039/c8ob01515e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The linear lipopeptide holrhizin is an important mediator of the Burkholderia-Rhizopus interaction that promotes bacterial colonization of the fungal host.
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Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Research and Infection Biology (HKI)
- 07745 Jena
- Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Research and Infection Biology (HKI)
- 07745 Jena
- Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry
- Leibniz Institute for Natural Product Research and Infection Biology (HKI)
- 07745 Jena
- Germany
- Friedrich Schiller University Jena
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50
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Pratama AA, Haq IU, Nazir R, Chaib De Mares M, van Elsas JD. Draft genome sequences of three fungal-interactive Paraburkholderia terrae strains, BS007, BS110 and BS437. Stand Genomic Sci 2017; 12:81. [PMID: 29270249 PMCID: PMC5735546 DOI: 10.1186/s40793-017-0293-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/24/2017] [Indexed: 02/08/2023] Open
Abstract
Here, we report the draft genome sequences of three fungal-interactive 10.1601/nm.27008 strains, denoted BS110, BS007 and BS437. Phylogenetic analyses showed that the three strains belong to clade II of the genus 10.1601/nm.1619, which was recently renamed 10.1601/nm.26956. This novel genus primarily contains environmental species, encompassing non-pathogenic plant- as well as fungal-interactive species. The genome of strain BS007 consists of 11,025,273 bp, whereas those of strains BS110 and BS437 have 11,178,081 and 11,303,071 bp, respectively. Analyses of the three annotated genomes revealed the presence of (1) a large suite of substrate capture systems, and (2) a suite of genetic systems required for adaptation to microenvironments in soil and the mycosphere. Thus, genes encoding traits that potentially confer fungal interactivity were found, such as type 4 pili, type 1, 2, 3, 4 and 6 secretion systems, and biofilm formation (PGA, alginate and pel) and glycerol uptake systems. Furthermore, the three genomes also revealed the presence of a highly conserved five-gene cluster that had previously been shown to be upregulated upon contact with fungal hyphae. Moreover, a considerable number of prophage-like and CRISPR spacer sequences was found, next to genetic systems responsible for secondary metabolite production. Overall, the three 10.1601/nm.27008 strains possess the genetic repertoire necessary for adaptation to diverse soil niches, including those influenced by soil fungi.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG The Netherlands
| | - Irshad Ul Haq
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG The Netherlands
| | - Rashid Nazir
- Department of Environmental Sciences COMSATS Institute of Information Technology, University Road, Abbottabad, 22060 Pakistan
| | - Maryam Chaib De Mares
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen, 9747 AG The Netherlands
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