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Shankar G, Akhter Y. Stealing survival: Iron acquisition strategies of Mycobacteriumtuberculosis. Biochimie 2024:S0300-9084(24)00142-1. [PMID: 38901792 DOI: 10.1016/j.biochi.2024.06.006] [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: 05/06/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), faces iron scarcity within the host due to immune defenses. This review explores the importance of iron for Mtb and its strategies to overcome iron restriction. We discuss how the host limits iron as an innate immune response and how Mtb utilizes various iron acquisition systems, particularly the siderophore-mediated pathway. The review illustrates the structure and biosynthesis of mycobactin, a key siderophore in Mtb, and the regulation of its production. We explore the potential of targeting siderophore biosynthesis and uptake as a novel therapeutic approach for TB. Finally, we summarize current knowledge on Mtb's iron acquisition and highlight promising directions for future research to exploit this pathway for developing new TB interventions.
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Affiliation(s)
- Gauri Shankar
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226 025, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226 025, India.
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2
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Mannaa M, Lee D, Lee HH, Han G, Kang M, Kim TJ, Park J, Seo YS. Exploring the comparative genome of rice pathogen Burkholderia plantarii: unveiling virulence, fitness traits, and a potential type III secretion system effector. FRONTIERS IN PLANT SCIENCE 2024; 15:1416253. [PMID: 38845849 PMCID: PMC11153758 DOI: 10.3389/fpls.2024.1416253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
This study presents a comprehensive genomic analysis of Burkholderia plantarii, a rice pathogen that causes blight and grain rot in seedlings. The entire genome of B. plantarii KACC 18964 was sequenced, followed by a comparative genomic analysis with other available genomes to gain insights into its virulence, fitness, and interactions with rice. Multiple secondary metabolite gene clusters were identified. Among these, 12 demonstrated varying similarity levels to known clusters linked to bioactive compounds, whereas eight exhibited no similarity, indicating B. plantarii as a source of potentially novel secondary metabolites. Notably, the genes responsible for tropolone and quorum sensing were conserved across the examined genomes. Additionally, B. plantarii was observed to possess three complete CRISPR systems and a range of secretion systems, exhibiting minor variations among the analyzed genomes. Genomic islands were analyzed across the four genomes, and a detailed study of the B. plantarii KACC 18964 genome revealed 59 unique islands. These islands were thoroughly investigated for their gene contents and potential roles in virulence. Particular attention has been devoted to the Type III secretion system (T3SS), a crucial virulence factor. An in silico analysis of potential T3SS effectors identified a conserved gene, aroA. Further mutational studies, in planta and in vitro analyses validated the association between aroA and virulence in rice. Overall, this study enriches our understanding of the genomic basis of B. plantarii pathogenicity and emphasizes the potential role of aroA in virulence. This understanding may guide the development of effective disease management strategies.
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Affiliation(s)
- Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Duyoung Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Minhee Kang
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Tae-Jin Kim
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
| | - Jungwook Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Institute of System Biology, Pusan National University, Busan, Republic of Korea
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3
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Liu H, Sun L, Zhang J, Wang Y, Lu H. Siderophore-synthesizing NRPS reprogram lipid metabolic profiles for phenotype and function changes of Arthrobotrys oligospora. World J Microbiol Biotechnol 2023; 40:46. [PMID: 38114752 DOI: 10.1007/s11274-023-03840-9] [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: 05/15/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023]
Abstract
The objective of this paper is to explore the function of the AOL-s00215g415 (Aog415) gene, which encodes for the synthesis of siderophore in the nematode trapping fungal model strain A. oligospora, in order to understand the relationship between siderophore biosynthesis and nematode trapping activity. After a through sequence analysis, it was determined that Aog415 is a siderophore-synthesizing NRPS. The product of this gene was then identified to be the hydroxamate siderophore desferriferrichrome, using mass spectrometry analysis. When compared to the WT strains, the Aog415 knockout strain exhibited a 60% decrease in siderophore content in fermentation broth. Additionally, the number of predatory rings of decreased by 23.21%, while the spore yield increased by 37.34%. The deletion of Aog415 did not affect the growth of A. oligospora in diverse nutrient medium. Lipid metabolism-related pathways were the primary targets of Aog415 disruption as revealed by the metabolomic analysis. In comparison to the WT, a significant reduction in the levels of glycerophospholipids, and glycolipids was observed in the mutation. The metabolic alteration in fatty acyls and amino acid-like molecules were significantly disrupted. The knockout of Aog415 impaired the biosynthesis of the hydroxamate siderophore desferriferrichrome, remodeled the flow of fatty acid in A. oligospora, and mainly reprogrammed the membrane lipid metabolism in cells. Desferriferrichrome, a hydroxamate siderophore affects the growth, metabolism and nematode trapping ability of A. oligospora by regulating iron intake and cell membrane homeostasis. Our study uncovered the significant contribution of siderophores to the growth and nematode trapping ability and constructed the relationship among siderophores biosynthesis, lipid metabolism and nematode trapping activity of A. oligospora, which provides a new insight for the development of nematode biocontrol agents based on nematode trapping fungi.
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Affiliation(s)
- Huiwen Liu
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China
| | - Liangyin Sun
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China
| | - Jintao Zhang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601, Anhui, China.
| | - Hengqian Lu
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China.
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4
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Zhang W, Forester NT, Applegate ER, Liu X, Johnson LJ. High-affinity iron uptake is required for optimal Epichloë festucae colonization of Lolium perenne and seed transmission. MOLECULAR PLANT PATHOLOGY 2023; 24:1430-1442. [PMID: 37477276 PMCID: PMC10576175 DOI: 10.1111/mpp.13379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/14/2023] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
Epichloë festucae uses a siderophore-mediated system to acquire iron, which is important to maintain endophyte-grass symbioses. Here we investigate the roles of the alternative iron acquisition system, reductive iron assimilation (RIA), via disruption of the fetC gene, which encodes a multicopper ferroxidase, either alone (i.e., ΔfetC) or in combination with disruption of the gene sidA, which encodes a siderophore biosynthesis enzyme (i.e., ΔfetC/ΔsidA). The phenotypic characteristics of these mutants were compared to ΔsidA and wild-type (WT) strains during growth under axenic culture conditions (in culture) and in symbiosis with the host grass, perennial ryegrass (in planta). Under iron deficiency, the colony growth rate of ΔfetC was slightly slower than that of WT, while the growth of ΔsidA and ΔfetC/ΔsidA mutants was severely suppressed. Siderophore analyses indicated that ΔfetC mutants hyperaccumulate ferriepichloënin A (FEA) at low iron concentrations and ferricrocin and FEA at higher iron concentrations. When compared to WT, all mutant strains displayed hyperbranching hyphal structures and a reduced ratio of Epichloë DNA to total DNA in planta. Furthermore, host colonization and vertical transmission through infection of the host seed were significantly reduced in the ΔfetC/ΔsidA mutants, confirming that high-affinity iron uptake is a critical process for Epichloë transmission. Thus, RIA and siderophore iron uptake are complementary systems required for the maintenance of iron metabolism, fungal growth, and symbiosis between E. festucae and perennial ryegrass.
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Affiliation(s)
- Wei Zhang
- AgResearch Limited, Grasslands Research CentrePalmerston NorthNew Zealand
| | | | - Emma R. Applegate
- AgResearch Limited, Grasslands Research CentrePalmerston NorthNew Zealand
| | - Xinqi Liu
- AgResearch Limited, Grasslands Research CentrePalmerston NorthNew Zealand
| | - Linda J. Johnson
- AgResearch Limited, Grasslands Research CentrePalmerston NorthNew Zealand
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Happacher I, Aguiar M, Yap A, Decristoforo C, Haas H. Fungal siderophore metabolism with a focus on Aspergillus fumigatus: impact on biotic interactions and potential translational applications. Essays Biochem 2023; 67:829-842. [PMID: 37313590 PMCID: PMC10500206 DOI: 10.1042/ebc20220252] [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: 04/03/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
Iron is an essential trace element that is limiting in most habitats including hosts for fungal pathogens. Siderophores are iron-chelators synthesized by most fungal species for high-affinity uptake and intracellular handling of iron. Moreover, virtually all fungal species including those lacking siderophore biosynthesis appear to be able to utilize siderophores produced by other species. Siderophore biosynthesis has been shown to be crucial for virulence of several fungal pathogens infecting animals and plants revealing induction of this iron acquisition system during virulence, which offers translational potential of this fungal-specific system. The present article summarizes the current knowledge on the fungal siderophore system with a focus on Aspergillus fumigatus and its potential translational application including noninvasive diagnosis of fungal infections via urine samples, imaging of fungal infections via labeling of siderophores with radionuclides such as Gallium-68 for detection with positron emission tomography, conjugation of siderophores with fluorescent probes, and development of novel antifungal strategies.
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Affiliation(s)
- Isidor Happacher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Mario Aguiar
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Annie Yap
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Clemens Decristoforo
- Department of Nuclear Medicine, Medical University Innsbruck, Innsbruck, Austria
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
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He R, Zhang J, Shao Y, Gu S, Song C, Qian L, Yin WB, Li Z. Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements. PLoS Comput Biol 2023; 19:e1011100. [PMID: 37186644 DOI: 10.1371/journal.pcbi.1011100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 05/25/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) is a diverse family of biosynthetic enzymes for the assembly of bioactive peptides. Despite advances in microbial sequencing, the lack of a consistent standard for annotating NRPS domains and modules has made data-driven discoveries challenging. To address this, we introduced a standardized architecture for NRPS, by using known conserved motifs to partition typical domains. This motif-and-intermotif standardization allowed for systematic evaluations of sequence properties from a large number of NRPS pathways, resulting in the most comprehensive cross-kingdom C domain subtype classifications to date, as well as the discovery and experimental validation of novel conserved motifs with functional significance. Furthermore, our coevolution analysis revealed important barriers associated with re-engineering NRPSs and uncovered the entanglement between phylogeny and substrate specificity in NRPS sequences. Our findings provide a comprehensive and statistically insightful analysis of NRPS sequences, opening avenues for future data-driven discoveries.
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Affiliation(s)
- Ruolin He
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yuanzhe Shao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Long Qian
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, PR China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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7
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Narh Mensah DL, Wingfield BD, Coetzee MPA. Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae. Curr Genet 2023; 69:7-24. [PMID: 36369495 DOI: 10.1007/s00294-022-01256-w] [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: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022]
Abstract
Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)3(TC)2. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Council for Scientific and Industrial Research-Food Research Institute (CSIR-FRI), P. O. Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
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Miller TA, Hudson DA, Johnson RD, Singh JS, Mace WJ, Forester NT, Maclean PH, Voisey CR, Johnson LJ. Dissection of the epoxyjanthitrem pathway in Epichloë sp. LpTG-3 strain AR37 by CRISPR gene editing. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:944234. [PMID: 37746172 PMCID: PMC10512260 DOI: 10.3389/ffunb.2022.944234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/18/2022] [Indexed: 09/26/2023]
Abstract
Epichloë festucae var. lolii and Epichloë sp. LpTG-3 are filamentous fungal endophytes of perennial ryegrass (Lolium perenne) that have a substantial impact on New Zealand's agricultural economy by conferring biotic advantages to the host grass. Overall, Epichloë endophytes contribute NZ$200 million to the economy annually, with strain AR37 estimated to contribute NZ$3.6 billion to the New Zealand economy over a 20-year period. This strain produces secondary metabolites, including epoxyjanthitrems, which are a class of indole diterpenes, associated with the observed effects of AR37 on livestock and insect pests. Until very recently, AR37 was intractable to genetic modification but this has changed with the application of CRISPR-Cas9 based gene editing techniques. In this paper, gene inactivation by CRISPR-Cas9 was used to deconvolute the genetic basis for epoxyjanthitrem biosynthesis, including creating an AR37 strain that has been edited to remove the biosynthesis of all indole diterpenes. We show that gene editing of Epichloë can be achieved without off-target events or introduction of foreign DNA (footprint-less) through an AMA1-based plasmid that simultaneously expresses the CRISPR-Cas9 system and selectable marker. Genetic modification events in these transformants were investigated through genome sequencing and in planta chemistry.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Linda J. Johnson
- Grasslands Research Centre, AgResearch, Palmerston North, New Zealand
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Liu Q, Johnson LJ, Applegate ER, Arfmann K, Jauregui R, Larking A, Mace WJ, Maclean P, Walker T, Johnson RD. Identification of Genetic Diversity, Pyrrocidine-Producing Strains and Transmission Modes of Endophytic Sarocladium zeae Fungi from Zea Crops. Microorganisms 2022; 10:microorganisms10071415. [PMID: 35889134 PMCID: PMC9316807 DOI: 10.3390/microorganisms10071415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/10/2022] Open
Abstract
Genotyping by sequencing (GBS) was used to reveal the inherent genetic variation within the haploid fungi Sarocladium zeae isolated from diverse Zea germplasm, including modern Zea mays and its wild progenitors—the teosintes. In accordance with broad host relationship parameters, GBS analysis revealed significant host lineages of S. zeae genetic diversity, indicating that S. zeae genetic variation may associate with different evolutionary histories of host species or varieties. Based on a recently identified PKS-NRPS gene responsible for pyrrocidine biosynthesis in S. zeae fungi, a novel PCR assay was developed to discriminate pyrrocidine-producing S. zeae strains. This molecular method for screening bioactive strains of S. zeae is complementary to other approaches, such as chemical analyses. An eGFP-labelled S. zeae strain was also developed to investigate the endophytic transmission of S. zeae in Z. mays seedlings, which has further improved our understanding of the transmission modes of S. zeae endophytes in maize tissues.
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Wang Y, Glukhov E, He Y, Liu Y, Zhou L, Ma X, Hu X, Hong P, Gerwick WH, Zhang Y. Secondary Metabolite Variation and Bioactivities of Two Marine Aspergillus Strains in Static Co-Culture Investigated by Molecular Network Analysis and Multiple Database Mining Based on LC-PDA-MS/MS. Antibiotics (Basel) 2022; 11:antibiotics11040513. [PMID: 35453264 PMCID: PMC9031932 DOI: 10.3390/antibiotics11040513] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Co-culture is known as an efficient way to explore the metabolic potential of fungal strains for new antibiotics and other therapeutic agents that could counter emerging health issues. To study the effect of co-culture on the secondary metabolites and bioactivities of two marine strains, Aspergillus terreus C23-3 and Aspergillus. unguis DLEP2008001, they were co-cultured in live or inactivated forms successively or simultaneously. The mycelial morphology and high-performance thin layer chromatography (HPTLC) including bioautography of the fermentation extracts were recorded. Furthermore, the agar cup-plate method was used to compare the antimicrobial activity of the extracts. Based on the above, liquid chromatography-photodiode array-tandem mass spectrometry (LC-PDA-MS/MS) together with Global Natural Products Social molecular networking (GNPS) and multiple natural products database mining were used to further analyze their secondary metabolite variations. The comprehensive results showed the following trends: (1) The strain first inoculated will strongly inhibit the growth and metabolism of the latter inoculated one; (2) Autoclaved A. unguis exerted a strong inducing effect on later inoculated A. terreus, while the autoclaved A. terreus showed high stability of its metabolites and still potently suppressed the growth and metabolism of A. unguis; (3) When the two strains are inoculated simultaneously, they both grow and produce metabolites; however, the A. terreus seemed to be more strongly induced by live A. unguis and this inducing effect surpassed that of the autoclaved A. unguis. Under some of the conditions, the extracts showed higher antimicrobial activity than the axenic cultures. Totally, A. unguis was negative in response but potent in stimulating its rival while A. terreus had the opposite effect. Fifteen MS detectable and/or UV active peaks showed different yields in co-cultures vs. the corresponding axenic culture. GNPS analysis assisted by multiple natural products databases mining (PubChem, Dictionary of Natural Products, NPASS, etc.) gave reasonable annotations for some of these peaks, including antimicrobial compounds such as unguisin A, lovastatin, and nidulin. However, some of the peaks were correlated with antagonistic properties and remain as possible novel compounds without mass or UV matching hits from any database. It is intriguing that the two strains both synthesize chemical ‘weapons’ for antagonism, and that these are upregulated when needed in competitive co-culture environment. At the same time, compounds not useful in this antagonistic setting are downregulated in their expression. Some of the natural products produced during antagonism are unknown chlorinated metabolites and deserve further study for their antimicrobial properties. In summary, this study disclosed the different responses of two Aspergillus strains in co-culture, revealed their metabolic variation, and displayed new opportunities for antibiotic discovery.
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Affiliation(s)
- Yuan Wang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yifan He
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yayue Liu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Longjian Zhou
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xiaoxiang Ma
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xueqiong Hu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
| | - Pengzhi Hong
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yi Zhang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
- Correspondence: or ; Tel.: +86-759-2396046
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11
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Berry D, Lee K, Winter D, Mace W, Becker Y, Nagabhyru P, Treindl AD, Bogantes EV, Young CA, Leuchtmann A, Johnson LJ, Johnson RD, Cox MP, Schardl CL, Scott B. Cross-species transcriptomics identifies core regulatory changes differentiating the asymptomatic asexual and virulent sexual life cycles of grass-symbiotic Epichloë fungi. G3 (BETHESDA, MD.) 2022; 12:jkac043. [PMID: 35191483 PMCID: PMC8982410 DOI: 10.1093/g3journal/jkac043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/07/2022] [Indexed: 02/04/2023]
Abstract
Fungi from the genus Epichloë form systemic endobiotic infections of cool season grasses, producing a range of host-protective natural products in return for access to nutrients. These infections are asymptomatic during vegetative host growth, with associations between asexual Epichloë spp. and their hosts considered mutualistic. However, the sexual cycle of Epichloë spp. involves virulent growth, characterized by the envelopment and sterilization of a developing host inflorescence by a dense sheath of mycelia known as a stroma. Microscopic analysis of stromata revealed a dramatic increase in hyphal propagation and host degradation compared with asymptomatic tissues. RNAseq was used to identify differentially expressed genes in asymptomatic vs stromatized tissues from 3 diverse Epichloë-host associations. Comparative analysis identified a core set of 135 differentially expressed genes that exhibited conserved transcriptional changes across all 3 associations. The core differentially expressed genes more strongly expressed during virulent growth encode proteins associated with host suppression, digestion, adaptation to the external environment, a biosynthetic gene cluster, and 5 transcription factors that may regulate Epichloë stroma formation. An additional 5 transcription factor encoding differentially expressed genes were suppressed during virulent growth, suggesting they regulate mutualistic processes. Expression of biosynthetic gene clusters for natural products that suppress herbivory was universally suppressed during virulent growth, and additional biosynthetic gene clusters that may encode production of novel host-protective natural products were identified. A comparative analysis of 26 Epichloë genomes found a general decrease in core differentially expressed gene conservation among asexual species, and a specific decrease in conservation for the biosynthetic gene cluster expressed during virulent growth and an unusual uncharacterized gene.
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Affiliation(s)
- Daniel Berry
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Kate Lee
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - David Winter
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Wade Mace
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - Yvonne Becker
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
| | - Padmaja Nagabhyru
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
| | - Artemis D Treindl
- Institute of Integrative Biology, ETH Zurich, 8092 Zürich, Switzerland
| | | | | | - Adrian Leuchtmann
- Institute of Integrative Biology, ETH Zurich, 8092 Zürich, Switzerland
| | | | | | - Murray P Cox
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | | | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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12
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Hettiarachchige IK, Vander Jagt CJ, Mann RC, Sawbridge TI, Spangenberg GC, Guthridge KM. Global Changes in Asexual Epichloë Transcriptomes during the Early Stages, from Seed to Seedling, of Symbiotum Establishment. Microorganisms 2021; 9:microorganisms9050991. [PMID: 34064362 PMCID: PMC8147782 DOI: 10.3390/microorganisms9050991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 11/16/2022] Open
Abstract
Asexual Epichloë fungi are strictly seed-transmitted endophytic symbionts of cool-season grasses and spend their entire life cycle within the host plant. Endophyte infection can confer protective benefits to its host through the production of bioprotective compounds. Inversely, plants provide nourishment and shelter to the resident endophyte in return. Current understanding of the changes in global gene expression of asexual Epichloë endophytes during the early stages of host-endophyte symbiotum is limited. A time-course study using a deep RNA-sequencing approach was performed at six stages of germination, using seeds infected with one of three endophyte strains belonging to different representative taxa. Analysis of the most abundantly expressed endophyte genes identified that most were predicted to have a role in stress and defence responses. The number of differentially expressed genes observed at early time points was greater than those detected at later time points, suggesting an active transcriptional reprogramming of endophytes at the onset of seed germination. Gene ontology enrichment analysis revealed dynamic changes in global gene expression consistent with the developmental processes of symbiotic relationships. Expression of pathway genes for biosynthesis of key secondary metabolites was studied comprehensively and fuzzy clustering identified some unique expression patterns. Furthermore, comparisons of the transcriptomes from three endophyte strains in planta identified genes unique to each strain, including genes predicted to be associated with secondary metabolism. Findings from this study highlight the importance of better understanding the unique properties of individual endophyte strains and will serve as an excellent resource for future studies of host-endophyte interactions.
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Affiliation(s)
- Inoka K. Hettiarachchige
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (I.K.H.); (C.J.V.J.); (R.C.M.); (T.I.S.); (G.C.S.)
| | - Christy J. Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (I.K.H.); (C.J.V.J.); (R.C.M.); (T.I.S.); (G.C.S.)
| | - Ross C. Mann
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (I.K.H.); (C.J.V.J.); (R.C.M.); (T.I.S.); (G.C.S.)
| | - Timothy I. Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (I.K.H.); (C.J.V.J.); (R.C.M.); (T.I.S.); (G.C.S.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (I.K.H.); (C.J.V.J.); (R.C.M.); (T.I.S.); (G.C.S.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Kathryn M. Guthridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (I.K.H.); (C.J.V.J.); (R.C.M.); (T.I.S.); (G.C.S.)
- Correspondence:
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13
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Burragoni SG, Jeon J. Applications of endophytic microbes in agriculture, biotechnology, medicine, and beyond. Microbiol Res 2021; 245:126691. [PMID: 33508761 DOI: 10.1016/j.micres.2020.126691] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 12/26/2022]
Abstract
Endophytes are emerging as integral components of plant microbiomes. Some of them play pivotal roles in plant development and plant responses to pathogens and abiotic stresses, whereas others produce useful and/or interesting secondary metabolites. The appreciation of their abilities to affect plant phenotypes and produce useful compounds via genetic and molecular interactions has paved the way for these abilities to be exploited for health and welfare of plants, humans and ecosystems. Here we comprehensively review current and potential applications of endophytes in the agricultural, pharmaceutical, and industrial sectors. In addition, we briefly discuss the research objectives that should be focused upon in the coming years in order for endophytes and their metabolites to be fully harnessed for potential use in diverse areas.
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Affiliation(s)
- Sravanthi Goud Burragoni
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| | - Junhyun Jeon
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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14
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Bioinformatics Applications in Fungal Siderophores: Omics Implications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-53077-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Fungal Siderophores: Prospects and Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-53077-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Caradus JR, Johnson LJ. Epichloë Fungal Endophytes-From a Biological Curiosity in Wild Grasses to an Essential Component of Resilient High Performing Ryegrass and Fescue Pastures. J Fungi (Basel) 2020; 6:E322. [PMID: 33261217 PMCID: PMC7720123 DOI: 10.3390/jof6040322] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
The relationship between Epichloë endophytes found in a wide range of temperate grasses spans the continuum from antagonistic to mutualistic. The diversity of asexual mutualistic types can be characterised by the types of alkaloids they produce in planta. Some of these are responsible for detrimental health and welfare issues of ruminants when consumed, while others protect the host plant from insect pests and pathogens. In many temperate regions they are an essential component of high producing resilient tall fescue and ryegrass swards. This obligate mutualism between fungus and host is a seed-borne technology that has resulted in several commercial products being used with high uptake rates by end-user farmers, particularly in New Zealand and to a lesser extent Australia and USA. However, this has not happened by chance. It has been reliant on multi-disciplinary research teams undertaking excellent science to understand the taxonomic relationships of these endophytes, their life cycle, symbiosis regulation at both the cellular and molecular level, and the impact of secondary metabolites, including an understanding of their mammalian toxicity and bioactivity against insects and pathogens. Additionally, agronomic trials and seed biology studies of these microbes have all contributed to the delivery of robust and efficacious products. The supply chain from science, through seed companies and retailers to the end-user farmer needs to be well resourced providing convincing information on the efficacy and ensuring effective quality control to result in a strong uptake of these Epichloë endophyte technologies in pastoral agriculture.
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Affiliation(s)
- John R. Caradus
- Grasslanz Technology Ltd., Palmerston North PB11008, New Zealand
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17
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Misslinger M, Hortschansky P, Brakhage AA, Haas H. Fungal iron homeostasis with a focus on Aspergillus fumigatus. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118885. [PMID: 33045305 DOI: 10.1016/j.bbamcr.2020.118885] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 02/08/2023]
Abstract
To maintain iron homeostasis, fungi have to balance iron acquisition, storage, and utilization to ensure sufficient supply and to avoid toxic excess of this essential trace element. As pathogens usually encounter iron limitation in the host niche, this metal plays a particular role during virulence. Siderophores are iron-chelators synthesized by most, but not all fungal species to sequester iron extra- and intracellularly. In recent years, the facultative human pathogen Aspergillus fumigatus has become a model for fungal iron homeostasis of siderophore-producing fungal species. This article summarizes the knowledge on fungal iron homeostasis and its links to virulence with a focus on A. fumigatus. It covers mechanisms for iron acquisition, storage, and detoxification, as well as the modes of transcriptional iron regulation and iron sensing in A. fumigatus in comparison to other fungal species. Moreover, potential translational applications of the peculiarities of fungal iron metabolism for treatment and diagnosis of fungal infections is addressed.
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Affiliation(s)
- Matthias Misslinger
- Institute of Molecular Biology - Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, Germany; Department Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hubertus Haas
- Institute of Molecular Biology - Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
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18
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19
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Hume DE, Stewart AV, Simpson WR, Johnson RD. Epichloëfungal endophytes play a fundamental role in New Zealand grasslands. J R Soc N Z 2020. [DOI: 10.1080/03036758.2020.1726415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- David E. Hume
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Alan V. Stewart
- PGG Wrightson Seeds Limited, Kimihia Research Centre, Lincoln, New Zealand
| | - Wayne R. Simpson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
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20
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Hassing B, Eaton CJ, Winter D, Green KA, Brandt U, Savoian MS, Mesarich CH, Fleissner A, Scott B. Phosphatidic acid produced by phospholipase D is required for hyphal cell-cell fusion and fungal-plant symbiosis. Mol Microbiol 2020; 113:1101-1121. [PMID: 32022309 DOI: 10.1111/mmi.14480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/15/2022]
Abstract
Although lipid signaling has been shown to serve crucial roles in mammals and plants, little is known about this process in filamentous fungi. Here we analyze the contribution of phospholipase D (PLD) and its product phosphatidic acid (PA) in hyphal morphogenesis and growth of Epichloë festucae and Neurospora crassa, and in the establishment of a symbiotic interaction between E. festucae and Lolium perenne. Growth of E. festucae and N. crassa PLD deletion strains in axenic culture, and for E. festucae in association with L. perenne, were analyzed by light-, confocal- and electron microscopy. Changes in PA distribution were analyzed in E. festucae using a PA biosensor and the impact of these changes on the endocytic recycling and superoxide production investigated. We found that E. festucae PldB, and the N. crassa ortholog, PLA-7, are required for polarized growth and cell fusion and contribute to ascospore development, whereas PldA/PLA-8 are dispensable for these functions. Exogenous addition of PA rescues the cell-fusion phenotype in E. festucae. PldB is also crucial for E. festucae to establish a symbiotic association with L. perenne. This study identifies a new component of the cell-cell communication and cell fusion signaling network for hyphal morphogenesis and growth of filamentous fungi.
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Affiliation(s)
- Berit Hassing
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Carla J Eaton
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Kimberly A Green
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Ulrike Brandt
- Institute for Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Matthew S Savoian
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Carl H Mesarich
- Bio-Protection Research Centre, Lincoln, New Zealand.,School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Andre Fleissner
- Institute for Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
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21
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Forte FP, Schmid J, Dijkwel PP, Nagy I, Hume DE, Johnson RD, Simpson WR, Monk SM, Zhang N, Sehrish T, Asp T. Fungal Endophyte Colonization Patterns Alter Over Time in the Novel Association Between Lolium perenne and Epichloë Endophyte AR37. FRONTIERS IN PLANT SCIENCE 2020; 11:570026. [PMID: 33193501 PMCID: PMC7658011 DOI: 10.3389/fpls.2020.570026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/22/2020] [Indexed: 05/16/2023]
Abstract
Infection of the pasture grass Lolium perenne with the seed-transmitted fungal endophyte Epichloë festucae enhances its resilience to biotic and abiotic stress. Agricultural benefits of endophyte infection can be increased by generating novel symbiotic associations through inoculating L. perenne with selected Epichloë strains. Natural symbioses have coevolved over long periods. Thus, artificial symbioses will probably not have static properties, but symbionts will coadapt over time improving the fitness of the association. Here we report for the first time on temporal changes in a novel association of Epichloë strain AR37 and the L. perenne cultivar Grasslands Samson. Over nine generations, a seed maintenance program had increased the endophyte seed transmission rates to > 95% (from an initial 76%). We observed an approximately fivefold decline in endophyte biomass concentration in vegetative tissues over time (between generations 2 and 9). This indicates strong selection pressure toward reducing endophyte-related fitness costs by reducing endophyte biomass, without compromising the frequency of endophyte transmission to seed. We observed no obvious changes in tillering and only minor transcriptomic changes in infected plants over time. Functional analysis of 40 plant genes, showing continuously decreasing expression over time, suggests that adaptation of host metabolism and defense mechanisms are important for increasing the fitness of this association, and possibly fitness of such symbioses in general. Our results indicate that fitness of novel associations is likely to improve over time and that monitoring changes in novel associations can assist in identifying key features of endophyte-mediated enhancement of host fitness.
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Affiliation(s)
- Flavia Pilar Forte
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- *Correspondence: Flavia Pilar Forte,
| | - Jan Schmid
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Ferguson Street Laboratories, Palmerston North, New Zealand
| | - Paul P. Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - David E. Hume
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Wayne R. Simpson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Ningxin Zhang
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Tina Sehrish
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
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22
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Rahnama M, Maclean P, Fleetwood DJ, Johnson RD. VelA and LaeA are Key Regulators of Epichloë festucae Transcriptomic Response during Symbiosis with Perennial Ryegrass. Microorganisms 2019; 8:microorganisms8010033. [PMID: 31878026 PMCID: PMC7023048 DOI: 10.3390/microorganisms8010033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/29/2022] Open
Abstract
VelA (or VeA) is a key global regulator in fungal secondary metabolism and development which we previously showed is required during the symbiotic interaction of Epichloë festucae with perennial ryegrass. In this study, comparative transcriptomic analyses of ∆velA mutant compared to wild-type E. festucae, under three different conditions (in culture, infected seedlings, and infected mature plants), were performed to investigate the impact of VelA on E. festucae transcriptome. These comparative transcriptomic studies showed that VelA regulates the expression of genes encoding proteins involved in membrane transport, fungal cell wall biosynthesis, host cell wall degradation, and secondary metabolism, along with a number of small secreted proteins and a large number of proteins with no predictable functions. In addition, these results were compared with previous transcriptomic experiments that studied the impact of LaeA, another key global regulator of secondary metabolism and development that we have shown is important for E. festucae–perennial ryegrass interaction. The results showed that although VelA and LaeA regulate a subset of E. festucae genes in a similar manner, they also regulated many other genes independently of each other suggesting specialised roles.
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Affiliation(s)
- Mostafa Rahnama
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand; (P.M.); (D.J.F.)
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Correspondence: (M.R.); (R.D.J.)
| | - Paul Maclean
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand; (P.M.); (D.J.F.)
| | - Damien J. Fleetwood
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand; (P.M.); (D.J.F.)
- Biotelliga Ltd, Auckland 1052, New Zealand
| | - Richard D. Johnson
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand; (P.M.); (D.J.F.)
- Correspondence: (M.R.); (R.D.J.)
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23
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Jia SL, Ma Y, Chi Z, Liu GL, Hu Z, Chi ZM. Genome sequencing of a yeast-like fungal strain P6, a novel species of Aureobasidium spp.: insights into its taxonomy, evolution, and biotechnological potentials. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01531-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Abstract
Purpose
This study aimed to look insights into taxonomy, evolution, and biotechnological potentials of a yeast-like fungal strain P6 isolated from a mangrove ecosystem.
Methods
The genome sequencing for the yeast-like fungal strain P6 was conducted on a Hiseq sequencing platform, and the genomic characteristics and annotations were analyzed. The central metabolism and gluconate biosynthesis pathway were studied through the genome sequence data by using the GO, KOG, and KEGG databases. The secondary metabolite potentials were also evaluated.
Results
The whole genome size of the P6 strain was 25.41Mb and the G + C content of its genome was 50.69%. Totally, 6098 protein-coding genes and 264 non-coding RNA genes were predicted. The annotation results showed that the yeast-like fungal strain P6 had complete metabolic pathways of TCA cycle, EMP pathway, pentose phosphate pathway, glyoxylic acid cycle, and other central metabolic pathways. Furthermore, the inulinase activity associated with β-fructofuranosidase and high glucose oxidase activity in this strain have been demonstrated. It was found that this yeast-like fungal strain was located at root of most species of Aureobasidium spp. and at a separate cluster of all the phylogenetic trees. The P6 strain was predicted to contain three NRPS gene clusters, five type-I PKS gene clusters, and one type-I NRPS/PKS gene cluster via analysis at the antiSMASH Website. It may synthesize epichloenin A, fusaric acid, elsinochromes, and fusaridione A.
Conclusions
Based on its unique DNA sequence, taxonomic position in the phylogenetic tree and evolutional position, the yeast-like fungal strain P6 was identified as a novel species Aureobasidium hainanensis sp. nov. P6 isolate and had highly potential applications.
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24
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Mucha J, Pawłowski TA, Klupczyńska EA, Guzicka M, Zadworny M. The Effect of Hydroxamic Siderophores Structure on Acetylation of Histone H3 and Alpha Tubulin in Pinus sylvestris Root Cells. Int J Mol Sci 2019; 20:E6099. [PMID: 31816938 PMCID: PMC6928989 DOI: 10.3390/ijms20236099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/18/2019] [Accepted: 11/30/2019] [Indexed: 12/03/2022] Open
Abstract
Protein acetylation affects gene expression, as well as other processes in cells, and it might be dependent on the availability of the metals. However, whether iron chelating compounds (siderophores) can have an effect on the acetylation process in plant roots is largely unknown. In the present study, western blotting and confocal microscopy was used to examine the degree of acetylation of histone H3 and alpha tubulin in Pinus sylvestris root cells in the presence of structurally different siderophores. The effect of metabolites that were produced by pathogenic and mycorrhizal fungi was also assessed. No effect was observed on histone acetylation. By contrast, the metabolites of the pathogenic fungus were able to decrease the level of microtubule acetylation, whereas treatment with iron-free ferrioxamine (DFO) was able to increase it. This latter was not observed when ferrioxamine-iron complexes were used. The pathogen metabolites induced important modifications of cytoskeleton organization. Siderophores also induced changes in the tubulin skeleton and these changes were iron-dependent. The effect of siderophores on the microtubule network was dependent on the presence of iron. More root cells with a depolymerized cytoskeleton were observed when the roots were exposed to iron-free siderophores and the metabolites of pathogenic fungi; whereas, the metabolites from mycorrhizal fungi and iron-enriched forms of siderophores slightly altered the cytoskeleton network of root cells. Collectively, these data indicated that the metabolites of pathogenic fungi mirror siderophore action, and iron limitation can lead to enhanced alternations in cell structure and physiology.
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Affiliation(s)
- Joanna Mucha
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland; (T.A.P.); (E.A.K.); (M.G.); (M.Z.)
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Forester NT, Lane GA, McKenzie CM, Lamont IL, Johnson LJ. The Role of SreA-Mediated Iron Regulation in Maintaining Epichloë festucae- Lolium perenne Symbioses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1324-1335. [PMID: 31107632 DOI: 10.1094/mpmi-03-19-0060-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In ascomycetes and basidiomycetes, iron-responsive GATA-type transcriptional repressors are involved in regulating iron homeostasis, notably to prevent iron toxicity through control of iron uptake. To date, it has been unknown whether this iron regulator contributes toward mutualistic endosymbiosis of microbes with plants, a system where the endophyte must function within the constraints of an in-host existence, including a dependency on the host for nutrient acquisition. Functional characterization of one such protein, SreA from Epichloë festucae, a fungal endosymbiont of cool-season grasses, indicates that regulation of iron homeostasis processes is important for symbiotic maintenance. The deletion of the sreA gene (ΔsreA) led to iron-dependent aberrant hyphal growth and the gradual loss of endophyte hyphae from perennial ryegrass. SreA negatively regulates the siderophore biosynthesis and high-affinity iron uptake systems of E. festucae, similar to other fungi, resulting in iron accumulation in mutants. Our evidence suggests that SreA is involved in the processes that moderate Epichloë iron acquisition from the plant apoplast, because overharvesting of iron in ΔsreA mutants was detected as premature chlorosis of the host using a hydroponic plant growth assay. E. festucae appears to have a tightly regulated iron management system, involving SreA that balances endophyte growth with its survival and prevents overcompetition with the host for iron in the intercellular niche, thus promoting mutualistic associations. Mutations that interfere with Epichloë iron management negatively affect iron-dependent fungal growth and destabilize mutualistic Epichloë -ryegrass associations.
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Affiliation(s)
- Natasha T Forester
- AgResearch Ltd., Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Geoffrey A Lane
- AgResearch Ltd., Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Catherine M McKenzie
- AgResearch Ltd., Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Linda J Johnson
- AgResearch Ltd., Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
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Hermenau R, Mehl JL, Ishida K, Dose B, Pidot SJ, Stinear TP, Hertweck C. Genomics‐Driven Discovery of NO‐Donating Diazeniumdiolate Siderophores in Diverse Plant‐Associated Bacteria. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906326] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ron Hermenau
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Jule L. Mehl
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute University of Melbourne Melbourne VIC 3000 Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology at the Doherty Institute University of Melbourne Melbourne VIC 3000 Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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Hermenau R, Mehl JL, Ishida K, Dose B, Pidot SJ, Stinear TP, Hertweck C. Genomics-Driven Discovery of NO-Donating Diazeniumdiolate Siderophores in Diverse Plant-Associated Bacteria. Angew Chem Int Ed Engl 2019; 58:13024-13029. [PMID: 31276269 PMCID: PMC6771848 DOI: 10.1002/anie.201906326] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/05/2019] [Indexed: 01/13/2023]
Abstract
Siderophores are key players in bacteria–host interactions, with the main function to provide soluble iron for their producers. Gramibactin from rhizosphere bacteria expands siderophore function and diversity as it delivers iron to the host plant and features an unusual diazeniumdiolate moiety for iron chelation. By mutational analysis of the grb gene cluster, we identified genes (grbD and grbE) necessary for diazeniumdiolate formation. Genome mining using a GrbD‐based network revealed a broad range of orthologous gene clusters in mainly plant‐associated Burkholderia/Paraburkholderia species. Two new types of diazeniumdiolate siderophores, megapolibactins and plantaribactin were fully characterized. In vitro assays and in vivo monitoring experiments revealed that the iron chelators also liberate nitric oxide (NO) in plant roots. This finding is important since NO donors are considered as biofertilizers that maintain iron homeostasis and increase overall plant fitness.
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Affiliation(s)
- Ron Hermenau
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jule L Mehl
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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Green KA, Eaton CJ, Savoian MS, Scott B. A homologue of the fungal tetraspanin Pls1 is required for Epichloë festucae expressorium formation and establishment of a mutualistic interaction with Lolium perenne. MOLECULAR PLANT PATHOLOGY 2019; 20:961-975. [PMID: 31008572 PMCID: PMC6589725 DOI: 10.1111/mpp.12805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Epichloë festucae is an endophytic fungus that forms a mutualistic symbiotic association with the grass host Lolium perenne. Endophytic hyphae exit the host by an appressorium-like structure known as an expressorium. In plant-pathogenic fungi, the tetraspanin Pls1 and the NADPH oxidase component Nox2 are required for appressorium development. Previously we showed that the homologue of Nox2, NoxB, is required for E. festucae expressorium development and establishment of a mutualistic symbiotic interaction with the grass host. Here we used a reverse genetics approach to functionally characterize the role of the E. festucae homologue of Pls1, PlsA. The morphology and growth of ΔplsA in axenic culture was comparable to wild-type. The tiller length of plants infected with ΔplsA was significantly reduced. Hyphae of ΔplsA had a proliferative pattern of growth within the leaves of L. perenne with increased colonization of the intercellular spaces and the vascular bundles. The ΔplsA mutant was also defective in expressorium development although the phenotype was not as severe as for ΔnoxB, highlighting potentially distinct roles for PlsA and NoxB in signalling through the NoxB complex. Hyphae of ΔplsA proliferate below the cuticle surface but still occasionally form an expressorium-like structure that enables the mutant hyphae to exit the leaf to grow on the surface. These expressoria still form a septin ring-like structure at the point of cuticle exit as found in the wild-type strain. These results establish that E. festucae PlsA has an important, but distinct, role to NoxB in expressorium development and plant symbiosis.
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Affiliation(s)
- Kimberly A. Green
- Institute of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Carla J. Eaton
- Institute of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Matthew S. Savoian
- Institute of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Barry Scott
- Institute of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
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Rahnama M, Maclean P, Fleetwood DJ, Johnson RD. The LaeA orthologue in Epichloë festucae is required for symbiotic interaction with Lolium perenne. Fungal Genet Biol 2019; 129:74-85. [PMID: 31071427 DOI: 10.1016/j.fgb.2019.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
Abstract
LaeA is a conserved global regulator of secondary metabolism and development in fungi. It is often required for successful pathogenic interactions. In this study, the laeA homologue in the fungal grass endophyte E. festucae was deleted and functionally characterised in vitro and its role in the mutualistic E. festucae interaction with Lolium perenne (perennial ryegrass) was determined. We showed that laeA in E. festucae is required for normal hyphal morphology, resistance to oxidative stress, and conidiation under nutrient-limited in vitro conditions. In planta studies revealed that laeA is expressed in a tissue-specific manner and is required to form a compatible plant interaction, with the majority of seedlings inoculated with a laeA deletion mutant either dying or being uninfected. In mature infected plants no difference was observed in the number or morphology of endophytic hyphae. However, the number of epiphyllous hyphae were greatly increased. Comparative transcriptomics analyses suggested roles for plant cell wall degradation, fungal cell wall composition, secondary metabolism and small-secreted proteins in Epichloë foliar symbiosis.
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Affiliation(s)
- M Rahnama
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; School of Biological Sciences, University of Auckland, New Zealand
| | - P Maclean
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - D J Fleetwood
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; Biotelliga Ltd, Auckland, New Zealand.
| | - R D Johnson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.
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Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis. Fungal Genet Biol 2019; 125:71-83. [DOI: 10.1016/j.fgb.2019.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/29/2019] [Accepted: 02/03/2019] [Indexed: 01/10/2023]
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Domka AM, Rozpaądek P, Turnau K. Are Fungal Endophytes Merely Mycorrhizal Copycats? The Role of Fungal Endophytes in the Adaptation of Plants to Metal Toxicity. Front Microbiol 2019; 10:371. [PMID: 30930857 PMCID: PMC6428775 DOI: 10.3389/fmicb.2019.00371] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/12/2019] [Indexed: 12/04/2022] Open
Abstract
The contamination of soil with toxic metals is a worldwide problem, resulting in the disruption of plant vegetation and subsequent crop production. Thus, remediation techniques for contaminated soil and water remain a constant interest of researchers. Phytoremediation, which utilizes plants to remove or stabilize contaminants, is perceived to be a promising strategy. However, phytoremediation's use to date is limited because of constraints associated with such factors as slow plant growth rates or metal toxicity. Microbial-assisted phytoremediation serves as an alternative solution, since the impact of the microbial symbionts on plant growth and stress tolerance has frequently been described. Endophytic fungi occur in almost every plant in the natural environment and contribute to plant growth and tolerance to environmental stress conditions. Although this group of symbiotic fungi was found to form association with a wide range of hosts, including the non-mycorrhizal Brassicaceae metallophytes, their role in the response of plants to metal toxicity has not been thoroughly elucidated to date. This review summarizes the current knowledge regarding the role of endophytic fungi in the tolerance of plants to toxic metals and highlights the similarities and differences between this group of symbiotic fungi and mycorrhizal associations in terms of the survival of the plant during heavy metal stress.
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Affiliation(s)
| | - Piotr Rozpaądek
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Katarzyna Turnau
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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Nagabhyru P, Dinkins RD, Schardl CL. Transcriptomics of Epichloë-Grass Symbioses in Host Vegetative and Reproductive Stages. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:194-207. [PMID: 30145935 DOI: 10.1094/mpmi-10-17-0251-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epichloë species are fungal symbionts (endophytes) of cool-season grasses that transmit vertically via inflorescence primordia (IP), ovaries (OV), and ultimately, embryos. Epichloë coenophiala, an endophyte of tall fescue (Schedonorus arundinaceus), provides multiple protective benefits to the grass. We conducted transcriptome analysis of the tall fescue-E. coenophiala symbiosis, comparing IP, OV, vegetative pseudostems (PS), and the lemma and palea (LP) (bracts) of the young floret. Transcriptomes of host OV and PS exhibited almost no significant differences attributable to endophyte presence or absence. Comparison of endophyte gene expression in different plant parts revealed numerous differentially expressed genes (DEGs). The 150 endophyte DEGs significantly higher in PS over OV included genes for alkaloid biosynthesis and sugar or amino acid transport. The 277 endophyte DEGs significantly higher in OV over PS included genes for protein chaperones (including most heat-shock proteins), trehalose synthesis complex, a bax inhibitor-1 protein homolog, the CLC chloride ion channel, catalase, and superoxide dismutase. Similar trends were apparent in the Brachypodium sylvaticum-Epichloë sylvatica symbiosis. Gene expression profiles in tall fescue IP and LP indicated that the endophyte transcriptome shift began early in host floral development. We discuss possible roles of the endophyte DEGs in colonization of reproductive grass tissues.
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Affiliation(s)
- Padmaja Nagabhyru
- 1 Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A.; and
| | - Randy D Dinkins
- 2 USDA-ARS, Forage-Animal Production Research Unit, Lexington, KY 40546, U.S.A
| | - Christopher L Schardl
- 1 Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A.; and
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Esmaeel Q, Miotto L, Rondeau M, Leclère V, Clément C, Jacquard C, Sanchez L, Barka EA. Paraburkholderia phytofirmans PsJN-Plants Interaction: From Perception to the Induced Mechanisms. Front Microbiol 2018; 9:2093. [PMID: 30214441 PMCID: PMC6125355 DOI: 10.3389/fmicb.2018.02093] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022] Open
Abstract
The use of plant-associated bacteria has received many scientific and economic attention as an effective and alternative method to reduce the chemical pesticides use in agriculture. The genus Burkholderia includes at least 90 species including pathogenic strains, plant pathogens, as well as plant beneficial species as those related to Paraburkholderia, which has been reported to be associated with plants and exerts a positive effect on plant growth and fitness. Paraburkholderia phytofirmans PsJN, a beneficial endophyte able to colonize a wide range of plants, is an established model for plant-associated endophytic bacteria. Indeed, in addition to its plant growth promoting ability, it can also induce plant resistance against biotic as well as abiotic stresses. Here, we summarized an inventory of knowledge on PsJN-plant interaction, from the perception to the resistance mechanisms induced in the plant by a way of the atypical colonization mode of this endophyte. We also have carried out an extensive genome analysis to identify all gene clusters which contribute to the adaptive mechanisms under different environments and partly explaining the high ecological competence of P. phytofirmans PsJN.
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Affiliation(s)
- Qassim Esmaeel
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Lidiane Miotto
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Marine Rondeau
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, SFR Condorcet FR CNRS 3417, Lille, France
| | - Christophe Clément
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Cédric Jacquard
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Essaid A Barka
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
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Scott B, Green K, Berry D. The fine balance between mutualism and antagonism in the Epichloë festucae-grass symbiotic interaction. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:32-38. [PMID: 29454183 DOI: 10.1016/j.pbi.2018.01.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 05/27/2023]
Abstract
Epichloë endophytes form mutualistic symbiotic associations with aerial tissues of temperate grasses. Intercalary growth of hyphae within the leaves enables fungal growth to be synchronized with host leaf growth, leading to formation of a highly structured and tightly regulated symbiotic network. Mutations in fungal genes that disrupt cell-cell fusion and other key signalling pathways lead to an antagonistic interaction characterized by unregulated growth of endophytic hyphae and detrimental effects on host growth. Transcriptome analysis of these mutant associations provides key insights into the regulation of the symbiosis. In nature a similar switch in growth occurs when hyphae transition into the sexual cycle forming stromata that abort host inflorescences. Endophyte infection of the grass host leads to a major reprogramming of host metabolism and alters host development. Changes in endophyte cell wall structure and the repertoire of effectors secreted into the host apoplast accompany establishment of a mutualistic interaction within the leaves.
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Affiliation(s)
- Barry Scott
- Institute of Molecular BioSciences and Bioprotection Research Centre, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Kimberly Green
- Institute of Molecular BioSciences and Bioprotection Research Centre, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Daniel Berry
- Institute of Molecular BioSciences and Bioprotection Research Centre, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
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Rahnama M, Johnson RD, Voisey CR, Simpson WR, Fleetwood DJ. The Global Regulatory Protein VelA Is Required for Symbiosis Between the Endophytic Fungus Epichloë festucae and Lolium perenne. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:591-604. [PMID: 29315021 DOI: 10.1094/mpmi-11-17-0286-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Epichloë species fungi form bioprotective endophytic symbioses with many cool-season grasses, including agriculturally important forage grasses. Despite its importance, relatively little is known about the molecular details of the interaction and the regulatory genes involved. The conserved velvet-domain protein VelA (or VeA) is a global regulator of a number of cellular and developmental functions in fungi. In this study, the E. festucae velA gene was functionally characterized in vitro and during interaction with perennial ryegrass. The velA gene is required in E. festucae for resistance to osmotic and cell wall-damaging stresses, repression of conidiation, and normal hyphal morphology during nutrient-limited in-vitro conditions. Expression of velA in E. festucae is light- and nitrogen-dependent and is tissue-specific in mature infected plants. In-planta studies showed that velA is required in E. festucae for a compatible interaction. Inoculating seedlings with mutant ΔvelA induced callose deposition and H2O2 production, and a high level of seedling death was observed. In surviving plants infected with ΔvelA mutant fungi, plants were stunted and we observed increased biomass and invasion of vascular bundles. Overall, this work characterizes a key fungal regulatory factor in this increasingly important model symbiotic association.
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Affiliation(s)
- M Rahnama
- 1 AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; and
- 2 School of Biological Sciences, University of Auckland, New Zealand
| | - R D Johnson
- 1 AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; and
| | - C R Voisey
- 1 AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; and
| | - W R Simpson
- 1 AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; and
| | - D J Fleetwood
- 1 AgResearch, Grasslands Research Centre, Palmerston North, New Zealand; and
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Tamayo E, Knight SAB, Valderas A, Dancis A, Ferrol N. The arbuscular mycorrhizal fungus Rhizophagus irregularis
uses a reductive iron assimilation pathway for high-affinity iron uptake. Environ Microbiol 2018; 20:1857-1872. [DOI: 10.1111/1462-2920.14121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Elisabeth Tamayo
- Departamento de Microbiología del Suelo y Sistemas Simbióticos; Estación Experimental del Zaidín, CSIC; Granada Spain
| | - Simon A. B. Knight
- Department of Medicine, Division of Hematology-Oncology; Perelman School of Medicine, University of Pennsylvania; Philadelphia PA USA
| | - Ascensión Valderas
- Departamento de Microbiología del Suelo y Sistemas Simbióticos; Estación Experimental del Zaidín, CSIC; Granada Spain
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology; Perelman School of Medicine, University of Pennsylvania; Philadelphia PA USA
| | - Nuria Ferrol
- Departamento de Microbiología del Suelo y Sistemas Simbióticos; Estación Experimental del Zaidín, CSIC; Granada Spain
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37
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Chagas FO, Pessotti RDC, Caraballo-Rodríguez AM, Pupo MT. Chemical signaling involved in plant-microbe interactions. Chem Soc Rev 2018; 47:1652-1704. [PMID: 29218336 DOI: 10.1039/c7cs00343a] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.
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Affiliation(s)
- Fernanda Oliveira Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (FCFRP-USP), Avenida do Café, s/n, 14040-903, Ribeirão Preto-SP, Brazil.
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Contrasting roles of fungal siderophores in maintaining iron homeostasis in Epichloë festucae. Fungal Genet Biol 2018; 111:60-72. [DOI: 10.1016/j.fgb.2017.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/11/2017] [Accepted: 11/14/2017] [Indexed: 11/23/2022]
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Gagic M, Faville MJ, Zhang W, Forester NT, Rolston MP, Johnson RD, Ganesh S, Koolaard JP, Easton HS, Hudson D, Johnson LJ, Moon CD, Voisey CR. Seed Transmission of Epichloë Endophytes in Lolium perenne Is Heavily Influenced by Host Genetics. FRONTIERS IN PLANT SCIENCE 2018; 9:1580. [PMID: 30483280 PMCID: PMC6242978 DOI: 10.3389/fpls.2018.01580] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/10/2018] [Indexed: 05/14/2023]
Abstract
Vertical transmission of symbiotic Epichloë endophytes from host grasses into progeny seed is the primary mechanism by which the next generation of plants is colonized. This process is often imperfect, resulting in endophyte-free seedlings which may have poor ecological fitness if the endophyte confers protective benefits to its host. In this study, we investigated the influence of host genetics and environment on the vertical transmission of Epichloë festucae var. lolii strain AR37 in the temperate forage grass Lolium perenne. The efficiency of AR37 transmission into the seed of over 500 plant genotypes from five genetically diverse breeding populations was determined. In Populations I-III, which had undergone previous selection for high seed infection by AR37, mean transmission was 88, 93, and 92%, respectively. However, in Populations IV and V, which had not undergone previous selection, mean transmission was 69 and 70%, respectively. The transmission values, together with single-nucleotide polymorphism data obtained using genotyping-by-sequencing for each host, was used to develop a genomic prediction model for AR37 seed transmission. The predictive ability of the model was estimated at r = 0.54. While host genotype contributed greatly to differences in AR37 seed transmission, undefined environmental variables also contributed significantly to seed transmission across different years and geographic locations. There was evidence for a small host genotype-by-environment effect; however this was less pronounced than genotype or environment alone. Analysis of endophyte infection levels in parent plants within Populations I and IV revealed a loss of endophyte infection over time in Population IV only. This population also had lower average tiller infection frequencies than Population I, suggesting that AR37 failed to colonize all the daughter tillers and therefore seeds. However, we also observed that infection of seed by AR37 may fail during or after initiation of floral development from plants where all tillers remained endophyte-infected over time. While the effects of environment and host genotype on fungal endophyte transmission have been evaluated previously, this is the first study that quantifies the relative impacts of host genetics and environment on endophyte vertical transmission.
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Affiliation(s)
- Milan Gagic
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Marty J. Faville
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wei Zhang
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | | | | | - Siva Ganesh
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - John P. Koolaard
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - H. Sydney Easton
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Debbie Hudson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Linda J. Johnson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Christina D. Moon
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Christine R. Voisey
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- *Correspondence: Christine R. Voisey,
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Efficient targeted mutagenesis in Epichloë festucae using a split marker system. J Microbiol Methods 2017; 134:62-65. [DOI: 10.1016/j.mimet.2016.12.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 11/17/2022]
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Green KA, Becker Y, Tanaka A, Takemoto D, Fitzsimons HL, Seiler S, Lalucque H, Silar P, Scott B. SymB and SymC, two membrane associated proteins, are required forEpichloë festucaehyphal cell-cell fusion and maintenance of a mutualistic interaction withLolium perenne. Mol Microbiol 2016; 103:657-677. [DOI: 10.1111/mmi.13580] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Kimberly A. Green
- Institute of Fundamental Sciences, Massey University; Palmerston North 4442 New Zealand
- Bioprotection Research Centre, Massey University; Palmerston North 4442 New Zealand
| | - Yvonne Becker
- Institute of Fundamental Sciences, Massey University; Palmerston North 4442 New Zealand
- Leibniz Institute of Vegetable and Ornamental Crops; Großbeeren 14979 Germany
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences; Nagoya University; Nagoya 464-8601 Japan
| | - Daigo Takemoto
- Graduate School of Bioagricultural Sciences; Nagoya University; Nagoya 464-8601 Japan
| | - Helen L. Fitzsimons
- Institute of Fundamental Sciences, Massey University; Palmerston North 4442 New Zealand
| | - Stephan Seiler
- Freiburg Institute for Advanced Studies, Albert-Ludwigs Universität Freiburg; Freiburg Germany
| | - Hervé Lalucque
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire des Energies de Demain; Paris 75205 France
| | - Philippe Silar
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire des Energies de Demain; Paris 75205 France
| | - Barry Scott
- Institute of Fundamental Sciences, Massey University; Palmerston North 4442 New Zealand
- Bioprotection Research Centre, Massey University; Palmerston North 4442 New Zealand
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Green KA, Becker Y, Fitzsimons HL, Scott B. An Epichloë festucae homologue of MOB3, a component of the STRIPAK complex, is required for the establishment of a mutualistic symbiotic interaction with Lolium perenne. MOLECULAR PLANT PATHOLOGY 2016; 17:1480-1492. [PMID: 27277141 PMCID: PMC5132070 DOI: 10.1111/mpp.12443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 05/13/2023]
Abstract
In both Sordaria macrospora and Neurospora crassa, components of the conserved STRIPAK (striatin-interacting phosphatase and kinase) complex regulate cell-cell fusion, hyphal network development and fruiting body formation. Interestingly, a number of Epichloë festucae genes that are required for hyphal cell-cell fusion, such as noxA, noxR, proA, mpkA and mkkA, are also required for the establishment of a mutualistic symbiotic interaction with Lolium perenne. To determine whether MobC, a homologue of the STRIPAK complex component MOB3 in S. macrospora and N. crassa, is required for E. festucae hyphal fusion and symbiosis, a mobC deletion strain was generated. The ΔmobC mutant showed reduced rates of hyphal cell-cell fusion, formed intrahyphal hyphae and exhibited enhanced conidiation. Plants infected with ΔmobC were severely stunted. Hyphae of ΔmobC showed a proliferative pattern of growth within the leaves of Lolium perenne with increased colonization of the intercellular spaces and vascular bundles. Although hyphae were still able to form expressoria, structures allowing the colonization of the leaf surface, the frequency of formation was significantly reduced. Collectively, these results show that the STRIPAK component MobC is required for the establishment of a mutualistic symbiotic association between E. festucae and L. perenne, and plays an accessory role in the regulation of hyphal cell-cell fusion and expressorium development in E. festucae.
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Affiliation(s)
- Kimberly A. Green
- Institute of Fundamental Sciences, Massey UniversityPalmerston North 4442New Zealand
| | - Yvonne Becker
- Institute of Fundamental Sciences, Massey UniversityPalmerston North 4442New Zealand
| | - Helen L. Fitzsimons
- Institute of Fundamental Sciences, Massey UniversityPalmerston North 4442New Zealand
| | - Barry Scott
- Institute of Fundamental Sciences, Massey UniversityPalmerston North 4442New Zealand
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Penselin D, Münsterkötter M, Kirsten S, Felder M, Taudien S, Platzer M, Ashelford K, Paskiewicz KH, Harrison RJ, Hughes DJ, Wolf T, Shelest E, Graap J, Hoffmann J, Wenzel C, Wöltje N, King KM, Fitt BDL, Güldener U, Avrova A, Knogge W. Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses. BMC Genomics 2016; 17:953. [PMID: 27875982 PMCID: PMC5118889 DOI: 10.1186/s12864-016-3299-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/15/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts. RESULTS The genomes of the different Rhynchosporium species were sequenced, assembled and annotated using ab initio gene predictors trained on several fungal genomes as well as on Rhynchosporium expressed sequence tags. Structures of the rDNA regions and genome-wide single nucleotide polymorphisms provided a hypothesis for intra-genus evolution. Homology screening detected core meiotic genes along with most genes crucial for sexual recombination in ascomycete fungi. In addition, a large number of cell wall-degrading enzymes that is characteristic for hemibiotrophic and necrotrophic fungi infecting monocotyledonous hosts were found. Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding for polyketide synthases and non-ribosomal peptide synthetases. Several of these genes are missing from the genome of the closest sequenced relative, the poplar pathogen Marssonina brunnea, and are possibly involved in adaptation to the grass hosts. Most importantly, six species-specific genes coding for protein effectors were identified in R. commune. Their deletion yielded mutants that grew more vigorously in planta than the wild type. CONCLUSION Both cryptic sexuality and secondary metabolites may have contributed to host adaptation. Most importantly, however, the growth-retarding activity of the species-specific effectors suggests that host adaptation of R. commune aims at extending the biotrophic stage at the expense of the necrotrophic stage of pathogenesis. Like other apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host leaves relatively slowly without causing symptoms, reminiscent of the development of endophytic fungi. Rhynchosporium may therefore become an object for studying the mutualism-parasitism transition.
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Affiliation(s)
- Daniel Penselin
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kirsten
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Marius Felder
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Stefan Taudien
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Matthias Platzer
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Kevin Ashelford
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | | | | | - David J. Hughes
- Applied Bioinformatics, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Thomas Wolf
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Ekaterina Shelest
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Jenny Graap
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Jan Hoffmann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Claudia Wenzel
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany ,Present address: Food Quality and Nutrition, Agroscope, Bern, Switzerland
| | - Nadine Wöltje
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Kevin M. King
- Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Bruce D. L. Fitt
- Biological and Environmental Sciences, University of Hertfordshire, Hatfield, Hertfordshire UK
| | - Ulrich Güldener
- Department of Genome-Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Anna Avrova
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Wolfgang Knogge
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
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Voisey CR, Christensen MT, Johnson LJ, Forester NT, Gagic M, Bryan GT, Simpson WR, Fleetwood DJ, Card SD, Koolaard JP, Maclean PH, Johnson RD. cAMP Signaling Regulates Synchronised Growth of Symbiotic Epichloë Fungi with the Host Grass Lolium perenne. FRONTIERS IN PLANT SCIENCE 2016; 7:1546. [PMID: 27833620 PMCID: PMC5082231 DOI: 10.3389/fpls.2016.01546] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
The seed-transmitted fungal symbiont, Epichloë festucae, colonizes grasses by infecting host tissues as they form on the shoot apical meristem (SAM) of the seedling. How this fungus accommodates the complexities of plant development to successfully colonize the leaves and inflorescences is unclear. Since adenosine 3', 5'-cyclic monophosphate (cAMP)-dependent signaling is often essential for host colonization by fungal pathogens, we disrupted the cAMP cascade by insertional mutagenesis of the E. festucae adenylate cyclase gene (acyA). Consistent with deletions of this gene in other fungi, acyA mutants had a slow radial growth rate in culture, and hyphae were convoluted and hyper-branched suggesting that fungal apical dominance had been disrupted. Nitro blue tetrazolium (NBT) staining of hyphae showed that cAMP disruption mutants were impaired in their ability to synthesize superoxide, indicating that cAMP signaling regulates accumulation of reactive oxygen species (ROS). Despite significant defects in hyphal growth and ROS production, E. festucae ΔacyA mutants were infectious and capable of forming symbiotic associations with grasses. Plants infected with E. festucae ΔacyA were marginally less robust than the wild-type (WT), however hyphae were hyper-branched, and leaf tissues heavily colonized, indicating that the tight regulation of hyphal growth normally observed in maturing leaves requires functional cAMP signaling.
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Affiliation(s)
- Christine R. Voisey
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Michael T. Christensen
- Formally of Forage Improvement, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Linda J. Johnson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Natasha T. Forester
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Milan Gagic
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Gregory T. Bryan
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Wayne R. Simpson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Damien J. Fleetwood
- Biotelliga Ltd., Institute for Innovation in BiotechnologyAuckland, New Zealand
| | - Stuart D. Card
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - John P. Koolaard
- Bioinformatics and Statistics Team, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
| | - Paul H. Maclean
- Bioinformatics and Statistics Team, AgResearch Ltd., Lincoln Research CentreChristchurch, New Zealand
| | - Richard D. Johnson
- Forage Science, AgResearch Ltd., Grasslands Research CentrePalmerston North, New Zealand
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Abstract
The nonribosomal peptide synthetases are modular enzymes that catalyze synthesis of important peptide products from a variety of standard and non-proteinogenic amino acid substrates. Within a single module are multiple catalytic domains that are responsible for incorporation of a single residue. After the amino acid is activated and covalently attached to an integrated carrier protein domain, the substrates and intermediates are delivered to neighboring catalytic domains for peptide bond formation or, in some modules, chemical modification. In the final module, the peptide is delivered to a terminal thioesterase domain that catalyzes release of the peptide product. This multi-domain modular architecture raises questions about the structural features that enable this assembly line synthesis in an efficient manner. The structures of the core component domains have been determined and demonstrate insights into the catalytic activity. More recently, multi-domain structures have been determined and are providing clues to the features of these enzyme systems that govern the functional interaction between multiple domains. This chapter describes the structures of NRPS proteins and the strategies that are being used to assist structural studies of these dynamic proteins, including careful consideration of domain boundaries for generation of truncated proteins and the use of mechanism-based inhibitors that trap interactions between the catalytic and carrier protein domains.
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46
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A novel family of cyclic oligopeptides derived from ribosomal peptide synthesis of an in planta-induced gene, gigA, in Epichloë endophytes of grasses. Fungal Genet Biol 2015; 85:14-24. [DOI: 10.1016/j.fgb.2015.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 10/16/2015] [Accepted: 10/26/2015] [Indexed: 11/19/2022]
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Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015; 79:293-320. [PMID: 26136581 PMCID: PMC4488371 DOI: 10.1128/mmbr.00050-14] [Citation(s) in RCA: 1048] [Impact Index Per Article: 116.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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Affiliation(s)
- Pablo R. Hardoim
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Stéphane Compant
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Andrea Campisano
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | | | - Angela Sessitsch
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
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48
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The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015. [PMID: 26136581 DOI: 10.1128/mmbr.00050-14.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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Giuliano Garisto Donzelli B, Gibson DM, Krasnoff SB. Intracellular siderophore but not extracellular siderophore is required for full virulence in Metarhizium robertsii. Fungal Genet Biol 2015; 82:56-68. [PMID: 26135511 DOI: 10.1016/j.fgb.2015.06.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/26/2015] [Accepted: 06/27/2015] [Indexed: 10/23/2022]
Abstract
Efficient iron acquisition mechanisms are fundamental for microbial survival in the environment and for pathogen virulence within their hosts. M. robertsii produces two known iron-binding natural products: metachelins, which are used to scavenge extracellular iron, and ferricrocin, which is strictly intracellular. To study the contribution of siderophore-mediated iron uptake and storage to M. robertsii fitness, we generated null mutants for each siderophore synthase gene (mrsidD and mrsidC, respectively), as well as for the iron uptake transcriptional repressor mrsreA. All of these mutants showed impaired germination speed, differential sensitivity to hydrogen peroxide, and differential ability to overcome iron chelation on growth-limiting iron concentrations. RT-qPCR data supported regulation of mrsreA, mrsidC, and mrsidD by supplied iron in vitro and during growth within the insect host, Spodoptera exigua. We also observed strong upregulation of the insect iron-binding proteins, transferrins, during infection. Insect bioassays revealed that ferricrocin is required for full virulence against S. exigua; neither the loss of metachelin production nor the deletion of the transcription factor mrsreA significantly affected M. robertsii virulence.
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Affiliation(s)
- Bruno Giuliano Garisto Donzelli
- School of Integrative Plant Science - Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, United States.
| | - Donna M Gibson
- USDA ARS, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, United States
| | - Stuart B Krasnoff
- USDA ARS, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, United States
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50
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Sociality in Escherichia coli: Enterochelin Is a Private Good at Low Cell Density and Can Be Shared at High Cell Density. J Bacteriol 2015; 197:2122-2128. [PMID: 25733620 DOI: 10.1128/jb.02596-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 02/25/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Many bacteria produce secreted iron chelators called siderophores, which can be shared among cells with specific siderophore uptake systems regardless of whether the cell produces siderophores. Sharing secreted products allows freeloading, where individuals use resources without bearing the cost of production. Here we show that the Escherichia coli siderophore enterochelin is not evenly shared between producers and nonproducers. Wild-type Escherichia coli grows well in low-iron minimal medium, and an isogenic enterochelin synthesis mutant (ΔentF) grows very poorly. The enterochelin mutant grows well in low-iron medium supplemented with enterochelin. At high cell densities the ΔentF mutant can compete equally with the wild type in low-iron medium. At low cell densities the ΔentF mutant cannot compete. Furthermore, the growth rate of the wild type is unaffected by cell density. The wild type grows well in low-iron medium even at very low starting densities. Our experiments support a model where at least some enterochelin remains associated with the cells that produce it, and the cell-associated enterochelin enables iron acquisition even at very low cell density. Enterochelin that is not retained by producing cells at low density is lost to dilution. At high cell densities, cell-free enterochelin can accumulate and be shared by all cells in the group. Partial privatization is a solution to the problem of iron acquisition in low-iron, low-cell-density habitats. Cell-free enterochelin allows for iron scavenging at a distance at higher population densities. Our findings shed light on the conditions under which freeloaders might benefit from enterochelin uptake systems. IMPORTANCE Sociality in microbes has become a topic of great interest. One facet of sociality is the sharing of secreted products, such as the iron-scavenging siderophores. We present evidence that the Escherichia coli siderophore enterochelin is relatively inexpensive to produce and is partially privatized such that it can be efficiently shared only at high producer cell densities. At low cell densities, cell-free enterochelin is scarce and only enterochelin producers are able to grow in low-iron medium. Because freely shared products can be exploited by freeloaders, this partial privatization may help explain how enterochelin production is stabilized in E. coli and may provide insight into when enterochelin is available for freeloaders.
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