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Rahnama M, Maclean P, Fleetwood DJ, Johnson RD. Comparative Transcriptomics Profiling of Perennial Ryegrass Infected with Wild Type or a Δ velA Epichloë festucae Mutant Reveals Host Processes Underlying Mutualistic versus Antagonistic Interactions. J Fungi (Basel) 2023; 9:jof9020190. [PMID: 36836305 PMCID: PMC9959145 DOI: 10.3390/jof9020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 02/05/2023] Open
Abstract
Epichloë species 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. VelA is a key global regulator in fungal secondary metabolism and development. In previous studies, we showed the requirement of velA for E. festucae to form a mutualistic interaction with Lolium perenne. We 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 several small-secreted proteins in Epichloë festucae. Here, by a comparative transcriptomics analysis on perennial ryegrass seedlings and mature plants, which are endophyte free or infected with wild type (mutualistic interaction) or mutant ΔvelA E. festucae (antagonistic or incompatible interaction), regulatory effects of the endophytic interaction on perennial ryegrass development was studied. We show that ΔvelA mutant associations influence the expression of genes involved in primary metabolism, secondary metabolism, and response to biotic and abiotic stresses compared with wild type associations, providing an insight into processes defining mutualistic versus antagonistic interactions.
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Affiliation(s)
- Mostafa Rahnama
- Department of Biology, Tennessee Tech University, Cookeville, TN 38505, USA
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
- Correspondence: (M.R.); (R.D.J.)
| | - Paul Maclean
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | | | - Richard D. Johnson
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
- Correspondence: (M.R.); (R.D.J.)
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Rahnama M, Fleetwood DJ, Johnson RD. Histological Methods to Detect Early-stage Plant Defense Responses during Artificial Inoculation of Lolium perenne with Epichloë festucae. Bio Protoc 2021; 11:e4013. [PMID: 34124312 PMCID: PMC8161103 DOI: 10.21769/bioprotoc.4013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 12/31/2022] Open
Abstract
Epichloë species form agriculturally important symbioses with many cool season grasses. To study these symbioses, such as the interaction of Epichloë festucae with perennial ryegrass (Lolium perenne), host plants can be infected by artificial inoculation of etiolated seedlings. This inoculation is performed by placing mycelium into an incision in the meristem, as previously described by Latch and Christensen (1985). In recent years, this method has been broadly used to study this interaction at the molecular level using different Epichloë festucae mutants that can cause incompatible interactions. We have developed and adapted methods to study four of the most important host plant responses to infection, including cell death, callose deposition, lignin production, and hydrogen peroxide (H2O2) production, which are useful in defining the host response to infection at a very early time point.
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Affiliation(s)
- Mostafa Rahnama
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- School of Biological Sciences, University of Auckland, New Zealand
| | - Damien J. Fleetwood
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- Biotelliga Ltd, Auckland, New Zealand
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Mol Plant Microbe Interact 2018; 31:591-604. [PMID: 29315021 DOI: 10.1094/mpmi-11-17-0286-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML, Jaromczyk JW, Roe BA, O'Sullivan DM, Scott B, Tudzynski P, An Z, Arnaoudova EG, Bullock CT, Charlton ND, Chen L, Cox M, Dinkins RD, Florea S, Glenn AE, Gordon A, Güldener U, Harris DR, Hollin W, Jaromczyk J, Johnson RD, Khan AK, Leistner E, Leuchtmann A, Li C, Liu J, Liu J, Liu M, Mace W, Machado C, Nagabhyru P, Pan J, Schmid J, Sugawara K, Steiner U, Takach JE, Tanaka E, Webb JS, Wilson EV, Wiseman JL, Yoshida R, Zeng Z. Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genet 2013; 9:e1003323. [PMID: 23468653 PMCID: PMC3585121 DOI: 10.1371/journal.pgen.1003323] [Citation(s) in RCA: 271] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 12/31/2012] [Indexed: 01/01/2023] Open
Abstract
The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some-including the infamous ergot alkaloids-have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.
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Fleetwood DJ, Khan AK, Johnson RD, Young CA, Mittal S, Wrenn RE, Hesse U, Foster SJ, Schardl CL, Scott B. Abundant degenerate miniature inverted-repeat transposable elements in genomes of epichloid fungal endophytes of grasses. Genome Biol Evol 2011; 3:1253-64. [PMID: 21948396 PMCID: PMC3227409 DOI: 10.1093/gbe/evr098] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2011] [Indexed: 12/20/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are abundant repeat elements in plant and animal genomes; however, there are few analyses of these elements in fungal genomes. Analysis of the draft genome sequence of the fungal endophyte Epichloë festucae revealed 13 MITE families that make up almost 1% of the E. festucae genome, and relics of putative autonomous parent elements were identified for three families. Sequence and DNA hybridization analyses suggest that at least some of the MITEs identified in the study were active early in the evolution of Epichloë but are not found in closely related genera. Analysis of MITE integration sites showed that these elements have a moderate integration site preference for 5' genic regions of the E. festucae genome and are particularly enriched near genes for secondary metabolism. Copies of the EFT-3m/Toru element appear to have mediated recombination events that may have abolished synthesis of two fungal alkaloids in different epichloae. This work provides insight into the potential impact of MITEs on epichloae evolution and provides a foundation for analysis in other fungal genomes.
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Affiliation(s)
- Damien J Fleetwood
- Forage Biotechnology Section, AgResearch, Palmerston North, New Zealand.
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Abstract
Clavicipitaceous fungal endophytes of the genera Epichloë and Neotyphodium form symbioses with grasses of the subfamily Pooideae, in which they can synthesize an array of bioprotective alkaloids. Some strains produce the ergopeptine alkaloid ergovaline, which is implicated in livestock toxicoses caused by ingestion of endophyte-infected grasses. Cloning and analysis of a nonribosomal peptide synthetase (NRPS) gene from Neotyphodium lolii revealed a putative gene cluster for ergovaline biosynthesis containing a single-module NRPS gene, lpsB, and other genes orthologous to genes in the ergopeptine gene cluster of Claviceps purpurea and the clavine cluster of Aspergillus fumigatus. Despite conservation of gene sequence, gene order is substantially different between the N. lolii, C. purpurea, and A. fumigatus ergot alkaloid gene clusters. Southern analysis indicated that the N. lolii cluster was linked with previously identified ergovaline biosynthetic genes dmaW and lpsA. The ergovaline genes are closely associated with transposon relics, including retrotransposons and autonomous and nonautonomous DNA transposons. All genes in the cluster were highly expressed in planta, but expression was very low or undetectable in mycelia from axenic culture. This work provides a genetic foundation for elucidating biochemical steps in the ergovaline pathway, the ecological role of individual ergot alkaloid compounds, and the regulation of their synthesis in planta.
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Affiliation(s)
- Damien J Fleetwood
- AgResearch, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand
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Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD, Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS, Weaver JE, Webby RJ, De Bruijn FJ, Ronson CW. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol 2002; 184:3086-95. [PMID: 12003951 PMCID: PMC135072 DOI: 10.1128/jb.184.11.3086-3095.2002] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mesorhizobium loti strain R7A symbiosis island is a 502-kb chromosomally integrated element which transfers to nonsymbiotic mesorhizobia in the environment, converting them to Lotus symbionts. It integrates into a phenylalanine tRNA gene in a process mediated by a P4-type integrase encoded at the left end of the element. We have determined the nucleotide sequence of the island and compared its deduced genetic complement with that reported for the 611-kb putative symbiosis island of M. loti strain MAFF303099. The two islands share 248 kb of DNA, with multiple deletions and insertions of up to 168 kb interrupting highly conserved colinear DNA regions in the two strains. The shared DNA regions contain all the genes likely to be required for Nod factor synthesis, nitrogen fixation, and island transfer. Transfer genes include a trb operon and a cluster of potential tra genes which are also present on the strain MAFF303099 plasmid pMLb. The island lacks plasmid replication genes, suggesting that it is a site-specific conjugative transposon. The R7A island encodes a type IV secretion system with strong similarity to the vir pilus from Agrobacterium tumefaciens that is deleted from MAFF303099, which in turn encodes a type III secretion system not found on the R7A island. The 414 genes on the R7A island also include putative regulatory genes, transport genes, and an array of metabolic genes. Most of the unique hypothetical genes on the R7A island are strain-specific and clustered, suggesting that they may represent other acquired genetic elements rather than symbiotically relevant DNA.
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Affiliation(s)
- John T Sullivan
- Department of Microbiology, University of Otago, Dunedin, New Zealand
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