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Rodríguez-Romero J, Marconi M, Ortega-Campayo V, Demuez M, Wilkinson MD, Sesma A. Virulence- and signaling-associated genes display a preference for long 3'UTRs during rice infection and metabolic stress in the rice blast fungus. THE NEW PHYTOLOGIST 2019; 221:399-414. [PMID: 30169888 DOI: 10.1111/nph.15405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
Generation of mRNA isoforms by alternative polyadenylation (APA) and their involvement in regulation of fungal cellular processes, including virulence, remains elusive. Here, we investigated genome-wide polyadenylation site (PAS) selection in the rice blast fungus to understand how APA regulates pathogenicity. More than half of Magnaporthe oryzae transcripts undergo APA and show novel motifs in their PAS region. Transcripts with shorter 3'UTRs are more stable and abundant in polysomal fractions, suggesting they are being translated more efficiently. Importantly, rice colonization increases the use of distal PASs of pathogenicity genes, especially those participating in signalling pathways like 14-3-3B, whose long 3'UTR is required for infection. Cleavage factor I (CFI) Rbp35 regulates expression and distal PAS selection of virulence and signalling-associated genes, tRNAs and transposable elements, pointing its potential to drive genomic rearrangements and pathogen evolution. We propose a noncanonical PAS selection mechanism for Rbp35 that recognizes UGUAH, unlike humans, without CFI25. Our results showed that APA controls turnover and translation of transcripts involved in fungal growth and environmental adaptation. Furthermore, these data provide useful information for enhancing genome annotations and for cross-species comparisons of PASs and PAS usage within the fungal kingdom and the tree of life.
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Affiliation(s)
- Julio Rodríguez-Romero
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Marco Marconi
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Víctor Ortega-Campayo
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Marie Demuez
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Mark D Wilkinson
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Ane Sesma
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
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Marconi M, Sesma A, Rodríguez-Romero JL, González MLR, Wilkinson MD. Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae. Sci Data 2018; 5:180271. [PMID: 30480660 PMCID: PMC6257040 DOI: 10.1038/sdata.2018.271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/11/2018] [Indexed: 11/08/2022] Open
Abstract
Polyadenylation plays an important role in gene regulation, thus affecting a wide variety of biological processes. In the rice blast fungus Magnaporthe oryzae the cleavage factor I protein Rpb35 is required for pre-mRNA polyadenylation and fungal virulence. Here we present the bioinformatic approach and output data related to a global survey of polyadenylation site usage in M. oryzae wild-type and Δrbp35 strains under a variety of nutrient conditions, some of which simulate the conditions experienced by the fungus during part of its infection cycle.
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Affiliation(s)
- Marco Marconi
- Centro de Biotecnología y Genómica de Plantas UPM – INIA, Madrid, Spain
| | - Ane Sesma
- Centro de Biotecnología y Genómica de Plantas UPM – INIA, Madrid, Spain
| | | | | | - Mark D. Wilkinson
- Centro de Biotecnología y Genómica de Plantas UPM – INIA, Madrid, Spain
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Galhano R, Illana A, Ryder LS, Rodríguez-Romero J, Demuez M, Badaruddin M, Martinez-Rocha AL, Soanes DM, Studholme DJ, Talbot NJ, Sesma A. Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus. PLoS Pathog 2017; 13:e1006516. [PMID: 28742127 PMCID: PMC5542705 DOI: 10.1371/journal.ppat.1006516] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 08/03/2017] [Accepted: 07/06/2017] [Indexed: 01/05/2023] Open
Abstract
The establishment of polarity is a critical process in pathogenic fungi, mediating infection-related morphogenesis and host tissue invasion. Here, we report the identification of TPC1 (Transcription factor for Polarity Control 1), which regulates invasive polarized growth in the rice blast fungus Magnaporthe oryzae. TPC1 encodes a putative transcription factor of the fungal Zn(II)2Cys6 family, exclusive to filamentous fungi. Tpc1-deficient mutants show severe defects in conidiogenesis, infection-associated autophagy, glycogen and lipid metabolism, and plant tissue colonisation. By tracking actin-binding proteins, septin-5 and autophagosome components, we show that Tpc1 regulates cytoskeletal dynamics and infection-associated autophagy during appressorium-mediated plant penetration. We found that Tpc1 interacts with Mst12 and modulates its DNA-binding activity, while Tpc1 nuclear localisation also depends on the MAP kinase Pmk1, consistent with the involvement of Tpc1 in this signalling pathway, which is critical for appressorium development. Importantly, Tpc1 directly regulates NOXD expression, the p22phox subunit of the fungal NADPH oxidase complex via an interaction with Mst12. Tpc1 therefore controls spatial and temporal regulation of cortical F-actin through regulation of the NADPH oxidase complex during appressorium re-polarisation. Consequently, Tpc1 is a core developmental regulator in filamentous fungi, linking the regulated synthesis of reactive oxygen species and the Pmk1 pathway, with polarity control during host invasion. Cellular polarity is an intrinsic feature of filamentous fungal growth and pathogenesis. In this study, we identified a gene required for fungal polar growth and virulence in the rice blast fungus Magnaporthe oryzae. This gene has been named TPC1 (Transcription factor for Polarity Control 1). The Tpc1 protein belongs to the fungal Zn(II)2Cys6 binuclear cluster family. This DNA-binding motif is present exclusively in the fungal kingdom. We have characterised defects associated with lack of Tpc1 in M. oryzae. We show that Tpc1 is involved in polarised growth and virulence. The M. oryzae Δtpc1 mutant shows a delay in glycogen and lipid metabolism, and infection-associated autophagy–processes that regulate appressorium-mediated M. oryzae plant infection. The saprophytic fungus Neurospora crassa contains a Tpc1 homolog (NcTpc1) involved in vegetative growth and sustained tip elongation, suggesting that Tpc1-like proteins act as core regulators of polarised growth and development in filamentous fungi. A comparative transcriptome analysis has allowed us to identify genes regulated by Tpc1 in M. oryzae including NoxD, an important component of the fungal NADPH complex. Significantly, Tpc1 interacts with Mst12, a component of the Pmk1 signalling pathway essential for appressorium development, and modulates Mst12 binding affinity to NOXD promoter region. We conclude that Tpc1 is a key regulator of polarity in M. oryzae that regulates growth, autophagy and septin-mediated reorientation of the F-actin cytoskeleton to facilitate plant cell invasion.
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Affiliation(s)
- Rita Galhano
- Disease & Stress Biology Dept. John Innes Centre, Norwich, United Kingdom
- School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, United Kingdom
| | - Adriana Illana
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid, (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Madrid, Spain
- Dept. Biotecnología y Biología Vegetal, UPM, Madrid, Spain
| | - Lauren S. Ryder
- School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, United Kingdom
| | - Julio Rodríguez-Romero
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid, (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Madrid, Spain
- Dept. Biotecnología y Biología Vegetal, UPM, Madrid, Spain
| | - Marie Demuez
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid, (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Madrid, Spain
- Dept. Biotecnología y Biología Vegetal, UPM, Madrid, Spain
| | - Muhammad Badaruddin
- School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, United Kingdom
| | | | - Darren M. Soanes
- School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, United Kingdom
| | - David J. Studholme
- School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, United Kingdom
| | - Nicholas J. Talbot
- School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, United Kingdom
| | - Ane Sesma
- Disease & Stress Biology Dept. John Innes Centre, Norwich, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid, (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Madrid, Spain
- Dept. Biotecnología y Biología Vegetal, UPM, Madrid, Spain
- * E-mail:
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Marroquin-Guzman M, Wilson RA. GATA-Dependent Glutaminolysis Drives Appressorium Formation in Magnaporthe oryzae by Suppressing TOR Inhibition of cAMP/PKA Signaling. PLoS Pathog 2015; 11:e1004851. [PMID: 25901357 PMCID: PMC4406744 DOI: 10.1371/journal.ppat.1004851] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 04/03/2015] [Indexed: 01/14/2023] Open
Abstract
Fungal plant pathogens are persistent and global food security threats. To invade their hosts they often form highly specialized infection structures, known as appressoria. The cAMP/ PKA- and MAP kinase-signaling cascades have been functionally delineated as positive-acting pathways required for appressorium development. Negative-acting regulatory pathways that block appressorial development are not known. Here, we present the first detailed evidence that the conserved Target of Rapamycin (TOR) signaling pathway is a powerful inhibitor of appressorium formation by the rice blast fungus Magnaporthe oryzae. We determined TOR signaling was activated in an M. oryzae mutant strain lacking a functional copy of the GATA transcription factor-encoding gene ASD4. Δasd4 mutant strains could not form appressoria and expressed GLN1, a glutamine synthetase-encoding orthologue silenced in wild type. Inappropriate expression of GLN1 increased the intracellular steady-state levels of glutamine in Δasd4 mutant strains during axenic growth when compared to wild type. Deleting GLN1 lowered glutamine levels and promoted appressorium formation by Δasd4 strains. Furthermore, glutamine is an agonist of TOR. Treating Δasd4 mutant strains with the specific TOR kinase inhibitor rapamycin restored appressorium development. Rapamycin was also shown to induce appressorium formation by wild type and Δcpka mutant strains on non-inductive hydrophilic surfaces but had no effect on the MAP kinase mutant Δpmk1. When taken together, we implicate Asd4 in regulating intracellular glutamine levels in order to modulate TOR inhibition of appressorium formation downstream of cPKA. This study thus provides novel insight into the metabolic mechanisms that underpin the highly regulated process of appressorium development. Many fungal pathogens destroy important crops by first gaining entrance to the host using specialized appressorial cells. Understanding the molecular mechanisms that control appressorium formation could provide new routes for managing severe plant diseases. Here, we describe a previously unknown regulatory pathway that suppresses appressorium formation by the rice pathogen Magnaporthe oryzae. We provide evidence that a mutant M. oryzae strain, unable to form appressoria, accumulates intracellular glutamine that, in turn, inappropriately activates a conserved signaling pathway called TOR. Reducing intracellular glutamine levels, or inactivating TOR, restored appressorium formation to the mutant strain. TOR activation is thus a powerful inhibitor of appressorium formation and could be leveraged to develop sustainable mitigation practices against recalcitrant fungal pathogens.
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Affiliation(s)
- Margarita Marroquin-Guzman
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Richard A. Wilson
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
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