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Clairet C, Gay EJ, Porquier A, Blaise F, Marais CL, Balesdent MH, Rouxel T, Soyer JL, Fudal I. Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-player game. New Phytol 2024; 242:247-261. [PMID: 38358035 DOI: 10.1111/nph.19581] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Effector genes, encoding molecules involved in disease establishment, are concertedly expressed throughout the lifecycle of plant-pathogenic fungi. However, little is known about how effector gene expression is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in their regulation was recently investigated, notably establishing that the repressive histone modification H3K9me3, deposited by KMT1, was involved in several fungal species including Leptosphaeria maculans. Nevertheless, previous data suggest that a second regulatory layer, probably involving a specific transcription factor (TF), might be required. In L. maculans, a Dothideomycete causing stem canker of oilseed rape, we identified the ortholog of Pf2, a TF belonging to the Zn2Cys6 fungal-specific family, and described as essential for pathogenicity and effector gene expression. We investigated its role together with KMT1, by inactivating and over-expressing LmPf2 in a wild-type strain and a ∆kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis and we found a major effect of LmPf2 on the induction of effector gene expression once KMT1 repression is lifted. Our results show, for the first time, a dual control of effector gene expression.
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Affiliation(s)
- Colin Clairet
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Antoine Porquier
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
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Soyer JL, Clairet C, Gay EJ, Lapalu N, Rouxel T, Stukenbrock EH, Fudal I. Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization. Chromosome Res 2021; 29:219-236. [PMID: 34018080 PMCID: PMC8159818 DOI: 10.1007/s10577-021-09658-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022]
Abstract
Leptosphaeria maculans 'brassicae' (Lmb) and Leptosphaeria maculans 'lepidii' (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains.
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Affiliation(s)
- Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
| | - Colin Clairet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
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Mary V, Schnell Ramos M, Gillet C, Socha AL, Giraudat J, Agorio A, Merlot S, Clairet C, Kim SA, Punshon T, Guerinot ML, Thomine S. Bypassing Iron Storage in Endodermal Vacuoles Rescues the Iron Mobilization Defect in the natural resistance associated-macrophage protein3natural resistance associated-macrophage protein4 Double Mutant. Plant Physiol 2015; 169:748-59. [PMID: 26232490 PMCID: PMC4577389 DOI: 10.1104/pp.15.00380] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/29/2015] [Indexed: 05/03/2023]
Abstract
To improve seed iron (Fe) content and bioavailability, it is crucial to decipher the mechanisms that control Fe storage during seed development. In Arabidopsis (Arabidopsis thaliana) seeds, most Fe is concentrated in insoluble precipitates, with phytate in the vacuoles of cells surrounding the vasculature of the embryo. NATURAL RESISTANCE ASSOCIATED-MACROPHAGE PROTEIN3 (AtNRAMP3) and AtNRAMP4 function redundantly in Fe retrieval from vacuoles during germination. When germinated under Fe-deficient conditions, development of the nramp3nramp4 double mutant is arrested as a consequence of impaired Fe mobilization. To identify novel genes involved in seed Fe homeostasis, we screened an ethyl methanesulfonate-mutagenized population of nramp3nramp4 seedlings for mutations suppressing their phenotypes on low Fe. Here, we report that, among the suppressors, two independent mutations in the VACUOLAR IRON TRANSPORTER1 (AtVIT1) gene caused the suppressor phenotype. The AtVIT1 transporter is involved in Fe influx into vacuoles of endodermal and bundle sheath cells. This result establishes a functional link between Fe loading in vacuoles by AtVIT1 and its remobilization by AtNRAMP3 and AtNRAMP4. Moreover, analysis of subcellular Fe localization indicates that simultaneous disruption of AtVIT1, AtNRAMP3, and AtNRAMP4 limits Fe accumulation in vacuolar globoids.
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Affiliation(s)
- Viviane Mary
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Magali Schnell Ramos
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Cynthia Gillet
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Amanda L Socha
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Jérôme Giraudat
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Astrid Agorio
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Sylvain Merlot
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Colin Clairet
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Sun A Kim
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Tracy Punshon
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Mary Lou Guerinot
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
| | - Sébastien Thomine
- Institute for Integrative Biology of the Cell, Saclay Plant Sciences, Université Paris-Saclay, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Paris-Sud, F-91198 Gif-sur-Yvette, France (V.M., M.S.R., C.G., J.G., A.A., S.M., C.C., S.T.); andDepartment of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 (A.L.S., S.A.K., T.P., M.L.G.)
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