Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection
Alternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple mRNA and protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS isoforms un...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2022-12-01
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| Series: | RNA Biology |
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| Online Access: | http://dx.doi.org/10.1080/15476286.2022.2043040 |
| _version_ | 1797403953644699648 |
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| author | Jongbum Jeon Ki-Tae Kim Jaeyoung Choi Kyeongchae Cheong Jaeho Ko Gobong Choi Hyunjun Lee Gir-Won Lee Sook-Young Park Seongbeom Kim Sun Tae Kim Cheol Woo Min Seogchan Kang Yong-Hwan Lee |
| author_facet | Jongbum Jeon Ki-Tae Kim Jaeyoung Choi Kyeongchae Cheong Jaeho Ko Gobong Choi Hyunjun Lee Gir-Won Lee Sook-Young Park Seongbeom Kim Sun Tae Kim Cheol Woo Min Seogchan Kang Yong-Hwan Lee |
| author_sort | Jongbum Jeon |
| collection | DOAJ |
| description | Alternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple mRNA and protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS isoforms under a limited number of conditions. We analysed AS profiles in the rice blast fungus Magnaporthe oryzae, a global threat to rice production, using high-quality transcriptome data representing its vegetative growth (mycelia) and multiple host infection stages. We identified 4,270 AS isoforms derived from 2,413 genes, including 499 genes presumably regulated by infection-specific AS. AS appears to increase during infection, with 32.7% of the AS isoforms being produced during infection but absent in mycelia. Analysis of the isoforms observed at each infection stage showed that 636 AS isoforms were more abundant than corresponding annotated mRNAs, especially after initial hyphal penetration into host cell. Many such dominant isoforms were predicted to encode regulatory proteins such as transcription factors and phospho-transferases. We also identified the genes encoding distinct proteins via AS and confirmed the translation of some isoforms via a proteomic analysis, suggesting potential AS-mediated neo-functionalization of some genes during infection. Comprehensive profiling of the pattern of genome-wide AS during multiple stages of rice-M. oryzae interaction established a foundational resource that will help investigate the role and regulation of AS during rice infection. |
| first_indexed | 2024-03-09T02:47:06Z |
| format | Article |
| id | doaj.art-2b3cda9e129c410f9c9cbfffa0a8d416 |
| institution | Directory Open Access Journal |
| issn | 1547-6286 1555-8584 |
| language | English |
| last_indexed | 2024-03-09T02:47:06Z |
| publishDate | 2022-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | RNA Biology |
| spelling | doaj.art-2b3cda9e129c410f9c9cbfffa0a8d4162023-12-05T16:09:51ZengTaylor & Francis GroupRNA Biology1547-62861555-85842022-12-0119137338610.1080/15476286.2022.20430402043040Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infectionJongbum Jeon0Ki-Tae Kim1Jaeyoung Choi2Kyeongchae Cheong3Jaeho Ko4Gobong Choi5Hyunjun Lee6Gir-Won Lee7Sook-Young Park8Seongbeom Kim9Sun Tae Kim10Cheol Woo Min11Seogchan Kang12Yong-Hwan Lee13Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySunchon National UniversitySmart Farm Research Center, Korea Institute of Science and TechnologyInterdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul National UniversityInterdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul National UniversityNGeneBio Co LtdSunchon National UniversitySeoul National UniversityPusan National UniversityPusan National UniversityPennsylvania State University, University ParkInterdisciplinary Program in Agricultural Genomics, Seoul National UniversityAlternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple mRNA and protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS isoforms under a limited number of conditions. We analysed AS profiles in the rice blast fungus Magnaporthe oryzae, a global threat to rice production, using high-quality transcriptome data representing its vegetative growth (mycelia) and multiple host infection stages. We identified 4,270 AS isoforms derived from 2,413 genes, including 499 genes presumably regulated by infection-specific AS. AS appears to increase during infection, with 32.7% of the AS isoforms being produced during infection but absent in mycelia. Analysis of the isoforms observed at each infection stage showed that 636 AS isoforms were more abundant than corresponding annotated mRNAs, especially after initial hyphal penetration into host cell. Many such dominant isoforms were predicted to encode regulatory proteins such as transcription factors and phospho-transferases. We also identified the genes encoding distinct proteins via AS and confirmed the translation of some isoforms via a proteomic analysis, suggesting potential AS-mediated neo-functionalization of some genes during infection. Comprehensive profiling of the pattern of genome-wide AS during multiple stages of rice-M. oryzae interaction established a foundational resource that will help investigate the role and regulation of AS during rice infection.http://dx.doi.org/10.1080/15476286.2022.2043040alternative splicingfunctional diversificationmagnaporthe oryzaepathogenicityproteomericetranscriptome |
| spellingShingle | Jongbum Jeon Ki-Tae Kim Jaeyoung Choi Kyeongchae Cheong Jaeho Ko Gobong Choi Hyunjun Lee Gir-Won Lee Sook-Young Park Seongbeom Kim Sun Tae Kim Cheol Woo Min Seogchan Kang Yong-Hwan Lee Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection RNA Biology alternative splicing functional diversification magnaporthe oryzae pathogenicity proteome rice transcriptome |
| title | Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection |
| title_full | Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection |
| title_fullStr | Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection |
| title_full_unstemmed | Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection |
| title_short | Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection |
| title_sort | alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection |
| topic | alternative splicing functional diversification magnaporthe oryzae pathogenicity proteome rice transcriptome |
| url | http://dx.doi.org/10.1080/15476286.2022.2043040 |
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