Larissa C Laforest, Tuan-Anh M Nguyen, Gabriel Oliveira Matsumoto, Pavithra Ramachandria, Andre Chanderbali, Siva Rama Raju Kanumuri, Abhisheak Sharma, Christopher R McCurdy, Thu-Thuy T Dang, Satya Swathi Nadakuduti
Monoterpene indole alkaloids (MIAs) found in the Rubiaceae have varied pharmaceutical uses. Spirooxindole alkaloids are a structural subtype of MIAs with a unique spiro[pyrrolidine-3,3'-oxindole] ring system. Despite their intriguing structures and potent bioactivities, the evolution and diversification of spirooxindole alkaloids remain poorly understood. We report a high-quality chromosome-scale genome assembly of Mitragyna parvifolia, a tree species of the Rubiaceae family that predominantly produces the spirooxindole alkaloid mitraphylline. Comparative genomics, including comprehensive synteny and phylogeny analyses across the MIA-producing order Gentianales revealed a whole-genome duplication event underlying the divergence of the Cinchonoideae alliance from the Coffeeae alliance, leading to diversification of MIA biosynthesis. Transcriptome analyses of young and mature leaves, stems, stipules, and roots integrated with MIA profiling and genome analyses revealed several candidates in the MIA biosynthetic pathway. Functional characterization of selected candidates led to the elucidation of the biosynthesis of the antiproliferative spirooxindole mitraphylline in M. parvifolia. These genomic and transcriptomic resources are invaluable to identify the evolutionary origins and diversification of MIAs and spirooxindole alkaloids.
{"title":"A chromosome-level Mitragyna parvifolia genome unveils spirooxindole alkaloid diversification and mitraphylline biosynthesis.","authors":"Larissa C Laforest, Tuan-Anh M Nguyen, Gabriel Oliveira Matsumoto, Pavithra Ramachandria, Andre Chanderbali, Siva Rama Raju Kanumuri, Abhisheak Sharma, Christopher R McCurdy, Thu-Thuy T Dang, Satya Swathi Nadakuduti","doi":"10.1093/plcell/koaf207","DOIUrl":"10.1093/plcell/koaf207","url":null,"abstract":"<p><p>Monoterpene indole alkaloids (MIAs) found in the Rubiaceae have varied pharmaceutical uses. Spirooxindole alkaloids are a structural subtype of MIAs with a unique spiro[pyrrolidine-3,3'-oxindole] ring system. Despite their intriguing structures and potent bioactivities, the evolution and diversification of spirooxindole alkaloids remain poorly understood. We report a high-quality chromosome-scale genome assembly of Mitragyna parvifolia, a tree species of the Rubiaceae family that predominantly produces the spirooxindole alkaloid mitraphylline. Comparative genomics, including comprehensive synteny and phylogeny analyses across the MIA-producing order Gentianales revealed a whole-genome duplication event underlying the divergence of the Cinchonoideae alliance from the Coffeeae alliance, leading to diversification of MIA biosynthesis. Transcriptome analyses of young and mature leaves, stems, stipules, and roots integrated with MIA profiling and genome analyses revealed several candidates in the MIA biosynthetic pathway. Functional characterization of selected candidates led to the elucidation of the biosynthesis of the antiproliferative spirooxindole mitraphylline in M. parvifolia. These genomic and transcriptomic resources are invaluable to identify the evolutionary origins and diversification of MIAs and spirooxindole alkaloids.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12419693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Seasons change and so do trees: Expression profiling of aspen reveals season-specific gene hubs.","authors":"Renuka Kolli","doi":"10.1093/plcell/koaf213","DOIUrl":"https://doi.org/10.1093/plcell/koaf213","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144965130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Expression of Concern: HAB1-SWI3B Interaction Reveals a Link between Abscisic Acid Signaling and Putative SWI/SNF Chromatin-Remodeling Complexes in Arabidopsis.","authors":"","doi":"10.1093/plcell/koaf193","DOIUrl":"10.1093/plcell/koaf193","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":"37 8","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carsten Poul Skou Nielsen, Laura Arribas-Hernández, Peter Brodersen
{"title":"Response to \"The action of Arabidopsis DICER-LIKE2 in plant growth inhibition\".","authors":"Carsten Poul Skou Nielsen, Laura Arribas-Hernández, Peter Brodersen","doi":"10.1093/plcell/koaf163","DOIUrl":"https://doi.org/10.1093/plcell/koaf163","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":"37 8","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12396379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144965102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Expression of Concern: Ubiquitin Ligases RGLG1 and RGLG5 Regulate Abscisic Acid Signaling by Controlling the Turnover of Phosphatase PP2CA.","authors":"","doi":"10.1093/plcell/koaf192","DOIUrl":"10.1093/plcell/koaf192","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":"37 8","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12641515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Expression of Concern: C2-Domain Abscisic Acid-Related Proteins Mediate the Interaction of PYR/PYL/RCAR Abscisic Acid Receptors with the Plasma Membrane and Regulate Abscisic Acid Sensitivity in Arabidopsis.","authors":"","doi":"10.1093/plcell/koaf191","DOIUrl":"10.1093/plcell/koaf191","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":"37 8","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12641514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alternative splicing (AS) is an important regulatory mechanism for fine-tuning gene transcription in eukaryotes. H3K36me3 affects AS, but the underlying mechanisms remain obscure. In this study, we showed that the Arabidopsis thaliana H3K36me3 reader protein MORF-RELATED GENE 2 (MRG2) directly interacts with eIF4A3, a component of the exon junction complex within the spliceosome. The eif4a3 mutant displays a late-flowering phenotype similar to that of the mrg1 mrg2 double mutant under long-day, but not short-day, photoperiod conditions. Transcriptome analysis showed that deleting either eIF4A3 or MRG1/MRG2 causes similar changes in gene transcription and AS, which are involved in diverse processes including circadian rhythm regulation and responses to environmental stimuli. Both eIF4A3 and MRG1/MRG2 are required for the AS of key circadian clock genes and the maintenance of an appropriate circadian rhythm. RNA immunoprecipitation sequencing (RIP-seq) showed that MRG1/MRG2 promote eIF4A3 binding to the transcripts of a set of genes, including the key circadian clock genes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and PRR9. Moreover, eIF4A3 and MRG2 directly target and enhance each other's binding to PRR7 and PRR9 chromatin. Collectively, our findings reveal that the reader protein MRG2 recognizes histone methylation signals and recruits eIF4A3 to regulate co-transcriptional AS events, establishing a direct link between histone modification and the splicing machinery in plants.
{"title":"The Arabidopsis histone methylation reader MRG2 interacts with eIF4A3 to regulate alternative splicing and circadian rhythms.","authors":"Yaxue Huang, Jiabing Wu, Xiang Li, Jiachen Wang, Mengmeng Ma, Wen Jiang, Wen-Hui Shen, Yu Yu, Aiwu Dong","doi":"10.1093/plcell/koaf209","DOIUrl":"10.1093/plcell/koaf209","url":null,"abstract":"<p><p>Alternative splicing (AS) is an important regulatory mechanism for fine-tuning gene transcription in eukaryotes. H3K36me3 affects AS, but the underlying mechanisms remain obscure. In this study, we showed that the Arabidopsis thaliana H3K36me3 reader protein MORF-RELATED GENE 2 (MRG2) directly interacts with eIF4A3, a component of the exon junction complex within the spliceosome. The eif4a3 mutant displays a late-flowering phenotype similar to that of the mrg1 mrg2 double mutant under long-day, but not short-day, photoperiod conditions. Transcriptome analysis showed that deleting either eIF4A3 or MRG1/MRG2 causes similar changes in gene transcription and AS, which are involved in diverse processes including circadian rhythm regulation and responses to environmental stimuli. Both eIF4A3 and MRG1/MRG2 are required for the AS of key circadian clock genes and the maintenance of an appropriate circadian rhythm. RNA immunoprecipitation sequencing (RIP-seq) showed that MRG1/MRG2 promote eIF4A3 binding to the transcripts of a set of genes, including the key circadian clock genes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and PRR9. Moreover, eIF4A3 and MRG2 directly target and enhance each other's binding to PRR7 and PRR9 chromatin. Collectively, our findings reveal that the reader protein MRG2 recognizes histone methylation signals and recruits eIF4A3 to regulate co-transcriptional AS events, establishing a direct link between histone modification and the splicing machinery in plants.</p>","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dark-responsive BGH2 and light-responsive BPG4: Taming the GLK1/2 master transcription factors for etioplast and chloroplast homeostasis.","authors":"Jiajun Wang","doi":"10.1093/plcell/koaf190","DOIUrl":"10.1093/plcell/koaf190","url":null,"abstract":"","PeriodicalId":20186,"journal":{"name":"Plant Cell","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144837315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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