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Impact of alternative splicing on Arabidopsis proteome.
Reyes, Andres V; Shrestha, Ruben; Grismer, TaraBryn S; Byun, Danbi; Xu, Shou-Ling.
Afiliación
  • Reyes AV; Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA.
  • Shrestha R; Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA.
  • Grismer TS; Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA.
  • Byun D; Division of biosphere science and engineering, Carnegie Institution for Science, Stanford, California, USA.
  • Xu SL; Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA.
bioRxiv ; 2024 Mar 04.
Article en En | MEDLINE | ID: mdl-38496481
ABSTRACT
Alternative splicing is an important regulatory process in eukaryotes. In plants, the major form of alternative splicing is intron retention. Despite its importance, the global impact of AS on the Arabidopsis proteome has not been investigated. In this study, we address this gap by performing a comprehensive integrated analysis of how changes in AS can affect the Arabidopsis proteome using mutants that disrupt ACINUS and PININ, two evolutionarily conserved alternative splicing factors. We used tandem mass tagging (TMT) with real-time search MS3 (RTS-SPS-MS3) coupled with extensive sample fractionations to achieve very high coverage and accurate protein quantification. We then integrated our proteomic data with transcriptomic data to assess how transcript changes and increased intron retention (IIR) affect the proteome. For differentially expressed transcripts, we have observed a weak to moderate correlation between transcript changes and protein changes. Our studies revealed that some IIRs have no effect on either transcript or protein levels, while some IIRs can significantly affect protein levels. Surprisingly, we found that IIRs have a much smaller effect on increasing protein diversity. Notably, the increased intron retention events detected in the double mutant are also detected in the WT under various biotic or abiotic stresses. We further investigated the characteristics of the retained introns. Our extensive proteomic data help to guide the phenotypic analysis and reveal that collective protein changes contribute to the observed phenotypes of the increased anthocyanin, pale green, reduced growth, and short root observed in the acinus pnn double mutant. Overall, our study provides insight into the intricate regulatory mechanism of intron retention and its impact on protein abundance in plants.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos