PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in <i>Arabidopsis thaliana</i>

Kanno, Tohru; Venhuizen, Peter; Teng, Wen; Lin, Wen-Dar; Chiou, Phebe; Kalyna, Maria; Matzke, A. J. M.; Matzke, Marjori

doi:10.1534/genetics.118.301515

Cited by 21 publications

(21 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is well known that many proteins involved in splicing are regulated by phosphorylation [22] [3]. PRP4KA (PRE-MRNA PROCESSING 4 KINASE A) is a spliceosome-associated kinase in Arabidopsis that affects alternative splicing patterns by phosphorylating different splicing target regulators [23]. Interestingly, we found PRP4KA as a phosphorylated protein in the Et sample (AT3G25840, Additional File 1: Table S6).…”

Section: Discussionmentioning

confidence: 79%

“…Interestingly, we found PRP4KA as a phosphorylated protein in the Et sample (AT3G25840, Additional File 1: Table S6). More surprisingly, we found 7 targets of PRP4KA phosphorylation: 3 splicing factors (ATSF1, RS40 and RS41), 3 RNA binding proteins (BTR1L, CCR2 and ELF9) and 1 mRNA decapping protein (VCS) (Additional File 1: Table S6 and [23]. We found PRP40A (PRE-MRNA-PROCESSING PROTEIN 40A) and PRP40B (PRE-MRNA-PROCESSING PROTEIN 40B) in Et samples, two phosphoproteins that binds the phosphorylated C-terminal domain of the largest subunit of RNA polymerase II.…”

Section: Discussionmentioning

confidence: 97%

See 1 more Smart Citation

A Novel Strategy to Uncover Specific Go Terms/phosphorylation Pathways in Phosphoproteomic Data in Arabidopsis Thaliana

Arico

Beati

Wengier

et al. 2021

Preprint

View full text Add to dashboard Cite

Background. Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to an experimental query from a list of phosphoproteins. Comparison of the frequency distribution of GO (Gene Ontology) terms in a given phosphoproteome set with that observed in the genome reference set (GenRS) is the most widely used tool to infer biological significance. Yet, this comparison assumes that GO term distribution between the phosphoproteome and the genome are identical. However, this hypothesis has not been tested due to the lack of a comprehensive phosphoproteome database.Results. In this study, we test this hypothesis by constructing three phosphoproteome databases in Arabidopsis thaliana: one based in experimental data (ExpRS), another based in in silico phosphorylation protein prediction (PredRS) and a third that is the union of both (UnRS). Our results show that the three phosphoproteome reference sets show default enrichment of several GO terms compared to GenRS, indicating that GO term distribution in the phosphoproteomes does not match that of the genome. Moreover, these differences overshadow the identification of GO terms that are specifically enriched in a particular condition. To overcome this limitation, we present an additional comparison of the sample of interest with UnRS to uncover GO terms specifically enriched in a particular phosphoproteome experiment. Using this strategy, we found that mRNA splicing and cytoplasmic microtubule compounds are important processes specifically enriched in the phosphoproteome of dark-grown Arabidopsis seedlings. Conclusions. This study provides a novel strategy to uncover GO specific terms in phosphoproteome data of Arabidopsis that could be applied to any other organism. We also highlight the importance of specific phosphorylation pathways that take place during dark-grown Arabidopsis development.

show abstract

Section: Discussionmentioning

confidence: 79%

Section: Discussionmentioning

confidence: 97%

A Novel Strategy to Uncover Specific Go Terms/phosphorylation Pathways in Phosphoproteomic Data in Arabidopsis Thaliana

Arico

Beati

Wengier

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…It is well known that many proteins involved in splicing are regulated by phosphorylation [ 3 , 22 ]. PRP4KA (PRE-MRNA PROCESSING 4 KINASE A) is a spliceosome-associated kinase in Arabidopsis that affects alternative splicing patterns by phosphorylating different splicing target regulators [ 23 ]. Interestingly, we found PRP4KA as a phosphorylated protein in the Et sample (AT3G25840, Table S6 ).…”

Section: Discussionmentioning

confidence: 99%

A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana

et al. 2021

View full text Add to dashboard Cite

Background Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to an experimental query from a list of phosphoproteins. Comparison of the frequency distribution of GO (Gene Ontology) terms in a given phosphoproteome set with that observed in the genome reference set (GenRS) is the most widely used tool to infer biological significance. Yet, this comparison assumes that GO term distribution between the phosphoproteome and the genome are identical. However, this hypothesis has not been tested due to the lack of a comprehensive phosphoproteome database. Results In this study, we test this hypothesis by constructing three phosphoproteome databases in Arabidopsis thaliana: one based in experimental data (ExpRS), another based in in silico phosphorylation protein prediction (PredRS) and a third that is the union of both (UnRS). Our results show that the three phosphoproteome reference sets show default enrichment of several GO terms compared to GenRS, indicating that GO term distribution in the phosphoproteomes does not match that of the genome. Moreover, these differences overshadow the identification of GO terms that are specifically enriched in a particular condition. To overcome this limitation, we present an additional comparison of the sample of interest with UnRS to uncover GO terms specifically enriched in a particular phosphoproteome experiment. Using this strategy, we found that mRNA splicing and cytoplasmic microtubule compounds are important processes specifically enriched in the phosphoproteome of dark-grown Arabidopsis seedlings. Conclusions This study provides a novel strategy to uncover GO specific terms in phosphoproteome data of Arabidopsis that could be applied to any other organism. We also highlight the importance of specific phosphorylation pathways that take place during dark-grown Arabidopsis development.

show abstract

“…Moreover, these systems have also been instrumental in identifying the factors upstream of some of these AS events [ 2 , 3 , 5 , 6 , 7 ]. The usage of AS reporters in plant model organisms is scarce and has practically never been purposed for assessing cell-specific expression of splice isoforms [ 9 , 43 , 44 ]. To our knowledge, genetic screening with the marker, such as DAAO, has never been used in plants for such purpose at all.…”

Section: Discussionmentioning

confidence: 99%

In Vivo Reporters for Visualizing Alternative Splicing of Hormonal Genes

Kashkan

Timofeyenko

Kollárová

et al. 2020

Plants

View full text Add to dashboard Cite

Rapid progress in plant molecular biology in recent years has uncovered the main players in hormonal pathways and characterized transcriptomic networks associated with hormonal response. However, the role of RNA processing, in particular alternative splicing (AS), remains largely unexplored. Here, using example genes involved in cytokinin signaling, brassinosteroid synthesis and auxin transport, we present a set of reporters devised to visualize their AS events in vivo. These reporters show a differential tissue-specific expression of certain transcripts and reveal that expression of some of the them can be changed by the application of the exogenous hormone. Finally, based on the characterized AS event of the PIN7 auxin efflux carrier, we designed a system that allows a rapid genetic screening for the factors upstream of this AS event. Our innovative toolset can be therefore highly useful for exploring novel regulatory nodes of hormonal pathways and potentially helpful for plant researchers focusing on developmental aspects of AS.

show abstract

PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in Arabidopsis thaliana

Abstract: Prp4 kinase (Prp4k) is the first spliceosome-associated kinase shown to regulate splicing in fungi and metazoans, but nothing is yet known about its functions in plants. Here, Kanno and Venhuizen et al. report...

Cited by 21 publications

References 79 publications

A Novel Strategy to Uncover Specific Go Terms/phosphorylation Pathways in Phosphoproteomic Data in Arabidopsis Thaliana

A Novel Strategy to Uncover Specific Go Terms/phosphorylation Pathways in Phosphoproteomic Data in Arabidopsis Thaliana

A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana

In Vivo Reporters for Visualizing Alternative Splicing of Hormonal Genes

Contact Info

Product

Resources

About