Exploring the Arabidopsis RNA-binding proteome and its dynamics under salinity stress

Authors: ZHANG, YONG - University Of California, Riverside; XU, YE - University Of California, Riverside; Skaggs, Todd; Ferreira, Jorge; CHEN, XUEMI - Peking University; Sandhu, Devinder

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/15/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: RNA-binding proteins (RBPs) play crucial roles in regulating cell fate and essential developmental processes. Therefore, systematic profiling of the RBP proteome (RBPome) becomes a prerequisite for scientists to understand how posttranscriptional gene regulation is achieved. While methods developed for humans, mice, and bacteria have successfully identified RBPomes in these organisms, the complexity of plant tissues has posed challenges for their effectiveness in plants. Herein, we introduced the plant phase extraction (PPE) method, which yielded a highly comprehensive RNA-binding proteome, revealing 2,517 RBPs from Arabidopsis leaf and root tissues, with a diverse array of RNA-binding domains. Notably, PPE identified 40% non-poly(A) RBPs that were not previously annotated, distinguishing it from RNA-interactome capture (RIC), a previously prevalent approach in plants for capturing poly(A)-RNA binding proteins. In contrast to quantitative proteomics methods that identify salt-responsive proteins based on changes in overall protein levels, PPE focuses on the entire RBP-RNA complex. This unique feature enables the detection of changes in RBP-RNA dynamics under salt stress, irrespective of protein abundance. Our results indicate that less than 20% of previously identified salt-responsive RBPs displayed altered interactions with RNAs. In contrast, 100% of salt-responsive RBPs captured by PPE, including 327 novel ones, exhibited changed dynamics between RBPs and RNAs when plants were exposed to salt stress. In summary, our findings demonstrate that PPE is an impactful approach for identifying RBPs from complex plant tissues. The advantage of PPE will undoubtedly reshape and advance our understanding of how RBPs function under physiological and stress conditions at the post-transcriptional level.