Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings

Fu Yuan Zhu, Mo Xian Chen, Neng Hui Ye, Lu Shi, Kai Long Ma, Jing Fang Yang, Yun Ying Cao, Youjun Zhang, Takuya Yoshida, Alisdair R. Fernie, Guang Yi Fan, Bo Wen, Ruo Zhou, Tie Yuan Liu, Tao Fan, Bei Gao, Di Zhang, Ge Fei Hao, Shi Xiao, Ying Gao Liu*Jianhua ZHANG

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

61 Citations (Scopus)

Abstract

In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.

Original languageEnglish
Pages (from-to)518-533
Number of pages16
JournalPlant Journal
Volume91
Issue number3
DOIs
Publication statusPublished - Aug 2017

Scopus Subject Areas

  • Genetics
  • Plant Science
  • Cell Biology

User-Defined Keywords

  • abscisic acid
  • alternative splicing
  • Arabidopsis thaliana
  • proteogenomics
  • splicing factor
  • technical advance
  • translation

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