Premium
Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings
Author(s) -
Zhu FuYuan,
Chen MoXian,
Ye NengHui,
Shi Lu,
Ma KaiLong,
Yang JingFang,
Cao YunYing,
Zhang Youjun,
Yoshida Takuya,
Fernie Alisdair R.,
Fan GuangYi,
Wen Bo,
Zhou Ruo,
Liu TieYuan,
Fan Tao,
Gao Bei,
Zhang Di,
Hao GeFei,
Xiao Shi,
Liu YingGao,
Zhang Jianhua
Publication year - 2017
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13571
Subject(s) - biology , alternative splicing , arabidopsis , intron , exon , rna splicing , computational biology , translation (biology) , gene isoform , gene , genetics , abscisic acid , splicing factor , rna , messenger rna , mutant
Summary 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.