pr5009724_si_004.xlsx (107.37 kB)
Comprehensive Profiling of the Rice Ubiquitome Reveals the Significance of Lysine Ubiquitination in Young Leaves
dataset
posted on 2015-05-01, 00:00 authored by Xin Xie, Houxiang Kang, Wende Liu, Guo-Liang WangProtein
ubiquitination is a major post-translational modification
that regulates development, apoptosis, responses to environmental
cues, and other processes in eukaryotes. Although several ubiquitinated
proteins have been identified in rice, large-scale profiling of the
rice ubiquitome has not been reported because of limitations in the
current analytical methods. Here, we report the first rice ubiquitome,
determined by combining highly sensitive immune affinity purification
and high resolution LC–MS/MS. We identified 861 di-Gly-Lys-containing
peptides in 464 proteins in rice leaf cells. Bioinformatic analyses
of the ubiquitome identified a variety of cellular functions and diverse
subcellular localizations for the ubiquitinated proteins, and also
revealed seven putative ubiquitination motifs in rice. Proteins related
to binding and catalytic activity were predicted to be the preferential
targets of lysine ubiquitination. A protein interaction network and
KEGG analysis indicated that a wide range of signaling and metabolic
pathways are modulated by protein ubiquitination in rice. Our results
demonstrate the usefulness of the significantly improved method for
assaying proteome-wide ubiquitination in plants. The identification
of the 464 ubiquitinated proteins in rice leaves provides a foundation
for the analysis of the physiological roles of these ubiquitination-related
proteins.