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Protein ubiquitination during photomorphogenesis

Ubiquitination in Arabidopsis thaliana

222 modifications in 196 peptides, found in 419 proteins

Experiment Details

Exp 3


Experimental Setup
TissueWild-type Col-0 and hexa(6His-UBQ) seedlings
ConditionDark, 1h light exposed, MG132 treatment
PTM Enrichment Tandem repeated Ub binding entity (TUBE)
MS InstrumentLTQ Orbitrap Velos
MS/MS Search Parameters
Protein Database TAIR (IPI database version 3.85)
Decoy StrategyReverse decoy database
FDR Threshold0.01
Search Algorithm(s)SEQUEST version 1.2
Precursor Mass Tolerance10 ppm
ProteaseTrypsin
Fixed ModificationsCarbamidomethyl (C)
Variable ModificationsOxidation (M)
GlyGly (K)
Other Information
Comments Supplemental Table 4.


Publication Information

Aguilar-Hernández et al., 2017

PubMed ID: 28461270

No external accession available

Abstract

Mol Plant. 2017 Jun 5;10(6):846-865. doi: 10.1016/j.molp.2017.04.008. Epub 2017 
Apr 28.

Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in 
Remodeling the Arabidopsis Proteome during Photomorphogenesis.

Aguilar-Hernández V(1), Kim DY(2), Stankey RJ(2), Scalf M(3), Smith LM(3), 
Vierstra RD(4).

Author information:
(1)Department of Biology, Washington University in St. Louis, Campus Box 1137, 
One Brookings Drive, St. Louis, MO 63130, USA; Department of Genetics, 425-G 
Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA.
(2)Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, 
Madison, WI 53706, USA.
(3)Department of Chemistry, 1101 University Avenue, University of 
Wisconsin-Madison, Madison, WI 53706, USA.
(4)Department of Biology, Washington University in St. Louis, Campus Box 1137, 
One Brookings Drive, St. Louis, MO 63130, USA; Department of Genetics, 425-G 
Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic 
address: rdvierstra@wustl.edu.

The switch from skotomorphogenesis to photomorphogenesis is a key developmental 
transition in the life of seed plants. While much of the underpinning proteome 
remodeling is driven by light-induced changes in gene expression, the 
proteolytic removal of specific proteins by the ubiquitin-26S proteasome system 
is also likely paramount. Through mass spectrometric analysis of ubiquitylated 
proteins affinity-purified from etiolated Arabidopsis seedlings before and after 
red-light irradiation, we identified a number of influential proteins whose 
ubiquitylation status is modified during this switch. We observed a 
substantial enrichment for proteins involved in auxin, abscisic acid, ethylene, 
and brassinosteroid signaling, peroxisome function, disease resistance, protein 
phosphorylation and light perception, including the phytochrome (Phy) A and 
phototropin photoreceptors. Soon after red-light treatment, PhyA becomes the 
dominant ubiquitylated species, with ubiquitin attachment sites mapped to six 
lysines. A PhyA mutant protected from ubiquitin addition at these sites is 
substantially more stable in planta upon photoconversion to Pfr and is 
hyperactive in driving photomorphogenesis. However, light still stimulates 
ubiquitylation and degradation of this mutant, implying that other attachment 
sites and/or proteolytic pathways exist. Collectively, we expand the catalog of 
ubiquitylation targets in Arabidopsis and show that this post-translational 
modification is central to the rewiring of plants for photoautotrophic growth.

Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

DOI: 10.1016/j.molp.2017.04.008
PMCID: PMC5695678
PMID: 28461270 [Indexed for MEDLINE]