Agriculture Reference
In-Depth Information
Ubiquitins are encoded by a small-to-medium-sized multigene family compris-
ing two gene classes, monomeric and polymeric. Monomeric ubiquitin genes
consist of 228 nucleotides (76 codons) with an additional C-terminal sequence
that encodes a ribosomal protein. By contrast, polymeric genes known as
polyubiquitins are composed of tandem repeats of a 228-bp gene with no spacer
sequence between them (Nei et al.
2000
). In Arabdopsis, the Ub gene family
consists of at least 14 members (Callis et al.
1995
).
Three enzymes (E1-E3), working in a hierarchical cascade, attach a Ub tag to the
target proteins (Sadanandom et al.
2012
). E1 (ubiquitin-activating enzyme) hydro-
lyses ATP to adenylate the C-terminal carboxyl of Ub and form a thiolester bond
with E1 cysteinyl sulphydyl residue (E1-Ub intermediate). After completion of this
activation, E2 (ubiquitin-conjugating enzyme) accepts Ub on its cysteinyl
sulphydryl group and a thiolester bond is formed again (E2-Ub intermediate).
When conjugation is completed, E2 can either bind to E3 (ubiquitin ligase) to
transfer Ub to the protein substrate or transfer Ub to E3, which subsequently
transfers Ub to the target. Usually a Lys residue of the substrate accepts the
C-terminal Gly-76 of Ub. The E3 Ub ligases recognise and bind specific degrada-
tion signals in substrate proteins and thus confer specificity to the ubiquitination-
mediated degradation.
This ubiquitination cycle can be repeated multiple times. To add more complex-
ity, the protein family of deubiquitinating enzymes form an additional regulatory
step. A comprehensive repository of ubiquitinating and deubiquitinating enzymes
from 50 distinct genomes belonging to four of the five major phylogenetic super-
groups of eukaryotes was recently completed (Hutchins et al.
2013
) and it is
publicly available at the Database of Ubiquitinating and Deubiquitinating Enzymes
Proteins targeted for recycling by linkage of the Ub tag are degraded in two
evolutionary conserved degradation systems. The ubiquitin-proteasome system
(UPS) takes over the short-lived regulatory proteins (Dantuma et al.
2000
; Vierstra
2009
), while the autophagy pathway sequesters within double membrane structures
the longer-lived and bigger proteinaceous material, such as protein aggregates
(Yang and Klionsky
2010
). Autophagy and the UPS are critical in the maintenance
of cellular homeostasis, thus their activities need to be carefully orchestrated
(Korolchuk et al.
2010
). The limited degradative capacity of UPS is complemented
with autophagy and crosstalk mechanisms between both systems exist (Schreiber
and Peter
2013
). Moreover, both recycling mechanisms are in crosstalk with
senescence, programmed cell death (PCD) and prematurate aging (Madeo
et al.
2010
). The literature shows that when some autophagy related genes (ATG)
are impaired, accelerated senescence overtakes the plant destiny (Hanaoka
et al.
2002
; Thompson and Vierstra
2005
) presumably by impairment of autophagic
recycling that contributes to plant energy availability (Izumi et al.
2013
).
An overview of the ubiquitination cascade and UPS is shown in Fig.
7.1
. The
26S proteasome structures in mammals, yeast and plants indicate a similar overall
design (Sadanandom et al.
2012
). However, UPS-dependent regulation of signaling
and metabolic pathways appears to be more complex and prevalent in plants than in
yeast and animals.
