Ubiquitin-Proteasome System-Mediated Protein Degradation in Defense Signaling - PAMP Signals in Plant Innate Immunity: Signal Perception and Transduction - page 408

the proteasome lid (Thrower et al. 2000 ). Ubiquitin-ubiquitin linkages may serve as
proteolytic signals (Kirkpatrick et al. 2006 ).
The common 26S proteasome contains one 20S core particle structure and two
19S regulatory caps. The core is hollow and provides an enclosed cavity in which
proteins are degraded; openings at the two ends of the core allow the target protein
to enter. Each end of the core particle associates with a 19S regulatory subunit that
contains multiple ATPase active sites and ubiquitin binding sites. This structure
recognizes polyubiquitinated proteins and transfers them to the catalytic core. After
delivery to the proteasome mediated in part by ubiquitin binding proteins, the
polyubiquitylated substrate can be deubiquitylated by the proteasome's regulatory
cap or associated proteases. The deubiquitylated substrate is fed into the proteolytic
core of the proteasome where it is cleaved into small peptides (Book et al. 2005 ;
Zhu et al. 2005 ; Dreher and Callis 2007 ).
E3 ligases play a key role in the ubiquitin-proteasome system (UPS). Two mech-
anistic classes of E3 ligases have been recognized. In case of HECT (for Homologous
to E6-AP COOH terminus) domain E3 ligases, ubiquitin forms a covalent thioester
linkage with a cysteinyl sulfhydryl group on HECT protein before being transferred
to a lysine on the substrate (Downes et al. 2003 ). The other E3 ligase class non-
covalently interacts with an E2 protein carrying ubiquitin. There are two groups
within this class, the U-box (UFD2-homology) domain- and RING (for Really
Interesting New Gene) domain-containing proteins (Zheng et al. 2000 ; Pickart
2001 ; Andersen et al. 2004 ). Several proteins containing U-box and RING domains
have been reported in plants. Approximately 61 proteins containing U-box domain
and more than 450 proteins with one or more RING domains have been identifi ed
in Arabidopsis thaliana (Stone et al. 2005 ).
The RING domain has a consensus sequence containing Cys and His
residues (Cys-X 2 -Cys-X 9-39 -Cys-X 1-3 -His-X 2-3 -Cys/His-X 2 -Cys-X 4-48 -Cys-X 2 -Cys),
which functions as a binding site for the ubiquitin-conjugating enzyme (E2) inter-
mediate that has a zinc-binding domain formed by conserved Cys and His residues
(Lee et al. 2011 ). Based on the presence of Cys or His in the fi fth position, the RING
domains of RING fi nger type proteins can be divided into two types (Borden and
Freemont 1996 ).
Major types of E3 ligases belong to the Skp, Cullin, F-box containing complex
(SCF complex), which are composed of four primary subunits: SKP1 (for S-phase
Kinase-associated Protein 1); a cullin family member protein (e.g. CUL1); a RING
fi nger protein; and an F-box protein (Guo and Ecker 2003 ; Potuschak et al. 2003 ;
Risseeuw et al. 2003 ; Dreher and Callis 2007 ). Within this complex, the F-box pro-
tein directly binds the substrate through protein-protein interaction domains, the
cullin binds the RING fi nger protein, together they recruit E2 ubiquitin-conjugating
enzyme, and SKP1 helps to link the F-box protein and cullin (Deshaies 1999 ).
The cullins are modifi ed covalently by NEDDB/RUB1, a ubiquitin-like protein, in
a process called neddylation. This modifi cation stimulates SCF ubiquitin ligase
activity in plants (Kawakami et al. 2001 ; del Pozo et al. 2002 ).
A nucleus-enriched multisubunit protein complex, called “COP9 signalosome
(CSN)” is known to regulate ubiquitin-proteasome-mediated protein degradation