Hongyong Fu

Subunit interaction maps for the regulatory particle of the 26S proteasome and the COP9 signalosome

The 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin‐tagged proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. To help define the molecular organization of the RP, we tested all possible paired interactions among subunits from Saccharomyces cerevisiae by yeast two‐hybrid analysis. Within the base, a Rpt4/5/3/6 interaction cluster was evident. Within the lid, a structural cluster formed around Rpn5/11/9/8. Interactions were detected among synonymous subunits (Csn4/5/7/6) from the evolutionarily related COP9 signalosome (CSN) from Arabidopsis, implying a similar quaternary arrangement. No paired interactions were detected between lid, base or core particle subcomplexes, suggesting that stable contacts between them require prior assembly. Mutational analysis defined the ATPase, coiled‐coil, PCI and MPN domains as important for RP assembly. A single residue in the vWA domain of Rpn10 is essential for amino acid analog resistance, for degrading a ubiquitin fusion degradation substrate and for stabilizing lid—base association. Comprehensive subunit interaction maps for the 26S proteasome and CSN support the ancestral relationship of these two complexes.

IRT1 DEGRADATION FACTOR1, a RING E3 Ubiquitin Ligase, Regulates the Degradation of IRON-REGULATED TRANSPORTER1 in Arabidopsis

Plants strictly regulate uptake of the essential micronutrient iron by protein turnover of the major ferrous iron transporter IRON-REGULATED TRANSPORTER1 (IRT1). This study revealed that IRT1 DEGRADATION FACTOR1 directly functions in IRT1 turnover through its RING E3 ubiquitin ligase activity. Fe is an essential micronutrient for plant growth and development; plants have developed sophisticated strategies to acquire ferric Fe from the soil. Nongraminaceous plants acquire Fe by a reduction-based mechanism, and graminaceous plants use a chelation-based mechanism. In Arabidopsis thaliana, which uses the reduction-based method, IRON-REGULATED TRANSPORTER1 (IRT1) functions as the most important transporter for ferrous Fe uptake. Rapid and constitutive degradation of IRT1 allows plants to quickly respond to changing conditions to maintain Fe homeostasis. IRT1 degradation involves ubiquitination. To identify the specific E3 ubiquitin ligases involved in IRT1 degradation, we screened a set of insertional mutants in RING-type E3 ligases and identified a mutant that showed delayed degradation of IRT1 and loss of IRT1-ubiquitin complexes. The corresponding gene was designated IRT1 DEGRADATION FACTOR1 (IDF1). Evidence of direct interaction between IDF1 and IRT1 in the plasma membrane supported the role of IDF1 in IRT1 degradation. IRT1 accumulation was reduced when coexpressed with IDF1 in yeast or Xenopus laevis oocytes. IDF1 function was RING domain dependent. The idf1 mutants showed increased tolerance to Fe deficiency, resulting from increased IRT1 levels. This evidence indicates that IDF1 directly regulates IRT1 degradation through its RING-type E3 ligase activity.

The RAD23 Family Provides an Essential Connection between the 26S Proteasome and Ubiquitylated Proteins in Arabidopsis

This study describes the collection of UBL/UBA domain proteins in Arabidopsis that participate in the ubiquitin/26S proteasome system, with a focus on the RAD23 family. The data point to a specific role for RAD23s in plants and suggest that the four isoforms have both redundant and unique roles in Arabidopsis development by helping shuttle ubiquitin conjugates to the 26S proteasome. The ubiquitin (Ub)/26S proteasome system (UPS) directs the turnover of numerous regulatory proteins, thereby exerting control over many aspects of plant growth, development, and survival. The UPS is directed in part by a group of Ub-like/Ub-associated (UBL/UBA) proteins that help shuttle ubiquitylated proteins to the 26S proteasome for breakdown. Here, we describe the collection of UBL/UBA proteins in Arabidopsis thaliana, including four isoforms that comprise the RADIATION SENSITIVE23 (RAD23) family. The nuclear-enriched RAD23 proteins bind Ub conjugates, especially those linked internally through Lys-48, via their UBA domains, and associate with the 26S proteasome Ub receptor RPN10 via their N-terminal UBL domains. Whereas homozygous mutants individually affecting the four RAD23 genes are without phenotypic consequences (rad23a, rad23c, and rad23d) or induce mild phyllotaxy and sterility defects (rad23b), higher-order mutant combinations generate severely dwarfed plants, with the quadruple mutant displaying reproductive lethality. Both the synergistic effects of a rad23b-1 rpn10-1 combination and the response of rad23b plants to mitomycin C suggest that RAD23b regulates cell division. Taken together, RAD23 proteins appear to play an essential role in the cell cycle, morphology, and fertility of plants through their delivery of UPS substrates to the 26S proteasome.

Cross‐species divergence of the major recognition pathways of ubiquitylated substrates for ubiquitin/26S proteasome‐mediated proteolysis

The recognition of ubiquitylated substrates is an essential element of ubiquitin/26S proteasome‐mediated proteolysis (UPP), which is mediated directly by the proteasome subunit RPN10 and/or RPN13, or indirectly by ubiquitin receptors containing ubiquitin‐like and ubiquitin‐associated domains. By pull‐down and mutagenesis assays, we detected cross‐species divergence of the major recognition pathways. RPN10 plays a major role in direct recognition in Arabidopsis and yeast based on the strong affinity for the long and K48‐linked ubiquitin chains. In contrast, both the RPN10 and RPN13 homologs play major roles in humans. For indirect recognition, the RAD23 and DSK2 homologs (except for the human DSK2 homolog) are major receptors. The human RAD23 homolog is targeted to the 26S proteasome by the RPN10 and RPN13 homologs. In comparison, Arabidopsis uses UIM1 and UIM3 of RPN10 to bind DSK2 and RAD23, respectively. Yeast uses UIM in RPN10 and LRR in RPN1. Overall, multiple proteasome subunits are responsible for the direct and/or indirect recognition of ubiquitylated substrates in yeast and humans. In contrast, a single proteasome subunit, RPN10, is critical for both the direct and indirect recognition pathways in Arabidopsis. In agreement with these results, the accumulation of ubiquitylated substrates and severe pleiotropic phenotypes of vegetative and reproductive growth are associated with the loss of RPN10 function in an Arabidopsis T‐DNA insertion mutant. This implies that the targeting and proteolysis of the critical regulators involved are affected. These results support a cross‐species mechanistic and functional divergence of the major recognition pathways for ubiquitylated substrates of UPP.

Proteasomal recognition of ubiquitylated substrates

Ubiquitin/26S proteasome-mediated proteolysis controls the half-life of numerous critical regulatory proteins and is an intimate regulatory component for nearly all aspects of cellular processes. In addition to ubiquitin conjugation, an additional level of substrate specificity is regulated at the step of proteasomal recognition of ubiquitylated substrates, which serves as an important mechanistic and regulatory component to connect the substrate from the conjugation machinery to the 26S proteasome. In this review, we discuss current knowledge and future challenges relevant to understanding the mechanism, regulation, functions and substrate specificity of proteasomal recognition mediated by a multitude of ubiquitin receptors. The mechanistic details of major recognition pathways for ubiquitylated substrates are clearly divergent within and across species, which implies functional differentiation.

The defective proteasome but not substrate recognition function is responsible for the null phenotypes of the Arabidopsis proteasome subunit RPN10.

This study shows that the major ubiquitin receptors involved in targeting ubiquitylated proteins for proteasome-mediated proteolysis are functionally redundant in Arabidopsis. Interestingly, in addition to playing a redundant role in substrate recognition, the Arabidopsis proteasome subunit RPN10 maintains the structural integrity of proteasome, which is critical for vegetative and reproductive growth. Ubiquitylated substrate recognition during ubiquitin/proteasome-mediated proteolysis (UPP) is mediated directly by the proteasome subunits RPN10 and RPN13 and indirectly by ubiquitin-like (UBL) and ubiquitin-associated (UBA) domain-containing factors. To dissect the complexity and functional roles of UPP substrate recognition in Arabidopsis thaliana, potential UPP substrate receptors were characterized. RPN10 and members of the UBL-UBA–containing RAD23 and DSK2 families displayed strong affinities for Lys-48–linked ubiquitin chains (the major UPP signals), indicating that they are involved in ubiquitylated substrate recognition. Additionally, RPN10 uses distinct interfaces as primary proteasomal docking sites for RAD23s and DSK2s. Analyses of T-DNA insertion knockout or RNA interference knockdown mutants of potential UPP ubiquitin receptors, including RPN10, RPN13, RAD23a-d, DSK2a-b, DDI1, and NUB1, demonstrated that only the RPN10 mutant gave clear phenotypes. The null rpn10-2 showed decreased double-capped proteasomes, increased 20S core complexes, and pleiotropic vegetative and reproductive growth phenotypes. Surprisingly, the observed rpn10-2 phenotypes were rescued by a RPN10 variant defective in substrate recognition, indicating that the defectiveness of RPN10 in proteasome but not substrate recognition function is responsible for the null phenotypes. Our results suggest that redundant recognition pathways likely are used in Arabidopsis to target ubiquitylated substrates for proteasomal degradation and that their specific roles in vivo require further examination.

Pollen-Specific SKP1-Like Proteins are Components of Functional SCF Complexes and Essential for Lily Pollen Tube Elongation

The ubiquitin-proteasome pathway mediates protein degradation and is involved in diverse aspects of plant development and differentiation, including pollen tube elongation and self-incompatibility. We characterized three lily (Lilium longiflorum) SKP1-like genes, LSK1-LSK3, that are specifically expressed in late pollen developmental stages and the elongating pollen tube. The encoded peptide sequences reveal that LSK1-LSK3 share high identity with Arabidopsis ASK1 and contain a putative N-terminal CUL1- and a C-terminal F-box-interacting domain. Yeast two-hybrid and in vitro affinity binding assays revealed that the LSKs associate with lily CULLIN1. In addition, the LSK genes can functionally complement the yeast skp1 deletion mutant YDR328C. To investigate their biological functions in pollen tube elongation, an in vivo approach for green fluorescent protein (GFP)-tagged dominant-negative LSK1-LSK3 was developed. Microprojectile bombardment with N-terminally truncated LSK1-LSK3 (LSK1-LSK3Delta-GFP) significantly retarded pollen tube elongation in both in vitro germination and in vivo self- and cross-pollination after >12 h incubation. Interestingly, elongation of pollen tubes harboring overexpressed LSK2Delta-GFP and LSK3Delta-GFP was substantially inhibited within the self-pollinated styles. The elongation of most LSK2Delta-GFP-transformed pollen tubes could germinate only on the stigmatic surface of self style and showed statistically significant growth arrest as compared with control pollen tubes. Lily exhibits typical gametophytic self-incompatibility via an unknown mechanism, but LSK2 and LSK3 may be involved in this complex machinery. These results suggest critical roles for LSK1-LSK3 in regulating fundamental pollen tube elongation in vitro and in vivo and that the 26S proteasome-mediated protein pathway plays an important role in pollen tube elongation.

Distinct phylogenetic relationships and biochemical properties of Arabidopsis ovarian tumor-related deubiquitinases support their functional differentiation

The reverse reaction of ubiquitylation is catalyzed by different classes of deubiquitylation enzymes (DUBs), including ovarian tumor domain (OTU)-containing DUBs; experiments using Homo sapiens proteins have demonstrated that OTU DUBs modulate various cellular processes. With the exception of OTLD1, plant OTU DUBs have not been characterized. We identified 12 Arabidopsis thaliana OTU loci and analyzed 11 of the encoded proteins in vitro to determine their preferences for the ubiquitin (UB) chains of M1, K48, and K63 linkages as well as the UB-/RUB-/SUMO-GST fusions. The A. thaliana OTU DUBs were shown to be cysteine proteases and classified into four groups with distinct linkage preferences: OTU1 (M1 = K48 > K63), OTU3/4/7/10 (K63 > K48 > M1), OTU2/9 (K48 = K63), and OTU5/11/12/OTLD1 (inactive). Five active OTU DUBs (OTU3/4/7/9/10) also cleaved RUB fusion. OTU1/3/4 cleaved M1 UB chains, suggesting a possible role for M1 chains in plant cellular signaling. The different substrate specificities of the various A. thaliana OTU DUBs indicate the involvement of distinct structural elements; for example, the OTU1 oxyanion residue D89 is essential for cleaving isopeptide bond-linked chains but dispensable for M1 chains. UB-binding activities were detected only for OTU2 and OTLD1, with distinct linkage preferences. These differences in biochemical properties support the involvement of A. thaliana OTU DUBs in different functions. Moreover, based on the established phylogenetic tree, plant- and H. sapiens-specific clades exist, which suggests that the proteins within these clades have taxa-specific functions. We also detected five OTU clades that are conserved across species, which suggests that the orthologs in different species within each clade are involved in conserved cellular processes, such as ERAD and DNA damage responses. However, different linkage preferences have been detected among potential cross-species OTU orthologs, indicating functional and mechanistic differentiation.

Reversible ubiquitylation in plant biology

Post-translational modification by ubiquitin plays a critical regulatory function in nearly all aspects of plant biology (Vierstra, 2009). Diverse conjugation enzymes attach monoubiquitin or polyubiquitin, with eight different linkages, as distinct signals to the regulatory and mechanistic components of various cellular processes. This ebook updates the functions, targets, and mechanisms of the conjugation components involved in the monoubiquitination of histones H2A and H2B and the polyubiquitination of all linkage types. Additionally, the roles and mechanisms of E3 ligases in biotic and abiotic stress responses and self-incompatibility (SI) and the regulation of cullin-based ligases (CRLs) by neddylation/deneddylation are updated. Finally, the functional roles of deubiquitination enzymes (DUBs) are reviewed together with a report on the biochemical and phylogenetic analyses of Arabidopsis OTU DUBs that support their functional differences.

The Deubiquitinase OTU5 Regulates Root Responses to Phosphate Starvation

The deubiquitinase OTU5 is required for the interpretation of environmental cues that alter the abundance of root hair- and chromatin-related proteins. Phosphorus, taken up by plants as inorganic phosphate (Pi), is an essential but often growth-limiting mineral nutrient for plants. As part of an orchestrated response to improve its acquisition, insufficient Pi supply triggers alterations in root architecture and epidermal cell morphogenesis. Arabidopsis (Arabidopsis thaliana) mutants defective in the expression of the OVARIAN TUMOR DOMAIN-CONTAINING DEUBIQUITINATING ENZYME5 (OTU5) exhibited a constitutive Pi deficiency root phenotype, comprising the formation of long and dense root hairs and attenuated primary root growth. Quantitative protein profiling of otu5 and wild-type roots using the isobaric tag for relative and absolute quantification methodology revealed genotype- and Pi-dependent alterations in protein profiles. In otu5 plants, Pi starvation caused a short-root-hair phenotype and decreased abundance of a suite of Pi-responsive root hair-related proteins. Mutant plants also showed the accumulation of proteins involved in chromatin remodeling and altered distribution of reactive oxygen species along the root, which may be causative for the alterations in root hair morphogenesis. The root hair phenotype of otu5 was synergistic to that of actin-related protein6 (arp6), harboring a mutation in the SWR1 chromatin-remodeling complex. Genetic analysis of otu5/arp6 double mutants suggests independent but functionally related roles of the two proteins in chromatin organization. The root hair phenotype of otu5 is not caused by a general up-regulation of the Pi starvation response, indicating that OTU5 acts downstream of or interacts with Pi signaling. It is concluded that OTU5 is involved in the interpretation of environmental information, probably by altering chromatin organization and maintaining redox homeostasis.