Ubiquitination-mediated protein degradation and modification： an emerging theme in plant-microbe interactions

Post-translational modification is central to protein stability and to the naodulation of protein activity.Various types ofprotein modification,such as phosphorylation,methylation,acetylation,myristoylation,glycosylation,and ubiquitina-tion,have been reported.Among them,ubiquitination distinguishes itself from others in that most of the ubiquitinatedproteins are targeted to the 26S proteasome for degradation.The ubiquitin/26S proteasome system constitutes the majorprotein degradation pathway in the cell.In recent years,the importance of the ubiquitination machinery in the controlof numerous eukaryotic cellular functions has been increasingly appreciated.Increasing number of E3 ubiquitin ligasesand their substrates,including a variety of essential cellular regulators have been identified.Studies in the past severalyears have revealed that the ubiquitination system is important for a broad range of plant developmental processes andresponses to abiotic and biotic stresses.This review discusses recent advances in the functional analysis of ubiquitina-tion-associated proteins from plants and pathogens that play important roles in plant-microbe interactions.     

Cullin-containing E3 ubiquitin ligases in plant development

In eukaryotes, the ubiquitin-proteasome system participates in the control of signal transduction events by selectively eliminating regulatory proteins. E3 ubiquitin ligases specifically bind degradation substrates and mediate their poly-ubiquitylation, a prerequisite for their degradation by the 26S proteasome. On the basis of the analysis of the Arabidopsis genome sequence, it is predicted that there are more than 1000 E3 ubiquitin ligases in plants. Several types of E3 ubiquitin ligases have already been characterized in eukaryotes. Recently, some of these E3 enzymes have been implicated in specific plant signaling pathways.     

PHOR1: A U-Box GA Signaling Component With a Role in Proteasome Degradation?

Recent identification of U-box proteins as E3 ubiquitin ligases suggests that the U-box arm-repeat protein PHOR1, for which we have demonstrated a role in GA signal transduction, may play a role in GA signaling by ubiquitinating one or more components of the GA response pathway to target them for proteasome degradation. Here we show that PHOR1 function in GA signaling is not exclusive of potato plants, but it is also conserved in Arabidopsis. Three PHOR1-homologs have been identified in this plant species, which would correspond to PHOR1-orthologs. Experimental evidence has recently been obtained for the involvement of proteasome-dependent protein degradation in GA-mediated destabilization of the SLN1 DELLA protein, thus pointing to this repressor as a likely substrate for ubiquitination by the PHOR1 ubiquitin ligase activity.     

Plant ubiquitylation and proteolytic systems, the key elements in hormonal signaling pathways

The general function of the ubiquitylation systems is to conjugate ubiquitin to lysine residues within substrate proteins, thus targeting them for degradation by the proteasome. In Arabidopsis thaliana more than 1300 genes (approximately 5% of the proteome) encode components of the ubiquitin/26S proteasome pathway. Approximately 90% of these genes encode subunits of the E3 ubiquitin ligases, which confer substrate specificity to the ubiquitin/26S proteasome pathway. The plant E3 ubiquitin ligases comprise a large and diverse family of proteins or protein complexes containing either a HECT domain, a RING-finger or U-box domain. The SCF class of E3 ligases is the most thoroughly studied in plants because some of them participate in regulation of hormone signaling pathways. The role of the SCF is to ubiquitylate repressors of hormone response (auxin, gibberellins), whereas in response to ethylene, abscisic acid and brassinosteroids the SCF participate in degradation of positive regulators in the absence of the hormone.     

泛素化在植物抗病中的作用

泛素化作为植物体内一种广泛存在的调控细胞反应的机制,参与调控植物抗病反应。本文综述了泛素化系统在植物抗病反应中的功能及作用机制,重点介绍了CRLs型E3泛素连接酶和RING/U-box型E3泛素连接酶如何参与调控植物抗病信号途径,以及病原物通过效应蛋白和毒性因子调控植物抗病性的分子机理,为阐明植物抗病机理和植物病害防治方法提供参考。     

Identification of ubiquitinated proteins in Arabidopsis

Ubiquitin (Ub) is a small peptide that is covalently attached to proteins in a posttranslational reaction. Ubiquitination is a precise regulatory system that is present in all eukaryotic organisms and regulates the stability, the activity, the localization and the transport of proteins. Ubiquitination involves different enzymatic activities, in which the E3 ligases catalyze the last step recruiting of the target for labelling with ubiquitin. Genomic analyses have shown that the ubiquitin-proteasome system involves a large number of proteins in plants, as approximately 5% of the total protein belongs to this pathway. In contrast to the high number of E3 ligases of ubiquitin identified, very few proteins regulated by ubiquitination have been described. To solve this, we have undertaken a new proteomic approach aimed to identify proteins modified with ubiquitin. This is based on affinity purification and identification for ubiquitinated proteins using the ubiquitin binding domain (UBA) polypeptide of the P62 protein attached to agarose beads. This P62-agarose matrix is capable of specifically binding ubiquitinated proteins. These bound proteins were digested with trypsin and the peptides separated by HPLC chromatography, spotted directly onto a MALDI target and analyzed by MALDI-TOF/TOF off-line coupled LC/MALDI-MS/MS. A total of 200 putative ubiquitinated proteins were identified. From these we found that several of the putative targets were already described in plants, as well as in other organisms, as ubiquitinated proteins. In addition, we have found that some of these proteins were indeed modified with ubiquitin in vivo. Taken together, we have shown that this approach is useful for identifying ubiquitinated protein in plants.     

Type III secretion effectors of the IpaH family are E3 ubiquitin ligases

Many bacteria pathogenic for plants or animals, including Shigella spp., which is responsible for shigellosis in humans, use a type III secretion apparatus to inject effector proteins into host cells. Effectors alter cell signaling and host responses induced upon infection; however, their precise biochemical activities have been elucidated in very few cases. Utilizing Saccharomyces cerevisiae as a surrogate host, we show that the Shigella effector IpaH9.8 interrupts pheromone response signaling by promoting the proteasome-dependent destruction of the MAPKK Ste7. In vitro, IpaH9.8 displayed ubiquitin ligase activity toward ubiquitin and Ste7. Replacement of a Cys residue that is invariant among IpaH homologs of plant and animal pathogens abolished the ubiquitin ligase activity of IpaH9.8. We also present evidence that the IpaH homolog SspH1 from Salmonella enterica can ubiquitinate ubiquitin and PKN1, a previously identified SspH1 interaction partner. This study assigns a function for IpaH family members as E3 ubiquitin ligases.     

U-box泛素连接酶调控植物抗逆和生长发育

泛素化是真核生物蛋白质转录后修饰的重要方式之一。泛素连接酶决定了泛素化过程底物的特异性, 在植物抗病、抗旱、耐盐、抗寒和生长发育各个阶段都发挥重要作用。泛素连接酶包括RING、U-box、HECT和F-box四大类。该文对U-box泛素连接酶在植物抗逆和生长发育过程中的作用进行了总结, 并对今后的研究提出了建议, 以期为进一步了解植物泛素化调控通路提供依据。     

Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison

The conjugation of the small ubiquitin-related modifier, SUMO, to substrate proteins is a reversible and dynamic process, and an important response of plants to environmental challenges. Nevertheless, reliable data have so far been restricted largely to the model plant Arabidopsis thaliana. The increasing availability of genome information for other plant species offers the possibility to identify a core set of indispensable components, and to discover species-specific features of the sumoylation pathway. We analyzed the enzymes responsible for the conjugation of SUMO to substrates for their conservation between dicots and monocots. We thus assembled gene sets that relate the Arabidopsis SUMO conjugation system to that of the dicot species tomato, grapevine and poplar, and to four plant species from the monocot class: rice, Brachypodium distachyon, Sorghum bicolor and maize. We found that a core set of genes with clear assignment in Arabidopsis had highly conserved homologs in all tested plants. However, we also observed a variation in the copy number of homologous genes, and sequence variations that suggested monocot-specific variants. Generally, SUMO ligases and proteases showed the most pronounced differences. Finally, we identified potential SUMO chain-binding ubiquitin ligases, pointing to an in vivo function of SUMO chains as degradation signals in plants.     

The Arabidopsis DDB1 interacting protein WDR55 is required for vegetative development

The CULLIN family of E3 ubiquitin ligases are important regulators of plant development and function. A newly identified class of CULLIN4-RING-E3 ligases (CRL4s) interacts with substrate receptors referred to as DDB1-CUL4 ASSOCIATED FACTORS (DCAFs) via a DDB1 linker protein. We have previously reported that the WD40 protein WDR55 interacts with DDB1A and is thus a putative DCAF. Mutants of WDR55 are embryo lethal, suggesting that a DDB1^WDR55 complex could regulate embryo and endosperm development. Here we report that a weak allele homozygous for wdr55 display pleiotropic phenotypes in the seedling and adult stages, suggesting a novel regulatory role for WDR55 in vegetative development.     

PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues

The gene PRT1 of Arabidopsis, encoding a 45-kD protein with two RING finger domains, is essential for the degradation of F-dihydrofolate reductase, a model substrate of the N-end rule pathway of protein degradation. We have determined the function of PRT1 by expression in yeast (Saccharomyces cerevisiae). PRT1 can act as a ubiquitin protein ligase in the heterologous host. The identified substrates of PRT1 have an aromatic residue at their amino-terminus, indicating that PRT1 mediates degradation of N-end rule substrates with aromatic termini but not of those with aliphatic or basic amino-termini. Expression of model substrates in mutant and wild-type plants confirmed this substrate specificity. A ligase activity exclusively devoted to aromatic amino-termini of the N-end rule pathway is apparently unique to plants. The results presented also imply that other known substrates of the plant N-end rule pathway are ubiquitylated by one or more different ubiquitin protein ligases.     

A Competitive binding mechanism between Skp1 and exportin 1 (CRM1) controls the localization of a subset of F-box proteins

SCF-type E3 ubiquitin ligases are crucial regulators of cell cycle progression. As the F-box protein is the substrate-specifying subunit of this family of ligases, their availability dictates the timing and the location of the ubiquitination of substrates. We report here our investigation into the regulation of the localization of F-box proteins, in particular Fbxo7, whose mislocalization is associated with human disease. We identified a motif in Fbxo7 that we have characterized as a functional leucine-rich nuclear export sequence (NES), and which allowed binding to the nuclear export protein, exportin 1 (CRM1). Unusually, the NES was embedded within the F-box domain, which is bound by Skp1 and enables the F-box protein to form part of an E3 ubiquitin ligase. The NES of Fbxo7 controlled its localization and was conserved in Fbxo7 homologues in other species. Skp1 binding prevented Fbxo7 from contacting CRM1. We propose that this competitive binding allowed Fbxo7 to accumulate within the nucleus starting at the G1/S transition. More than ten other F-box proteins also contain an NES at the same location in their F-box domains, indicating that this competitive binding mechanism may contribute to the regulation of a sixth of the known F-box proteins.     

A plant‐specific in vitro ubiquitination analysis system

Protein ubiquitination requires the concerted action of three enzymes: ubiquitin‐activating enzyme (E1), ubiquitin‐conjugating enzyme (E2) and ubiquitin ligase (E3). These ubiquitination enzymes belong to an abundant protein family that is encoded in all eukaryotic genomes. Describing their biochemical characteristics is an important part of their functional analysis. It has been recognized that various E2/E3 specificities exist, and that detection of E3 ubiquitination activity in vitro may depend on the recruitment of E2s. Here, we describe the development of an in vitro ubiquitination system based on proteins encoded by genes from Arabidopsis. It includes most varieties of Arabidopsis E2 proteins, which are tested with several RING‐finger type E3 ligases. This system permits determination of E3 activity in combination with most of the E2 sub‐groups that have been identified in the Arabidopsis genome. At the same time, E2/E3 specificities have also been explored. The components used in this system are all from plants, particularly Arabidopsis, making it very suitable for ubiquitination assays of plant proteins. Some E2 proteins that are not easily expressed in Escherichia coli were transiently expressed and purified from plants before use in ubiquitination assays. This system is also adaptable to proteins of species other than plants. In this system, we also analyzed two mutated forms of ubiquitin, K48R and K63R, to detect various types of ubiquitin conjugation.     

Translational suppression of atrophic regulators by microRNA-23a integrates resistance to skeletal muscle atrophy

Muscle atrophy is caused by accelerated protein degradation and occurs in many pathological states. Two muscle-specific ubiquitin ligases, MAFbx/atrogin-1 and muscle RING-finger 1 (MuRF1), are prominently induced during muscle atrophy and mediate atrophy-associated protein degradation. Blocking the expression of these two ubiquitin ligases provides protection against muscle atrophy. Here we report that miR-23a suppresses the translation of both MAFbx/atrogin-1 and MuRF1 in a 3'-UTR-dependent manner. Ectopic expression of miR-23a is sufficient to protect muscles from atrophy in vitro and in vivo. Furthermore, miR-23a transgenic mice showed resistance against glucocorticoid-induced skeletal muscle atrophy. These data suggest that suppression of multiple regulators by a single miRNA can have significant consequences in adult tissues.     

Overexpression of a Soybean Ariadne-Like Ubiquitin Ligase Gene GmARI1 Enhances Aluminum Tolerance in Arabidopsis

Ariadne (ARI) subfamily of RBR (Ring Between Ring fingers) proteins have been found as a group of putative E3 ubiquitin ligases containing RING (Really Interesting New Gene) finger domains in fruitfly, mouse, human and Arabidopsis. Recent studies showed several RING-type E3 ubiquitin ligases play important roles in plant response to abiotic stresses, but the function of ARI in plants is largely unknown. In this study, an ariadne-like E3 ubiquitin ligase gene was isolated from soybean, Glycine max (L.) Merr., and designated as GmARI1. It encodes a predicted protein of 586 amino acids with a RBR supra-domain. Subcellular localization studies using Arabidopsis protoplast cells indicated GmARI protein was located in nucleus. The expression of GmARI1 in soybean roots was induced as early as 2–4 h after simulated stress treatments such as aluminum, which coincided with the fact of aluminum toxicity firstly and mainly acting on plant roots. In vitro ubiquitination assay showed GmARI1 protein has E3 ligase activity. Overexpression of GmARI1 significantly enhanced the aluminum tolerance of transgenic Arabidopsis. These findings suggest that GmARI1 encodes a RBR type E3 ligase, which may play important roles in plant tolerance to aluminum stress.