The covalent attachment of ubiquitin is an important determinant for selective protein degradation by the 26S proteasome in plants and animals. The specificity of ubiquitination is often controlled by ubiquitin-protein ligases (or E3s), which facilitate the transfer of ubiquitin to appropriate targets. One ligase type, the SCF E3s are composed of four proteins, cullin1͞Cdc53, Rbx1͞Roc1͞Hrt1, Skp1, and an F-box protein. The F-box protein, which identifies the targets, binds to the Skp1 component of the complex through a degenerate N-terminal Ϸ60-aa motif called the F-box. Using published F-boxes as queries, we have identified 694 potential F-box genes in Arabidopsis, making this gene superfamily one of the largest currently known in plants. Most of the encoded proteins contain interaction domains C-terminal to the F-box that presumably participate in substrate recognition. The F-box proteins can be classified via a phylogenetic approach into five major families, which can be further organized into multiple subfamilies. Sequence diversity within the subfamilies suggests that many F-box proteins have distinct functions and͞or substrates. Representatives of all of the major families interact in yeast two-hybrid experiments with members of the Arabidopsis Skp family supporting their classification as F-box proteins. For some, a limited preference for Skps was observed, suggesting that a hierarchical organization of SCF complexes exists defined by distinct Skp͞F-box protein pairs. Collectively, the data shows that Arabidopsis has exploited the SCF complex and the ubiquitin͞26S proteasome pathway as a major route for cellular regulation and that a diverse array of SCF targets is likely present in plants.
SummaryAttachment of one or more ubiquitins (Ubs) to various intracellular proteins has a number of roles in plants including the selective removal of regulatory proteins by the 26S proteasome. The ®nal step in this modi®cation is performed by ubiquitin-protein ligases (E3s) that promote Ub transfer to appropriate targets. One important family of E3s is de®ned by the presence of a HECT domain, an active site ®rst found at the C-terminus of the human E3 (E6-AP). Using a consensus HECT domain as the query, we identi®ed a family of seven HECT-containing ubiquitin-protein ligases (UPL1±UPL7) in Arabidopsis thaliana that can be grouped into four subfamilies. The UPL3 and UPL4 subfamily encodes approximately 200-kDa proteins with four Armadillo repeats similar to those in the nuclear pore protein importin-a, suggesting that these E3s identify their targets through binding to nuclear localization sequences. Although T-DNA disruptions of the UPL3 locus do not affect overall growth and development of Arabidopsis, the mutants show aberrant trichome morphology. Instead of developing three branches, many upl3 trichomes contain ®ve or more branches. The upl3 trichomes also often undergo an additional round of endoreplication resulting in enlarged nuclei with ploidy levels of up to 64C. upl3 plants are hypersensitive to gibberellic acid-3 (GA 3 ), consistent with the role of gibberellins in trichome development. The phenotype of upl3 mutants is similar to that of kaktus, a previously described set of trichome mutants with supernumerary branches. Genetic analyses con®rmed that upl3 mutants and kaktus-2 are allelic with kaktus-2 plants harboring a splice-site mutation within the UPL3-transcribed region. Collectively, the data indicate that the ubiquitination of one or more activator proteins by UPL3 is necessary to repress excess branching and endoreplication of Arabidopsis trichomes.
The concept that plants exploit polypeptides as post-translational modifiers is rapidly emerging as an important method to manipulate various cellular processes. The best known is Ub (ubiquitin) that serves as reusable tag for selective protein degradation by the 26 S proteasome and for endosomal trafficking. Genomic analyses indicate that Ub pathway alone comprises over 6% of the Arabidopsis proteome with thousands of proteins being targets. Consequently, this pathway influences much of plant biology. Others tags include RUB-1 (related to Ub-1; also known as NEDD8), SUMO (small Ub-like modifier), ATG-8 (autophagy-8) and ATG-12, UFM-1 (Ub-fold modifier-1) and HUB-1 (homology to Ub-1). Preliminary studies indicate that these tags have much more limited sets of targets and provide more specialized functions, including transcriptional regulation, protein localization, autophagic turnover and antagonizing the effects of Ub. On the basis of their widespread distribution and pervasive functions, peptide tags can now be considered as prime players in plant cell regulation.
Ubiquitin (Ub)-fold proteins are rapidly emerging as an important class of eukaryotic modifiers, which often exert their influence by post-translational addition to other intracellular proteins. Despite assuming a common -grasp threedimensional structure, their functions are highly diverse because of distinct surface features and targets and include tagging proteins for selective breakdown, nuclear import, autophagic recycling, vesicular trafficking, polarized morphogenesis, and the stress response. Here we describe a novel family of Membrane-anchored Ub-fold (MUB) proteins that are present in animals, filamentous fungi, and plants. Extending from the C terminus of the Ub-fold is typically a cysteinecontaining CAAX (where A indicates aliphatic amino acid) sequence that can direct the attachment of either a 15-carbon farnesyl or a 20-carbon geranylgeranyl moiety in vitro. Modified forms of several MUBs were detected in transgenic Arabidopsis thaliana, suggesting that these MUBs are prenylated in vivo. Both cell fractionation and confocal microscopic analyses of Arabidopsis plants expressing GFP-MUB fusions showed that the modified forms are membrane-anchored with a significant enrichment on the plasma membrane. This plasma membrane location was blocked in vivo in prenyltransferase mutants and by mevinolin, which inhibits the synthesis of prenyl groups. In addition to the five MUBs with CAAX boxes, Arabidopsis has one MUB variant with a cysteine-rich C terminus distinct from the CAAX box that is also membrane-anchored, possibly through the attachment of a long chain acyl group. Although the physiological role(s) of MUBs remain unknown, the discovery of these prenylated forms further expands the diversity and potential functions of Ub-fold proteins in eukaryotic biology.The superfamily of ubiquitin (Ub) 4 -type proteins has emerged over the last decade as an influential set of post-translational modifiers in eukaryotes. These small proteins (ϳ75-180 amino acids) contain a signature -grasp (or Ub-fold) core domain, created by an ␣-helix transversing a groove created by an arched four-strand -sheet (1). Extending from the core is a short flexible C-terminal extension that enables their attachment to other molecules through the terminal carboxyl group. The first and best-known member of this family is Ub (2, 3). It functions by becoming ligated to other proteins through an isopeptide bond between the C-terminal glycine of Ub and free lysine ⑀-amino groups in the target. The main role of Ub is to direct selective proteolysis by assembling chains of Ub monomers linked internally through Lys-48 onto various target proteins to promote their recognition by the 26 S proteasome. Others include roles in DNA repair via attachment of Lys-63-linked chains and endomembrane trafficking, transcription, and chromatin remodeling via attachment of Ub monomers (2, 3).Since the discovery of Ub, a number of related modifiers have been found, including Related to Ub-1 (RUB1 or NEDD8), Small-Ub-like Modifier (SUMO), Autophagy (ATG)-8 an...
Expansin proteins are essential components of acid-induced cell wall loosening in plants. -Expansins, which constitute a subfamily of related expansin proteins, include the group I grass pollen allergens. To provide a better description of -expansin expression, we have characterized a cytokinin-inducible -expansin from soybean (Glycine max cv Mandarin) called Cim1. Our results demonstrate that the hormones cytokinin and auxin act synergistically to induce the accumulation and proteolytic processing of Cim1. Carboxyl terminal truncation of a 35-kD form of Cim1 is predicted to remove the putative cellulose binding domain from the amino terminal cysteine-rich domain, resulting in a 20-kD form of the protein. Furthermore, the identical amino termini of the 35-and 20-kD forms of Cim1 correspond to a position 11 amino acids downstream of the predicted signal sequence cleavage site, suggesting proteolysis of a short amino terminal propeptide after removal of the signal peptide. This propeptide fragment contains a consensus site for N-glycosylation and our data suggest that it is glycosylated by a tunicamycin-sensitive mechanism in cultured soybean cells. The onset of Cim1 expression correlates with increased growth of soybean cultures. Ultimately, Cim1 is rapidly and specifically proteolyzed as soybean cultures reach stationary phase. These findings are consistent with the hypothesis that -expansin proteins are extensively modified by post-translational N-glycosylation and proteolysis.
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