Tamar Ziv

A novel site for ubiquitination: the N-terminal residue, and not internal lysines of MyoD, is essential for conjugation and degradation of the protein.

The ubiquitin proteolytic pathway is a major system for selective protein degradation in eukaryotic cells. One of the first steps in the degradation of a protein via this pathway involves selective modification of ϵ‐NH2 groups of internal lysine residues by ubiquitination. To date, this amino group has been the only known target for ubiquitination. Here we report that the N‐terminal residue of MyoD is sufficient and necessary for promotion of conjugation and subsequent degradation of the protein. Substitution of all lysine residues in the protein did not affect significantly its conjugation and degradation either in vivoor in vitro. In cells, degradation of the lysine‐less protein is inhibited by the proteasome inhibitors MG132 and lactacystin. Inhibition is accompanied by accumulation of high molecular mass ubiquitinated forms of the modified MyoD. In striking contrast, wild‐type MyoD, in which all the internal Lys residues have been retained but the N‐terminus has been extended by fusion of a short peptide, is stable both in vivo and in vitro. In a cell‐free system, ATP and multiple ubiquitination are essential for degradation of the lysine‐less protein. Specific chemical modifications have yielded similar results. Selective blocking of the α‐NH2 group of wild‐type protein renders it stable, while modification of the internal Lys residues with preservation of the free N‐terminal group left the protein susceptible to degradation. Our data suggest that conjugation of MyoD occurs via a novel modification involving attachment of ubiquitin to the N‐terminal residue. The polyubiquitin chain is then synthesized on an internal Lys residue of the linearly attached first ubiquitin moiety.

The Polycomb Protein Ring1B Generates Self Atypical Mixed Ubiquitin Chains Required for Its In Vitro Histone H2A Ligase Activity

Polycomb complexes mediate gene silencing, in part by modifying histones. Ring1B and Bmi1 are RING finger proteins that are members of the Polycomb repressive complex 1 (PRC1). Ring1B is an E3 that mediates its own polyubiquitination and monoubiquitination of histone H2A. In contrast, Bmi1 has no self-ubiquitinating activity. We show that unlike other RING finger proteins that are believed to mediate their own ubiquitination and degradation, Ring1B and Bmi1 are degraded by an exogenous E3, independent of their RING domain. The RING domains of both proteins mediate their association and subsequent stabilization. Consistent with the nonproteolytic self-ligase activity of Ring1B, it generates atypical mixed K6-, K27-, and K48-based polyubiquitin chains, which require the presence of all these lysine residues on the same ubiquitin molecule. The modification is required for Ring1B ability to monoubiquitinate H2A in vitro, unraveling an as yet undescribed mechanism for ligase activation via noncanonical self-ubiquitination.

The E2 ubiquitin conjugating enzymes direct polyubiquitination to preferred lysines

The ubiquitin-proteasome pathway plays a crucial role in many cellular processes by degrading substrates tagged by polyubiquitin chains, linked mostly through lysine 48 of ubiquitin. Although polymerization of ubiquitin via its six other lysine residues exists in vivo as part of various physiological pathways, the molecular mechanisms that determine the type of polyubiquitin chains remained largely unknown. We undertook a systematic, in vitro, approach to evaluate the role of E2 enzymes in determining the topology of polyubiquitin. Because this study was performed in the absence of an E3 enzyme, our data indicate that the E2 enzymes are capable of directing the ubiquitination process to distinct subsets of ubiquitin lysines, depending on the specific E2 utilized. Moreover, our findings are in complete agreement with prior analyses of lysine preference assigned to certain E2s in the context of E3 (in vitro and in vivo). Finally, our findings support the rising notion that the functional unit of E2 is a dimer. To our knowledge, this is the first systematic indication for the involvement of E2 enzymes in specifying polyubiquitin chain assembly.

Metabolic Turnover of Synaptic Proteins: Kinetics, Interdependencies and Implications for Synaptic Maintenance

Chemical synapses contain multitudes of proteins, which in common with all proteins, have finite lifetimes and therefore need to be continuously replaced. Given the huge numbers of synaptic connections typical neurons form, the demand to maintain the protein contents of these connections might be expected to place considerable metabolic demands on each neuron. Moreover, synaptic proteostasis might differ according to distance from global protein synthesis sites, the availability of distributed protein synthesis facilities, trafficking rates and synaptic protein dynamics. To date, the turnover kinetics of synaptic proteins have not been studied or analyzed systematically, and thus metabolic demands or the aforementioned relationships remain largely unknown. In the current study we used dynamic Stable Isotope Labeling with Amino acids in Cell culture (SILAC), mass spectrometry (MS), Fluorescent Non–Canonical Amino acid Tagging (FUNCAT), quantitative immunohistochemistry and bioinformatics to systematically measure the metabolic half-lives of hundreds of synaptic proteins, examine how these depend on their pre/postsynaptic affiliation or their association with particular molecular complexes, and assess the metabolic load of synaptic proteostasis. We found that nearly all synaptic proteins identified here exhibited half-lifetimes in the range of 2–5 days. Unexpectedly, metabolic turnover rates were not significantly different for presynaptic and postsynaptic proteins, or for proteins for which mRNAs are consistently found in dendrites. Some functionally or structurally related proteins exhibited very similar turnover rates, indicating that their biogenesis and degradation might be coupled, a possibility further supported by bioinformatics-based analyses. The relatively low turnover rates measured here (∼0.7% of synaptic protein content per hour) are in good agreement with imaging-based studies of synaptic protein trafficking, yet indicate that the metabolic load synaptic protein turnover places on individual neurons is very substantial.

Analysis of endogenous peptides bound by soluble MHC class I molecules: a novel approach for identifying tumor‐specific antigens

The Human MHC Project aims at comprehensive cataloging of peptides presented within the context of different human leukocyte antigens (HLA) expressed by cells of various tissue origins, both in health and in disease. Of major interest are peptides presented on cancer cells, which include peptides derived from tumor antigens that are of interest for immunotherapy. Here, HLA‐restricted tumor‐specific antigens were identified by transfecting human breast, ovarian and prostate tumor cell lines with truncated genes of HLA‐A2 and HLA‐B7. Soluble HLA secreted by these cell lines were purified by affinity chromatography and analyzed by nano‐capillary electrospray ionization‐tandem mass spectrometry. Typically, a large peptide pool was recovered and sequenced including peptides derived from MAGE‐B2 and mucin and other new tumor‐derived antigens that may serve as potential candidates for immunotherapy.

Nanofibers made of globular proteins.

Strong nanofibers composed entirely of a model globular protein, namely, bovine serum albumin (BSA), were produced by electrospinning directly from a BSA solution without the use of chemical cross-linkers. Control of the spinnability and the mechanical properties of the produced nanofibers was achieved by manipulating the protein conformation, protein aggregation, and intra/intermolecular disulfide bonds exchange. In this manner, a low-viscosity globular protein solution could be modified into a polymer-like spinnable solution and easily spun into fibers whose mechanical properties were as good as those of natural fibers made of fibrous protein. We demonstrate here that newly formed disulfide bonds (intra/intermolecular) have a dominant role in both the formation of the nanofibers and in providing them with superior mechanical properties. Our approach to engineer proteins into biocompatible fibrous structures may be used in a wide range of biomedical applications such as suturing, wound dressing, and wound closure.

Proteomics of the response of Arabidopsis thaliana to infection with Alternaria brassicicola.

We have studied the proteome of the model plant Arabidopsis thaliana infected with a necrotrophic fungal pathogen, Alternaria brassicicola. The Arabidopsis-A. brassicicola host-pathogen pair is being developed as a model genetic system for incompatible plant-fungal interactions, in which the spread of disease is limited by plant defense responses. After confirming that a defense response was induced at the transcriptional level, we identified proteins whose abundance on 2-DE gels increased or decreased in infected leaves. At least 11 protein spots showed reproducible differences in abundance, increasing or decreasing during the progress of the infection. The pathogenesis-related protein PR4, a glycosyl hydrolase, and the antifungal protein osmotin are strongly up-regulated. Two members of the Arabidopsis glutathione S-transferase (GST) family increased in abundance in infected leaves. The spots in which these GST proteins were identified contain additional members of the GST family. Representation of GST family members in several protein spots migrating at similar molecular weight suggests post-translational modifications. The signature of GST regulation may be specific for the type of plant-pathogen interaction. The proteomic view of the defense response to A. brassicicola can be compared with other types of plant-pathogen interactions, and to leaf senescence, identifying unique regulatory patterns.

Autophosphorylation restrains the apoptotic activity of DRP‐1 kinase by controlling dimerization and calmodulin binding

DRP‐1 is a pro‐apoptotic Ca2+/calmodulin (CaM)‐regulated serine/threonine kinase, recently isolated as a novel member of the DAP‐kinase family of proteins. It contains a short extra‐catalytic tail required for homodimerization. Here we identify a novel regulatory mechanism that controls its pro‐apoptotic functions. It comprises a single autophosphorylation event mapped to Ser308 within the CaM regulatory domain. A negative charge at this site reduces both the binding to CaM and the formation of DRP‐1 homodimers. Conversely, the dephosphorylation of Ser308, which takes place in response to activated Fas or tumour necrosis factor‐α death receptors, increases the formation of DRP‐1 dimers, facilitates the binding to CaM and activates the pro‐apoptotic effects of the protein. Thus, the process of enzyme activation is controlled by two unlocking steps that must work in concert, i.e. dephosphorylation, which probably weakens the electrostatic interactions between the CaM regulatory domain and the catalytic cleft, and homodimerization. This mechanism of negative autophosphorylation provides a safety barrier that restrains the killing effects of DRP‐1, and a target for efficient activation of the kinase by various apoptotic stimuli.

Comparative proteomics of the developing fish (zebrafish and gilthead seabream) oocytes.

The maturation process of fish oocytes involves both protein biosynthesis within the oocytes and uptake from the plasma. To follow the changes in the proteins repertoires of fish oocytes during maturation, we performed a large-scale proteomics analysis using one and two-dimensional electrophoresis, multi-dimensional protein identification technology (MudPIT) and tandem mass-spectrometry. A large number of proteins were identified and a map of the vitellogenin derived yolk proteins; lipovitellin and phosvitin, was established (the vitellogenin map), reflecting the posttranslational processing of the different vitellogenins gene-products and their accumulation. Such protein patterns are potentially useful for molecular staging and for quality-control of maturing oocytes. Furthermore, proteomics analyses of single oocytes were used to demonstrate molecular variability between morphologically similar oocytes of same or different fish specimens. Proteins of interest detected in this study include proteins that may serve as maternal factors, such as TCP1, serpin A1 and importin alpha1. The large similarity between the proteins repertoires of fish oocytes and other species, such as mammals and insects, demonstrate the evolutionary conservation of oocyte maturation across diverse species gap.

E3 Ligases Determine Ubiquitination Site and Conjugate Type by Enforcing Specificity on E2 Enzymes

Ubiquitin-conjugating enzymes (E2s) have a dominant role in determining which of the seven lysine residues of ubiquitin is used for polyubiquitination. Here we show that tethering of a substrate to an E2 enzyme in the absence of an E3 ubiquitin ligase is sufficient to promote its ubiquitination, whereas the type of the ubiquitin conjugates and the identity of the target lysine on the substrate are promiscuous. In contrast, when an E3 enzyme is introduced, a clear decision between mono- and polyubiquitination is made, and the conjugation type as well as the identity of the target lysine residue on the substrate becomes highly specific. These features of the E3 can be further regulated by auxiliary factors as exemplified by MDMX (Murine Double Minute X). In fact, we show that this interactor reconfigures MDM2-dependent ubiquitination of p53. Based on several model systems, we propose that although interaction with an E2 is sufficient to promote substrate ubiquitination the E3 molds the reaction into a specific, physiologically relevant protein modification.