EBS7 is a plant-specific component of a highly conserved endoplasmic reticulum-associated degradation system in Arabidopsis

Endoplasmic reticulum (ER)-associated degradation (ERAD) is an essential part of an ER-localized protein quality-control system for eliminating terminally misfolded proteins. Recent studies have demonstrated that the ERAD machinery is conserved among yeast, animals, and plants; however, it remains unknown if the plant ERAD system involves plant-specific components. Here we report that the Arabidopsis ethyl methanesulfonate-mutagenized brassinosteroid-insensitive 1 suppressor 7 (EBS7) gene encodes an ER membrane-localized ERAD component that is highly conserved in land plants. Loss-of-function ebs7 mutations prevent ERAD of brassinosteroid insensitive 1-9 (bri1-9) and bri1-5, two ER-retained mutant variants of the cell-surface receptor for brassinosteroids (BRs). As a result, the two mutant receptors accumulate in the ER and consequently leak to the plasma membrane, resulting in the restoration of BR sensitivity and phenotypic suppression of the bri1-9 and bri1-5 mutants. EBS7 accumulates under ER stress, and its mutations lead to hypersensitivity to ER and salt stresses. EBS7 interacts with the ER membrane-anchored ubiquitin ligase Arabidopsis thaliana HMG-CoA reductase degradation 1a (AtHrd1a), one of the central components of the Arabidopsis ERAD machinery, and an ebs7 mutation destabilizes AtHrd1a to reduce polyubiquitination of bri1-9. Taken together, our results uncover a plant-specific component of a plant ERAD pathway and also suggest its likely biochemical function.Endoplasmic reticulum (ER)-associated degradation (ERAD) is an integral part of an ER-mediated protein quality-control system in eukaryotes, which permits export of only correctly folded proteins but retains misfolded proteins in the ER for repair via additional folding attempts or removal through ERAD. Genetic and biochemical studies in yeast and mammalian cells have revealed that the core ERAD machinery is highly conserved between yeast and mammals and that ERAD involves four tightly coupled steps: substrate selection, retrotranslocation through the ER membrane, ubiquitination, and proteasome-mediated degradation (1, 2).Because the great majority of secretory/membrane proteins are glycosylated in the ER, diversion of most ERAD substrates from their futile folding cycles into ERAD is initiated through progressive mannose trimming of their asparagine-linked glycans (N-glycans) by ER/Golgi-localized class I mannosidases, including homologous to α-mannosidase 1 (Htm1) and its mammalian homologs ER degradation-enhancing α-mannosidase-like proteins (EDEMs) (3). The processed glycoproteins are captured by two ER resident proteins, yeast amplified in osteosarcoma 9 (OS9 in mammals) homolog (Yos9) and HMG-CoA reductase degradation 3 (Hrd3) [suppressor/enhancer of Lin-12–like (SEL1L) in mammals], which recognize the mannose-trimmed N-glycans and surface-exposed hydrophobic amino acid residues, respectively (4, 5). The selected ERAD clients are delivered to an ER membrane-anchored ubiquitin ligase (E3), which is the core component of the ERAD machinery (6), for polyubiquitination. Yeast has two known ERAD E3 ligases, Hrd1 and degradation of alpha 10 (Doa10), both containing a catalytically active RING finger domain, whereas mammals have a large collection of ER membrane-anchored E3 ligases, including Hrd1 and gp78 (7). The yeast Hrd1/Doa10-containing ERAD complexes target different substrates, with the former ubiquitinating substrates with misfolded transmembrane or luminal domains and the latter acting on clients with cytosolic structural lesions (8).Because of the cytosolic location of the E3′s catalytic domain and proteasome, all ERAD substrates must retrotranslocate through the ER membrane. It is well known that the retrotranslocation step is tightly coupled with substrate ubiquitination and is powered by an AAA-type ATPase, cell division cycle 48 (Cdc48) in yeast and p97 in mammals. However, the true identity of the retrotranslocon remains controversial. Earlier studies implicated the secretory 61 (Sec61) translocon, degradation in the endoplasmic reticulum 1 (Der1) [Der1-like proteins (Derlins) in mammals], and Hrd1 in retrotranslocating ERAD substrates (9). After retrotranslocation, ubiquitinated ERAD clients are delivered to the cytosolic proteasome with the help of Cdc48/p97 and their associated factors for proteolysis (10). In addition to the above-mentioned proteins, the yeast/mammalian ERAD systems contain several other components, including several ubiquitin-conjugating enzymes (E2), a membrane-anchored E2-recruiting factor, Cue1 that has no mammalian homolog, a scaffold protein U1-Snp1–associating 1 (Usa1) [homocysteine-induced ER protein (HERP) in mammals] of the E3 ligases, and a membrane-anchored Cdc48-recruiting factor, Ubx2 (Ubxd8 in mammals) (6).For many years ERAD has been known to operate in plants (11), but the research on the plant ERAD pathway lagged far behind similar studies in yeast and mammalian systems. Recent molecular and genetic studies in the reference plant Arabidopsis, especially two Arabidopsis dwarf mutants, brassinosteroid-insensitive 1-5 (bri1-5) and bri1-9, carrying ER-retained mutant variants of the brassinosteroid receptor (BR) BRASSINOSTEROID-INSENSITIVE 1 (BRI1) (12–14), revealed that the ERAD system also is conserved in plants (reviewed in refs. 15 and 16). For example, the ERAD N-glycan signal to mark misfolded glycoproteins in Arabidopsis was found to be the same as that in yeast/mammalian cells (17, 18). Both forward and reverse genetic studies have shown that Arabidopsis homologs of the yeast/mammalian ERAD components, including Yos9/OS9 (19, 20), Hrd3/Sel1L (21, 22), Hrd1 (21), EDEMs (23), and a membrane-anchored E2 (24), are involved in degrading misfolded glycoproteins. However, it remains unknown if the plant ERAD requires one or more plant-specific components to degrade terminally misfolded proteins efficiently. In this study, we took a forward genetic approach to identify a novel Arabidopsis ERAD mutant, ethyl methanesulfonate-mutagenized bri1 suppressor 7 (ebs7), and subsequently cloned the corresponding EBS7 gene. We discovered that EBS7 encodes an ER-localized membrane protein that is highly conserved in land plants but lacks a homolog in yeast or mammals. Our biochemical studies strongly suggested that EBS7 plays a key role in an Arabidopsis ERAD process by regulating the protein stability of the Arabidopsis thaliana HRD1a (AtHrd1a).     

Role of RAG1 autoubiquitination in V(D)J recombination

The variable domains of Ig and T-cell receptor genes in vertebrates are assembled from gene fragments by the V(D)J recombination process. The RAG1–RAG2 recombinase (RAG1/2) initiates this recombination by cutting DNA at the borders of recombination signal sequences (RSS) and their neighboring gene segments. The RAG1 protein is also known to contain a ubiquitin E3 ligase activity, located in an N-terminal region that is not strictly required for the basic recombination reaction but helps to regulate recombination. The isolated E3 ligase domain was earlier shown to ubiquitinate one site in a neighboring RAG1 sequence. Here we show that autoubiquitination of full-length RAG1 at this specific residue (K233) results in a large increase of DNA cleavage by RAG1/2. A mutational block of the ubiquitination site abolishes this effect and inhibits recombination of a test substrate in mouse cells. Thus, ubiquitination of RAG1, which can be promoted by RAG1’s own ubiquitin ligase activity, plays a significant role in governing the level of V(D)J recombination activity.V(D)J recombination plays a central role in the production of antigen receptors by recombining V, D, and J gene segments from their genomic clusters to give rise to the highly varied populations of immunoglobulins and T-cell receptors (1). Recombination starts with the introduction of double-strand breaks by the RAG1/RAG2 protein complex at a pair of recombination signal sequences (RSS) (2, 3), distinguished by the length of the spacer DNA separating their conserved heptamer and nonamer elements. Recombination requires one RSS with a 12-base pair spacer and another with a 23-base pair spacer. Each pair of breaks is then processed by the nonhomologous DNA end-joining group of proteins to produce a junction of two segments of coding sequence (a coding joint) and a junction of the two RSSs (a signal joint) (4). The purified RAG1/2 protein complex displays the correct specificity for pairs of RSSs (5, 6), and has thus been used as a model for the initiation of V(D)J recombination. Until recently, the RAG proteins used for these studies have generally been minimal “core” regions of RAG1 and RAG2 (amino acids 384–1,008 of 1,040 in mouse RAG1 and 1–387 of 527 in RAG2), which are sufficient for specific binding and cleavage activity in a purified cell-free system. Ectopic expression of these truncated proteins supports V(D)J recombination in suitable cell lines, although with differences from the full-length proteins that will be discussed here.A complex composed of core RAG1 and RAG2 is more active than its full-length counterpart in cleavage of extrachromosomal substrates in a hamster cell line, but overall recombination is reported to be lower (7), indicating a defect in the stages of recombination subsequent to DNA cleavage. Similarly, mice or pre-B cells missing the RAG2 C-terminal noncore region are defective in the V to DJ recombination step of Ig heavy chain joining, although the earlier D to J joining step is normal (8). The mice also display an increased prevalence of lymphomas (9). A plant homeo domain (PHD) within the RAG2 C terminus is known to bind to chromatin, and specifically to histone 3 trimethylated on lysine 4 (H3K4me3), which is presumably an important step in directing RAG1/2 to loci bearing this “activating” modification (10). The lack of this domain may largely explain the defective functions of the RAG2 core protein. Similarly, although core RAG1 can support D to J rearrangement at the Ig heavy chain locus in RAG1^−/− pro-B cells, the level is reduced compared with that of full-length RAG1 (FLRAG1) (11), and deletions of certain smaller regions within the RAG1 N terminus have even greater effects (11). Some naturally occurring truncations of the RAG1 N terminus lead to human immunodeficiency (12). The functions of the parts of RAG1 and RAG2 outside of the catalytically essential cores have been reviewed (13). There is also evidence that the RAG1 and RAG2 C termini interact: DNA cleavage by RAG1/2 combinations containing both regions was greatly reduced but was restored upon addition of an H3K4me3-containing peptide (14). Relief of this autoinhibition may synergize with the chromatin-binding effect of the PHD domain to target recombination to the appropriate loci.The significant modulation of recombination in cells, and/or of DNA cleavage in vitro, by these “dispensable” regions of both RAG1 and RAG2 is further modified by covalent modifications of the proteins, which affect their stability or activity. RAG2 becomes phosphorylated at a specific site in its C terminus (T490) at the G1/S stage of the cell cycle, and is then ubiquitinated by the Skp2-SCF ubiquitin ligase, a central regulator of cell cycle progression, leading to its degradation in S phase (15, 16). Phosphorylation of RAG1 at residue S528 by the AMP-dependent protein kinase has also been described (17), in this case leading to increased activity of RAG1/2 both for cell-free DNA cleavage and for recombination in cells.The N terminus of RAG1 contains a Zn-binding motif (amino acids 264–389) that includes a C₃HC₄ RING (really interesting new gene) finger motif closely associated with an adjacent C₂H₂ Zn finger. This domain was shown to have ubiquitin ligase (E3) activity (18, 19), a common feature of RING finger domains, when combined with ubiquitin, the ubiquitin-activating (E1) enzyme, and an appropriate ubiquitin-conjugating (E2) enzyme. A naturally occurring human mutation in this RING finger motif (C328Y) was found to cause the primary immunodeficiency disease Omenn’s syndrome (20). A study of the equivalent mutation in mouse RAG1 (C325Y) showed that it greatly reduced recombination of an extrachromosomal plasmid, as did mutation of the neighboring residue (P326G) (21). Other RING finger residues critical for ubiquitin ligase activity appeared to contribute to robust recombination of extrachromosomal substrates (22). In biochemical experiments carried out with an N-terminal fragment of RAG1 (residues 218–389), the principal site of autoubiquitination was found to be a residue neighboring the RING finger, K233; mutation of this residue (K233M) essentially abolished autoubiquitination of the fragment (18).In this article, we assess the site or sites and extent of autoubiquitination of RAG1, the consequences of this modification for RAG1/RAG2 activity in a cell-free system and in cells, and the functional relationship between this modification and the histone-recognizing PHD domain of RAG2. We prepare FLRAG1 in complex with either full-length RAG2 (FLRAG2) or core RAG2 and find that FLRAG1 undergoes autoubiquitination specifically at K233. The ubiquitination of RAG1 protein enhances coupled cleavage by the RAG1/RAG2 complex of a 12/23 RSS pair by about fivefold. RAG1 autoubiquitination also ap-pears to be important for supporting V(D)J recombination in cells.     

Distinct activation of an E2 ubiquitin-conjugating enzyme by its cognate E3 ligases

A significant portion of ubiquitin (Ub)-dependent cellular protein quality control takes place at the endoplasmic reticulum (ER) in a process termed “ER-associated degradation” (ERAD). Yeast ERAD employs two integral ER membrane E3 Ub ligases: Hrd1 (also termed “Der3”) and Doa10, which recognize a distinct set of substrates. However, both E3s bind to and activate a common E2-conjugating enzyme, Ubc7. Here we describe a novel feature of the ERAD system that entails differential activation of Ubc7 by its cognate E3s. We found that residues within helix α2 of Ubc7 that interact with donor Ub were essential for polyUb conjugation. Mutagenesis of these residues inhibited the in vitro activity of Ubc7 by preventing the conjugation of donor Ub to the acceptor. Unexpectedly, Ub chain formation by mutant Ubc7 was restored selectively by the Hrd1 RING domain but not by the Doa10 RING domain. In agreement with the in vitro data, Ubc7 α2 helix mutations selectively impaired the in vivo degradation of Doa10 substrates but had no apparent effect on the degradation of Hrd1 substrates. To our knowledge, this is the first example of distinct activation requirements of a single E2 by two E3s. We propose a model in which the RING domain activates Ub transfer by stabilizing a transition state determined by noncovalent interactions between the α2 helix of Ubc7 and Ub and that this transition state may be stabilized further by some E3 ligases, such as Hrd1, through additional interactions outside the RING domain.The ubiquitin (Ub) conjugation machinery employs three basic enzymatic activities, E1, E2, and E3, that work in concert to transfer Ub to client substrates and to form polyUb chains (1). Initially, an E1 Ub-activating enzyme forms a high-energy thioester bond with the C terminus of Ub, after which the Ub molecule is transferred to the active-site Cys of an E2 Ub-conjugating (Ubc) enzyme. The Ub-charged E2 binds to an E3 ligase and catalyzes the transfer of Ub to the ε-amino group of a Lys side chain within the substrate. Additional Ubs then can be ligated to the initial Ub molecule through sequential ubiquitylation cycles, ultimately forming a polyUb chain. Ub can be conjugated to itself via specific Lys residues, resulting in diverse types of chain linkages. Linkage through Lys48 is linked primarily to substrate degradation. Consequently, protein substrates carrying Lys48-linked polyUb chains bind to and are degraded by 26S proteasome.Although it is well established that E3 ligases activate Ub ligation by E2s via their RING domains, very little is actually known about the underlying regulatory mechanism. Several recent studies determined the structure of RING domain complexes with Ub-charged UbcH5 (2–4). In one of these studies, the structure in solution of Ub-charged UbcH5c together with the mouse E3 ligase E4B U-box domain revealed that Ub can adopt an array of “open” and “closed” conformations (2). The productive closed conformation promotes a nucleophilic attack on the Ub∼E2 thioester by an incoming Lys (acceptor) residue (2). A similar closed conformation was identified in the structures of UbcH5a and UbcH5b, together with their cognate RING domains (3, 4). Taken together, these structural studies suggest that RING domains can catalyze Ub transfer by stabilizing a transition state of a closed conformation of the E2-bound (donor) Ub (5).Among the fundamental intracellular functions of the Ub–proteasome system is maintenance of cellular protein quality control (PQC) by targeting a diverse array of transiently or permanently misfolded substrates for proteolysis. A central branch of PQC degradation takes place in the endoplasmic reticulum (ER) in a process termed “ER-associated degradation” (ERAD) (6). Despite the multitude of misfolded substrates, ERAD employs only a few E3–ligase complexes (7). In fact, the bakers'' yeast S. cerevisiae ERAD system employs only two Ub-ligation complexes, specified by their E3 ligase components, Hrd1 and Doa10 (8–12). Importantly, each of the two E3 ligase complexes recognizes a distinct set of substrates, with minor overlaps (13).Degradation by the yeast ERAD Ub-ligation system entails the combined activity of two E2 enzymes: Ubc6 and Ubc7 for the Doa10 pathway and Ubc1 and Ubc7 for the Hrd1 pathway (14, 15). The shared E2 enzyme, Ubc7, is a soluble cytosolic protein whose binding to either of the E3–ligase complexes at the ER membrane is mediated by the auxiliary ER membrane protein Cue1. Binding to Cue1 not only mediates the interaction with the E3–ligase complex but also protects Ubc7 from degradation and stimulates its Ub-transfer activity (16–20). Ubc7 is highly conserved in evolution, as evident from substantial sequence and structure similarities with its orthologs from other species (21). The human Ubc7 ortholog, Ube2g2 (21), functions together with several ER membrane-embedded E3 ligases, the best characterized of which is the tumor autocrine motility factor receptor, gp78 (22). Ubc7 and Ube2g2 are subjected to similar regulatory mechanisms: They bind to and are activated by the RING domains of their cognate E3s as well as by the E2-binding regions and CUE domains within Cue1 and gp78 (19, 20, 23–26). The evolutionarily conserved sequence, structure, and regulatory mechanisms of the Ubc7 E2s imply an essential physiological function.In this study we explored the role of helix α2 of Ubc7 in enzyme activation. Based on our in vivo and in vitro observations and on the available structural information, we propose a mechanism whereby activation of Ubc7, mediated by noncovalent interaction with Ub at helix α2, is differentially affected by the RING domains of its cognate E3 ligases Hrd1 and Doa10.     

The role and therapeutic implications of RING‐finger E3 ubiquitin ligases in hepatocellular carcinoma

Increasing evidence indicates that deregulation of RING‐finger ubiquitin‐protein ligases (E3s) involves in the development of hepatocellular carcinoma (HCC). These RING‐finger E3s serve as oncoproteins or tumor suppressors in HCC under specific conditions. In this review, we summarize current knowledge about abnormal RING‐finger E3s and their clinical significance in the development of HCC, and discuss parts of critical substrates for these RING‐finger E3s in detail. Furthermore, in light of success of Bortezomib in treating hematological malignancies, we describe the preclinical and clinical studies of therapeutic approaches targeting aberrant RING‐finger E3s in HCC.     

Screening analysis of ubiquitin ligases reveals G2E3 as a potential target for chemosensitizing cancer cells

Cisplatin is widely used against various tumors, but resistance is commonly encountered. By inducing DNA crosslinks, cisplatin triggers DNA damage response (DDR) and cell death. However, the molecular determinants of how cells respond to cisplatin are incompletely understood. Since ubiquitination plays a major role in DDR, we performed a high-content siRNA screen targeting 327 human ubiquitin ligases and 92 deubiquitinating enzymes in U2OS cells, interrogating the response to cisplatin. We quantified γH2AX by immunofluorescence and image analysis as a read-out for DNA damage. Among known mediators of DDR, the screen identified the ubiquitin ligase G2E3 as a new player in the response to cisplatin. G2E3 depletion led to decreased γH2AX levels and decreased phosphorylation of the checkpoint kinase 1 (Chk1) upon cisplatin. Moreover, loss of G2E3 triggered apoptosis and decreased proliferation of cancer cells. Treating cells with the nucleoside analogue gemcitabine led to increased accumulation of single-stranded DNA upon G2E3 depletion, pointing to a defect in replication. Furthermore, we show that endogenous G2E3 levels in cancer cells were down-regulated upon chemotherapeutic treatment. Taken together, our results suggest that G2E3 is a molecular determinant of the DDR and cell survival, and that its loss sensitizes tumor cells towards DNA-damaging treatment.     

Mechanistic basis for ubiquitin modulation of a protein energy landscape

Ubiquitin is a common posttranslational modification canonically associated with targeting proteins to the 26S proteasome for degradation and also plays a role in numerous other nondegradative cellular processes. Ubiquitination at certain sites destabilizes the substrate protein, with consequences for proteasomal processing, while ubiquitination at other sites has little energetic effect. How this site specificity—and, by extension, the myriad effects of ubiquitination on substrate proteins—arises remains unknown. Here, we systematically characterize the atomic-level effects of ubiquitination at various sites on a model protein, barstar, using a combination of NMR, hydrogen–deuterium exchange mass spectrometry, and molecular dynamics simulation. We find that, regardless of the site of modification, ubiquitination does not induce large structural rearrangements in the substrate. Destabilizing modifications, however, increase fluctuations from the native state resulting in exposure of the substrate’s C terminus. Both of the sites occur in regions of barstar with relatively high conformational flexibility. Nevertheless, destabilization appears to occur through different thermodynamic mechanisms, involving a reduction in entropy in one case and a loss in enthalpy in another. By contrast, ubiquitination at a nondestabilizing site protects the substrate C terminus through intermittent formation of a structural motif with the last three residues of ubiquitin. Thus, the biophysical effects of ubiquitination at a given site depend greatly on local context. Taken together, our results reveal how a single posttranslational modification can generate a broad array of distinct effects, providing a framework to guide the design of proteins and therapeutics with desired degradation and quality control properties.

Ubiquitin is an 8.5-kDa protein appended to target proteins as a posttranslational modification (PTM). Typically, ubiquitin is conjugated to the primary amine of substrate lysine residues, though noncanonical linkages to serine and cysteine also exist in vivo. Ubiquitin itself contains seven lysine residues, which allows building of ubiquitin chains with various linkages and topologies. Ubiquitination is most typically associated with targeting condemned proteins to the 26S proteasome for degradation; however, it is also involved in a large and ever-growing list of crucial regulatory, nondegradative cellular processes (1). A complex and highly regulated enzymatic cascade attaches ubiquitin to substrates and therefore plays a key role in determining the specific downstream effects of an individual ubiquitination event. There are several hundred E3 ligases, the terminal enzymes in this cascade (2), which give rise to broad proteome coverage and allow for some level of site specificity (3, 4).Multiple different ubiquitin chain linkages and topologies bind with high affinity to proteasomal ubiquitin receptors and promote degradation (5–8). However, the presence of a ubiquitin tag alone is not sufficient to ensure proteasomal degradation. In fact, a substantial proportion of ubiquitin-modified proteins that interact with the 26S proteasome are ultimately released (9, 10) and not degraded. The proteasome also relies on substrate conformational properties, initiating degradation at an unstructured region on the condemned protein (11, 12). Much work has been done to understand the requirements of this unstructured region with regard to length, sequence composition, and topological position (13–15), yet at least 30% of known proteasome clients lack such a region (16). While evidence suggests that well-folded proteins are processed by diverse cellular unfoldases, such as Cdc48/p97/VCP (17, 18), an intriguing possibility is that the ubiquitin modification itself can modulate the conformational landscape and thus regulate proteasome substrate selection. Simulations have suggested that ubiquitination can destabilize the folded state of the substrate protein, thereby allowing it to more readily adopt unfolded or partially unfolded conformations (19, 20).Recently, we demonstrated that this is indeed the case: ubiquitin can exert significant effects on a substrate’s energy landscape depending on the site of ubiquitination and the identity of the substrate protein. Moreover, these changes can have direct consequences for proteasomal processing (21). By examining the energetic effects of native, isopeptide-linked ubiquitin attachment to three different sites within the small protein barstar from Bacillus amyloliquefaciens, we found that ubiquitin attached at either lysine 2 or lysine 60 destabilizes the protein both globally and via subglobal fluctuations, and we thus refer to these residues as sensitive sites. By contrast, ubiquitination at lysine 78 produces little effect on the energy landscape (21), and we therefore term it a nonsensitive site. Another study found that ubiquitin, appended through a nonnative linkage, can destabilize a folded substrate as measured by changes in the midpoints for thermally induced unfolding transitions (22).Ubiquitination at the two sensitive sites in barstar increases the population of partially unfolded, high-energy states on the landscape sufficient for proteasomal engagement and degradation. Ubiquitination at the single nondestabilizing site does not allow for proteasomal degradation. These results suggest that ubiquitin-mediated destabilization can reveal an obligate unstructured region in substrates that otherwise lack such a region. Furthermore, ubiquitination at sensitive sites results in more rapid degradation of these barstar variants when a proteasome-engageable unstructured tail is fused to their C termini (21).This previous work clearly demonstrates that ubiquitin-mediated changes to the protein landscape can play an important role in proteasomal selectivity and processing; it did not, however, uncover the molecular mechanisms through which these site-specific effects arise. Here, we interrogate the molecular mechanisms of ubiquitin-induced changes for these same single-lysine variants of barstar. We investigate differences in the intrinsic dynamics of these regions within barstar and differences in how the protein responds to ubiquitination at these individual sites. We employed two sets of complementary approaches: 1) NMR and HDX-MS (hydrogen–deuterium exchange mass spectrometry) to characterize the equilibrium conformational fluctuations of the substrate protein in the presence and absence of ubiquitin and 2) molecular dynamics (MD) simulations to track the position of every atom in barstar, in the presence and absence of ubiquitin, starting from its native conformation over the timescale of microseconds.We find that ubiquitination has only subtle effects on the native structure of barstar. Ubiquitination at the sensitive sites, however, selectively increases fluctuations that expose barstar’s C terminus. While both of the sensitive sites arise in regions of barstar with relatively high conformational flexibility, the observed destabilization appears to occur through different thermodynamic mechanisms. By contrast, ubiquitination at the nonsensitive site has a protective effect on barstar’s C terminus. Thus, the effects of ubiquitination at each site are highly dependent on the local context. This mechanistic understanding of the site-specific effects of ubiquitination should aid in developing predictive models of the energetic consequences of individual ubiquitination events and also of the ways in which aberrant lysine targeting leads to disease (23–25).     

SUMO化反应在肾脏疾病中的作用探索

小泛素相关修饰物(SUMO)与靶蛋白的共价结合是一种真核基因表达的翻译后加工形式。SU-MO化能够使蛋白质更加稳定,进而调节许多关键的细胞活动,如核运输、信号传递、凋亡、细胞周期调控以及基因表达的调控等。此外SUMO化还可通过过氧化物酶体增殖物激活受体-γ、核转录因子-κB及转化生长因子-β依赖的途径参与抗炎和致纤维化过程,本文就这一机制可能在肾脏疾病中发挥的作用作一综述。     

Effects of Chronic Administration with Nilvadipine Against Immunohistochemical Changes Related to Aging in the Mouse Hippocampus

We investigated the effect of Ca²⁺ antagonist nilvadipine on age-related immunohistochemical alterations in ubiquitin and S100 protein of the hippocampal CA1 sector in mice using 8-, 18-, 40-, and 59-week-old mice. No significant changes in the number of neuronal cells were observed in the hippocampal CA1 sector up to 59 weeks after birth. The administration of nilvadipine did not affect the number of the hippocampal CA1 cells of 40-week-old mice. Age-dependent increases in ubiquitin immunoreactivity were observed in the hippocampal CA1 neurons up to 59 weeks after birth. The administration of nilvadipine prevented dose-dependently the increases in the number of ubiquitin-immunoreactive neurons in the hippocampal CA1 sector of 40-week-old mice. S100 immunoreactivity was unchanged in the hippocampal CA1 sector up to 40 weeks after birth. In 59-week-old mice, the level of staining of S100-immunoreactive cells increased significantly in the hippocampal CA1 sector. The administration of nilvadipine decreased dose-dependently the number of S100-immunoreactive cells in the hippocampal CA1 sector of 40-week-old mice. The present study demonstrates that age-related increases in ubiquitin system may play a pivotal role in protecting neuronal cell damage during aging. In contrast, our results suggest that expression of S100 protein in the hippocampal CA1 sector may play an exacerbating factor in some neuronal cells damaged by aging. Our results also demonstrate that nilvadipine, a dihydropyridine-type calcium channel blocker, can prevent dose-dependently the increases in the ubiquitin immunoreactive neurons and decrease the number of S100 immunoreactive cells in the hippocampal CA1 neurons of aged mice. These results suggest that nilvadipine may offer a new approach for the treatment of neuronal dysfunction in aged humans.     

小鼠睾丸组织特异表达基因Rnf148的鉴定及其编码E3泛素连接酶的功能分析

目的 研究小鼠Rnf148基因表达的时空特异性及其环指结构域的E3泛素连接酶功能。 方法 提取不同成年小鼠组织、不同胚胎期组织和出生后小鼠睾丸组织的总RNA,通过实时荧光RT-PCR和Northern杂交分析小鼠Rnf148基因的表达谱。构建包含整个Rnf148蛋白的环指结构域与谷胱甘肽-S-转移酶（GST）的融合蛋白原核表达载体,在BL21细菌中诱导表达后,经GST琼脂糖凝胶纯化GST-Rnf148重组蛋白。体外泛素化反应试验检测GST-Rnf148重组蛋白的E3泛素连接酶功能。 结果 在小鼠13种不同器官组织中,Rnf148 mRNA仅存在于睾丸组织中。进一步Northern杂交验证了只在小鼠睾丸组织表达一个1.2 kb左右的Rnf148基因mRNA片段。小鼠Rnf148基因在胚胎期及出生后3周内不表达,出生后21 d开始表达,25 d后达到表达高峰并一直持续表达。实验成功诱导表达并纯化了GST-Rnf148重组蛋白,体外蛋白泛素化反应显示该重组蛋白具有E3泛素连接酶的功能。 结论 小鼠Rnf148基因特异地表达在出生3周后的睾丸组织中,Rnf148蛋白的环指结构域具有泛素连接酶活性。