Ubiquitylation of proteins in livers of hibernating golden-mantled ground squirrels,Spermophilus lateralis

Rodent hibernators experience low core body temperature (as low as −2 °C) and reduced metabolic rates during hibernation. Concordant with energetic constraints, protein synthesis is negligible during torpor. To maintain pools of key regulatory proteins, proteolysis must be depressed as well. Ubiquitin-dependent proteolysis consists of two major steps: (1) ubiquitylation or tagging of a protein substrate by ubiquitin and (2) the protein substrate’s subsequent degradation by the 26S proteasome. Earlier, we demonstrated that the low temperatures typical of torpor virtually arrest proteolytic processing. Here, we demonstrate that in vitro ubiquitylation still continues at greater than 30% of maximal rates at temperatures as low as 0 °C. Continued ubiquitylation in the presence of severely depressed proteolysis may explain the previously observed 2- to 3-fold increase of ubiquitin conjugates during torpor. We determined if there is a qualitative change in the type of ubiquitylation e.g., monoubiquitylation vs polyubiquitylation that occurs during torpor. We found no bias for monoubiquitylation in any state of the torpor cycle. We further determined that substrate limitation of free ubiquitin is not limiting ubiquitylation during torpor. We conclude that while the cold temperatures of torpor may limit proteolysis in accordance with metabolic demands, continued ubiquitylation may result in increased ubiquitin conjugate concentrations that must be processed upon arousal.     

Proteolysis is depressed during torpor in hibernators at the level of the 20S core protease

Protein synthesis is depressed during mammalian hibernation in concordance with metabolic demands. In the absence of significant protein synthesis, continued proteolysis would rapidly deplete protein pools. Since ubiquitin-dependent proteolysis is implicated in the turnover of most regulatory proteins, we examined the fate of this system during hibernation. Ubiquitin-dependent proteolysis consists of two major steps: (1) the tagging of a protein substrate by ubiquitin and (2) the protein substrates subsequent degradation by the 26S proteasome. An earlier study revealed a two to threefold elevation of ubiquitin conjugate concentrations during hibernation: an unexpected result that seemingly would suggest increased proteolytic activity. A more likely explanation for these data would be that proteolysis per se was depressed and that the increased levels of ubiquitylated proteins reflect an inability to degrade tagged proteins. We employed an assay based on the cleavage of fluorogenic substrates to address the well characterized proteolytic activities of the proteasome. All activities show little to no activity at temperatures associated with deep torpor. Coordinated depression of proteolytic activities by low temperature supports the hypothesis that the increased levels of ubiquitylated proteins during hibernation is explained by a net accumulation due to an inability to degrade the tagged proteins.     

Ubiquitin conjugate dynamics in the gut and liver of hibernating ground squirrels

Protein synthesis is severely depressed in hibernating mammals. In the absence of significant protein synthesis, the continued turnover of proteins as a function of normal cellular activity would result in the net depletion of protein pools. We measured levels of ubiquitylated proteins in the gut of thirteen-lined ground squirrels ( Spermophilus tridecemlineatus) and liver of golden-mantled ground squirrels ( Spermophilus lateralis). In both tissues, ubiquitin conjugate concentrations increased during entrance into torpor and were elevated 2-3 fold by late torpor compared with levels in active animals. The data are consistent with a depression of proteolysis with a resultant high level of ubiquitylated proteins during the natural hypothermia of torpor. The periodic returns to euthermy during the hibernation season allow for degradation of these conjugated proteins and may serve to restore protein pools.     

Ubiquitin acetylation inhibits polyubiquitin chain elongation

Ubiquitylation is a versatile post-translational modification (PTM). The diversity of ubiquitylation topologies, which encompasses different chain lengths and linkages, underlies its widespread cellular roles. Here, we show that endogenous ubiquitin is acetylated at lysine (K)-6 (AcK6) or K48. Acetylated ubiquitin does not affect substrate monoubiquitylation, but inhibits K11-, K48-, and K63-linked polyubiquitin chain elongation by several E2 enzymes in vitro. In cells, AcK6-mimetic ubiquitin stabilizes the monoubiquitylation of histone H2B—which we identify as an endogenous substrate of acetylated ubiquitin—and of artificial ubiquitin fusion degradation substrates. These results characterize a mechanism whereby ubiquitin, itself a PTM, is subject to another PTM to modulate mono- and polyubiquitylation, thus adding a new regulatory layer to ubiquitin biology.     

Hibernation and daily torpor in an armadillo, the pichi (Zaedyus pichiy)

Hibernation and daily torpor are physiological strategies to cope with energetic challenges that occur in many mammalian and avian taxa, but no reliable information exists about daily torpor or hibernation for any xenarthran. Our objective was to determine whether the pichi (Zaedyus pichiy), a small armadillo (Xenarthra, Dasypodidae) that inhabits arid and semi-arid habitats in central and southern Argentina and Chile, enters shallow daily torpor or prolonged deep hibernation during winter when environmental temperature and food availability are low. We studied body temperature changes during winter in semi-captive pichis by means of temperature dataloggers implanted subcutaneously. All individuals entered hibernation, characterized by torpor events of 75 ± 20 h during which the subcutaneous temperature (T_sc) decreased to 14.6 ± 2.1 °C. These events were interrupted by periods of euthermia of 44 ± 38 h with a T_sc of 29.1 ± 0.7 °C. After the hibernation season, daily torpor bouts of 4 to 6 h occurred irregularly, with T_sc dropping to as low as 24.5 °C. We conclude that the pichi is a true hibernator and can enter daily torpor outside of the hibernation season.     

Identification of developmentally expressed proteins that functionally interact with Nedd4 ubiquitin ligase.

Nedd4 is a HECT domain-containing ubiquitin ligase that mediates ubiquitylation and proteasome degradation of target proteins. The molecular basis for the interaction of Nedd4 with substrates lies in its WW domains, which can bind proline-rich (PY) domains in target proteins. Nedd4 is a developmentally expressed protein and may have a fundamental role to play in embryonic processes. However, whether Nedd4 has such a function is currently unknown, in part because few developmentally regulated ubiquitylation substrates have been identified or characterized. We have carried out a yeast two-hybrid screen and identified four proteins expressed in the mid-gestation embryo that are able to interact with Nedd4. Characterization of their functional interaction with Nedd4 in vitro and in vivo demonstrated that three of the four are bona fide Nedd4 binding partners, and two have the capacity to be ubiquitylation substrates. One of these is the first identified nonviral substrate for Nedd4-mediated monoubiquitylation. Interestingly, neither of these two ubiquitylated proteins interacts with Nedd4 through PY-mediated mechanisms. For one of the three Nedd4 binding partners, there was no discernable evidence of ubiquitylation. However, this protein clearly associates with Nedd4 through its PY domains and can alter the location of Nedd4 in cells, suggesting a role other than as a ubiquitylation substrate.     

Depression of mitochondrial respiration during daily torpor of the Djungarian hamster,Phodopus sungorus,is specific for liver and correlates with body temperature

Small mammals actively decrease metabolism during daily torpor and hibernation to save energy. Increasing evidence suggests depression of mitochondrial respiration during daily torpor of the Djungarian hamster but tissue-specificity and relation to torpor depth is unknown. We first confirmed a previous study by Brown and colleagues reporting on the depressed substrate oxidation in isolated liver mitochondria of the Djungarian hamster (Phodopus sungorus) during daily torpor. Next, we show that mitochondrial respiration is not depressed in kidneys, skeletal muscle and heart. In liver mitochondria, we found that state 3 and state 4 respirations correlate with body temperature, suggesting inhibition related to torpor depth and to metabolic rate. We conclude that molecular events leading to depression of mitochondrial respiration during daily torpor are specific to liver and linked to a decrease in body temperature. Different tissue-specificity of mitochondrial depression may assist to compare and identify the molecular nature of mitochondrial alterations during torpor.     

Ubiquitin Pool Modulation and Protein Degradation in Wheat Roots during High Temperature Stress

Ubiquitin, a key component in an ATP-dependent proteolytic pathway, participates in the response of various eucaryotic organisms to high temperature stress. Our objective was to determine if ubiquitin serves a similar capacity for metabolizing altered proteins in higher plants during stress. Degradation of total proteins was measured, and ubiquitin pools (free versus conjugated) were extracted with an improved protocol from wheat (Triticum aestivum L. cv Len) roots treated at 22, 27, 32, 37, and 42°C for 1 hour and assayed by western blots and radioimmunoassays. Heat-shock protein synthesis was detected by in vivo labeling and autoradiography. Mean half-life of total root proteins decreased from 51 hours at 22°C to 23 hours at 40°C. Ubiquitin pools were extracted better and proteolysis was slowed more by the improved protocol than by a conventional procedure for plant proteins. Amounts of high molecular mass conjugates were elevated and levels of low molecular mass conjugates and free ubiquitin were depressed when roots were treated at 37 or 42°C than at lower temperatures; the same high temperatures also induced synthesis of heat-shock proteins. We concluded that high temperatures increase breakdown of root proteins, which are degraded via the ubiquitin proteolytic pathway. A conjugate with an apparent molecular mass of 23 kilodaltons was tentatively identified as an ubiquitinated histone.     

HOIL‐1 ubiquitin ligase activity targets unbranched glucosaccharides and is required to prevent polyglucosan accumulation

HOIL‐1, a component of the linear ubiquitin chain assembly complex (LUBAC), ubiquitylates serine and threonine residues in proteins by esterification. Here, we report that mice expressing an E3 ligase‐inactive HOIL‐1[C458S] mutant accumulate polyglucosan in brain, heart and other organs, indicating that HOIL‐1’s E3 ligase activity is essential to prevent these toxic polysaccharide deposits from accumulating. We found that HOIL‐1 monoubiquitylates glycogen and α1:4‐linked maltoheptaose in vitro and identify the C6 hydroxyl moiety of glucose as the site of ester‐linked ubiquitylation. The monoubiquitylation of maltoheptaose was accelerated > 100‐fold by the interaction of Met1‐linked or Lys63‐linked ubiquitin oligomers with the RBR domain of HOIL‐1. HOIL‐1 also transferred pre‐formed ubiquitin oligomers to maltoheptaose en bloc, producing polyubiquitylated maltoheptaose in one catalytic step. The Sharpin and HOIP components of LUBAC, but not HOIL‐1, bound to unbranched and infrequently branched glucose polymers in vitro, but not to highly branched mammalian glycogen, suggesting a potential function in targeting HOIL‐1 to unbranched glucosaccharides in cells. We suggest that monoubiquitylation of unbranched glucosaccharides may initiate their removal from cells, preventing precipitation as polyglucosan.     

Analysis of the role of ubiquitin-interacting motifs in ubiquitin binding and ubiquitylation

The ubiquitin-interacting motif (UIM) is a short peptide motif with the dual function of binding ubiquitin and promoting ubiquitylation. This motif is conserved throughout eukaryotes and is present in numerous proteins involved in a wide variety of cellular processes including endocytosis, protein trafficking, and signal transduction. We previously reported that the UIMs of epsin were both necessary and sufficient for its ubiquitylation. In this study, we found that many, but not all, UIM-containing proteins were ubiquitylated. When expressed as chimeric fusion proteins, most UIMs promoted ubiquitylation of the chimera. In contrast to previous studies, we found that UIMs do not exclusively promote monoubiquitylation but rather a mixture of mono-, multi-, and polyubiquitylation. However, UIM-dependent polyubiquitylation does not lead to degradation of the modified protein. UIMs also bind polyubiquitin chains of varying lengths and to different degrees, and this activity is required for UIM-dependent ubiquitylation. Mutational analysis of the UIM revealed specific amino acids that are important for both polyubiquitin binding and ubiquitin conjugation. Finally we provide evidence that UIM-dependent ubiquitylation inhibits the interaction of UIM-containing proteins with other ubiquitylated cellular proteins. Our results suggest a new model for the ubiquitylation of UIM-containing proteins.     

The effect of hibernation on protein phosphatases from ground squirrel organs

Protein phosphorylation has been identified as a reversible mechanism for the regulated suppression of metabolism and thermogenesis during mammalian hibernation. The effects of hibernation on the activity of serine/threonine and tyrosine protein phosphatases (PP1, PP2A, PP2C and PTPs) were assessed in five organs of Richardson’s ground squirrel. Each phosphatase subfamily responded differently during torpor, and each showed organ-specific patterns of activity changes. The distribution of PP1 catalytic subunit (PP1c) isoforms (α, δ, γ1) was assessed in five organs, and changes in the subcellular distribution of PP1 were observed during hibernation in liver and muscle. For example, in muscle, cytosolic PP1 content increased and myofibril-associated PP1 decreased during torpor. PP1c from ground squirrel liver was purified to homogeneity and characterized; temperature effects on PP1c maximal activity suggested that temperature had little or no effect on relative dephosphorylation potential at low temperatures. However, nucleotide inhibition of PP1c by ATP, ADP and AMP was much weaker at 5 °C compared with 37 °C assay temperatures. PP2A activity decreased in three organs (brown adipose, kidney, brain) during hibernation whereas PP2C activity was increased in liver and brain. PTPs were assessed using both a general substrate (ENDpYINASL) and a substrate (DADEpYLIPQQG) specific for PTPs containing the SH2-binding site; both revealed hibernation-associated changes in PTP activities. Changes in protein phosphatase activities suggest the relative importance of these modules in controlling metabolic function and cellular processes during mammalian hibernation.     

Endocytosis of receptor tyrosine kinases is driven by monoubiquitylation,not polyubiquitylation

Growth factors stimulate specific receptor tyrosine kinases, but subsequent receptor endocytosis terminates signaling. The ubiquitin ligase c-Cbl targets epidermal growth factor receptors (EGFRs) to endocytosis by tagging them with multiple ubiquitin molecules. However, the type of ubiquitylation is unknown; whereas polyubiquitin chains signal proteasomal degradation, ubiquitin monomers control other processes. We report that in isolation c-Cbl mediates monoubiquitylation rather than polyubiquitylation of EGFRs. Consistent with the sufficiency of monoubiquitylation, when fused to the tail of EGFR, a single ubiquitin induces receptor endocytosis and degradation in cells. By using receptor and ubiquitin mutants, we infer that c-Cbl attaches a founder monoubiquitin to the kinase domain of EGFR and this is complemented by the conjugation of additional monoubiquitins. Hence, receptor tyrosine kinases are desensitized through conjugation of multiple monoubiquitins, which is distinct from polyubiquitin-dependent proteasomal degradation.     

Dynamic regulation of PCNA ubiquitylation/deubiquitylation

Proliferating Cell Nuclear Antigen (PCNA) ubiquitylation plays a crucial role in maintaining genomic stability during DNA replication. DNA damage stalling the DNA replication fork induces PCNA ubiquitylation that activates DNA damage bypass to prevent the collapse of DNA replication forks that could potentially produce double-strand breaks and chromosomal rearrangements. PCNA ubiquitylation dictates the mode of bypass depending on the level of ubiquitylation; monoubiquitylation and polyubiquitylation activate error-prone translesion synthesis and error-free template switching, respectively. Due to the error-prone nature of DNA damage bypass, PCNA ubiquitylation needs to be tightly regulated. Here, we review the molecular mechanisms to remove ubiquitin from PCNA including the emerging role of USP1 and ELG1 in this fascinating process.     

Mitochondrial metabolism during daily torpor in the dwarf Siberian hamster: role of active regulated changes and passive thermal effects

During daily torpor in the dwarf Siberian hamster, Phodopus sungorus, metabolic rate is reduced by 65% compared with the basal rate, but the mechanisms involved are contentious. We examined liver mitochondrial respiration to determine the possible role of active regulated changes and passive thermal effects in the reduction of metabolic rate. When assayed at 37 degrees C, state 3 (phosphorylating) respiration, but not state 4 (nonphosphorylating) respiration, was significantly lower during torpor compared with normothermia, suggesting that active regulated changes occur during daily torpor. Using top-down elasticity analysis, we determined that these active changes in torpor included a reduced substrate oxidation capacity and an increased proton conductance of the inner mitochondrial membrane. At 15 degrees C, mitochondrial respiration was at least 75% lower than at 37 degrees C, but there was no difference between normothermia and torpor. This implies that the active regulated changes are likely more important for reducing respiration at high temperatures (i.e., during entrance) and/or have effects other than reducing respiration at low temperatures. The decrease in respiration from 37 degrees C to 15 degrees C resulted predominantly from a considerable reduction of substrate oxidation capacity in both torpid and normothermic animals. Temperature-dependent changes in proton leak and phosphorylation kinetics depended on metabolic state; proton leakiness increased in torpid animals but decreased in normothermic animals, whereas phosphorylation activity decreased in torpid animals but increased in normothermic animals. Overall, we have shown that both active and passive changes to oxidative phosphorylation occur during daily torpor in this species, contributing to reduced metabolic rate.     

Ubiquitin/SUMO modification of PCNA promotes replication fork progression in Xenopus laevis egg extracts

The homotrimeric DNA replication protein proliferating cell nuclear antigen (PCNA) is regulated by both ubiquitylation and sumoylation. We study the appearance and the impact of these modifications on chromosomal replication in frog egg extracts. Xenopus laevis PCNA is modified on lysine 164 by sumoylation, monoubiquitylation, and diubiquitylation. Sumoylation and monoubiquitylation occur during the replication of undamaged DNA, whereas diubiquitylation occurs specifically in response to DNA damage. When lysine 164 modification is prevented, replication fork movement through undamaged DNA slows down and DNA polymerase delta fails to associate with replicating chromatin. When sumoylation alone is prevented, replication occurs normally and neither monoubiquitylation nor sumoylation are required for the replication of simple single-strand DNA templates. Our findings expand the repertoire of functions for PCNA ubiquitylation and sumoylation by elucidating a role for these modifications during the replication of undamaged DNA. Furthermore, they suggest that PCNA monoubiquitylation serves as a molecular gas pedal that controls the speed of replisome movement during S phase.     

A versatile new tool derived from a bacterial deubiquitylase to detect and purify ubiquitylated substrates and their interacting proteins

Protein ubiquitylation is an important posttranslational modification affecting a wide range of cellular processes. Due to the low abundance of ubiquitylated species in biological samples, considerable effort has been spent on methods to purify and detect ubiquitylated proteins. We have developed and characterized a novel tool for ubiquitin detection and purification based on OtUBD, a high-affinity ubiquitin-binding domain (UBD) derived from an Orientia tsutsugamushi deubiquitylase (DUB). We demonstrate that OtUBD can be used to purify both monoubiquitylated and polyubiquitylated substrates from yeast and human tissue culture samples and compare their performance with existing methods. Importantly, we found conditions for either selective purification of covalently ubiquitylated proteins or co-isolation of both ubiquitylated proteins and their interacting proteins. As proof of principle for these newly developed methods, we profiled the ubiquitylome and ubiquitin-associated proteome of the budding yeast Saccharomyces cerevisiae. Combining OtUBD affinity purification with quantitative proteomics, we identified potential substrates for the E3 ligases Bre1 and Pib1. OtUBD provides a versatile, efficient, and economical tool for ubiquitin research with specific advantages over certain other methods, such as in efficiently detecting monoubiquitylation or ubiquitin linkages to noncanonical sites.

This study presents OtUBD, a new tool derived from a bacterial deubiquitylase, for the purification and analysis of a broad range of endogenous ubiquitylated proteins, including monoubiquitylation, polyubiquitylation, non-lysine ubiquitylation and potentially other macromolecules.     

Selective ubiquitylation of p21 and Cdt1 by UBCH8 and UBE2G ubiquitin-conjugating enzymes via the CRL4Cdt2 ubiquitin ligase complex

CRL4(Cdt2) is a cullin-based E3 ubiquitin ligase that promotes the ubiquitin-dependent proteolysis of various substrates implicated in the control of cell cycle and various DNA metabolic processes such as DNA replication and repair. Substrates for CRL4(Cdt2) E3 ubiquitin ligase include the replication licensing factor Cdt1 and the cyclin-dependent kinase (Cdk) inhibitor p21. Inhibition of this E3 ligase leads to serious abnormalities of the cell cycle and cell death. The ubiquitin-conjugating enzyme (UBC) involved in this important pathway, however, remains unknown. By a proteomic analysis of Cdt2-associated proteins and an RNA interference-based screening approach, we show that CRL4(Cdt2) utilizes two different UBCs to target different substrates. UBCH8, a member of the UBE2E family of UBCs, ubiquitylates and promotes the degradation of p21, both during the normal cell cycle and in UV-irradiated cells. Importantly, depletion of UBCH8 by small interfering RNA (siRNA) increases p21 protein level, delays entry into S phase of the cell cycle, and suppresses the DNA damage response after UV irradiation. On the other hand, members of the UBE2G family of UBCs (UBE2G1 and UBE2G2) cooperate with CRL4(Cdt2) to polyubiquitylate and degrade Cdt1 postradiation, an activity that is critical for preventing origin licensing in DNA-damaged cells. Finally, we show that UBCH8, but not UBE2G1 or UBE2G2, is required for CRL4(Cdt2)-mediated ubiquitylation and degradation of the histone H4 lysine 20 monomethyltransferase Set8, a previously identified CRL4(Cdt2) substrate, as well as for CRL4(Cdt2)-dependent monoubiquitylation of PCNA in unstressed cells. These findings identify the UBCs required for the activity of CRL4(Cdt2) on multiple substrates and demonstrate that different UBCs are involved in the selective ubiquitylation of different substrates by the same E3 complex.     

The ubiquitin ligase ability of IAPs regulates apoptosis

Accumulating evidence indicates that there is a critical role of the ubiquitin/proteasome pathway in the regulation of apoptosis. Among the important molecules that couple these two fundamental cellular activities are members of the inhibitor of apoptosis (IAP) protein family. In addition to their well-studied ability to directly bind and inhibit caspases, many IAPs contain RING domains that are necessary and sufficient to cause ubiquitylation and subsequent proteasome-mediated proteolysis. This review summarizes recent findings about the ubiquitin protein ligase activity of IAPs, and considers possible mechanisms for substrate selectivity.