Search

This is an open access article under the terms of the Creative Commons Attribution License.-- et al., DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination mediated (error-free) and translesion synthesis-mediated (errorprone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication- associated lesions into the errorfree DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability. © 2014 The Authors., SJ is supported by Max Planck Society, Deutsche Forschungsgemeinschaft, Fonds der chemischen Industrie, Center for Integrated Protein Science Munich, and Louis‐Jeantet Foundation; DB, by the ERC grant REPSUBREP 242928, the AIRC grant IG10637, the Telethon grant GGP12160 and by FIRC.

DNA double-strand breaks (DSBs) are one of the most toxic types of DNA damage, as their inaccurate repair results in mutations and chromosomal rearrangements.1 One of the earliest responses to a DSB is the formation of γH2AX around the break, a highly conserved process by which canonical yeast histone 2A (H2A) or the mammalian histone variant H2A.X are phosphorylated by DNA damage response kinases.2 Cells expressing the respective phosphorylation-defective H2A/H2A.X mutant are sensitive to DSB-inducing agents, and mice bearing the phosphorylation-defective H2A.X mutant exhibit chromosomal instability.3 These phenotypes have been mainly connected to γH2A serving as a recruitment scaffold for proteins assisting in repair or to a role of γH2A in the DNA damage checkpoint.2 Notably, γH2A can spread over very large regions surrounding the DSB encompassing hundreds of kilobases in yeast4 and up to megabases in mammals.5 However, the underlying causes and consequences of this broad distribution of γH2A remained enigmatic.2 We recently demonstrated that the distribution of γH2A does not simply reflect linear spreading of this modification to both sides of the DSB, but follows the pattern of homology search during homologous recombination.6 Homologous recombination relies on the usage of an intact homologous donor sequence to repair a DSB. How homology search, the exploration of the genome for intact homologous donor sequences, operates in the context of a crowded nuclear environment was puzzling for a long time.7 However, using time-resolved chromatin immunoprecipitation (ChIP) of the recombinase Rad51 in S. cerevisiae, we noticed that the distribution pattern of Rad51 on chromatin is a direct result of homology probing on chromosomes after DSB induction.6 Monitoring homology search by this approach in vivo, we found that the repair complex (presynaptic nucleoprotein filament) preferentially samples on the broken chromosome around the DSB, but also on regions of other chromosomes if they are in close proximity due to nuclear organization.6 In addition to these general findings regarding homology search, we discovered that the distribution of γH2A ChIP signals closely parallels the distribution of the homology search-linked Rad51 ChIP signals.6 When a DSB was induced at the S. cerevisiae mating-type (MAT) locus, homology search and Rad51 ChIP signals preferentially targeted the left chromosomal arm (HML) in MATa cells, and the right chromosomal arm (HMR) in MATα cells, according to the known donor preferences for repair of the 2 different mating types.6 Notably, the γH2A ChIP signal profiles almost precisely matched those for Rad51 in the 2 strains upon DSB induction at MAT,6 indicating that both Rad51 and γH2A ChIP signal distributions are direct consequences of homology search. Since the observed distribution of γH2A also paralleled the homology search in cases when a single DSB was induced on other chromosomes, γH2A signal spreading and homology search are apparently generally directly linked. Interestingly, when a DSB was induced close to the centromere of a chromosome, homology search monitored by Rad51 ChIP signals was also detectable around centromeres of all other chromosomes.6 This is most likely due to the fact that yeast centromeres cluster in the nucleus, thereby potentially facilitating proximity-guided homology search from the broken chromosome to centromeric regions of other chromosomes. Notably, γH2A ChIP signals also appeared at centromeric regions analogous to Rad51,6 indicating again that the observed ChIP signals for Rad51 and γH2A are both direct consequences of homology search. This finding demonstrates that γH2A formation does not necessarily occur only in cis on the broken chromosome, but also in trans on other chromosomes. An important corollary of this finding is that the widely used DSB marker γH2A does not exclusively label areas of DSBs. Based on these findings, we would like to propose that the broad chromosomal distribution of γH2A previously observed in yeast and mammalian cells4,5,8 are, in large part, consequences of DSB-triggered homology search. A plausible scenario is that checkpoint kinases travel along with the presynaptic filament during homology search, thereby phosphorylating histones encountered during the search process. If true, this model would predict that factors reported to impact γH2A distribution, like cohesion and transcription,5,8 might influence homology search as well. Despite these findings, one pressing question remains: what might be the function of γH2A during the homology-probing process? Hypothetically, γH2A might render the chromatin environment more accessible for homology probing or might recruit factors that facilitate the search. However, the finding that a phosphorylation-defective mutant variant of H2A had apparently no measurable deleterious effect on homology search in yeast6 may argue against this possibility. Alternatively, γH2A could mark the chromosomal sites that have already been sampled (and render them inaccessible) or amplify the checkpoint response until homology has been found. In whatever way, the finding that γH2A follows homology search adds an important new twist to DNA repair and suggests that studies in yeast and mammalian cells relying on γH2A foci and signals should consider homology search, and not only the DSBs per se, as a potential source for γH2A signals. (Fig. 1) Figure 1. γH2AX follows homology search. Homology search (depicted as black arrows) during homologous recombination can be monitored in vivo by Rad51-directed chromatin immunoprecipitations (ChIP). The profiles of ChIP signal distributions ...

The ubiquitin/proteasome system is the main eukaryotic nonlysosomal protein degradation system. Substrate selectivity of this pathway is thought to be mediated in part by members of a large family of ubiquitin-conjugating (E2) enzymes, which catalyze the covalent attachment of ubiquitin to proteolytic substrates. E2 enzymes have a conserved approximately 150-residue so-called UBC domain, which harbors the cysteine residue required for enzyme-ubiquitin thioester formation. Some E2 enzymes possess additional carboxyl-terminal extensions that are involved in substrate specificity and intracellular localization of the enzyme. Here we describe a novel family of E2 enzymes from higher eukaryotes (Drosophila, mouse, and man) that have amino-terminal extensions but lack carboxyl-terminal extensions. We have identified four different variants of these enzymes that have virtually identical UBC domains (94% identity) but differ in their amino-terminal extensions. In yeast, these enzymes can partially complement mutants deficient in the UBC4 E2 enzyme. This indicates that members of this novel E2 family may operate in UBC4-related proteolytic pathways.

Damaged DNA is an obstacle during DNA replication and a cause of genome instability and cancer. To bypass this problem, eukaryotes activate DNA damage tolerance (DDT) pathways that involve ubiquitylation of the DNA polymerase clamp proliferating cell nuclear antigen (PCNA). Monoubiquitylation of PCNA mediates an error-prone pathway by recruiting translesion polymerases, whereas polyubiquitylation activates an error-free pathway that utilizes undamaged sister chromatids as templates. The error-free pathway involves recombination-related mechanisms; however, the factors that act along with polyubiquitylated PCNA remain largely unknown. Here we report that the PCNA-related 9-1-1 complex, which is typically linked to checkpoint signaling, participates together with Exo1 nuclease in error-free DDT. Notably, 9-1-1 promotes template switching in a manner that is distinct from its canonical checkpoint functions and uncoupled from the replication fork. Our findings thus reveal unexpected cooperation in the error-free pathway between the two related clamps and indicate that 9-1-1 plays a broader role in the DNA damage response than previously assumed.

Protein translocation into the mammalian endoplasmic reticulum requires the Sec61p complex, which consists of three membrane proteins. The alpha-subunit, the homologue of Sec61p of yeast, shows some similarity to SecYp, a key component of the protein export apparatus of bacteria. In Escherichia coli, SecYp is also associated with two other proteins (SecEp and band-1 protein). We have now determined the sequences of the beta- and gamma-subunits of the mammalian Sec61p complex. Sec61-gamma is homologous to SSS1p, a suppressor of sec61 mutants in Saccharomyces cerevisiae, and can functionally replace it in yeast cells. Moreover, Sec61-gamma and SSS1p are structurally related to SecEp of E. coli and to putative homologues in various other bacteria. At least two subunits of the Sec61/SecYp complex therefore seem to be key components of the protein translocation apparatus in all classes of organisms.

All living organisms are vulnerable to DNA damage. Cells respond to this hazard by activating a complex network of checkpoint and repair proteins to preserve genomic integrity. The DNA-encircling, ring-shaped heterotrimeric 9-1-1 complex, a relative of the replication protein PCNA, is a central coordinator of these events. 9-1-1 is loaded to damaged sites where it serves as a platform for the selective recruitment of checkpoint and repair proteins. In this Opinion article, 9-1-1 and proliferating cell nuclear antigen (PCNA) are compared and discussed in light of their respective structures and functions. We propose that the interaction partners of 9-1-1 possess specific 9-1-1-interaction boxes, which discriminate between 9-1-1 and PCNA thereby enabling specific interactions with individual 9-1-1 subunits.

Ubiquitin and SUMO are structurally related protein modifiers that are covalently attached to lysine residues of target proteins. While ubiquitin is traditionally known as a signal for proteasomal degradation, its nondegradative actions are equally important in the control of cellular key processes. Similarly, the SUMO system primarily acts in a nondegradative manner. Accumulating evidence indicates that these nonproteolytic functions of ubiquitin and SUMO are particularly important in the control of the DNA damage response network, which coordinates a set of DNA repair pathways and allows cells to cope with different types of genotoxic stress. In this chapter we will illustrate some key functions of ubiquitin and SUMO in the control of selected DNA repair pathways.

The related transcription factors ACE1 of Saccharomyces cerevisiae and AMT1 of Candida glabrata are involved in copper metabolism by activating the transcription of copper metallothionein genes. ACE1 and AMT1 are 'copper-fist' transcription factors which possess a conserved cysteine-rich copper binding domain required for DNA binding. Here we report the identification of a nuclear protein from S. cerevisiae, MAC1, whose N-terminal region is highly similar to the copper and DNA binding domains of ACE1 and AMT1. Loss-of-function mutants of MAC1 have a defect in the plasma membrane Cu(II) and Fe(III) reductase activity, are slow growing, respiratory deficient, and hypersensitive to heat and exposure to cadmium, zinc, lead and H2O2. Conversely, a dominant gain-of-function mutant of MAC1 shows an elevated reductase activity and is hypersensitive to copper. We have identified two target genes of MAC1 whose altered expression in mutants of MAC1 can account for some of the observed mutant phenotypes. First, MAC1 is involved in basal level transcription of FRE1, encoding a plasma membrane component associated with both Cu(II) and Fe(III) reduction. Second, MAC1 is involved in the H2O2-induced transcription of CTT1, encoding the cytosolic catalase. This suggests that MAC1 may encode a novel metal-fist transcription factor required for both basal and regulated transcription of genes involved in Cu/Fe utilization and the stress response.

UBIQUITIN-conjugating enzymes function in selective proteolysis pathways and catalyse the covalent attachment of ubiquitin to proteolytic substrates1–4. Here we report the identification of an integral membrane ubiquitin-conjugating enzyme. This enzyme, UBC6, localizes to the endoplasmic reticulum (ER), with the cata-lytic domain facing the cytosol. ubc6 loss-of-function mutants sup-press the protein translocation defect caused by a mutation in SEC61, which encodes a key component of a multisubunit protein translocation apparatus of the ER5–11. The expression of the sec61 mutant phenotype requires both the activity of UBC6 and its localization at the ER membrane. This suggests that UBC6 may mediate selective degradation of ER membrane proteins and that the protein translocation defect of sec61 may be caused by proteolysis of components of a structurally distorted mutant translocation apparatus.

Selective ubiquitin-dependent autophagy mediates the disposal of superfluous cellular structures and clears cells of protein aggregates such as polyQ proteins linked to Huntington disease. Crucial selectivity factors of this pathway are ubiquitin-Atg8 receptors such as human SQSTM1/p62, which recognize ubiquitinated cargoes and deliver them to phagophores for degradation. Contrasting previous beliefs, we recently showed that ubiquitin-dependent autophagy is not restricted to higher eukaryotes but also exists in yeast with Cue5, harboring a ubiquitin-binding CUE domain, being a ubiquitin-Atg8 receptor. Notably, the human CUE domain protein TOLLIP is functionally similar to yeast Cue5, indicating that Cue5/TOLLIP (CUET) proteins represent a new and conserved class of autophagy receptors. Remarkably, both Cue5 in yeast and TOLLIP in human cells mediate efficient clearance of aggregation-prone polyQ proteins derived from human HTT/huntingtin. Indeed, TOLLIP is potentially more potent in polyQ clearance than SQSTM1/p62 in HeLa cells, suggesting that TOLLIP, also implicated in innate immunity, may be significant for human health and disease.

SUMO (small ubiquitin-related modifier) is a highly conserved eukaryotic member of the family of ubiquitin-related proteins. Despite limited sequence similarity, SUMO and ubiquitin have highly homologous structures (i.e., with a root-mean-square deviation [rmsd] difference of 2.1 A). Like ubiquitin, SUMO is covalently attached to other proteins (SUMOylation) and thus functions as a posttranslational modifier. Although a major function of ubiquitination is to promote protein degradation, SUMOylation does not usually trigger proteolyis of the conjugated protein. Instead, a main function of SUMOylation is to foster—and occasionally disrupt—protein-protein interactions.Although less frequent than ubiquitination, SUMOylation regulates numerous processes and has many substrates in the cytosol and the nucleus. Lower eukaryotes possess only one SUMO form, but higher eukaryotes express several, perhaps functionally distinct, SUMO variants. In most organisms, SUMO is essential for viability. This SnapShot depicts the reactions involved in SUMO ligation, the effects of SUMOylation on target proteins, and cellular processes regulated by SUMOylation.

Replication-factor C (RFC) is a protein complex that loads the processivity clamp PCNA onto DNA. Elg1 is a conserved protein with homology to the largest subunit of RFC, but its function remained enigmatic. Here, we show that yeast Elg1 interacts physically and genetically with PCNA, in a manner that depends on PCNA modification, and exhibits preferential affinity for SUMOylated PCNA. This interaction is mediated by three small ubiquitin-like modifier (SUMO)-interacting motifs and a PCNA-interacting protein box close to the N-terminus of Elg1. These motifs are important for the ability of Elg1 to maintain genomic stability. SUMOylated PCNA is known to recruit the helicase Srs2, and in the absence of Elg1, Srs2 and SUMOylated PCNA accumulate on chromatin. Strains carrying mutations in both ELG1 and SRS2 exhibit a synthetic fitness defect that depends on PCNA modification. Our results underscore the importance of Elg1, Srs2 and SUMOylated PCNA in the maintenance of genomic stability.

Meiosis generates four haploid daughters from a diploid parental cell. Central steps of meiosis are the pairing and recombination of homologous chromosomes followed by their segregation in two rounds of cell division. Meiotic recombination is monitored by a specialized DNA damage checkpoint pathway and is guided by a unique chromosomal structure called synaptonemal complex (SC), but how these events are coordinated is unclear. Here, we identify the SC protein Red1 as a crucial regulator of early meiosis. Red1 interacts with two subunits of the 9-1-1 checkpoint complex via two distinct 9-1-1 subunit-specific motifs. Association of 9-1-1 with Red1 is essential not only for meiotic checkpoint activation but for SC formation. Moreover, Red1 becomes SUMO-modified, which fosters interaction of Red1 with the central SC element Zip1, thereby securing timely SC formation. Thus, Red1, in addition to its structural role in the SC, is a crucial coordinator of meiosis by coupling checkpoint signaling to SC formation.

Ubiquitin and SUMO are structurally related protein modifiers that are covalently attached to lysine residues of target proteins. While ubiquitin is traditionally known as a signal for proteasomal degradation, its nondegradative actions are equally important in the control of cellular key processes. Similarly, the SUMO system primarily acts in a nondegradative manner. Accumulating evidence indicates that these nonproteolytic functions of ubiquitin and SUMO are particularly important in the control of the DNA damage response network, which coordinates a set of DNA repair pathways and allows cells to cope with different types of genotoxic stress. In this chapter we will illustrate some key functions of ubiquitin and SUMO in the control of selected DNA repair pathways.

The ubiquitin/proteasome system is believed to be the major nonlysosomal proteolytic system of eukaryotic cells. It is present in the cytosol and the nucleus but apparently absent from the lumen of membrane-enclosed organelles, i. e., the endoplasmic reticulum, the Golgi and vesicular system, mitochondria, chloroplasts, and peroxisomes (for reviews see Finley and Chau, 1991; Jentsch, 1992a,b; Hershko and Ciechanover, 1992; Ciechanover, 1994; Hochstrasser, 1995; Smith et al., 1996). Substrates of this pathway include soluble proteins, subunits of oligomeric protein complexes, and integral membrane proteins. An important function of this pathway is the elimination of abnormal proteins (e. g., misfolded, misassembled) generated under normal and, in particular, stress conditions. Moreover, it is assumed that most naturally short-lived proteins of the cytosol and the nucleus are degraded by this pathway. Known substrates include proteins with important regulatory roles such as transcription factors, cell cycle regulators, and signal transducers.

A major pathway for protein degradation in eukaryotes is ubiquitin dependent. Substrate-specific ubiquitin-conjugating enzymes and accessory factors recognize specific signals on proteolytic substrates and attach ubiquitin to defined lysine residues of substrate proteins. Ubiquitin-protein conjugates are then degraded by the proteasome, a multicatalytic protease complex. This proteolytic pathway is highly selective and tightly regulated. It mediates the elimination of abnormal proteins and controls the half-lifes of certain regulatory proteins. Targets include transcriptional regulators, p53 and cyclins, pointing to a role of the ubiquitin system in the regulation of gene expression and growth control.

Pin1, a conserved eukaryotic peptidyl-prolyl cis/trans isomerase, has important roles in cellular regulation. Because of its activity to switch the conformation of peptidyl-proline bonds in polypeptide chains, Pin1 operates as a binary switch, often in fate-determining pathways. Pin1 activity is usually controlled by substrate phosphorylation, but how Pin1 switches protein fates has been unclear. Here we show that Pin1 controls the degree of substrate ubiquitylation and thereby protein functions. We found that yeast Pin1 (Ess1) is essential for viability because it controls the NF-kappaB-related Spt23 transcription factor involved in unsaturated fatty-acid synthesis. High Pin1 activity results in low ubiquitylation of Spt23, which triggers Spt23 precursor processing and hence transcription factor activation. By contrast, decreased Pin1 activity leads to robust Spt23 polyubiquitylation and subsequent proteasomal degradation. Inhibition of Pin1 in mammalian cells changes the ubiquitylation status of the tumour suppressor protein p53 from oligoubiquitylation, which is known to trigger nuclear export, to polyubiquitylation, which causes nuclear p53 degradation. This suggests that the Pin1 activity is often translated into a fate-determining ubiquitylation switch, and that Pin1 may affect the degree of substrate ubiquitylation in other pathways as well.

With the discovery in the late 1980s that the DNA-repair gene RAD6 encodes a ubiquitin-conjugating enzyme, it became clear that protein modification by ubiquitin conjugation has a much broader significance than had previously been assumed. Now, two decades later, ubiquitin and its cousin SUMO are implicated in a range of human diseases, including breast cancer and Fanconi anaemia, giving fresh momentum to studies focused on the relationships between ubiquitin, SUMO and DNA-repair pathways.

DNA double-strand breaks (DSBs) are acutely hazardous for cells, as they can cause genome instability. DSB repair involves the sequential recruitment of repair factors to the DSBs, followed by Rad51-mediated homology probing, DNA synthesis, and ligation. However, little is known about how cells react if no homology is found and DSBs persist. Here, by monitoring a single persistent DNA break, we show that, following DNA resection and RPA recruitment, Rad51 spreads chromosome-wide bidirectionally from the DSB but selectively only on the broken chromosome. Remarkably, the persistent DSB is later fixed to the nuclear periphery in a process that requires Rad51, the histone variant H2A.Z, its SUMO modification, and the DNA-damage checkpoint. Indeed, H2A.Z is deposited close to the break early but transiently and directs DNA resection, single DSB-induced checkpoint activation, and DSB anchoring. Thus, a persistent DSB induces a multifaceted response, which is linked to a specific chromatin mark.

Members of the inhibitor of apoptosis protein (IAP) family are key regulators of apoptosis as they bind and inhibit caspases and other pro-apoptotic factors. Recent findings suggest that these proteins play additional roles, e.g., in cell cycle regulation, angiogenesis, and carcinogenesis. Here, we review the function of BRUCE (BIR repeat-containing ubiquitin-conjugating enzyme), an unusual 528-kDa IAP with ubiquitin ligase activity, and describe its role in apoptosis and cytokinesis. Additionally, we discuss how these seemingly unrelated functions might be linked.

The covalent attachment of ubiquitin to cellular proteins is catalyzed by members of a family of ubiquitin-conjugating enzymes. These enzymes participate in a variety of cellular processes, including selective protein degradation, DNA repair, cell cycle control, and sporulation. In the yeast Saccharomyces cerevisiae, two closely related ubiquitin-conjugating enzymes, UBC4 and UBC5, have recently been shown to mediate the selective degradation of short-lived and abnormal proteins. We have now identified a third distinct member of this class of ubiquitin-conjugating enzymes, UBC1. UBC1, UBC4 and UBC5 are functionally overlapping and constitute an enzyme family essential for cell growth and viability. All three mediate selective protein degradation, however, UBC1 appears to function primarily in the early stages of growth after germination of spores. ubc1 mutants generated by gene disruption display only a moderate slow growth phenotype, but are markedly impaired in growth following germination. Moreover, yeast carrying the ubc1ubc4 double mutation are viable as mitotic cells, however, these cells fail to survive after undergoing sporulation and germination. This specific requirement for UBC1 after a state of quiescence suggests that degradation of certain proteins may be crucial at this transition point in the yeast life cycle.

Ubiquitin-conjugating enzymes catalyse the covalent attachment of ubiquitin to target proteins. Members of this enzyme family are involved in strikingly diverse cellular functions: UBC2 (RAD6) is central to DNA repair, UBC3 (CDC34) is involved in cell cycle control. We have cloned the genes for two novel ubiquitin-conjugating enzymes, UBC4 and UBC5, from the yeast Saccharomyces cerevisiae. These enzymes mediate selective degradation of short-lived and abnormal proteins. UBC4 and UBC5 are closely related in sequence and complementing in function. Expression of UBC4 and UBC5 genes is heat inducible. UBC4 and UBC5 enzymes generate high mol. wt ubiquitin-protein conjugates in vivo consistent with previous studies which suggested that attachment of multiple ubiquitin molecules to proteolytic substrates is required for their selective degradation. UBC4 and UBC5 enzymes comprise a major part of total ubiquitin-conjugation activity in stressed cells. Turnover of short-lived proteins and canavanyl-peptides but not of long-lived proteins is markedly reduced in ubc4ubc5 mutants. Loss of UBC4 and UBC5 activity impairs cell growth, leads to inviability at elevated temperatures or in the presence of an amino acid analog, and induces the stress response.

Inheritance requires genome duplication, reproduction of chromatin and its epigenetic information, mechanisms to ensure genome integrity, and faithful transmission of the information to progeny. Proliferating cell nuclear antigen (PCNA)-a cofactor of DNA polymerases that encircles DNA-orchestrates several of these functions by recruiting crucial players to the replication fork. Remarkably, many factors that are involved in replication-linked processes interact with a particular face of PCNA and through the same interaction domain, indicating that these interactions do not occur simultaneously during replication. Switching of PCNA partners may be triggered by affinity-driven competition, phosphorylation, proteolysis, and modification of PCNA by ubiquitin and SUMO.

When times are hard, cells are sometimes forced to gather food from their own interiors. They can also use this mechanism - known as autophagy - to get rid of old or unwanted cell components. This process has now been dissected at a molecular level, and, surprisingly, the pathway by which it occurs is very similar to that used by ubiquitin, a protein that targets other proteins for destruction.

Cdc48 (p97), a conserved chaperone-like ATPase of eukaryotic cells, has attracted attention recently because of its wide range of cellular functions. Cdc48 is intimately linked to the ubiquitin pathway because its primary action is to segregate ubiquitinated substrates from unmodified partners. This ‘segregase' activity is crucial for certain proteasomal degradation pathways and for some nonproteolytic functions of ubiquitin. Cdc48 associates not only with different ‘substrate-recruiting cofactors' but also with distinct ‘substrate-processing cofactors'. The latter proteins control the degree of ubiquitination of bound substrates by shifting the polyubiquitination reaction into ‘forward', ‘neutral' or ‘reverse'. We discuss how Cdc48 might use this ‘gearbox activity' to control protein fate and propose a similar mode of action for the 19S cap of the proteasome.

The proteasome is a barrel-shaped protease that conceals its active sites within its central cavity. Proteasomes usually completely degrade substrates into small peptides, but in some cases, degradation yields biologically active protein fragments. Some transcription factors are generated from precursors by this activity, but the mechanism of proteasomal protein processing remains unclear. Here we show that proteasomal processing of the yeast NFkappaB-related transcription factors Spt23 and Mga2 is initiated by an internal cleavage, followed by bidirectional proteolysis of the polypeptides. Studies with protein fusions indicate that stable proteolytic fragments are generated if the protein contains tightly folded structures that prevent the complete degradation of the protein. Furthermore, we provide evidence that the ability of the proteasome to initiate proteolysis from an internal site and to proceed via bidirectional polypeptide degradation may be relevant for the complete degradation of proteins as well.

Modification of proteins by covalent attachment of ubiquitin and the ubiquitin-like modifier SUMO are widespread regulatory events of all eukaryotic cells. SUMOylation has received much attention, because several identified targets play prominent roles, in particular, in cell signaling, gene expression, and DNA repair. Notably, only a very small fraction of a substrate is usually SUMOylated at steady-state levels, which could be because modification is reversible and transient. Because of the low level of modification, SUMOylated proteins are often overlooked or sometimes misinterpreted as a less important fraction of a protein pool. Here we discuss procedures that can circumvent identification problems and describe methods for their verification.

Post-translational modification with small ubiquitin-related modifier (SUMO) alters the function of many proteins, but the molecular mechanisms and consequences of this modification are still poorly defined. During a screen for novel SUMO1 targets, we identified the ubiquitin-conjugating enzyme E2-25K (Hip2). SUMO attachment severely impairs E2-25K ubiquitin thioester and unanchored ubiquitin chain formation in vitro. Crystal structures of E2-25K(1-155) and of the E2-25K(1-155)-SUMO conjugate (E2-25K(*)SUMO) indicate that SUMO attachment interferes with E1 interaction through its location on the N-terminal helix. The SUMO acceptor site in E2-25K, Lys14, does not conform to the consensus site found in most SUMO targets (PsiKXE), and functions only in the context of an alpha-helix. In contrast, adjacent SUMO consensus sites are modified only when in unstructured peptides. The demonstration that secondary structure elements are part of SUMO attachment signals could contribute to a better prediction of SUMO targets.

Modification of proteins by covalent attachment of ubiquitin and the ubiquitin‐like modifier SUMO are widespread regulatory events of all eukaryotic cells. SUMOylation has received much attention, because several identified targets play prominent roles, in particular, in cell signaling, gene expression, and DNA repair. Notably, only a very small fraction of a substrate is usually SUMOylated at steady‐state levels, which could be because modification is reversible and transient. Because of the low level of modification, SUMOylated proteins are often overlooked or sometimes misinterpreted as a less important fraction of a protein pool. Here we discuss procedures that can circumvent identification problems and describe methods for their verification.

We are writing to express our enthusiasm that the discovery of the ubiquitin conjugation system has been acknowledged with the award of the Nobel Prize in Chemistry to three outstanding biochemists: Avram Hershko and Aaron Ciechanover of the Technion Institute in Israel, and Irwin Rose of the University of California at Irvine (“Gold medal from cellular trash,” G. Vogel, News Focus, 15 Oct., p. 400). Unraveling the chemistry that underlies the attachment of ubiquitin to proteins that are destined to be degraded was a magnificent achievement and is fully deserving of this recognition.

Ubiquitin and ubiquitin-like modifiers (UBLs) form covalent complexes with other proteins by isopeptide formation between their carboxyl (C)-termini and ɛ-amino groups of lysine residues of acceptor proteins. A hallmark of UBLs is a protruding C-terminal tail with a terminal glycine residue, which is required for ATP-dependent conjugation. Recently, the highly conserved protein HUB1 (homologous to ubiquitin 1) has been reported to function as a UBL following C-terminal processing. HUB1 exhibits sequence similarity with ubiquitin but lacks a C-terminal tail bearing a glycine residue. Here we show that HUB1 can form SDS-resistant complexes with cellular proteins, but provide evidence that these adducts are not formed through covalent C-terminal conjugation of HUB1 to substrates. The adducts are still formed when the C-terminus of HUB1 was altered by epitope tagging, amino-acid exchange or deletion, or when cells were depleted of ATP. We propose that HUB1 may act as a novel protein modulator through the formation of tight, possibly noncovalent interactions with target proteins.

The OLE pathway of yeast regulates the abundance of the ER-bound enzyme Delta-9 fatty acid desaturase OLE1, thereby controlling unsaturated fatty acid pools and membrane fluidity. Previously, we showed that this pathway is exquisitely regulated by the ubiquitin/proteasome system. Activation of the pathway involves proteasomal processing of a membrane-bound transcription factor and the subsequent mobilization of the cleaved, ubiquitylated transcription factor from its partner molecule by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone-like enzyme. Here we report that the OLE1 protein itself is naturally short-lived and is degraded by ubiquitin/proteasome-dependent ER-associated degradation (ERAD). We found that CDC48(UFD1/NPL4) plays a second role in the OLE pathway by mediating ERAD of OLE1. Intriguingly, other ERAD substrates also require CDC48(UFD1/NPL4) for degradation, indicating that this enzyme is a novel, constitutive component of the ERAD machinery. We propose that CDC48(UFD1/NPL4) functions as a segregase that liberates ubiquitylated proteins from non-modified partners.

The ubiquitin/proteasome pathway is the main non-lysosomal route for intracellular protein degradation in eukaryotes. It is instrumental to various cellular processes, such as cell-cycle progression, transcription and antigen processing. Recent findings also substantiate a pivotal role of the ubiquitin/proteasome pathway in the regulation of apoptosis. Regulatory molecules that are involved in programmed cell death have been identified as substrates of the proteasome. Moreover, key regulators of apoptosis themselves seem to have an active part in the proteolytic inactivation of death executors.

Cadmium is a potent poison for living cells. In man, chronic exposure to low levels of cadmium results in damage to kidneys and has been linked to neoplastic disease and ageing, and acute exposure can cause damage to a variety of organs and tissues. Cadmium reacts with thiol groups and can substitute for zinc in certain proteins, but the reason for its toxicity in vivo remains uncertain. In eukaryotes, an important selective proteolysis pathway for the elimination of abnormal proteins that are generated under normal or stress conditions is ATP-dependent and mediated by the ubiquitin system. Substrates of this pathway are first recognized by ubiquitin-conjugating enzymes (or auxiliary factors) which covalently attach ubiquitin, a small and highly conserved protein, to specific internal lysine residues of proteolytic substrates. Ubiquitinated substrates are then degraded by the proteasome, a multisubunit protease complex. Here we show that expression of this ubiquitin-dependent proteolysis pathway in yeast is activated in response to cadmium exposure and that mutants deficient in specific ubiquitin-conjugating enzymes are hypersensitive to cadmium. Moreover, mutants in the proteasome are hypersensitive to cadmium, suggesting that cadmium resistance is mediated in part by degradation of abnormal proteins. This indicates that a major reason for cadmium toxicity may be cadmium-induced formation of abnormal proteins.

Covalent modification of cellular proteins by the ubiquitin-like modifier SUMO regulates various cellular processes, such as nuclear transport, signal transduction, stress response and cell-cycle progression. But, in contrast to ubiquitylation, sumoylation does not tag proteins for degradation, but seems to enhance their stability or modulate their subcellular compartmentalization.

Proteins modified by multiubiquitin chains are the preferred substrates of the proteasome. Ubiquitination involves a ubiquitin-activating enzyme, E1, a ubiquitin-conjugating enzyme, E2, and often a substrate-specific ubiquitin–protein ligase, E3. Here we show that efficient multiubiquitination needed for proteasomal targeting of a model substrate requires an additional conjugation factor, named E4. This protein, previously known as UFD2 in yeast, binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3. Intriguingly, E4 defines a novel protein family that includes two human members and the regulatory protein NOSA from Dictyostelium required for fruiting body development. In yeast, E4 activity is linked to cell survival under stress conditions, indicating that eukaryotes utilize E4-dependent proteolysis pathways for multiple cellular functions.

Ubiquitin conjugation is known to target protein substrates primarily to degradation by the proteasome or via the endocytic route. Here we describe a novel protein modification pathway in yeast which mediates the conjugation of RUB1, a ubiquitin-like protein displaying 53% amino acid identity to ubiquitin. We show that RUB1 conjugation requires at least three proteins in vivo. ULA1 and UBA3 are related to the N- and C-terminal domains of the E1 ubiquitin-activating enzyme, respectively, and together fulfil E1-like functions for RUB1 activation. RUB1 conjugation also requires UBC12, a protein related to E2 ubiquitin-conjugating enzymes, which functions analogously to E2 enzymes in RUB1-protein conjugate formation. Conjugation of RUB1 is not essential for normal cell growth and appears to be selective for a small set of substrates. Remarkably, CDC53/cullin, a common subunit of the multifunctional SCF ubiquitin ligase, was found to be a major substrate for RUB1 conjugation. This suggests that the RUB1 conjugation pathway is functionally affiliated to the ubiquitin-proteasome system and may play a regulatory role.

Eukaryotic proteins are tagged for degradation by addition of ubiquitin or single amino acids. Now Jentsch discusses a new prokaryotic protein tagging system reported by Keiler et al. ([p. 990][1]) in this issue of Science . In this novel tagging pathway, nascent polypeptides, translated from truncated mRNAs lacking stop codons, receive short COOH-terminal peptide tags encoded by a separate RNA, 10Sa RNA. [1]: /lookup/doi/10.1126/science.271.5251.990

Intracellular protein levels are controlled by protein synthesis and degradation. A major proteolytic pathway of eukaryotes is ATP–dependent and requires the covalent attachment of ubiquitin, a small and highly conserved protein, to proteolytic substrates prior to degradation (for reviews see Finley & Chau 1991, Hershko & Ciechanover 1992, and Jentsch 1992a and b). This pathway is highly selective and mediates the elimination of abnormal proteins and controls the half–lives of some regulatory proteins. Known targets include transcriptional regulators (Hochstrasser et al. 1991), p53 (Scheffner et al. 1990), the Mos kinase (Nishizawa et al. 1992) and cyclins (Glotzer et al. 1991).

Adenovirus E1A encodes two nuclear phosphoproteins that can transform primary rodent fibroblasts in culture. Transformation by E1A is mediated at least in part through binding to several cellular proteins, including the three members of the retinoblastoma family of growth inhibitory proteins. We report here the cloning of a novel murine cDNA whose encoded protein interacts with both adenovirus type 5 and type 12 E1A proteins. The novel E1A-interacting protein shares significant sequence homology with ubiquitin-conjugating enzymes, a family of related proteins that is involved in the proteasome-mediated proteolysis of short-lived proteins. Highest homology was seen with a Saccharomyces cerevisiae protein named UBC9. Importantly, the murine E1A-interacting protein complements a cell cycle defect of a S. cerevisiae mutant which harbors a temperature-sensitive mutation in UBC9. We therefore named this novel E1A-interacting protein mUBC9. We mapped the region of E1A that is required for mUBC9 binding and found that the transformation-relevant conserved region 2 of E1A is required for interaction.

Entry into a new cell cycle is triggered by environmental signals at a point called Start in G1 phase. A key regulator of this transition step in yeast is the CDC28 kinase together with its short-lived regulatory subunits called G1-cyclins or CLN proteins. To identify genes involved in G1-cyclin degradation, we employed a genetic screen by selecting for stable CLN1-beta-galactosidase fusion proteins. Surprisingly, one group of mutants was found to be allelic to GRR1, a gene previously described to be involved in glucose uptake, glucose repression, and divalent cation transport. In grr1 mutants, both CLN1 and CLN2 cyclins are significantly stabilized. A suppressor analysis indicated that G1-cyclin stabilization in grr1 was not a consequence of the nutrient uptake defect. This suggests that the GRR1 gene product is part of a common regulatory pathway linking two functions important for cell growth, nutrient uptake, and G1 cyclin-controlled cell division.

Attachment of ubiquitin to proteins is catalyzed by a family of ubiquitin-conjugating (UBC) enzymes. Although these enzymes are essential for many cellular processes; their molecular functions remain unclear because no physiological target has been identified for any of them. Here we show that four UBC proteins (UBC4, UBC5, UBC6, and UBC7) target the yeast MAT alpha 2 transcriptional regulator for intracellular degradation by two distinct ubiquitination pathways. UBC6 and UBC7 define one of the pathways and can physically associate. The UBC6/UBC7-containing complex targets the Deg1 degradation signal of alpha 2, a conclusion underscored by the finding that UBC6 is encoded by DOA2, a gene previously implicated in Deg1-mediated degradation. These data reveal an unexpected overlap in substrate specificity among diverse UBC enzymes and suggest a combinatorial mechanism of substrate selection in which UBC enzymes partition into multiple ubiquitination complexes.

The ubiquitin-protein conjugation system is involved in a variety of eukaryotic cell functions, including the degradation of abnormal and short-lived proteins, chromatin structure, cell cycle progression, and DNA repair. The ubiquitination of target proteins is catalyzed by a ubiquitin-activating enzyme (E1) and ubiquitin-conjugating enzymes (E2s) and in some cases also requires auxiliary substrate recognition proteins (E3s). Multiple E2s have been found, and these likely possess specificity for different classes of target proteins. Here we report the cloning and characterization of a gene (ubc-2) encoding a ubiquitin-conjugating enzyme which is involved in the selective degradation of abnormal and short-lived proteins in the nematode Caenorhabditis elegans. The nematode ubc-2 gene encodes a 16.7-kDa protein with striking amino acid sequence similarity to Saccharomyces cerevisiae UBC4 and UBC5 and Drosophila UbcD1. When driven by the UBC4 promoter, ubc-2 can functionally substitute for UBC4 in yeast cells; it rescues the slow-growth phenotype of ubc4 ubc5 mutants at normal temperature and restores their ability to grow at elevated temperatures. Western blots (immunoblots) of ubc4 ubc5 yeast cells transformed with ubc-2 reveal a protein of the expected size, which cross-reacts with anti-Drosophila UbcD1 antibody. C. elegans ubc-2 is constitutively expressed at all life cycle stages and, unlike yeast UBC4 and UBC5, is not induced by heat shock. Both trans and cis splicing are involved in the maturation of the ubc-2 transcript. These data suggest that yeast UBC4 and UBC5, Drosophila UbcD1, and C. elegans ubc-2 define a highly conserved gene family which plays fundamental roles in all eukaryotic cells.

Intracellular protein levels are controlled by protein synthesis and degradation. One major proteolytic pathway of eukaryotes requires the covalent attachment of ubiquitin, a small (8.5 kDa) and highly conserved protein, to proteolytic substrates prior to degradation (for reviews see Hershko 1991, Finley and Chau 1991, Jentsch et al. 1991, Jentsch 1992a, Jentsch 1992b). This pathway is highly selective and mediates the elimination of abnormal proteins and controls the half-lives of some regulatory proteins. Known targets include transcriptional regulators (Hochstrasser et al. 1991) p53 (Scheffner et al. 1990) and cyclins (Glotzer et al. 1991).