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In eukaryotic cells, proteasomes exist primarily as 26S holoenzymes, the most efficient configuration for ubiquitinated protein degradation. Here, we show that acute oxidative stress caused by environmental insults or mitochondrial defects results in rapid disassembly of 26S proteasomes into intact 20S core and 19S regulatory particles. Consequently, polyubiquitinated substrates accumulate, mitochondrial networks fragment, and cellular reactive oxygen species (ROS) levels increase. Oxidation of cysteine residues is sufficient to induce proteasome disassembly, and spontaneous reassembly from existing components is observed both in vivo and in vitro upon reduction. Ubiquitin-dependent substrate turnover also resumes after treatment with antioxidants. Reversible attenuation of 26S proteasome activity induced by acute mitochondrial or oxidative stress may be a short-term response distinct from adaptation to long-term ROS exposure or changes during aging.

Cdc48/p97 is an evolutionary conserved ubiquitin-dependent chaperone involved in a broad array of cellular functions due to its ability to associate with multiple cofactors. Aside from its role in removing RNA polymerase II from chromatin after DNA damage, little is known about how this AAA-ATPase is involved in the transcriptional process. Here, we show that yeast Cdc48 is recruited to chromatin in a transcription-coupled manner and modulates gene expression. Cdc48, together with its cofactor Ubx3 controls monoubiquitylation of histone H2B, a conserved modification regulating nucleosome dynamics and chromatin organization. Mechanistically, Cdc48 facilitates the recruitment of Lge1, a cofactor of the H2B ubiquitin ligase Bre1. The function of Cdc48 in controlling H2B ubiquitylation appears conserved in human cells because disease-related mutations or chemical inhibition of p97 function affected the amount of ubiquitylated H2B in muscle cells. Together, these results suggest a prominent role of Cdc48/p97 in the coordination of chromatin remodeling with gene transcription to define cellular differentiation processes.

Proteome stability is central to cellular function and the lifespan of an organism. This is apparent in muscle cells, where incorrect folding and assembly of the sarcomere contributes to disease and aging. Apart from the myosin-assembly factor UNC-45, the complete network of chaperones involved in assembly and maintenance of muscle tissue is currently unknown. To identify additional factors required for sarcomere quality control, we performed genetic screens based on suppressed or synthetic motility defects in Caenorhabditis elegans. In addition to ethyl methyl sulfonate-based mutagenesis, we employed RNAi-mediated knockdown of candidate chaperones in unc-45 temperature-sensitive mutants and screened for impaired movement at permissive conditions. This approach confirmed the cooperation between UNC-45 and Hsp90. Moreover, the screens identified three novel co-chaperones, CeHop (STI-1), CeAha1 (C01G10.8) and Cep23 (ZC395.10), required for muscle integrity. The specific identification of Hsp90 and Hsp90 co-chaperones highlights the physiological role of Hsp90 in myosin folding. Our work thus provides a clear example of how a combination of mild perturbations to the proteostasis network can uncover specific quality control modules.

The endoplasmic reticulum (ER) is a cellular compartment that has a key function in protein translation and folding. Maintaining its integrity is of fundamental importance for organism's physiology and viability. The dynamic regulation of intraluminal ER Ca2+ concentration directly influences the activity of ER-resident chaperones and stress response pathways that balance protein load and folding capacity. We review the emerging evidence that microRNAs play important roles in adjusting these processes to frequently changing intracellular and environmental conditions to modify ER Ca2+ handling and storage and maintain ER homeostasis.

The BH3-only protein NOXA represents one of the critical mediators of DNA-damage-induced cell death. In particular, its involvement in cellular responses to cancer chemotherapy is increasingly evident. Here, we identify a strategy of cancer cells to escape genotoxic chemotherapy by increasing proteasomal degradation of NOXA. We show that the deubiquitylating enzyme UCH-L1 is a key regulator of NOXA turnover, which protects NOXA from proteasomal degradation by removing Lys(48)-linked polyubiquitin chains. In the majority of tumors from patients with melanoma or colorectal cancer suffering from high rates of chemoresistance, NOXA fails to accumulate because UCH-L1 expression is epigenetically silenced. Whereas UCH-L1/NOXA-positive tumor samples exhibit increased sensitivity to genotoxic chemotherapy, downregulation of UCH-L1 or inhibition of its deubiquitylase activity resulted in reduced NOXA stability and resistance to genotoxic chemotherapy in both human and C. elegans cells. Our data identify the UCH-L1/NOXA interaction as a therapeutic target for overcoming cancer chemoresistance.

DNA damage responses have been well characterized with regard to their cell-autonomous checkpoint functions leading to cell cycle arrest, senescence and apoptosis(1). In contrast, systemic responses to tissue-specific genome instability remain poorly understood. In adult Caenorhabditis elegans worms germ cells undergo mitotic and meiotic cell divisions, whereas somatic tissues are entirely post-mitotic. Consequently, DNA damage checkpoints function specifically in the germ line(2), whereas somatic tissues in adult C. elegans are highly radio-resistant(3). Some DNA repair systems such as global-genome nucleotide excision repair (GG-NER) remove lesions specifically in germ cells(4). Here we investigated how genome instability in germ cells affects somatic tissues in C. elegans. We show that exogenous and endogenous DNA damage in germ cells evokes elevated resistance to heat and oxidative stress. The somatic stress resistance is mediated by the ERK MAP kinase MPK-1 in germ cells that triggers the induction of putative secreted peptides associated with innate immunity. The innate immune response leads to activation of the ubiquitin-proteasome system (UPS) in somatic tissues, which confers enhanced proteostasis and systemic stress resistance. We propose that elevated systemic stress resistance promotes endurance of somatic tissues to allow delay of progeny production when germ cells are genomically compromised.

Sirtuins, a family of histone deacetylases, have a fiercely debated role in regulating lifespan. In contrast with recent observations, here we find that overexpression of sir-2.1, the ortholog of mammalian SirT1, does extend Caenorhabditis elegans lifespan. Sirtuins mandatorily convert NAD(+) into nicotinamide (NAM). We here find that NAM and its metabolite, 1-methylnicotinamide (MNA), extend C. elegans lifespan, even in the absence of sir-2.1. We identify a previously unknown C. elegans nicotinamide-N-methyltransferase, encoded by a gene now named anmt-1, to generate MNA from NAM. Disruption and overexpression of anmt-1 have opposing effects on lifespan independent of sirtuins, with loss of anmt-1 fully inhibiting sir-2.1-mediated lifespan extension. MNA serves as a substrate for a newly identified aldehyde oxidase, GAD-3, to generate hydrogen peroxide, which acts as a mitohormetic reactive oxygen species signal to promote C. elegans longevity. Taken together, sirtuin-mediated lifespan extension depends on methylation of NAM, providing an unexpected mechanistic role for sirtuins beyond histone deacetylation.

Fehlgefaltete Proteine des sekretorischen Weges werden aus dem Endoplasmatischen Retikulum (ER) in das Zytosol transportiert und dort durch das Ubiquitin-Proteasom-System abgebaut. Dieser Qualitätskontrollmechanismus wird als Endoplasmatisches Retikulum-assoziierte Proteindegradation bezeichnet (ERAD). In der Bäckerhefe Saccharomyces cerevisiae stellt die HRD-Ubiquitinligase eine zentrale Komponente dieses Abbausystems dar. Eine Untereinheit dieses Multienzymkomplexes ist das ER-ständige Membranprotein Der1, das über den Faktor Usa1 an die Ubiquitinligase Hrd1 rekrutiert wird und ausschließlich für den Abbau löslicher luminaler ERAD-Substrate notwendig ist. Im Rahmen dieser Arbeit konnte gezeigt werden, dass der C-Terminus von Der1 die Interaktion zu Usa1 und damit die Rekrutierung des Proteins zur HRD-Ligase vermittelt. Usa1 wirkt nicht nur als Rekrutierungsfaktor, sondern induziert auch die Der1-Oligomerisierung. Punktmutationen in den Transmembrandomänen von Der1 beeinträchtigen die Dislokation luminaler Substratproteine aus dem ER. Um weitere Hinweise für eine Beteiligung von Der1 beim Substrattransport zu erhalten, wurde die Methode des zielgerichtetem in vivo photocrosslinking für Der1 angewendet. Hierbei wurden bestimmte Positionen von Der1 mit dem photoreaktiven Aminosäureanalogon p-Benzoylphenylalanin markiert, was die Ausbildung von Quervernetzungen von Der1 zu Interaktionspartnern nach einer UV-Bestrahlung ermöglichte. Schließlich konnte auf diese Weise eine räumliche Nähe der luminal exponierten Bereiche von Der1 zum Substratrezeptor Hrd3 gezeigt werden, während die Transmembransegmente Quervernetzungen zu Hrd1 ausbildeten. Beide Bereiche von Der1 konnten zudem mit einem luminalen ERAD-Substrat quervernetzt werden. Anhand dieser Ergebnisse wurde somit erstmals eine direkte Beteiligung von Der1 insbesondere in den ersten Schritten der Substratdislokation gezeigt, was eine Funktion von Der1 als zentrale Komponente des Exportkomplexes nahelegt., Newly synthesized proteins of the secretory pathway are subjected to an efficient quality control system in the endoplasmic reticulum. In order to prevent a harmful aggregation misfolded proteins are exported via a largely unknown mechanism into the cytosol and degraded by the ubiquitin-proteasome system in a process termed ER associated degradation (ERAD). In the yeast Saccharomyces cerevisiae the HRD-ligase constitutes a central component of ERAD. A subunit of this multi-enzyme complex is the small multispanning membrane protein Der1, which is exclusively required for the degradation of misfolded ER luminal proteins but dispensable for the turnover of membrane-bound substrates. In this study a short conserved motif in the cytosolic carboxyterminus of Der1 was identified that mediates the binding to the HRD-ligase. Moreover, co-immunoprecipitation experiments show that Der1 forms oligomers, which relies on its assembly into the degradation complex. Mutations in the transmembrane domains of Der1 block the export of soluble proteins across the ER-membrane. To further investigate the function of Der1 in substrate dislocation an in vivo site-specific photocrosslinking approach was applied. Various positions of Der1 were labelled with the photoreactive amino acid analogue p-benzoyl-phenylalanine followed by UV irradiation of living cells expressing these Der1 constructs. The crosslinking experiments reveal a spatial proximity of ER luminal exposed parts of Der1 to the substrate receptor Hrd3. By contrast, the membrane-embedded domains of Der1 reside adjacent to the ubiquitin ligase Hrd1. Intriguingly, both regions also form crosslinks to a client protein. In summary the data of this work imply that multimeric Der1 initiates the export of aberrant polypeptides from the ER-lumen by threading such molecules into the ER-membrane and routing them to Hrd1 for ubiquitylation.

Ubiquitination plays a crucial role in neurodevelopment as exemplified by Angelman syndrome, which is caused by genetic alterations of the ubiquitin ligase-encoding UBE3A gene. Although the function of UBE3A has been widely studied, little is known about its paralog UBE3B. By using exome and capillary sequencing, we here identify biallelic UBE3B mutations in four patients from three unrelated families presenting an autosomal-recessive blepharophimosis-ptosis-intellectual-disability syndrome characterized by developmental delay, growth retardation with a small head circumference, facial dysmorphisms, and low cholesterol levels. UBE3B encodes an uncharacterized E3 ubiquitin ligase. The identified UBE3B variants include one frameshift and two splice-site mutations as well as a missense substitution affecting the highly conserved HECT domain. Disruption of mouse Ube3b leads to reduced viability and recapitulates key aspects of the human disorder, such as reduced weight and brain size and a downregulation of cholesterol synthesis. We establish that the probable Caenorhabditis elegans ortholog of UBE3B, oxi-1, functions in the ubiquitin/proteasome system in vivo and is especially required under oxidative stress conditions. Our data reveal the pleiotropic effects of UBE3B deficiency and reinforce the physiological importance of ubiquitination in neuronal development and function in mammals.

Faithful transmission of genomic information requires tight spatiotemporal regulation of DNA replication factors. In the licensing step of DNA replication, CDT-1 is loaded onto chromatin to subsequently promote the recruitment of additional replication factors, including CDC-45 and GINS. During the elongation step, the CDC-45/GINS complex moves with the replication fork; however, it is largely unknown how its chromatin association is regulated. Here, we show that the chaperone-like ATPase CDC-48/p97 coordinates degradation of CDT-1 with release of the CDC-45/GINS complex. C. elegans embryos lacking CDC-48 or its cofactors UFD-1/NPL-4 accumulate CDT-1 on mitotic chromatin, indicating a critical role of CDC-48 in CDT-1 turnover. Strikingly, CDC-48(UFD-1/NPL-4)-deficient embryos show persistent chromatin association of CDC-45/GINS, which is a consequence of CDT-1 stabilization. Moreover, our data confirmed a similar regulation in Xenopus egg extracts, emphasizing a conserved coordination of licensing and elongation events during eukaryotic DNA replication by CDC-48/p97.

The accumulation of the human tumor suppressor 53BP1 at DNA damage sites requires the ubiquitin ligases RNF8 and RNF168. As 53BP1 recognizes dimethylated Lys20 in histone H4 (H4K20me2), the requirement for RNF8- and RNF168-mediated ubiquitylation has been unclear. Here we show that RNF8-mediated ubiquitylation facilitates the recruitment of the AAA-ATPase valosin-containing protein (VCP, also known as p97) and its cofactor NPL4 to sites of double-strand breaks. RIDDLE cells, which lack functional RNF168, also show impaired recruitment of VCP to DNA damage. The ATPase activity of VCP promotes the release of the Polycomb protein L3MBTL1 from chromatin, which also binds the H4K20me2 histone mark, thereby facilitating 53BP1 recruitment. Consistent with this, nematodes lacking the VCP orthologs CDC-48.1 or CDC-48.2, or cofactors UFD-1 or NPL-4, are highly sensitive to ionizing radiation. Our data suggest that human RNF8 and RNF168 promote VCP-mediated displacement of L3MBTL1 to unmask 53BP1 chromatin binding sites.