Orphan quality control shapes network dynamics and gene expression

All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-Myc oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over unpaired transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers opportunities to modulate gene expression in disease.

An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes

Ribosomes frequently stall during mRNA translation, resulting in the context-dependent activation of quality control pathways to maintain proteostasis. However, surveillance mechanisms that specifically respond to stalled ribosomes with an occluded A site have not been identified. We discovered that the elongation factor-1α (eEF1A) inhibitor, ternatin-4, triggers the ubiquitination and degradation of eEF1A on stalled ribosomes. Using a chemical genetic approach, we unveiled a signaling network comprising two E3 ligases, RNF14 and RNF25, which are required for eEF1A degradation. Quantitative proteomics revealed the RNF14 and RNF25-dependent ubiquitination of eEF1A and a discrete set of ribosomal proteins. The ribosome collision sensor GCN1 plays an essential role by engaging RNF14, which directly ubiquitinates eEF1A. The site-specific, RNF25-dependent ubiquitination of the ribosomal protein RPS27A/eS31 provides a second essential signaling input. Our findings illuminate a ubiquitin signaling network that monitors the ribosomal A site and promotes the degradation of stalled translation factors, including eEF1A and the termination factor eRF1.

Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion

Autophagy is essential for protein quality control and regulation of the functional proteome. Failure of autophagy pathways with age contributes to loss of proteostasis in aged organisms and accelerates the progression of age-related diseases. In this work, we show that activity of endosomal microautophagy (eMI), a selective type of autophagy occurring in late endosomes, declines with age and identify the sub-proteome affected by this loss of function. Proteomics of late endosomes from old mice revealed an aberrant glycation signature for Hsc70, the chaperone responsible for substrate targeting to eMI. Age-related Hsc70 glycation reduces its stability in late endosomes by favoring its organization into high molecular weight protein complexes and promoting its internalization/degradation inside late endosomes. Reduction of eMI with age associates with an increase in protein secretion, as late endosomes can release protein-loaded exosomes upon plasma membrane fusion. Our search for molecular mediators of the eMI/secretion switch identified the exocyst-RalA complex, known for its role in exocytosis, as a novel physiological eMI inhibitor that interacts with Hsc70 and acts directly at the late endosome membrane. This inhibitory function along with the higher exocyst-RalA complex levels detected in late endosomes from old mice could explain, at least in part, reduced eMI activity with age. Interaction of Hsc70 with components of the exocyst-RalA complex places this chaperone in the switch from eMI to secretion. Reduced intracellular degradation in favor of extracellular release of undegraded material with age may be relevant to the spreading of proteotoxicity associated with aging and progression of proteinopathies.

Compromised function of the ESCRT pathway promotes endolysosomal escape of tau seeds and propagation of tau aggregation

Intercellular propagation of protein aggregation is emerging as a key mechanism in the progression of several neurodegenerative diseases, including Alzheimer's disease and frontotemporal dementia (FTD). However, we lack a systematic understanding of the cellular pathways controlling prion-like propagation of aggregation. To uncover such pathways, here we performed CRISPR interference (CRISPRi) screens in a human cell-based model of propagation of tau aggregation monitored by FRET. Our screens uncovered that knockdown of several components of the endosomal sorting complexes required for transport (ESCRT) machinery, including charged multivesicular body protein 6 (CHMP6), or CHMP2A in combination with CHMP2B (whose gene is linked to familial FTD), promote propagation of tau aggregation. We found that knocking down the genes encoding these proteins also causes damage to endolysosomal membranes, consistent with a role for the ESCRT pathway in endolysosomal membrane repair. Leakiness of the endolysosomal compartment significantly enhanced prion-like propagation of tau aggregation, likely by making tau seeds more available to pools of cytoplasmic tau. Together, these findings suggest that endolysosomal escape is a critical step in tau propagation in neurodegenerative diseases.

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover 'shared sensitized positions' localized to areas around the hydrophobic patch and the C-terminus. In addition, we identified perturbation specific effects such as a sensitization of His68 in HU and a tolerance to mutation at Lys63 in DTT. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum.

DOI:http://dx.doi.org/10.7554/eLife.15802.001

The ability of an organism to grow and reproduce, that is, it’s “fitness”, is determined by how its genes interact with the environment. Yeast is a model organism in which researchers can control the exact mutations present in the yeast’s genes (its genotype) and the conditions in which the yeast cells live (their environment). This allows researchers to measure how a yeast cell’s genotype and environment affect its fitness.

Ubiquitin is a protein that many organisms depend on to manage cell stress by acting as a tag that targets other proteins for degradation. Essential proteins such as ubiquitin often remain unchanged by mutation over long periods of time. As a result, these proteins evolve very slowly. Like all proteins, ubiquitin is built from a chain of amino acid molecules linked together, and the ubiquitin proteins of yeast and humans are made of almost identical sequences of amino acids.

Although ubiquitin has barely changed its sequence over evolution, previous studies have shown that – under normal growth conditions in the laboratory – most amino acids in ubiquitin can be mutated without any loss of cell fitness. This led Mavor et al. to hypothesize that treating the yeast cells with chemicals that cause cell stress might lead to amino acids in ubiquitin becoming more sensitive to mutation.

To test this idea, a class of graduate students at the University of California, San Francisco grew yeast cells with different ubiquitin mutations together, and with different chemicals that induce cell stress, and measured their growth rates. Sequencing the ubiquitin gene in the thousands of tested yeast cells revealed that three of the chemicals cause a shared set of amino acids in ubiquitin to become more sensitive to mutation.

This result suggests that these amino acids are important for the stress response, possibly by altering the ability of yeast cells to target certain proteins for degradation. Conversely, another chemical causes yeast to become more tolerant to changes in the ubiquitin sequence. The experiments also link changes in particular amino acids in ubiquitin to specific stress responses.

Mavor et al. show that many of ubquitin’s amino acids are sensitive to mutation under different stress conditions, while others can be mutated to form different amino acids without effecting fitness. By testing the effects of other chemicals, future experiments could further characterize how the yeast’s genotype and environment interact.

DOI:http://dx.doi.org/10.7554/eLife.15802.002

Cytoplasmic Dynein Antagonists with Improved Potency and Isoform Selectivity

Cytoplasmic dyneins 1 and 2 are related members of the AAA+ superfamily (ATPases associated with diverse cellular activities) that function as the predominant minus-end-directed microtubule motors in eukaryotic cells. Dynein 1 controls mitotic spindle assembly, organelle movement, axonal transport, and other cytosolic, microtubule-guided processes, whereas dynein 2 mediates retrograde trafficking within motile and primary cilia. Small-molecule inhibitors are important tools for investigating motor protein-dependent mechanisms, and ciliobrevins were recently discovered as the first dynein-specific chemical antagonists. Here, we demonstrate that ciliobrevins directly target the heavy chains of both dynein isoforms and explore the structure–activity landscape of these inhibitors in vitro and in cells. In addition to identifying chemical motifs that are essential for dynein blockade, we have discovered analogs with increased potency and dynein 2 selectivity. These antagonists effectively disrupt Hedgehog signaling, intraflagellar transport, and ciliogenesis, making them useful probes of these and other cytoplasmic dynein 2-dependent cellular processes.

Redefining therapeutic success with virtual reality exposure therapy

The success rate for treating phobias with in vivo exposure is high. Unfortunately, few phobics (less than 15-20%) ever seek treatment. Virtual reality (VR) exposure therapy is also proving to be highly effective. The present surveys assessed 162 students high in fear of spiders. In Study 1, when asked to choose between multisession in vivo exposure vs. multisession VR exposure therapy, 81% chose VR. In Study 2, comparing one-session in vivo versus multisession VR exposure therapy, 89% chose VR. Results suggest that VR exposure therapy may prove valuable for increasing the number of phobics who seek treatment.

Perceived job image among police officers in Singapore: factorial dimensions and differential effects

The authors examined the perceived job image of police officers in Singapore and its differential effects on their work-related attitudes (e.g., job satisfaction, organizational commitment, and intention to quit). The authors obtained data from questionnaire surveys and focus-group interviews. Perceived job image consisted of 4 dimensions: (a) prestige, (b) integrity, (c) competence, and (d) nonroutine job nature. Results of hierarchical regression analyses suggested that the first 2 dimensions of the perceived job image construct were salient in affecting the police officers' work-related attitudes.

Listening to discourse in distracting settings: the effects of aging

Younger and older adults listened to discourse in quiet and in conversational noise, before answering questions concerning the material. Some questions required listeners to recall specific details; others were of a more integrative nature. When the listening situation was adjusted for individual differences in hearing, younger and older adults were equally adept at remembering the gist of the passages in both quiet and in two levels of noise. The two age groups also did not differ with respect to memory for specific details when listening in quiet or in a moderate level of noise, even when required to perform a concurrent task. Only at the loudest noise level did younger adults tend to recall more detail than older adults. However, when no adjustments were made to compensate for the poorer hearing of older adults (all participants tested under identical listening conditions), older adults could not recall as much detail as younger adults, either in quiet or in noise. The results indicate that the speech-comprehension difficulties of older adults primarily reflect declines in hearing rather than in cognitive ability.

Listening to discourse in distracting settings: the effects of aging

Younger and older adults listened to discourse in quiet and in conversational noise, before answering questions concerning the material. Some questions required listeners to recall specific details; others were of a more integrative nature. When the listening situation was adjusted for individual differences in hearing, younger and older adults were equally adept at remembering the gist of the passages in both quiet and in two levels of noise. The two age groups also did not differ with respect to memory for specific details when listening in quiet or in a moderate level of noise, even when required to perform a concurrent task. Only at the loudest noise level did younger adults tend to recall more detail than older adults. However, when no adjustments were made to compensate for the poorer hearing of older adults (all participants tested under identical listening conditions), older adults could not recall as much detail as younger adults, either in quiet or in noise. The results indicate that the speech-comprehension difficulties of older adults primarily reflect declines in hearing rather than in cognitive ability.

Patronizing the old: how do younger and older adults respond to baby talk in the nursing home?

To test the implications of Communication Accommodation Theory for intergenerational talk to dependent older persons, eighty young adults and seventy-one older adults evaluated speakers in a brief taped conversation. Specifically, the study was conducted to determine whether the apparent nurturant quality of the baby talk tone of voice and parental style would compensate for the lack of respect associated with this type of patronizing talk to elders. The talk was either secondary baby talk or a neutral variant addressed to an elderly resident in a nursing home by either a nurse or a volunteer. The caregivers who used baby talk were rated as significantly less respectful and competent than their peers in the neutral condition, but no differences were observed for nurturance of the caregiver. The recipients of baby talk were perceived to be less satisfied with the interaction. These findings were true for both caregiver roles and both respondent age groups.

Age-based beliefs about memory changes for self and others across adulthood

This study is intended to clarify the nature of beliefs about aging and memory. Earlier experiments (e.g., Ryan, 1992) had demonstrated that more frequent everyday memory problems are expected for typical older adults than for typical young adults. We used three self-efficacy scales of the Metamemory in Adulthood instrument (Dixon & Hultsch, 1983) to examine whether age changes are anticipated for oneself as well as for typical adults. Volunteers (N = 224; mean age = 35 years) completed the questionnaire about the memory of either typical adults (aged 25, 45, 65, or 85 years) or themselves at one of these ages. The anticipation of decline was obtained on two of the three self-efficacy scales (i.e., capacity and change) for both typical adults and for oneself. In contrast to Ryan's 1992 study, significant differentiation between target ages of 45 and 65 was observed on these more age-sensitive measures. Beliefs about memory change across adulthood were no weaker for the self than for typical others. Hence, this study supports the potential influence of general age-based beliefs upon individual self-efficacy beliefs and memory performance.