Mechanisms Linking Mitochondrial Dysfunction and Proteostasis Failure

TICB 1577 No. of Pages 12

Trends in Cell Biology

Review

Mechanisms Linking Mitochondrial Dysfunction and Proteostasis Failure Bingwei Lu1,* and Su Guo2 Maintaining cellular protein homeostasis (proteostasis) is an essential task for all eukaryotes. Proteostasis failure worsens with aging and is considered a cause of and a therapeutic target for age-related diseases including neurodegenerative disorders. The cellular networks regulating proteostasis and the pathogenic events driving proteostasis failure in disease remain poorly understood. Model organism studies in yeast and Drosophila reveal an intriguing link between mitochondrial function and proteostasis. In this review we examine recent findings on mitochondrial outer membrane (MOM)-associated mRNA translation, how this process is sensitive to mitochondrial dysfunction and constantly surveyed by ribosome-associated quality control (RQC), and how defects in this process generate aberrant proteins with unusual C-terminal extensions (CTEs) that promote aggregation and drive proteostasis failure. We also discuss the implications for human diseases.

Highlights

An Intimate Connection between Mitochondrial Function and Cytosolic Proteostasis

Translation stalling-induced protein Cterminal extension can cause protein aggregation, proteostasis failure, and contribute to disease.

Proteostasis refers to a cellular state in which protein synthesis, folding, and degradation are maintained in a homeostatic state such that an intact yet dynamic proteome is preserved to meet the changing demands of cellular functions under differing conditions [1]. It is generally believed that cellular mechanisms preserving proteostasis decline with age, contributing to the pathogenesis of age-related diseases [2]. Previous studies have emphasized the importance of the quality control of fully synthesized mature proteins in proteostasis maintenance. However, the life cycle of a protein begins when it is synthesized on ribosomes, and a RQC mechanism is closely surveying the quality of nascent peptides [3,4]. Defects in RQC can lead to perturbed proteostasis and is associated with neurodegeneration in mammals [5,6]. Recent studies in yeast and metazoans highlight the intimate connection between RQC and mitochondrial health [7,8]. Mitochondria are archetypal organelles in biology. In addition to producing ATP, these morphologically dynamic organelles possess highly varied proteome landscapes, are home to a vast array of metabolic pathways, and control essential cellular signaling processes from Ca2+ homeostasis to apoptosis [9]. We are still learning new roles of mitochondria as important signaling organelles [10,11]. For example, in yeast, mitochondria serve as a site where heat shock-induced misfolded proteins are imported and degraded [12], and ROS released by defective mitochondria has been shown to influence the cytosolic translation machinery, presumably through redox regulation of ribosomal proteins [13]. These studies strongly support the existence of an intimate link between mitochondrial function and cytosolic protein translation and proteostasis (Figure 1). Proteostasis failure manifested as the formation of aberrant protein aggregates is a defining feature of age-related neurodegenerative diseases [14–16]. These hallmark aggregates include those composed of the amyloid beta peptide in Alzheimer’s disease (AD) (amyloid plaques), α-synuclein in Parkinson’s disease (PD) and other synucleinopathies (Lewy bodies), tau in AD and related tauopathies (neurofibrillary tangles), SOD1, TDP-43, FUS, and dipeptide Trends in Cell Biology, Month 2020, Vol. xx, No. xx

Co-translational import of nucleusencoded mitochondrial proteins is a common feature in eukaryotes. Defects in the synthesis of nucleusencoded mitochondrial proteins on the mitochondrial surface are found in Parkinson’s disease. Mitochondrial stress can cause inefficient translation termination and/or recycling of mitochondrial outer membraneassociated ribosomes, triggering translation stalling and ribosome-associated quality control.

Mitochondrial stress-induced aberrant protein C-terminal extension mechanistically links mitochondrial dysfunction with cytosolic proteostasis failure. Mitochondrial dysfunction and proteostasis failure, along with oxidative stress and inflammation, are hallmarks of aging and age-related diseases

1

Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA 2 Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, UCSF, San Francisco, CA 94158, USA

*Correspondence: [email protected] (B. Lu).

https://doi.org/10.1016/j.tcb.2020.01.008 © 2020 Elsevier Ltd. All rights reserved.

1

Trends in Cell Biology

Glossary

Trends in Cell Biology

Figure 1. Possible Mechanisms of Mitochondrial Involvement in Cellular Proteostasis. Protein synthesis, chaperone-assisted protein folding, and the degradation of aberrant proteins represent major events in the proteostasis network. These events are performed by megamachineries and consume a large amount of ATP, which is provided primarily by mitochondria under normal conditions (A). Under extreme conditions, such as when yeast cells are under heat shock, many cellular proteins are denatured and misfolded and form aggregates. Persistent stress will overwhelm the cytosolic protein quality control systems. While a majority of misfolded proteins are targeted for degradation by the cytosolic proteasome, some of the protein aggregates are imported into mitochondria through the translocase of outer membrane (TOM)/translocase of inner membrane (TIM) complex and targeted for degradation by mitochondrial proteases. If the burden of protein aggregates exceeds the capacity of mitochondrial proteases, mitophagy may be triggered to target the whole organelle containing aberrant proteins for degradation (B). Cells also synthesize certain nucleus-encoded mitochondrial proteins on mitochondrial surfaces using the cytosolic ribosomes. This process ensures that components of the multiprotein complexes such as the respiratory chain complexes, which are encoded by both the nuclear and mitochondrial genomes and are translated by both cytosolic and mitochondrial ribosomes, are made at the right stoichiometry. Dysregulation in this process can perturb mitochondrial proteostasis and trigger the mitochondrial unfolded protein response (C).

repeats (DPRs) in amyotrophic lateral sclerosis (ALS), and polyglutamine tracks in trinucleotide repeat disorders such as Huntington’s disease (HD). While protein aggregation may serve some normal function in biology and be protective at times [17], its persistence in cells can impair essential cellular proteins or structures and be detrimental. Another common pathological feature of neurodegenerative diseases is mitochondrial dysfunction [16,18,19]. Mitochondrial dysfunction has been profoundly implicated in other major human diseases, including cancer and diabetes, and in the aging process [20]. Gene products disrupted in major neurodegenerative diseases such as AD and PD associate with or enter into mitochondria and regulate essential mitochondrial functions [19,21–24]. Moreover, at least in the case of PD, certain environmental toxins [25] and genetic lesions [26] cause disease by specifically targeting mitochondria, supporting a primary 2

Trends in Cell Biology, Month 2020, Vol. xx, No. xx

CAT-tailing: unusual protein CTE by random Ala and Thr addition, which occurs on stalled NPCs still attached on the 60S subunit of stalled ribosomes after the 40S and the template mRNA have been removed. Its physiological role remains unclear. Co-translational import: a cell biological process whereby nucleusencoded mitochondrial protein mRNAs are translated by cytoplasmic ribosomes on the mitochondrial surface and the nascent peptides are simultaneously imported into mitochondria through the import complex. Defective ribosome-associated peptides (DRiPs): peptides derived from newly synthesized proteins that are somehow defective in sequence or folding and degraded. Such peptides are thought to be the major source of MHC class I peptides presented to T cells. MISTERMINATE: mitochondrial stress-induced translational termination impairment and protein carboxyl terminal extension; since such C-terminally extended proteins are aggregation prone, MISTERMINATE is considered a process that links mitochondrial stress to cytosolic proteostasis failure seen in neurodegenerative diseases. Mitophagy: cell biological process by which dysfunctional or defective mitochondria are targeted for degradation by the autophagy machinery. Mitophagy is considered a cytoprotective mechanism. However, under certain conditions excessive mitophagy can be detrimental to cells. PINK1–Parkin pathway: a genetic pathway in which PINK1 and Parkin, two genes mutated in familial PD, work together to protect mitochondrial health, with PINK1 working upstream of Parkin. This pathway was initially defined through genetic studies in Drosophila and later shown to be conserved in mammals. PINK1 encodes a Ser/Thr kinase targeted to mitochondria and Parkin encodes an E3 ubiquitin ligase. Prion: a term coined by Stanley Prusiner for infectious protein assemblies that can convert normal proteins to pathogenic conformations and thus transmit disease between individuals. Although prions were initially discovered in scrapie, an infectious degenerative disease affecting sheep and goats, recent studies suggest that

Trends in Cell Biology

role of mitochondrial dysfunction in disease pathogenesis. How mitochondrial dysfunction arises and moreover contributes to the often tissue- and cell type-specific neurodegenerative disease pathologies remains enigmatic. While mitochondria metabolism are important to neuronal function, including synaptic transmission [27], and bioenergetics failure may partially explain the susceptibility of energy-demanding neuromuscular tissues, energy supplementation has been largely ineffective in treating diseases associated with mitochondrial dysfunction, necessitating therapeutic strategies targeting other pathogenic events originating from mitochondrial impairment [20]. The coexistence of proteostasis failure and mitochondrial dysfunction as hallmarks of neurodegenerative diseases raises the tantalizing possibility that these two pathologies are mechanistically linked. Consistent with this notion, in animal PD models featuring prominent mitochondrial dysfunction, genetic manipulation of protein synthesis has proved to be beneficial [7,28–31]. Similarly, in a mouse model of Leigh syndrome caused by genetic disruption of the mitochondrial complex-I subunit NDUFS1, treatment with rapamycin, a specific inhibitor of the mechanistic target of rapamycin (mTOR) pathway that stimulates cytosolic mRNA translation and other anabolic processes, enhances survival and attenuates disease progression [32]. In AD, conserved features of the mitochondrial stress response have been observed [33]. In worm and mouse models of AD, genetic or pharmacological manipulation of mitochondrial translation or mitophagy (see Glossary) reduces amyloid aggregation, improves cognitive capacity, and increases animal fitness [33,34]. However, molecular mechanisms linking mitochondria to proteostasis regulation that are relevant to disease remain to be delineated [35]. Recent studies are starting to provide some clues.

the seemingly noninfectious major neurodegenerative diseases, including AD and PD, may be caused by agents with prion-like properties, such as amyloid beta, tau and α-synuclein. Translocase of outer membrane (TOM)/translocase of inner membrane (TIM) complex: a protein complex located on the MOM and IMM that conducts protein import from the cytosol into mitochondrial compartments. It comprises proteins that form import channels and peripheral proteins that assist in protein docking, translocation, and folding.

Cytosolic Ribosomes Are Recruited to the MOM Mitochondria are complex organelles the MOM), the inner mitochondrial membrane (IMM), the intermembrane space (IMS), and the matrix. Of the more than 1000 protein components of human mitochondria [36], only 13 are encoded by the mitochondrial genome. Therefore, most mitochondrial proteins are encoded by the nuclear genome, synthesized in the cytosol, and delivered to mitochondria, primarily through the translocase of outer membrane (TOM)/translocase of inner membrane (TIM) complex. The conventional view is that these proteins are fully synthesized in the cytoplasm as pre-proteins and then imported into mitochondria with the help of mitochondrial targeting sequences [37], which are subsequently cleaved from the mature protein after import. Studies in yeast and metazoans, however, have challenged this view by demonstrating that many mitochondrial proteins are synthesized on the MOM and engage in co-translational import [29,38,39]. These new findings corroborate a previous observation made by Ronald Butow and colleagues in the 1970s. By electron microscopy, they showed that cytosolic ribosomes were present on the MOM and that their abundance responded to cellular metabolic status [40]. Recent studies in yeast using electron cryotomography offered structural insights on the cytosolic ribosomes associated with the MOM [41]. The logic of deploying a co-translational import mechanism at mitochondria is not immediately clear. It is possible that cotranslational import of these often hydrophobic, membrane-embedded mitochondrial proteins serves to avoid their misfolding, aggregation, or mistargeting in the cytoplasm. It is also possible that by making multisubunit complexes such as complex-I on demand, through coordinating the synthesis of nuclear and mitochondrial DNA-encoded subunits, cells may prevent the accumulation of unassembled subunits in the cytosol or inside mitochondria, which could perturb proteostasis at both locations [35]. Other styles of protein import into mitochondria may also exist (e.g., an ER surface retrieval pathway is shown to safeguard mitochondrial membrane protein import in yeast [42]). Co-translational import of nucleus-encoded mitochondrial proteins is regulated by the Pteninduced kinase 1 (PINK1)–Parkin pathway [29], mutations in which cause familial PD. The Trends in Cell Biology, Month 2020, Vol. xx, No. xx

3

Trends in Cell Biology

PINK1–Parkin pathway was initially shown in Drosophila to critically maintain mitochondrial function [43–45]. Previous studies have emphasized its role in mitophagy, a cellular process that targets dysfunctional or damaged mitochondria for autophagic clearance [46,47]. Recent studies reveal that PINK1 and Parkin also regulate the recruitment of nucleus-encoded respiratory chain component (nRCC) mRNAs, including complex-I 30 kD (C-I30) mRNA, to the MOM and direct their local translation in both Drosophila neuromuscular tissues and mammalian induced dopaminergic neurons (iDNs) (Figure 2). Defects in this process affect mitochondrial structure and function and contribute to PD pathogenesis in Drosophila and human iDN models [29]. It appears that co-translational import of nRCC mRNA into the mitochondria represents an earlier event in the continuum of a PINK1/Parkin-directed mitochondrial quality control (MQC) program (Box 1). nRCC mRNAs have also been shown to be localized to axonal mitochondria [48], and the position of axonal mitochondria plays an important role in coordinating intra-axonal protein synthesis and marking axonal branching sites [49]. It will be interesting to test whether the PINK1–Parkin pathway is involved.

MOM-Associated Translation Is Stalled by Mitochondrial Stress The strategic positioning of select nRCC mRNAs on the MOM for co-translational import also makes their translation sensitive to the functional status of mitochondria. For example, a drop in mitochondrial membrane potential, the driving force of protein import through the TIM complex [50], would cause a slowdown of the import of MOM-associated nascent peptides. This would lead to the collision of translating ribosomes on the MOM, a triggering event for RQC [51,52]. RQC is a recently described cellular quality control mechanism that handles stalled translation (Box 2). During nascent peptide chain (NPC) synthesis, the translating ribosomes could be stalled for a number of reasons, including mRNA defects, strong mRNA secondary structures, insufficient supply of aminoacyl-

Trends in Cell Biology

Figure 2. Mitochondrial Outer Membrane (MOM)-Associated mRNA Translation and Its Regulation by PtenInduced Kinase 1 (PINK1)/Parkin. Select nRCC mRNAs such as C-I30 mRNA are recruited to mitochondrial surfaces and the newly synthesized proteins are co-translationally imported into mitochondria through the translocase of outer membrane (TOM)/translocase of inner membrane (TIM) complex in Drosophila neuromuscular tissues and mammalian cells. This process is regulated by the PINK1–Parkin pathway in metazoans. PINK1 plays a role first in recruiting the mRNA/ribosome/mRNP complex from the cytosol to the MOM (Step I). During this process, the mRNA/ribosome/mRNP complex is translationally repressed by RNA-binding proteins such as Pumillio and Gloround/hnRNP-F bound to the 3′UTRs of the mRNA. On arrival of the mRNP complex at the MOM, PINK1 releases translational repression by promoting the degradation of the repressors by Parkin and further recruiting translational activators such as PABP and eIF4G (Step II). Since C-I30 and PINK1/Parkin are not present in yeast, this mechanism is specific to metazoans. It remains to be seen whether similar mechanisms but different players are involved in regulating MOM-associated mRNA translation in yeast.

4

Trends in Cell Biology, Month 2020, Vol. xx, No. xx

Trends in Cell Biology

Box 1. MQC Mechanism and Function Mitochondria are dynamic and complex organelles with essential roles in many aspects of biology, from energy production to intermediary metabolism to apoptosis. While a great deal has been learned about the physiological and pathophysiological roles of mitochondria, how eukaryotes monitor mitochondrial health and maintain organelle function, however, are relatively underexplored. In its simplest form, MQC can be envisioned as a cellular response mechanism to deal with dysfunctional mitochondria. This can be achieved by refolding or removal of misfolded/damaged proteins by chaperones/proteases from the inside and outside of the mitochondria, fusion with healthy mitochondria to restore organelle function via complementation and exchange of metabolites, or autophagic removal of badly damaged mitochondria that are beyond repair [46,47,84]. A mechanistic understanding and holistic view of this critical cellular process is currently lacking. Drosophila has served as a model system to uncover basic mechanisms underlying the regulation and function of MQC, thanks to the powerful tools available in this model organism and the generally high-level conservation of the mechanisms and function of mitochondrial regulation. Genetic studies in Drosophila have delineated a conserved signaling pathway governing MQC. This pathway was initially defined by PINK1 and the E3 ubiquitin ligase Parkin, with PINK1 acting upstream of Parkin [43–45]. The physiological importance of MQC to post-mitotic neurons is demonstrated by the association of mutations in PINK1 and Parkin with familial PD featuring degeneration of dopaminergic (DA) neurons, which has also been observed in Drosophila PINK1 and Parkin mutants. Although the involvement of the PINK1–Parkin pathway in mitophagy regulation is broad and has been extended to mammalian systems, it is now becoming clear that there exist PINK1/Parkin-independent mitophagy pathways [85–87] and that before its triggering of mitophagy, the PINK1–Parkin pathway performs other functions to help to preserve MOM-associated RQC, mitochondrial proteostasis, and even cytosolic proteostasis, suggesting that PINK1–Parkin signaling is an integral part of the cellular proteostasis network [7,29,31,88].

tRNAs, and electrostatic interaction between NPCs and the ribosome exit tunnel [3,4]. Consequently, the co-translational quality control complexes are recruited to stalled ribosomes to target the aberrant translation products and the template mRNAs for degradation. Factors such as ZNF598 and Rack1 sense colliding ribosomes, while Dom34/Pelo, HBS1, and ABCE1 separate 40S and 60S ribosome subunits and recycle them. Key RQC factors involved in protein quality control include Listerin (an E3 ubiquitin ligase), RQC1, RQC2 (Tae2/Clbn/NEMF), and Cdc48/p97/VCP. RNA quality control involves the 5′-to-3′ exonuclease Xrn1 and the exosome complex that degrades mRNA in the 3′-to5′ direction. Although most of these factors are conserved in metazoans, their functions in RQC were largely limited to studies in yeast using artificial mRNA substrates [4] until recently. Using both cultured mammalian cells and in vivo Drosophila models, it was found that when mitochondria suffer damage, there is an early attempt to repair the damage, via PINK1-dependent Box 2. Co-translational Quality Control Mechanisms and Function Proteome integrity is essential for cellular health. Quality control of cellular proteins starts when proteins are being synthesized on ribosomes. Ubiquitination and degradation of NPCs still associated with ribosomes is a widespread phenomenon [89]. It is estimated that more than 30% of newly synthesized peptides are ubiquitinated in mammalian cells [90]. An interconnected network of co-translational quality control pathways, including the nonsense-mediated decay (NMD), no-go decay (NGD), non-stop decay (NSD), and RQC pathways are deployed to survey the quality of translation. These distinct pathways target aberrant mRNAs containing premature termination codons (PTCs) or no stop codons or undergoing translational stalling due to mRNA damage, secondary structure, or aminoacyl-tRNA shortage [3]. A common theme of these various types of co-translational quality control is the splitting of stalled ribosomes before the clearance of stalled NPCs. A fundamental question is whether the protein CTE by a CAT-tailing like process occurs in all aberrant NPCs associated with the split 60S ribosome. The eRFs have been implicated in the resolution of more than one type of stalled ribosomes. In the case of PTC-containing mRNAs targeted by the NMD pathway, the NMD factors SMG1 and UPF1 form a complex with eRF1/eRF3 (the SURF complex), which interacts with the exon junction complex (EJC) containing UPF2, UPF3, eIF4AIII, Y14, and Magoh to trigger the degradation of PTC-containing mRNAs [91]. The faulty NPCs are also degraded during NMD [92], but the mechanism remains poorly understood. Two components of the EJC, UPF3 and Y14, are found to act in the MISTERMINATE of C-I30 [7]. Inhibition of UPF3 was sufficient to induce C-I30-u formation and phenocopy the PINK1 mutant, which was rescued by eRF1 overexpression. The mechanism of action of UPF3 in NMD is not well understood. It acts as a nucleocytoplasmic shuttling factor and interacts with Y14 and the NMD factors UPF1/UPF2, and mutations in UPF3B cause mental retardation [93]. UPF3, but not UPF2, is shown to be required for the E3 ligase activity of UPF1. Moreover, UPF3B participates in translational termination by interacting with eRF factors [94]. It would be interesting to test whether the termination function of UPF3B is important for its role in C-I30-u regulation and whether it is related to the pathogenesis of mental retardation.

Trends in Cell Biology, Month 2020, Vol. xx, No. xx

5

Trends in Cell Biology

recruitment of C-I30 mRNA and its associated ribosome/RNP complex to the MOM in mammalian cells [31]. However, persistent mitochondrial damage results in stalled translation of C-I30 mRNA on the MOM, recruitment of RQC factors and ribosome separation/recycling factors to C-I30 mRNP, and remodeling of the C-I30 mRNP complex. One of the key events occurring in C-I30 mRNP is the ubiquitination of ABCE1 by the ribosome-associated NOT4 E3 ligase, resulting in ABCE1 polyubiquitination [31]. Ubiquitinated ABCE1 then recruits autophagy receptors to C-I30 mRNP, triggering the autophagy of damaged mitochondria. This chain of events is critical for mitochondrial regulation and maintenance, as genetic manipulation of key factors including ABCE1 effectively rescues the PINK1-mutant phenotypes. Moreover, downregulation of ABCE1 and HBS1 is found in transcriptome analyses of PD patient brain samples [31], supporting the importance of these factors and RQC in PD pathogenesis.

Inefficient Resolution of Stalled Translation Generates Aberrant Proteins with Unusual CTEs by CAT-Tailing in Yeast and MISTERMINATE in Metazoans Consistent with stalled translation of C-I30 mRNA on mitochondrial stress, there is reduced C-I30 protein abundance in PINK1- or Parkin-mutant flies or when wild-type animals are exposed to mitochondrial toxins [7]. Detailed analysis of C-I30 protein revealed the generation of an upshifted C-I30 band (C-I30-u) under mitochondrial stress conditions. After excluding post-translational modifications (ubiquitination, phosphorylation, MTS cleavage) and alternative splicing as possible sources of C-I30-u generation, and after the demonstration of CTE as a possible mechanism of C-I30-u formation, a picture of C-I30 modification by a C-terminal Ala and Thr addition (CAT-tailing)-like phenomenon started to emerge [7]. Studies in yeast have shown that NPCs on stalled ribosomes can be modified while still attached to 60S subunits, in a 40S- and mRNA template-independent CAT-tailing process [53]. So far CAT-tailing has been studied mainly using artificial substrates and under conditions preventing the degradation-stalled NPCs [4]. The physiological role of CAT-tailing in the context of intact RQC is unknown. It has been proposed that CAT-tailing may induce the heat shock response [54], expose lysine residues in stalled NPCs hidden in the exit tunnel by pushing them out of the exit tunnel for ubiquitination by Listerin [55], or drive the degradation of stalled NPCs on and off the ribosomes [56]. However, whether CAT-tailing-like CTE of stalled NPCs occurs in metazoans, the compositions of the CTEs, and the pathological consequences of such CTEs in disease settings was not known due to the lack of identified endogenous CAT-tailed substrates. Studies in yeast have shown that the cytosolic Vms1 protein protects cells against mitochondrial toxicity from ribosome-stalled proteins and that Vms1 or its mammalian counterpart cleaves the peptidyl-tRNA bond and antagonizes CAT-tailing activity [8,57–60]. However, the CAT-tailing studies were done using reporter constructs. So far, no endogenous yeast protein has been shown to be CAT-tailed, and C-I30 is not conserved in yeast. Various evidence supports Drosophila and mammalian C-I30-u as the first endogenous CATtailed substrate: (i) its reduction by knocking down Clbn/NEMF or AARS and TARS, factors needed for the CAT-tailing reaction; (ii) its reduction by overexpression of the Vms1/ANKZF1 family of mitochondrial stress-responsive factors that antagonize CAT-tailing activity; (iii) its reduction by overexpression of various RQC factors including ABCE1, VCP, and Pelo; and (iv) mass spectrometry identification of CTEs containing A and T [7]. Distinct from CAT-tails in yeast that comprise exclusively A and T, CTEs of C-I30-u purified from PINK1-mutant flies also contain other amino acids (e.g., S, Y, C, E/P). Moreover, in contrast to the CAT-tails in yeast, which are added to the C-terminal poly-K of the GFP reporter without a stop codon [53], the CTE in CI30-u is added to C-I30 protein by ribosomes stalled at the canonical stop codon. This is caused by mitochondrial stress-induced impairment of the translation termination factor eRF1 and 6

Trends in Cell Biology, Month 2020, Vol. xx, No. xx

Trends in Cell Biology

Key Figure

Mechanism of MISTERMINATE and Its Role in Disease

Trends in Cell Biology

Figure 3. In response to mitochondrial stress, levels of the translation termination factor eRF1 and the recycling factor ABCE1 are reduced. While the exact mechanism remains to be elucidated, ABCE1, an iron–sulfur cluster containing protein that is redox sensitive and forms a complex with eRF1, might be the primary target. Loss of ABCE1/eRF1 creates ribosome-stalling signals that activate the ribosome-associated quality control (RQC) machinery. In the process of RQC, C-terminal extensions (CTEs) containing A, T, and select other amino acids are added to the C-I30 protein, generating CI30-CTE in a process termed MISTERMINATE. C-I30-CTE can be imported into mitochondria where it is assembled into C-I and may also form protein aggregates, resulting in mitochondrial toxicity. C-I30-CTE can also be released into the cytosol, where it forms protein aggregates in a CTE-dependent manner and such aggregates also recruit cellular metastable proteins, altering cytosolic proteostasis. Persistent activation of the RQC process on the mitochondrial outer membrane (MOM) may also titrate RQC factors away from their normal substrates, creating a deficit of overall cellular RQC activity. All of these events may contribute to disease pathogenesis.

recycling factor ABCE1 [7]. Thus, although the CTE in C-I30-u in metazoans is generated by a mechanism thematically like CAT-tailing in yeast, there are fundamental differences. This process is termed MISTERMINATE (Figure 3, Key Figure). Elucidation of the MISTERMINATE process in C-I30-u formation highlights the importance of translational termination and ribosome recycling factors in RQC. The availability of functional eRF1/eRF3 can strongly influence the amount of ubiquitinated NPCs associated with 60S in yeast [61]. Studies in yeast also showed that the ribosome recycling factor Dom34, the yeast homolog of Pelo, functions in rescuing ribosomes wandering past canonical stop codons. Such events occur more often under stress conditions, and Dom34 and ABCE1 functionally interact to limit translation re-initiation by terminating ribosomes in the 3′-UTR [62]. The relevance of this process to human brain aging and age-related brain diseases is highlighted by recent findings of ribosome-associated 3′-UTRs that lack 5′-UTRs and open reading frames [63,64]. These isolated 3′-UTRs are proposed to be the mRNA remnants of RNA quality control of stalled translation. They accumulate in an age-specific and brainregion-specific manner and encode short peptides [64]. Moreover, their accumulation correlates with mitochondrial dysfunction and oxidative stress and can be induced by the depletion of ABCE1 [64]. Thus, as in MISTERMINATE, mitochondrial stress and impairment of the translational termination/recycling factor ABCE1 results in altered RNA and protein quality control in the human brain. The pathogenic role of these aberrant mRNA and protein products remains to be tested. Trends in Cell Biology, Month 2020, Vol. xx, No. xx

7

Trends in Cell Biology

ABCE1 is a Fe–S cluster-containing protein and the Fe–S domain of ABCE1 interacts with eRF1 [65]. The Fe–S association with ABCE1 is sensitive to cellular redox state and essential for ABCE1 function in translation termination and ribosome recycling [66]. ABCE1 may serve as a key component of the translation machinery that senses mitochondrial health. In addition, at least in yeast cells, the physiological level of ABCE1 is below the threshold sufficient for complete ribosome recycling [62], and ABCE1 behaves as an intrinsically metastable protein that can be sequestered by protein aggregates formed by other proteins [67]. Future studies will test whether ABCE1 represents a weak link between mitochondrial function and cellular proteostasis.

Mitochondrial Stress-Induced C-I30 Protein with CTE Can Form Aggregates and Perturb Mitochondrial and Cytosolic Proteostasis In animal model studies, the presence of C-I30-u is shown to correlate strictly with toxicity in neuromuscular tissues [7]. In both fly models and mammalian cells, C-I30-u is imported into mitochondria, assembled into C-I and supercomplexes of the respiratory chain, and imposes mitochondrial toxicity [7]. Moreover, in both systems C-I30-u is also released into the cytosol, presumably by the action of Vms1/ANKZF1, where it forms protein aggregates. Such aggregates recruit cellular metastable proteins and perturb the proteostasis network, as indicated by the recruitment of molecular chaperones and the activation of signaling pathways responsive to proteostasis stress [7]. These findings are consistent with the propensity of A- and Tcontaining peptide polymers to form β-sheet and amyloid structures [68] and recent findings demonstrating that failure in the timely removal of CAT-tailed proteins can cause proteotoxicity in yeast [69–71].

Coordination between Mitochondrial Function and Proteostasis in Health and Disease It is unlikely that the formation of CAT-tails in yeast and MISTERMINATE-generated CTEs in metazoans is intended initially to cause proteotoxicity. Protein aggregate formation is a general phenomenon in biology, with possible functions ranging from the consolidation of aberrant proteins for quality control by the UPS or autophagy systems, or simply prevention of their interactions with other cellular proteins, to normal roles in development, translational regulation, the innate immune response, stress granule formation, or learning and memory [17,72–76]. Under normal conditions, protein aggregates formed in response to stress are resolved after stress stimuli are removed. However, under aging or pathological conditions, such aggregates persist, resulting in the sequestration of key cellular proteins like ABCE1, causing loss of essential cellular function and cell death (Box 3). These aggregates may also recruit disease-associated metastable Box 3. Pathogenic Mechanisms of Protein Conformational Diseases Protein conformational diseases are characterized by disease-associated proteins acquiring aberrant conformations that can self-propagate to spread the disease. This category of diseases includes the infectious prion diseases and the seemingly noninfectious age-related neurodegenerative diseases. The former comprises Creutzfeldt–Jakob disease (CJD) in humans, scrapie in sheep, chronic waste disease in deer and elk, and mad cow disease [79]. The latter include AD, PD, tauopathy, ALS, and multiple system atrophy [79–81]. A key tenet of conformational disease pathogenesis is that an aberrantly folded prion conformer would have the ability to force another prion protein in its native conformation to adopt the aberrant conformation. In the case of human CJD, 10–20% of patients carry familial mutations in the PRNP gene that encodes PrPC. The genetic mutations may directly induce the formation of PrPSc, the infectious and disease-causing conformer, or facilitate the adoption of the PrPSc conformation by mutant PrPC. However, in sporadic CJD patients, who account for the majority of CJD cases, no mutations in PRNP genes are found. How PrPSc arises in this situation is not understood [79]. The same holds true for the candidate prion-like conformers that cause other neurodegenerative diseases, such as Aβ, tau, α-synuclein, and SOD1, where familial mutations in protein sequences account for only a small portion of the disease cases. Even in the familial cases, the diseases tend to be late onset, despite the presence of the mutated proteins after birth. This may suggest that the process of prion formation is a sporadic process, probably aided by other cellular cofactors or post-translational modifications of the disease proteins. It is also possible that the prion conformers are constantly turned over by cellular quality control mechanisms and that only with age, when such quality control activities decline [2], are the toxic conformers able to accumulate and reach a threshold level that leads to disease.

8

Trends in Cell Biology, Month 2020, Vol. xx, No. xx

Trends in Cell Biology

Trends in Cell Biology

Figure 4. The Normal and Pathological Effect of MISTERMINATE-Generated C-Terminal Extensions (CTEs). Based on the propensity of A/T-rich sequences to form β-sheet structures and the heterogeneity of the sequence and composition of A/T-rich CTEs, it is proposed here that MISTERMINATE-generated C-I30-CTEs, or other ribosomeassociated quality control (RQC) substrates containing CTEs (Protein X-CTEs), may adopt differently shaped β-sheet structures, which will lead to the formation of CTE-dependent aggregates. The normal function of CTE-mediated aggregation may be to concentrate these stalled ribosome-generated peptides, making it more efficient for the cellular quality control machinery to refold them or target them for degradation. These aggregates are expected to be resolved after the stress signal is removed under normal conditions. However, under disease conditions when the stress signals persist or when RQC is impaired, CTE-containing proteins will accumulate and start to interact with other metastable proteins. These interactions will drive conformational changes of the metastable proteins to different conformers based on the CTEs involved, analogous to prion-like conversions. This may represent one of the mechanisms by which normal cellular proteins acquire prion-like conformations to form diverse prion ‘strains’ in sporadic forms of neurodegenerative diseases.

proteins such as amyloid-β, tau, α-synuclein, TDP-43, FUS, SOD1, or DPRs, driving the formation of disease-defining protein aggregates (Figure 4). Recent studies in yeast and metazoans emphasize the particular importance of RQC in maintaining mitochondrial function by protecting the integrity of nucleus-encoded mitochondrial proteins that are co-translationally imported [7,8]. A corollary of the finding of MISTERMINATE in linking mitochondrial stress to proteostasis failure is that mitochondrial dysfunction may contribute significantly to the pathological consequences of defective co-translational quality control. Mutations in the key RQC factors Listerin [5] and HBS1 [6] are linked to neurodegeneration in mouse models. Mutations in VCP are involved in inclusion bodies myopathy with Paget’s disease of bone and frontotemporal dementia (IBMPFD), familial ALS, and Charcot–Marie–Tooth disease type 2Y [77] and ANKZF1 defects are linked to infantile-onset inflammatory bowel disease [78]. Future studies will test whether defective RQC of MOM-associated translation and mitochondrial function is causally involved in these disease conditions, especially the neurodegeneration aspect. While mechanisms like MISTERMINATE may potentially explain the intimate relationship between mitochondrial dysfunction and proteostasis failure in disease, a fundamental question is whether the accumulation of the CTE forms of many cellular proteins is involved or whether a select few (e.g., C-I30-u) are the initial trigger for neurodegeneration. Available data suggest that accumulation of C-I30-u alone is sufficient to cause mitochondrial- and cytotoxicity in mammalian cells [7]. Given the heterogeneity of MISTERMINATE-generated CTEs, it would be interesting to test whether CTE variants have the capacity to ‘seed’ metastable proteins, resulting in the generation of diverse ‘strains’ of prion-like protein aggregates found in various neurodegenerative diseases [79–81] (Figure 4).

Therapeutic Implications Although the biochemical mechanisms of CAT-tailing in yeast and MISTERMINATE in metazoans remain to be elucidated, available data suggest that these non-templated peptide chain extension Trends in Cell Biology, Month 2020, Vol. xx, No. xx

9

Trends in Cell Biology

processes are distinct from canonical peptide chain elongation, offering an opportunity to inhibit this process without adversely inhibiting normal translation. For example, anisomycin, an antibiotic produced by Streptomyces griseolus, which inhibits eukaryotic protein synthesis by targeting the peptidyl-transfer center of 60S, potently inhibits CAT-tailing in vitro in yeast lysates [82] and MISTERMINATE in vivo in fly models and mammalian cells [7] in a manner distinct from other translational inhibitors. More work is needed to determine the exact mechanism of anisomycin action in these processes, as anisomycin can act independent of canonical translation [83]. Future preclinical studies in rodent models and patient-derived induced neuronal models are needed before anisomycin or its derivatives can be tested as candidate therapeutics. Genetic studies in fly models and human cells also indicate that activation of VCP or Vms1/ ANKZF1 and inhibition of Clbn/NEMF are effective approaches in inhibiting MISTERMINATE and preventing mitochondrial stress-induced neuromuscular degeneration [7]. Small-molecule compounds or gene therapy-based biologicals targeting these molecules may be pursued as novel therapies for disease conditions with prominent mitochondrial dysfunction. Finally, a potential application of MISTERMINATE-generated CTE is that it could be used as a biomarker for detecting mitochondrial stress in various age-related diseases. A specific antibody against a major subtype of MISTERMINATE-generated CTE populations could help to achieve this goal. C-I30-u may be just the first example of CTE-containing proteins that accumulate on the MOM under disease conditions. It is thus imperative to further characterize the MISTERMINATEgenerated CTEs under different disease conditions to discover novel sequences that could serve as biomarkers.

Concluding Remarks An intimate relationship between mitochondrial function and proteostasis exists across eukaryotes. Quality control of co-translationally imported mitochondrial proteins on MOM-associated ribosomes is critical for not only mitochondrial proteostasis but also global proteostasis in the cytosol. This provides a molecular framework for future studies to elucidate the mechanistic link between mitochondrial function and cytosolic proteostasis in health and disease. A limitation of current research is the paucity of knowledge of MISTERMINATE substrates, the compositions of the CTEs in these substrates, and the repertoire of disease-associated metastable proteins that are recruited by the CTEs. Many outstanding questions remain to be explored (see Outstanding Questions). For example, what is the nature of the mitochondrial stress signals that trigger MISTERMINATE? Do aging-related signaling pathways impinge on MISTERMINATE? What is the significance of the heterogeneity of the CTEs generated by MISTERMINATE? Do different diseases produce different CTEs? Is the accumulation of MISTERMINATE substrates a contributing factor in Listerin mutation-induced neurodegeneration in mouse? Could mitochondrial dysfunction and MISTERMINATE explain the regional and cell-type specificity of neurodegenerative diseases? Finally, is MISTERMINATE a viable target for therapeutic development? These questions will be avidly explored in the coming years and exciting new insights are expected to emerge. Acknowledgments We acknowledge the contributions of many investigators whose work lead to advances in the field, some of which could not be cited due to space limitations, and support by the United States National Institutes of Health (R01NS084412, R01NS083417, and R01AR0748750 to B.L.; R01NS095734 and R01GM132500 to S.G.) and the United States Department of Defense (PD17008 to S.G.).

References 1.

10

Sala, A.J. et al. (2017) Shaping proteostasis at the cellular, tissue, and organismal level. J. Cell Biol. 216, 1231–1241

Trends in Cell Biology, Month 2020, Vol. xx, No. xx

2.

Hipp, M.S. et al. (2019) The proteostasis network and its decline in ageing. Nat. Rev. Mol. Cell Biol. 20, 421–435

Outstanding Questions What is the nature of the mitochondrial stress signals that impinge on MOMassociated RQC and MISTERMINATE? Are mitochondrial membrane potential, Ca2+, ROS, or certain metabolites involved? What cellular signaling pathways act upstream to regulate MOM-associated RQC and MISTERMINATE? Are agingrelated pathways involved? What is the repertoire of MISTERMINATEgenerated CTEs in different diseases? What are the normal functions of the CAT-tails and CTEs induced by MISTERMINATE? Can the Listerin-like E3 ligase reach and modify stalled NPCs on the MOM? Are MISTERMINATE-induced CTEs involved in the neurodegeneration observed in the Listerin-mutant mouse? Could mitochondrial dysfunction and MISTERMINATE explain the regionand cell type-specificity of neurodegenerative diseases? Could MISTERMINATE-induced CTEs induce the formation of ‘prion’-like seeds of metastable proteins that form aggregates in the absence of disease-causing mutations in sporadic forms of conformational diseases? Could RQC failure result in the accumulation of defective ribosomeassociated peptides (DRiPs) that can induce an immune response? Can new therapeutic approaches be devised by targeting mitochondrial protein import, mitochondrial proteostasis, MISTERMINATE/CAT-tailing, or RQC?

Trends in Cell Biology

3. 4. 5.

6.

7.

8.

9. 10. 11. 12. 13.

14.

15. 16. 17. 18.

19. 20. 21.

22.

23. 24.

25.

26.

27.

28.

29.

30.

Brandman, O. and Hegde, R.S. (2016) Ribosome-associated protein quality control. Nat. Struct. Mol. Biol. 23, 7–15 Joazeiro, C.A.P. (2019) Mechanisms and functions of ribosomeassociated protein quality control. Nat. Rev. Mol. Cell Biol. 20, 368–383 Chu, J. et al. (2009) A mouse forward genetics screen identifies LISTERIN as an E3 ubiquitin ligase involved in neurodegeneration. Proc. Natl. Acad. Sci. U. S. A. 106, 2097–2103 Ishimura, R. et al. (2014) RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Science 345, 455–459 Wu, Z. et al. (2019) MISTERMINATE mechanistically links mitochondrial dysfunction with proteostasis failure. Mol. Cell 75, 835–848.e8 Izawa, T. et al. (2017) Cytosolic protein Vms1 links ribosome quality control to mitochondrial and cellular homeostasis. Cell 171, 890–903.e18 Friedman, J.R. and Nunnari, J. (2014) Mitochondrial form and function. Nature 505, 335–343 Chandel, N.S. (2015) Evolution of mitochondria as signaling organelles. Cell Metab. 22, 204–206 Topf, U. et al. (2019) Mitochondrial stress-dependent regulation of cellular protein synthesis. J. Cell Sci. 132, jcs226258 Ruan, L. et al. (2017) Cytosolic proteostasis through importing of misfolded proteins into mitochondria. Nature 543, 443–446 Topf, U. et al. (2018) Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species. Nat. Commun. 9, 324 Chiti, F. and Dobson, C.M. (2017) Protein misfolding, amyloid formation, and human disease: a summary of progress over the last decade. Annu. Rev. Biochem. 86, 27–68 Klaips, C.L. et al. (2018) Pathways of cellular proteostasis in aging and disease. J. Cell Biol. 217, 51–63 Hou, Y. et al. (2019) Ageing as a risk factor for neurodegenerative disease. Nat. Rev. Neurol. 15, 565–581 Si, K. (2015) Prions: what are they good for? Annu. Rev. Cell Dev. Biol. 31, 149–169 Johri, A. and Beal, M.F. (2012) Mitochondrial dysfunction in neurodegenerative diseases. J. Pharmacol. Exp. Ther. 342, 619–630 Coskun, P. et al. (2012) A mitochondrial etiology of Alzheimer and Parkinson disease. Biochim. Biophys. Acta 1820, 553–564 Sorrentino, V. et al. (2018) Repairing mitochondrial dysfunction in disease. Annu. Rev. Pharmacol. Toxicol. 58, 353–389 Anandatheerthavarada, H.K. et al. (2003) Mitochondrial targeting and a novel transmembrane arrest of Alzheimer’s amyloid precursor protein impairs mitochondrial function in neuronal cells. J. Cell Biol. 161, 41–54 Devi, L. et al. (2006) Accumulation of amyloid precursor protein in the mitochondrial import channels of human Alzheimer’s disease brain is associated with mitochondrial dysfunction. J. Neurosci. 26, 9057–9068 Lustbader, J.W. et al. (2004) ABAD directly links Aβ to mitochondrial toxicity in Alzheimer’s disease. Science 304, 448–452 Hansson Petersen, C.A. et al. (2008) The amyloid beta-peptide is imported into mitochondria via the TOM import machinery and localized to mitochondrial cristae. Proc. Natl. Acad. Sci. U. S. A. 105, 13145–13150 Betarbet, R. et al. (2000) Chronic systemic pesticide exposure reproduces features of Parkinson’s disease. Nat. Neurosci. 3, 1301–1306 Valente, E.M. et al. (2004) Hereditary early-onset Parkinson’s disease caused by mutations in PINK1. Science 304, 1158–1160 Devine, M.J. and Kittler, J.T. (2018) Mitochondria at the neuronal presynapse in health and disease. Nat. Rev. Neurosci. 19, 63–80 Gehrke, S. et al. (2010) Pathogenic LRRK2 negatively regulates microRNA-mediated translational repression. Nature 466, 637–641 Gehrke, S. et al. (2015) PINK1 and Parkin control localized translation of respiratory chain component mRNAs on mitochondria outer membrane. Cell Metab. 21, 95–108 Imai, Y. et al. (2008) Phosphorylation of 4E-BP by LRRK2 affects the maintenance of dopaminergic neurons in Drosophila. EMBO J. 27, 2432–2443

31. Wu, Z. et al. (2018) Ubiquitination of ABCE1 by NOT4 in response to mitochondrial damage links co-translational quality control to PINK1-directed mitophagy. Cell Metab. 28, 130–144.e7 32. Johnson, S.C. et al. (2013) mTOR inhibition alleviates mitochondrial disease in a mouse model of Leigh syndrome. Science 342 1524–1158 33. Sorrentino, V. et al. (2017) Enhancing mitochondrial proteostasis reduces amyloid-beta proteotoxicity. Nature 552, 187–193 34. Fang, E.F. et al. (2019) Mitophagy inhibits amyloid-beta and tau pathology and reverses cognitive deficits in models of Alzheimer’s disease. Nat. Neurosci. 22, 401–412 35. D’Amico, D. et al. (2017) Cytosolic proteostasis networks of the mitochondrial stress response. Trends Biochem. Sci. 42, 712–725 36. Calvo, S.E. and Mootha, V.K. (2010) The mitochondrial proteome and human disease. Annu. Rev. Genomics Hum. Genet. 11, 25–44 37. Neupert, W. and Herrmann, J.M. (2007) Translocation of proteins into mitochondria. Annu. Rev. Biochem. 76, 723–749 38. Williams, C.C. et al. (2014) Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. Science 346, 748–751 39. Lesnik, C. et al. (2015) Localized translation near the mitochondrial outer membrane: an update. RNA Biol. 12, 801–809 40. Kellems, R.E. and Butow, R.A. (1974) Cytoplasmic type 80 S ribosomes associated with yeast mitochondria. 3. Changes in the amount of bound ribosomes in response to changes in metabolic state. J. Biol. Chem. 249, 3304–3310 41. Gold, V.A. et al. (2017) Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo-tomography. EMBO Rep. 18, 1786–1800 42. Hansen, K.G. et al. (2018) An ER surface retrieval pathway safeguards the import of mitochondrial membrane proteins in yeast. Science 361, 1118–1122 43. Park, J. et al. (2006) Mitochondrial dysfunction in Drosophila PINK1 mutants is complemented by Parkin. Nature 441, 1157–1161 44. Clark, I.E. et al. (2006) Drosophila Pink1 is required for mitochondrial function and interacts genetically with Parkin. Nature 441, 1162–1166 45. Yang, Y. et al. (2006) Mitochondrial pathology and muscle and dopaminergic neuron degeneration caused by inactivation of Drosophila Pink1 is rescued by Parkin. Proc. Natl. Acad. Sci. U. S. A. 103, 10793–10798 46. Imai, Y. and Lu, B. (2011) Mitochondrial dynamics and mitophagy in Parkinson’s disease: disordered cellular power plant becomes a big deal in a major movement disorder. Curr. Opin. Neurobiol. 21, 935–941 47. Pickrell, A.M. and Youle, R.J. (2015) The roles of PINK1, Parkin, and mitochondrial fidelity in Parkinson’s disease. Neuron 85, 257–273 48. Aschrafi, A. et al. (2010) Regulation of axonal trafficking of cytochrome c oxidase IV mRNA. Mol. Cell. Neurosci. 43, 422–430 49. Spillane, M. et al. (2013) Mitochondria coordinate sites of axon branching through localized intra-axonal protein synthesis. Cell Rep. 5, 1564–1575 50. Bauer, M.F. et al. (1996) Role of Tim23 as voltage sensor and presequence receptor in protein import into mitochondria. Cell 87, 33–41 51. Juszkiewicz, S. et al. (2018) ZNF598 is a quality control sensor of collided ribosomes. Mol. Cell 72, 469–481 e7 52. Ikeuchi, K. et al. (2019) Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways. EMBO J. 38, e100276 53. Shen, P.S. et al. (2015) Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Science 347, 75–78 54. Brandman, O. et al. (2012) A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell 151, 1042–1054 55. Kostova, K.K. et al. (2017) CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides. Science 357, 414–417

Trends in Cell Biology, Month 2020, Vol. xx, No. xx

11

Trends in Cell Biology

56. Sitron, C.S. and Brandman, O. (2019) CAT tails drive degradation of stalled polypeptides on and off the ribosome. Nat. Struct. Mol. Biol. 26, 450–459 57. Verma, R. et al. (2018) Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes. Nature 557, 446–451 58. Zurita Rendon, O. et al. (2018) Vms1p is a release factor for the ribosome-associated quality control complex. Nat. Commun. 9, 2197 59. Kuroha, K. et al. (2018) Release of ubiquitinated and nonubiquitinated nascent chains from stalled mammalian ribosomal complexes by ANKZF1 and Ptrh1. Mol. Cell 72, 286–302.e8 60. Yip, M.C.J. et al. (2019) Mechanism for recycling tRNAs on stalled ribosomes. Nat. Struct. Mol. Biol. 26, 343–349 61. Shcherbik, N. et al. (2016) Distinct types of translation termination generate substrates for ribosome-associated quality control. Nucleic Acids Res. 44, 6840–6852 62. Young, D.J. et al. (2015) Rli1/ABCE1 recycles terminating ribosomes and controls translation reinitiation in 3′UTRs in vivo. Cell 162, 872–884 63. Kocabas, A. et al. (2015) Widespread differential expression of coding region and 3′ UTR sequences in neurons and other tissues. Neuron 88, 1149–1156 64. Sudmant, P.H. et al. (2018) Widespread accumulation of ribosome-associated isolated 3′ UTRs in neuronal cell populations of the aging brain. Cell Rep. 25, 2447–2456.e4 65. Preis, A. et al. (2014) Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1– eRF3 or eRF1–ABCE1. Cell Rep. 8, 59–65 66. Alhebshi, A. et al. (2012) The essential iron–sulfur protein Rli1 is an important target accounting for inhibition of cell growth by reactive oxygen species. Mol. Biol. Cell 23, 3582–3590 67. Olzscha, H. et al. (2011) Amyloid-like aggregates sequester numerous metastable proteins with essential cellular functions. Cell 144, 67–78 68. Fandrich, M. and Dobson, C.M. (2002) The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation. EMBO J. 21, 5682–5690 69. Choe, Y.J. et al. (2016) Failure of RQC machinery causes protein aggregation and proteotoxic stress. Nature 531, 191–195 70. Yonashiro, R. et al. (2016) The Rqc2/Tae2 subunit of the ribosome-associated quality control (RQC) complex marks ribosome-stalled nascent polypeptide chains for aggregation. Elife 5, e11794 71. Defenouillere, Q. et al. (2016) Rqc1 and Ltn1 prevent C-terminal alanine–threonine tail (CAT-tail)-induced protein aggregation by efficient recruitment of Cdc48 on stalled 60S subunits. J. Biol. Chem. 291, 12245–12253 72. Nil, Z. et al. (2019) Amyloid-like assembly activates a phosphatase in the developing Drosophila embryo. Cell 178, 1403–1420.e21 73. Khan, M.R. et al. (2015) Amyloidogenic oligomerization transforms Drosophila Orb2 from a translation repressor to an activator. Cell 163, 1468–1483 74. Majumdar, A. et al. (2012) Critical role of amyloid-like oligomers of Drosophila Orb2 in the persistence of memory. Cell 148, 515–529

12

Trends in Cell Biology, Month 2020, Vol. xx, No. xx

75. Li, Y.R. et al. (2013) Stress granules as crucibles of ALS pathogenesis. J. Cell Biol. 201, 361–372 76. Berke, I.C. et al. (2012) MDA5 assembles into a polar helical filament on dsRNA. Proc. Natl. Acad. Sci. U. S. A. 109, 18437–18441 77. Tang, W.K. and Xia, D. (2016) Mutations in the human AAA+ chaperone p97 and related diseases. Front. Mol. Biosci. 3, 79 78. van Haaften-Visser, D.Y. et al. (2017) Ankyrin repeat and zincfinger domain-containing 1 mutations are associated with infantile-onset inflammatory bowel disease. J. Biol. Chem. 292, 7904–7920 79. Prusiner, S.B. (2013) Biology and genetics of prions causing neurodegeneration. Annu. Rev. Genet. 47, 601–623 80. Jucker, M. and Walker, L.C. (2018) Propagation and spread of pathogenic protein assemblies in neurodegenerative diseases. Nat. Neurosci. 21, 1341–1349 81. Vaquer-Alicea, J. and Diamond, M.I. (2019) Propagation of protein aggregation in neurodegenerative diseases. Annu. Rev. Biochem. 88, 785–810 82. Osuna, B.A. et al. (2017) In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing. Elife 6, e27949 83. Hazzalin, C.A. et al. (1998) Anisomycin selectively desensitizes signalling components involved in stress kinase activation and fos and jun induction. Mol. Cell. Biol. 18, 1844–1854 84. Rugarli, E.I. and Langer, T. (2012) Mitochondrial quality control: a matter of life and death for neurons. EMBO J. 31, 1336–1349 85. Villa, E. et al. (2018) No Parkin zone: mitophagy without Parkin. Trends Cell Biol. 28, 882–895 86. Strappazzon, F. et al. (2015) AMBRA1 is able to induce mitophagy via LC3 binding, regardless of PARKIN and p62/ SQSTM1. Cell Death Differ. 22, 419–432 87. Di Rita, A. et al. (2018) HUWE1 E3 ligase promotes PINK1/ PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα. Nat. Commun. 9, 3755 88. Rana, A. et al. (2013) Parkin overexpression during aging reduces proteotoxicity, alters mitochondrial dynamics, and extends lifespan. Proc. Natl. Acad. Sci. U. S. A. 110, 8638–8643 89. Duttler, S. et al. (2013) Principles of cotranslational ubiquitination and quality control at the ribosome. Mol. Cell 50, 379–393 90. Wang, F. et al. (2013) A cotranslational ubiquitination pathway for quality control of misfolded proteins. Mol. Cell 50, 368–378 91. Kashima, I. et al. (2006) Binding of a novel SMG-1-Upf1-eRF1eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. Genes Dev. 20, 355–367 92. Kuroha, K. et al. (2009) Upf1 stimulates degradation of the product derived from aberrant messenger RNA containing a specific nonsense mutation by the proteasome. EMBO Rep. 10, 1265–1271 93. Tarpey, P.S. et al. (2007) Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation. Nat. Genet. 39, 1127–1133 94. Neu-Yilik, G. et al. (2017) Dual function of UPF3B in early and late translation termination. EMBO J. 36, 2968–2986