UFMylation of RPL26 links translocation-associated quality control to endoplasmic reticulum protein homeostasis

Wang, Lihui; Xu, Yue; Rogers, Heidi; Saidi, Layla; Noguchi, Constance Tom; Li, Honglin; Yewdell, Jonathan W.; Guydosh, Nicholas R.; Ye, Yihong

doi:10.1038/s41422-019-0236-6

Cited by 126 publications

(241 citation statements)

References 62 publications

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“…In a recent paper published in Cell Research, Wang et al 8 reported that RPL26 ufmylation increases upon stalling of ER translocon-associated ribosomes. During synthesis of most membrane and secreted proteins, nascent peptides are cotranslationally translocated from translocon-docked ribosomes into the ER lumen, where they are folded, post-translationally modified, and trafficked elsewhere.…”

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confidence: 99%

“…Interestingly, Wang et al show that degradation of their reporter is inhibited but still occurs gradually when RPL26 ufmylation is completely ablated, suggesting that some ufmylationindependent RQC is also active at the ER. 8 The division of labor between distinct RQC pathways at the ER, and the types of stalling that ribosomal ufmylation can resolve, remain to be explored. Future work may also identify additional factors necessary for processing ufmylated ER-associated ribosomes.…”

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confidence: 99%

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Cleaning up stalled ribosome-translocon complexes with ufmylation

Barna

2019

Cell Res

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Ufmylation, a metazoan-specific ubiquitin-like post-translational modification, is implicated in numerous cellular processes and mammalian phenotypes. Here, Wang et al. uncover an important function of ribosome ufmylation in protein quality control at ribosomes that have stalled during co-translational translocation of endoplasmic reticulum (ER)-targeted proteins. Post-translational modifications (PTMs) diversify the proteome and modulate protein function on faster time scales compared to transcriptional or translational regulation. While ubiquitination is one of the most common PTMs, several ubiquitin-like proteins have also been described. One intriguing example first described in 2004 is ufmylation, 1 in which the ubiquitin-like small protein Ubiquitin-Fold Modifier 1 (UFM1) is reversibly conjugated to lysine residues on substrates via a cascade of UFM1-specific ligases and proteases. Interestingly, this modification is found only in metazoans and can occur in plants, but not yeast, suggesting

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confidence: 99%

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Cleaning up stalled ribosome-translocon complexes with ufmylation

Barna

2019

Cell Res

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“…Our data set provides comprehensive evidence that different components of the translational machinery are UFMylated. We identified 27 ribosomal proteins as candidate substrates of the UFM1 system including RPS3 and RPL26, which recently have been characterized as UFM1 substrates (Simsek et al, 2017;Walczak et al, 2019;Wang et al, 2020). Mining peptides from a published deep proteome data set (Bekker-Jensen et al, 2017) for UFM1 modifications revealed that UFM1 remnant (valine-glycine, VG)-containing peptides were significantly enriched (p=0.00020929, Fisher's exact test) in candidates that passed our threshold ( Figure S4B and Table S2).…”

Section: The Translation Initiation Machinery Is Ufmylatedmentioning

confidence: 99%

“…However, thus far only reports by the Kopito, Cong and Ye laboratories provide a molecular explanation for a function of UFMylation in ER homeostasis: UFMylation and deUFMylation of the ribosomal subunit RPL26 contributes to co-translational protein insertion into the ER (Walczak et al, 2019) and promotes cotranslational quality control and degradation of stalled nascent polypeptides on ER-associated ribosomes (Wang et al, 2020). Further, UFMylation of DDRGK1 regulates the stability of the ER stress sensor IRE1a (Liu et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

UFMylation regulates translational homeostasis and cell cycle progression

Gak

Vasiljevic

Zerjatke

et al. 2020

Preprint

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UFMylation, the posttranslational modification of proteins with ubiquitin fold modifier 1 (UFM1) is essential for metazoan life and is associated with multiple human diseases.Although UFMylation has been linked to endoplasmic reticulum (ER) stress, its biological functions and relevant cellular targets beyond the ER are obscure. Here, we show that UFMylation directly controls translation and cell division in a manner otherwise known for cellular homeostasis-sensing pathways such as mTOR. By combining cell cycle analyses, mass spectrometry and ribosome profiling we demonstrate that UFMylation is required for eIF4F translation initiation complex assembly and recruitment of the ribosome. Interference with UFMylation shuts down global translation, which is sensed by cyclin D1 and halts the cell cycle independently of integrated stress response signalling. Our findings establish UFMylation as a key regulator of translation and uncover a pathway that couples translational homeostasis to cell cycle progression via a ubiquitin-like modification.

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“…7 C53 forms a tripartite receptor complex with the ufmylation E3 ligase UFL1 and its membrane adaptor DDRGK1 177 178 How is C53 recruited to the ER during ribosome stalling? Notably, C53 has been previously linked to 179 UFL1, an E3 ligase that mediates ufmylation of stalled, ER-bound ribosomes, modifying ribosomal protein 180 RPL26 Wang et al, 2019). To test if C53 forms a higher order receptor complex, we 181 analysed the interaction of C53 with UFL1 and its ER membrane adaptor DDRGK1 (Gerakis et al, 2019).…”

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A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress

Stephani

Picchianti

Gajic

et al. 2020

Preprint

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2Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the ER.3 Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a 4 major quality control mechanism. However, the degree to which ER-phagy is employed by other 5 branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, 6 that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. 7C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif 8 (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with 9 the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The 10 C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation 11 of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation 12 mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that 13 bridges selective autophagy with ribosome-associated quality control at the ER. 14 15 65 stress, we performed an immunoprecipitation coupled to mass spectrometry (IP-MS) screen to identify 66 AIM-dependent ATG8 interactions triggered by ER stress. We hypothesized that a synthetic AIM peptide 67 that has higher affinity for ATG8 can outcompete, and thus reveal, AIM-dependent ATG8 interactors. To 68 identify this synthetic peptide, we performed a peptide array analysis that revealed the AIM wt peptide 69 (Figure S1a, b; Table S1). Using isothermal titration calorimetry (ITC), we showed that the AIM wt binds 70 4 ATG8 with nanomolar affinity (KD=~700 nM), in contrast to the AIM mutant peptide (AIM mut), which 71 does not show any binding ( Figure S1c-f) or the low micromolar-range affinities measured for most cargo 72 receptors (Zaffagnini and Martens, 2016). As plants have an expanded set of ATG8 proteins, we first tested 73 if any of the ATG8 isoforms specifically responded to ER stress induced by tunicamycin (Kellner et al., 74 2016). Tunicamycin inhibits glycosylation and leads to proteotoxic stress at the ER (Bernales et al., 2006). 75 Quantification of ATG8 puncta in transgenic seedlings expressing GFP-ATG8A-I revealed that 76 tunicamycin treatment significantly induced all nine ATG8 isoforms (Figure S2). Since all ATG8 isoforms 77 were induced, we chose ATG8A, and performed peptide competition coupled IP-MS analysis (See methods 78 for detailed description). In addition to well-known AIM dependent ATG8 interactors such as ATG4 79 (Autophagy related gene 4) and NBR1 (Neighbour of BRCA1) (Wild et al., 2014), our analyses revealed 80 that the highly conserved cytosolic protein C53 (aliases: CDK5RAP3, LZAP, IC53, HSF-27) is an AIM-81 dependent ATG8 interactor (Figure 1a, Table S2, Figure S3). 83To confirm our IP-MS results, we performed in vitro pull-down experiments. Arabidopsis thaliana (At) 84 C53 specifically interacted with GST-ATG8A, and this interac...

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UFMylation of RPL26 links translocation-associated quality control to endoplasmic reticulum protein homeostasis

Cited by 126 publications

References 62 publications

Cleaning up stalled ribosome-translocon complexes with ufmylation

Cleaning up stalled ribosome-translocon complexes with ufmylation

UFMylation regulates translational homeostasis and cell cycle progression

A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress

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