bims-proteo 2024-07-28 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2024–07–28
thirty papers selected by
Eric Chevet, INSERM

Secondary interactions in ubiquitin-binding domains achieve linkage or substrate specificity.
CYYR1 promotes the degradation of the E3 ubiquitin ligase WWP1 and is associated with favorable prognosis in breast cancer.
UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome.
Pro-cathepsin D prevents aberrant protein aggregation dependent on endoplasmic reticulum protein CLN6.
Molecular insights into degron recognition by CRL5ASB7 ubiquitin ligase.
Spatial selectivity of ATase inhibition in mouse models of Charcot-Marie-Tooth disease.
GORASP2 promotes phagophore closure and autophagosome maturation into autolysosomes.
The ubiquitin-proteasome system degrades fatty acid synthase under nitrogen starvation when autophagy is dysfunctional in Saccharomyces cerevisiae.
Cellular turnover and degradation of the most common missense cystathionine beta-synthase variants causing homocystinuria.
Connexin43 promotes exocytosis of damaged lysosomes through actin remodelling.
A ligand discovery toolbox for the WWE domain family of human E3 ligases.
The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage.
Endoplasmic reticulum unfolded protein response transcriptional targets of XBP-1s mediate rescue from tauopathy.
ALS-linked VapB P56S mutation alters neuronal mitochondrial turnover at the synapse.
Selection for robust metabolism in domesticated yeasts is driven by adaptation to Hsp90 stress.
Fam134c and Fam134b shape axonal endoplasmic reticulum architecture in vivo.
Polysome collapse and RNA condensation fluidize the cytoplasm.
The ISR downstream target ATF4 represses long-term memory in a cell type-specific manner.
ATM facilitates autophagy and protects against oxidative stress and apoptosis in response to ER stress in vitro.
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile.
SMYD5 methylation of rpL40 links ribosomal output to gastric cancer.
Targeted degradation of extracellular mitochondrial aspartyl-tRNA synthetase modulates immune responses.
The COPII coat protein SEC24D is required for autophagosome closure in mammals.
Myeloid cells coordinately induce glioma cell-intrinsic and cell-extrinsic pathways for chemoresistance via GP130 signaling.
When less is more - A fast TurboID KI approach for high sensitivity endogenous interactome mapping.
Blending and separating dynamics of RNA-binding proteins develop architectural splicing networks spreading throughout the nucleus.
Unfolded protein response markers Grp78 and eIF2alpha are upregulated with increasing alpha-synuclein levels in Lewy body disease.
Decoding ribosome complexity: role of ribosomal proteins in cancer and disease.
TUnA: an uncertainty-aware transformer model for sequence-based protein-protein interaction prediction.
Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains.

Cell Rep. 2024 Jul 23. pii: S2211-1247(24)00874-X. [Epub ahead of print]43(8): 114545

Secondary interactions in ubiquitin-binding domains achieve linkage or substrate specificity.

Martin A Michel, Simon Scutts, David Komander.

  Small ubiquitin-binding domains (UBDs) recognize small surface patches on ubiquitin with weak affinity, and it remains a conundrum how specific cellular responses may be achieved. Npl4-type zinc-finger (NZF) domains are ∼30 amino acid, compact UBDs that can provide two ubiquitin-binding interfaces, imposing linkage specificity to explain signaling outcomes. We here comprehensively characterize the linkage preference of human NZF domains. TAB2 prefers Lys6 and Lys63 linkages phosphorylated on Ser65, explaining why TAB2 recognizes depolarized mitochondria. Surprisingly, most NZF domains do not display chain linkage preference, despite conserved, secondary interaction surfaces. This suggests that some NZF domains may specifically bind ubiquitinated substrates by simultaneously recognizing substrate and an attached ubiquitin. We show biochemically and structurally that the NZF1 domain of the E3 ligase HOIPbinds preferentially to site-specifically ubiquitinated forms of NEMO and optineurin. Thus, despite their small size, UBDs may impose signaling specificity via multivalent interactions with ubiquitinated substrates.

Keywords:  CP: Molecular biology; IKK; autophagy; mono-ubiquitination; optineurin; ubiquitin binding domain; ubiquitin chain linkage; ubiquitin code

DOI:  https://doi.org/10.1016/j.celrep.2024.114545
J Biol Chem. 2024 Jul 24. pii: S0021-9258(24)02102-1. [Epub ahead of print] 107601

CYYR1 promotes the degradation of the E3 ubiquitin ligase WWP1 and is associated with favorable prognosis in breast cancer.

Tiphaine Perron, Mathieu Boissan, Ivan Bièche, Laura Courtois, Florent Dingli, Damarys Loew, Mouna Chouchène, Sabrina Colasse, Laurence Levy, Céline Prunier.

  Ubiquitination plays a crucial role in cellular homeostasis by regulating the degradation, localization, and activity of proteins, ensuring proper cell function and balance. Among E3 ubiquitin ligases, WWP1 is implicated in cell proliferation, survival and apoptosis. Notably WWP1 is frequently amplified in breast cancer and associated with poor prognosis. Here we identify the protein CYYR1 that had previously no assigned function, as a regulator of WWP1 activity and stability. We show that CYYR1 binds to the WW domains of the E3 ubiquitin ligase WWP1 through its PPxY motifs. This interaction triggers K63-linked auto-ubiquitination and subsequent degradation of WWP1. We furthermore demonstrate that CYYR1 localizes to late endosomal vesicles and directs poly-ubiquitinated WWP1 toward lysosomal degradation through binding to ANKRD13A. Moreover, we found that CYYR1 expression attenuates breast cancer cell growth in anchorage-dependent and independent colony formation assays in a PPxY-dependent manner. Finally, we highlight that CYYR1 expression is significantly decreased in breast cancer and is associated with beneficial clinical outcome. Taken together our study suggests tumor suppressor properties for CYYR1 through regulation of WWP1 auto-ubiquitination and lysosomal degradation.

Keywords:  CYYR1; E3 ubiquitin ligase; WWP1; breast cancer; ubiquitination

DOI:  https://doi.org/10.1016/j.jbc.2024.107601
Nat Commun. 2024 Jul 25. 15(1): 6272

UNC-45 assisted myosin folding depends on a conserved FX3HY motif implicated in Freeman Sheldon Syndrome.

Antonia Vogel, Renato Arnese, Ricardo M Gudino Carrillo, Daria Sehr, Luiza Deszcz, Andrzej Bylicki, Anton Meinhart, Tim Clausen.

Myosin motors are critical for diverse motility functions, ranging from cytokinesis and endocytosis to muscle contraction. The UNC-45 chaperone controls myosin function mediating the folding, assembly, and degradation of the muscle protein. Here, we analyze the molecular mechanism of UNC-45 as a hub in myosin quality control. We show that UNC-45 forms discrete complexes with folded and unfolded myosin, forwarding them to downstream chaperones and E3 ligases. Structural analysis of a minimal chaperone:substrate complex reveals that UNC-45 binds to a conserved FX3HY motif in the myosin motor domain. Disrupting the observed interface by mutagenesis prevents myosin maturation leading to protein aggregation in vivo. We also show that a mutation in the FX3HY motif linked to the Freeman Sheldon Syndrome impairs UNC-45 assisted folding, reducing the level of functional myosin. These findings demonstrate that a faulty myosin quality control is a critical yet unexplored cause of human myopathies.

DOI: https://doi.org/10.1038/s41467-024-50442-6
Mol Genet Metab. 2024 Jul 16. pii: S1096-7192(24)00423-2. [Epub ahead of print]143(1-2): 108539

Pro-cathepsin D prevents aberrant protein aggregation dependent on endoplasmic reticulum protein CLN6.

Yuki Shiro, Syouichi Katayama, Haruka Tsukamoto, Tetsuo Yamazaki.

  We previously expressed a chimeric protein in which the small heat-shock protein αB-crystallin (αBC) is fused at its N-terminus to the C-terminus of the first transmembrane segment of the endoplasmic reticulum (ER) protein mitsugumin 23 and confirmed its localization to the ER. Moreover, overexpression of this N-terminally modified αBC was shown to prevent the aggregation of the coexpressed R120G αBC variant, which is highly aggregation-prone and associated with the hereditary myopathy αB-crystallinopathy. To uncover a molecular mechanism by which the ER-anchored αBC negatively regulates the protein aggregation, we isolated proteins that bind to the ER-anchored αBC and identified the lysosomal protease cathepsin D (CTSD) as one such interacting protein. Proteolytically active CTSD is produced by multi-step processing of pro-cathepsin D (proCTSD), which is initially synthesized in the ER and delivered to lysosomes. When overexpressed, CTSD itself prevented the coexpressed R120G αBC variant from aggregating. This anti-aggregate activity was also elicited upon overexpression of the W383C CTSD variant, which is predominantly sequestered in the ER and consequently remains unprocessed, suggesting that proCTSD, rather than mature CTSD, serves to suppress the aggregation of the R120G αBC variant. Meanwhile, overexpression of the A58V CTSD variant, which is identical to wild-type CTSD except for the Ala58Val substitution within the pro-peptide, did not suppress the protein aggregation, indicating that the integrity of the pro-peptide is required for proCTSD to exert its anti-aggregate activity. Based on our previous finding that overexpression of the ER transmembrane protein CLN6 (ceroid-lipofuscinosis, neuronal 6), identified as an interacting protein of the ER-anchored αBC, prevents the R120G αBC variant from aggregating, the CLN6-proCTSD coupling was hypothesized to underpin the functionality of proCTSD within the ER. Indeed, CTSD, when overexpressed in CLN6-depleted cells, was unable to exert its anti-aggregate activity, supporting our view. Collectively, we show here that proCTSD prevents the protein aggregation through the functional association with CLN6 in the microenvironment surrounding the ER membrane, shedding light on a novel aspect of proCTSD and its potential involvement in CTSD-related disorders characterized by the accumulation of aberrant protein aggregates.

Keywords:  Alzheimer's disease; CLN6; Cathepsin D; Endoplasmic reticulum; Neuronal ceroid Lipofuscinosis; Pro-cathepsin D; Pro-peptide

DOI:  https://doi.org/10.1016/j.ymgme.2024.108539
Nat Commun. 2024 Jul 22. 15(1): 6177

Molecular insights into degron recognition by CRL5ASB7 ubiquitin ligase.

Mengyu Zhou, Xiaolu Wang, Jiangtao Li, Jinfeng Ma, Ziyu Bao, Xiaojie Yan, Bing Zhang, Tong Liu, Ying Yu, Wenyi Mi, Cheng Dong.

The ankyrin (ANK) SOCS box (ASB) family, encompassing ASB1-18, is the largest group of substrate receptors of cullin 5 Ring E3 ubiquitin ligase. Nonetheless, the mechanism of substrate recognition by ASB family proteins has remained largely elusive. Here we present the crystal structure of ASB7-Elongin B-Elongin C ternary complex bound to a conserved helical degron. ASB7 employs its ANK3-6 to form an extended groove, effectively interacting with the internal α-helix-degron through a network of side-chain-mediated electrostatic and hydrophobic interactions. Our structural findings, combined with biochemical and cellular analyses, identify the key residues of the degron motif and ASB7 required for their recognition. This will facilitate the identification of additional physiological substrates of ASB7 by providing a defined degron motif for screening. Furthermore, the structural insights provide a basis for the rational design of compounds that can specifically target ASB7 by disrupting its interaction with its cognate degron.

DOI: https://doi.org/10.1038/s41467-024-50556-x
Brain Commun. 2024 ;6(4): fcae232

Spatial selectivity of ATase inhibition in mouse models of Charcot-Marie-Tooth disease.

Gonzalo Fernandez-Fuente, Mark A Farrugia, Yajing Peng, Andrew Schneider, John Svaren, Luigi Puglielli.

  The endoplasmic reticulum acetylation machinery has emerged as a new branch of the larger endoplasmic reticulum quality control system. It regulates the selection of correctly folded polypeptides as well as reticulophagy-mediated removal of toxic protein aggregates with the former being a particularly important aspect of the proteostatic functions of endoplasmic reticulum acetylation. Essential to this function is the Nε-lysine acetyltransferase activity of acetyltransferase 1 and acetyltransferase 2, which regulates the induction of endoplasmic reticulum-specific autophagy through the acetylation of the autophagy-related protein 9A. Here, we used three mouse models of Charcot-Marie-Tooth disease, peripheral myelin protein 22/Tr-J, C3-peripheral myelin protein 22 and myelin protein zero/ttrr, to study spatial and translational selectivity of endoplasmic reticulum acetyltransferase inhibitors. The results show that inhibition of the endoplasmic reticulum acetyltransferases selectively targets misfolding/pro-aggregating events occurring in the lumen of the organelle. Therefore, they establish acetyltransferase 1 and acetyltransferase 2 as the first proven targets for disease-causing proteotoxic states that initiate within the lumen of the endoplasmic reticulum/secretory pathway.

Keywords:  ATase; Charcot–Marie–Tooth disease; acetylation; endoplasmic reticulum; proteostasis

DOI:  https://doi.org/10.1093/braincomms/fcae232
Autophagy. 2024 Jul 26. 1-17

GORASP2 promotes phagophore closure and autophagosome maturation into autolysosomes.

Yusheng Xing, Lei Huang, Yannan Jian, Zhenqian Zhang, Xiaodan Zhao, Xing Zhang, Tingting Fu, Yue Zhang, Yijie Wang, Xiaoyan Zhang.

  As the central hub of the secretory pathway, the Golgi apparatus plays a crucial role in maintaining cellular homeostasis in response to stresses. Recent studies have revealed the involvement of the Golgi tether, GORASP2, in facilitating autophagosome-lysosome fusion by connecting LC3-II and LAMP2 during nutrient starvation. However, the precise mechanism remains elusive. In this study, utilizing super-resolution microscopy, we observed GORASP2 localization on the surface of autophagosomes during glucose starvation. Depletion of GORASP2 hindered phagophore closure by regulating the association between VPS4A and the ESCRT-III component, CHMP2A. Furthermore, we found that GORASP2 controls RAB7A activity by modulating its GEF complex, MON1A-CCZ1, thereby impacting RAB7A's interaction with the HOPS complex. The assembly of both STX17-SNAP29-VAMP8 and YKT6-SNAP29-STX7 SNARE complexes was also attenuated without GORASP2. These findings suggest that GORASP2 helps seal autophagosomes and activate the RAB7A-HOPS-SNAREs membrane fusion machinery for autophagosome maturation, highlighting its membrane tethering function in response to stresses.Abbreviations: BafA1: bafilomycin A1; ESCRT: endosomal sorting complex required for transport; FPP: fluorescence protease protection; GEF: guanine nucleotide exchange factor; GFP: green fluorescent protein; GORASP2: golgi reassembly stacking protein 2; GSB: glucose starvation along with bafilomycin A1; HOPS: homotypic fusion and protein sorting; LAMP2: lysosomal associated membrane protein 2; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; PBS: phosphate-buffered saline; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PK: proteinase K; SNARE: soluble N-ethylmaleimide-sensitive factor attachment protein receptor; SIM: structured illumination microscopy; UVRAG: UV radiation resistance associated.

Keywords:  Autophagosome maturation; ESCRT complex; GORASP2; RAB7A; SNAREs; phagophore closure

DOI:  https://doi.org/10.1080/15548627.2024.2375785
Biochem Biophys Res Commun. 2024 Jul 18. pii: S0006-291X(24)00959-8. [Epub ahead of print]733 150423

The ubiquitin-proteasome system degrades fatty acid synthase under nitrogen starvation when autophagy is dysfunctional in Saccharomyces cerevisiae.

Hae-Soo Jang, Yongook Lee, Yeonsoo Kim, Won-Ki Huh.

  Autophagy and the ubiquitin-proteasome system (UPS) are two major protein quality control mechanisms maintaining cellular proteostasis. In Saccharomyces cerevisiae, the de novo synthesis of saturated fatty acids is performed by a multienzyme complex known as fatty acid synthase (FAS). A recent study reported that yeast FAS is preferentially degraded by autophagy under nitrogen starvation. In this study, we examined the fate of FAS during nitrogen starvation when autophagy is dysfunctional. We found that the UPS compensates for FAS degradation in the absence of autophagy. Additionally, we discovered that the UPS-dependent degradation of Fas2 requires the E3 ubiquitin ligase Ubr1. Our findings highlight the complementary relationship between autophagy and the UPS.

Keywords:  Autophagy; Fatty acid synthase; Nitrogen starvation; Saccharomyces cerevisiae; Ubiquitin-proteasome system

DOI:  https://doi.org/10.1016/j.bbrc.2024.150423
Protein Sci. 2024 Aug;33(8): e5123

Cellular turnover and degradation of the most common missense cystathionine beta-synthase variants causing homocystinuria.

Ela Mijatovic, Kelly Ascenção, Csaba Szabo, Tomas Majtan.

  Homocystinuria (HCU) due to cystathionine beta-synthase (CBS) deficiency is the most common inborn error of sulfur amino acid metabolism. Recent work suggests that missense pathogenic mutations-regardless of their topology-cause instability of the C-terminal regulatory domain, which likely translates into CBS misfolding, impaired assembly, and loss of function. However, it is unknown how instability of the regulatory domain translates into cellular CBS turnover and which degradation pathways are involved in CBS proteostasis. Here, we developed a human HEK293-based cellular model lacking intrinsic CBS and stably overexpressing wild-type (WT) CBS or its 10 most common missense HCU mutants. We found that HCU mutants, except the I278T variant, expressed similarly or better than CBS WT, with some of them showing impaired oligomerization, activity and response to allosteric activator S-adenosylmethionine. Cellular stability of all HCU mutants, except P49L and A114V, was significantly lower than the stability of CBS WT, suggesting their increased degradation. Ubiquitination analysis of CBS WT and two representative CBS mutants (T191M and I278T) showed that proteasomal degradation is the major pathway for CBS disposal, with a minor involvement of lysosomal-autophagic and endoplasmic reticulum-associated degradation (ERAD) pathways for HCU mutants. Proteasomal inhibition significantly increased the half-life and activity of T191M and I278T CBS mutants. Lysosomal and ERAD inhibition had only a minor impact on CBS turnover, but ERAD inhibition rescued the activity of T191M and I278T CBS mutants similarly as proteasomal inhibition. In conclusion, the present study provides new insights into proteostasis of CBS in HCU.

Keywords:  conformational disorder; folding; proteostasis; ubiquitin signaling

DOI:  https://doi.org/10.1002/pro.5123
EMBO J. 2024 Jul 23.

Connexin43 promotes exocytosis of damaged lysosomes through actin remodelling.

Neuza Domingues, Steve Catarino, Beatriz Cristóvão, Lisa Rodrigues, Filomena A Carvalho, Maria João Sarmento, Mónica Zuzarte, Jani Almeida, Teresa Ribeiro-Rodrigues, Ânia Correia-Rodrigues, Fábio Fernandes, Paulo Rodrigues-Santos, Trond Aasen, Nuno C Santos, Viktor I Korolchuk, Teresa Gonçalves, Ira Milosevic, Nuno Raimundo, Henrique Girão.

  A robust and efficient cellular response to lysosomal membrane damage prevents leakage from the lysosome lumen into the cytoplasm. This response is understood to happen through either lysosomal membrane repair or lysophagy. Here we report exocytosis as a third response mechanism to lysosomal damage, which is further potentiated when membrane repair or lysosomal degradation mechanisms are impaired. We show that Connexin43 (Cx43), a protein canonically associated with gap junctions, is recruited from the plasma membrane to damaged lysosomes, promoting their secretion and accelerating cell recovery. The effects of Cx43 on lysosome exocytosis are mediated by a reorganization of the actin cytoskeleton that increases plasma membrane fluidity and decreases cell stiffness. Furthermore, we demonstrate that Cx43 interacts with the actin nucleator Arp2, the activity of which was shown to be necessary for Cx43-mediated actin rearrangement and lysosomal exocytosis following damage. These results define a novel mechanism of lysosomal quality control whereby Cx43-mediated actin remodelling potentiates the secretion of damaged lysosomes.

Keywords:  Actin-remodelling; Arp2; Connexin43; Exocytosis; Lysosomal Damage

DOI:  https://doi.org/10.1038/s44318-024-00177-3
Commun Biol. 2024 Jul 24. 7(1): 901

A ligand discovery toolbox for the WWE domain family of human E3 ligases.

Lena Münzker, Serah W Kimani, Milan M Fowkes, Aiping Dong, Hong Zheng, Yanjun Li, Morgan Dasovich, Krzysztof M Zak, Anthony K L Leung, Jonathan M Elkins, Dirk Kessler, Cheryl H Arrowsmith, Levon Halabelian, Jark Böttcher.

The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15N-NMR-based binding affinity assays and 19F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso-ADP-ribose (iso-ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.

DOI: https://doi.org/10.1038/s42003-024-06584-w
PLoS Biol. 2024 Apr;22(4): e3001767

The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage.

Melissa D Parker, Elise S Brunk, Adam J Getzler, Katrin Karbstein.

The 18S rRNA sequence is highly conserved, particularly at its 3'-end, which is formed by the endonuclease Nob1. How Nob1 identifies its target sequence is not known, and in vitro experiments have shown Nob1 to be error-prone. Moreover, the sequence around the 3'-end is degenerate with similar sites nearby. Here, we used yeast genetics, biochemistry, and next-generation sequencing to investigate a role for the ATPase Rio1 in monitoring the accuracy of the 18S rRNA 3'-end. We demonstrate that Nob1 can miscleave its rRNA substrate and that miscleaved rRNA accumulates upon bypassing the Rio1-mediated quality control (QC) step, but not in healthy cells with intact QC mechanisms. Mechanistically, we show that Rio1 binding to miscleaved rRNA is weaker than its binding to accurately processed 18S rRNA. Accordingly, excess Rio1 results in accumulation of miscleaved rRNA. Ribosomes containing miscleaved rRNA can translate, albeit more slowly, thereby inviting collisions with trailing ribosomes. These collisions result in degradation of the defective ribosomes utilizing parts of the machinery for mRNA QC. Altogether, the data support a model in which Rio1 inspects the 3'-end of the nascent 18S rRNA to prevent miscleaved 18S rRNA-containing ribosomes from erroneously engaging in translation, where they induce ribosome collisions. The data also demonstrate how ribosome collisions purify cells of altered ribosomes with different functionalities, with important implications for the concept of ribosome heterogeneity.

DOI: https://doi.org/10.1371/journal.pbio.3001767
Commun Biol. 2024 Jul 25. 7(1): 903

Endoplasmic reticulum unfolded protein response transcriptional targets of XBP-1s mediate rescue from tauopathy.

Sarah M Waldherr, Marina Han, Aleen D Saxton, Taylor A Vadset, Pamela J McMillan, Jeanna M Wheeler, Nicole F Liachko, Brian C Kraemer.

Pathological tau disrupts protein homeostasis (proteostasis) within neurons in Alzheimer's disease (AD) and related disorders. We previously showed constitutive activation of the endoplasmic reticulum unfolded protein response (UPRER) transcription factor XBP-1s rescues tauopathy-related proteostatic disruption in a tau transgenic Caenorhabditis elegans (C. elegans) model of human tauopathy. XBP-1s promotes clearance of pathological tau, and loss of function of the ATF-6 branch of the UPRER prevents XBP-1s rescue of tauopathy in C. elegans. We conducted transcriptomic analysis of tau transgenic and xbp-1s transgenic C. elegans and found 116 putative target genes significantly upregulated by constitutively active XBP-1s. Among these were five candidate XBP-1s target genes with human orthologs and a previously known association with ATF6 (csp-1, dnj-28, hsp-4, ckb-2, and lipl-3). We examined the functional involvement of these targets in XBP-1s-mediated tauopathy suppression and found loss of function in any one of these genes completely disrupts XBP-1s suppression of tauopathy. Further, we demonstrate upregulation of HSP-4, C. elegans BiP, partially rescues tauopathy independent of other changes in the transcriptional network. Understanding how the UPRER modulates pathological tau accumulation will inform neurodegenerative disease mechanisms and direct further study in mammalian systems with the long-term goal of identifying therapeutic targets in human tauopathies.

DOI: https://doi.org/10.1038/s42003-024-06570-2
J Neurosci. 2024 Jul 25. pii: e0879242024. [Epub ahead of print]

ALS-linked VapB P56S mutation alters neuronal mitochondrial turnover at the synapse.

Hiu-Tung C Wong, Angelica E Lang, Chris Stein, Catherine M Drerup.

Mitochondrial population maintenance in neurons is essential for neuron function and survival. Contact sites between mitochondria and the endoplasmic reticulum (ER) are poised to regulate mitochondrial homeostasis in neurons. These contact sites can function to facilitate transfer of calcium and lipids between the organelles and have been shown to regulate aspects of mitochondrial fission and fusion dynamics. VapB is an ER membrane protein present at a subset of ER-mitochondria contact sites. Mutations in VapB cause neurodegenerative disease. Specifically, a proline-to-serine mutation at amino acid 56 (P56S), correlates with susceptibility to amyotrophic lateral sclerosis (ALS) type 8. Given the relationship between failed mitochondrial health and neurodegenerative disease, we investigated the function of VapB in mitochondrial population maintenance. We demonstrate that transgenic expression of VapBP56S in zebrafish larvae (sex undetermined) increased mitochondrial biogenesis, causing increased mitochondrial population size in the axon terminal. Expression of wild type VapB did not alter biogenesis but, instead, increased mitophagy in the axon terminal. Using genetic manipulations to independently increase mitochondrial biogenesis in zebrafish neurons, we show that biogenesis is normally balanced by mitophagy to maintain a constant mitochondrial population size. VapBP56S transgenics fail to increase mitophagy to compensate for the increase in mitochondrial biogenesis, suggesting an impaired mitophagic response. Finally, using a synthetic ER-mitochondria tether, we show that VapB's function in mitochondrial turnover is likely independent of ER-mitochondrial tethering by contact sites. Our findings demonstrate that VapB can control mitochondrial turnover in the axon terminal, and this function is altered by the P56S ALS-linked mutation.Significance statement Mitochondrial population dysfunction is tightly tied to neurodegenerative diseases, including ALS. Maintenance of the mitochondrial population in neurons requires the birth of new mitochondria and the degradation of damaged organelles. ER-mitochondrial contact site proteins are in a position to regulate both processes in neurons. Our work demonstrates that an ALS-associated mutation in the contact site protein VapB disrupts both processes, identifying VapB as a mediator of regulated mitochondrial turnover to maintain a steady-state mitochondrial population.

DOI: https://doi.org/10.1523/JNEUROSCI.0879-24.2024
Science. 2024 Jul 26. 385(6707): eadi3048

Selection for robust metabolism in domesticated yeasts is driven by adaptation to Hsp90 stress.

Natalia Condic, Hatim Amiji, Dipak Patel, William Charles Shropshire, Nejla Ozirmak Lermi, Youssef Sabha, Beryl John, Blake Hanson, Georgios Ioannis Karras.

Protein folding both promotes and constrains adaptive evolution. We uncover this surprising duality in the role of the protein-folding chaperone heat shock protein 90 (Hsp90) in maintaining the integrity of yeast metabolism amid proteotoxic stressors within industrial domestication niches. Ethanol disrupts critical Hsp90-dependent metabolic pathways and exerts strong selective pressure for redundant duplications of key genes within these pathways, yielding the classical genomic signatures of beer and bread domestication. This work demonstrates a mechanism of adaptive canalization in an ecology of major economic importance and highlights Hsp90-dependent variation as an important source of phantom heritability in complex traits.

DOI: https://doi.org/10.1126/science.adi3048
EMBO Rep. 2024 Jul 22.

Fam134c and Fam134b shape axonal endoplasmic reticulum architecture in vivo.

Francescopaolo Iavarone, Marta Zaninello, Michela Perrone, Mariagrazia Monaco, Esther Barth, Felix Gaedke, Maria Teresa Pizzo, Giorgia Di Lorenzo, Vincenzo Desiderio, Eduardo Sommella, Fabrizio Merciai, Emanuela Salviati, Pietro Campiglia, Livio Luongo, Elvira De Leonibus, Elena Rugarli, Carmine Settembre.

  Endoplasmic reticulum (ER) remodeling is vital for cellular organization. ER-phagy, a selective autophagy targeting ER, plays an important role in maintaining ER morphology and function. The FAM134 protein family, including FAM134A, FAM134B, and FAM134C, mediates ER-phagy. While FAM134B mutations are linked to hereditary sensory and autonomic neuropathy in humans, the physiological role of the other FAM134 proteins remains unknown. To address this, we investigate the roles of FAM134 proteins using single and combined knockouts (KOs) in mice. Single KOs in young mice show no major phenotypes; however, combined Fam134b and Fam134c deletion (Fam134b/cdKO), but not the combination including Fam134a deletion, leads to rapid neuromuscular and somatosensory degeneration, resulting in premature death. Fam134b/cdKO mice show rapid loss of motor and sensory axons in the peripheral nervous system. Long axons from Fam134b/cdKO mice exhibit expanded tubular ER with a transverse ladder-like appearance, whereas no obvious abnormalities are present in cortical ER. Our study unveils the critical roles of FAM134C and FAM134B in the formation of tubular ER network in axons of both motor and sensory neurons.

Keywords:  Axon; Endoplasmic Reticulum; FAM134B; FAM134C

DOI:  https://doi.org/10.1038/s44319-024-00213-7
Mol Cell. 2024 Jul 25. pii: S1097-2765(24)00531-8. [Epub ahead of print]84(14): 2698-2716.e9

Polysome collapse and RNA condensation fluidize the cytoplasm.

Ying Xie, Tong Shu, Tiewei Liu, Marie-Christin Spindler, Julia Mahamid, Glen M Hocky, David Gresham, Liam J Holt.

  The cell interior is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cellular physiology. Cellular stress responses almost universally lead to inhibition of translation, resulting in polysome collapse and release of mRNA. The released mRNA molecules condense with RNA-binding proteins to form ribonucleoprotein (RNP) condensates known as processing bodies and stress granules. Here, we show that polysome collapse and condensation of RNA transiently fluidize the cytoplasm, and coarse-grained molecular dynamic simulations support this as a minimal mechanism for the observed biophysical changes. Increased mesoscale diffusivity correlates with the efficient formation of quality control bodies (Q-bodies), membraneless organelles that compartmentalize misfolded peptides during stress. Synthetic, light-induced RNA condensation also fluidizes the cytoplasm. Together, our study reveals a functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to enable efficient response of cells to stress conditions.

Keywords:  P-bodies; Q-bodies; biomolecular condensates; biophysics; cryo-electron tomography; microrheology; polysome; stress granules

DOI:  https://doi.org/10.1016/j.molcel.2024.06.024
Proc Natl Acad Sci U S A. 2024 Jul 30. 121(31): e2407472121

The ISR downstream target ATF4 represses long-term memory in a cell type-specific manner.

Niaz Mahmood, Jung-Hyun Choi, Pei You Wu, Sean W Dooling, Trent A Watkins, Ziying Huang, Jesse Lipman, Hanjie Zhao, Anqi Yang, Jake Silversmith, Yanis Inglebert, Constantinos Koumenis, Vijendra Sharma, Jean-Claude Lacaille, Wayne S Sossin, Arkady Khoutorsky, R Anne McKinney, Mauro Costa-Mattioli, Nahum Sonenberg.

  The integrated stress response (ISR), a pivotal protein homeostasis network, plays a critical role in the formation of long-term memory (LTM). The precise mechanism by which the ISR controls LTM is not well understood. Here, we report insights into how the ISR modulates the mnemonic process by using targeted deletion of the activating transcription factor 4 (ATF4), a key downstream effector of the ISR, in various neuronal and non-neuronal cell types. We found that the removal of ATF4 from forebrain excitatory neurons (but not from inhibitory neurons, cholinergic neurons, or astrocytes) enhances LTM formation. Furthermore, the deletion of ATF4 in excitatory neurons lowers the threshold for the induction of long-term potentiation, a cellular model for LTM. Transcriptomic and proteomic analyses revealed that ATF4 deletion in excitatory neurons leads to upregulation of components of oxidative phosphorylation pathways, which are critical for ATP production. Thus, we conclude that ATF4 functions as a memory repressor selectively within excitatory neurons.

Keywords:  integrated stress response; learning and memory; protein synthesis; synaptic plasticity

DOI:  https://doi.org/10.1073/pnas.2407472121
Biochem Biophys Res Commun. 2024 Jul 18. pii: S0006-291X(24)00958-6. [Epub ahead of print]732 150422

ATM facilitates autophagy and protects against oxidative stress and apoptosis in response to ER stress in vitro.

Danélle Bester, Marguerite Blignaut, Barbara Huisamen.

  The endoplasmic reticulum (ER) responds to cellular stress by initiating an unfolded protein response (UPR) that mitigates misfolded protein accumulation by promoting protein degradation pathways. Chronic ER stress leads to UPR-mediated apoptosis and is a common underlying feature of various diseases, highlighting the modulators of the UPR as attractive targets for therapeutic intervention. Ataxia-telangiectasia mutated protein kinase (ATM) is a stress-responsive kinase that initiates autophagy in response to reactive oxygen species (ROS), and ATM deficiency is associated with increased ER stress markers in vitro. However, whether ATM participates in the UPR remains unclear. In this in vitro study, a novel role for ATM in the ER stress response is described using the well-characterized HEK293 cells treated with the common ER stress-inducing agent, tunicamycin, with and without the potent ATM inhibitor, KU-60019. We show for the first time that ATM is activated in a time-dependent manner downstream of UPR initiation in response to tunicamycin treatment. Furthermore, we demonstrate that ATM is required for p62-bound protein cargo degradation through the autophagy pathway in response to ER stress. Lastly, our data suggest a protective role for ATM in ER stress-mediated oxidative stress and mitochondrial apoptosis. Taken together, we highlight ATM as a potential novel drug target in ER stress-related diseases.

Keywords:  ATM; Apoptosis; Autophagy; ER stress; Oxidative stress; UPR

DOI:  https://doi.org/10.1016/j.bbrc.2024.150422
PLoS Comput Biol. 2024 Jul 25. 20(7): e1012253

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile.

Patrick Bryant, Frank Noé.

Structure prediction of protein complexes has improved significantly with AlphaFold2 and AlphaFold-multimer (AFM), but only 60% of dimers are accurately predicted. Here, we learn a bias to the MSA representation that improves the predictions by performing gradient descent through the AFM network. We demonstrate the performance on seven difficult targets from CASP15 and increase the average MMscore to 0.76 compared to 0.63 with AFM. We evaluate the procedure on 487 protein complexes where AFM fails and obtain an increased success rate (MMscore>0.75) of 33% on these difficult targets. Our protocol, AFProfile, provides a way to direct predictions towards a defined target function guided by the MSA. We expect gradient descent over the MSA to be useful for different tasks.

DOI: https://doi.org/10.1371/journal.pcbi.1012253
Nature. 2024 Jul 24.

SMYD5 methylation of rpL40 links ribosomal output to gastric cancer.

Juhyung Park, Jibo Wu, Krzysztof J Szkop, Jinho Jeong, Predrag Jovanovic, Dylan Husmann, Natasha M Flores, Joel W Francis, Ying-Jiun C Chen, Ana Morales Benitez, Emily Zahn, Shumei Song, Jaffer A Ajani, Linghua Wang, Kamini Singh, Ola Larsson, Benjamin A Garcia, Ivan Topisirovic, Or Gozani, Pawel K Mazur.

Dysregulated transcription due to disruption in histone lysine methylation dynamics is an established contributor to tumorigenesis1,2. However, whether analogous pathologic epigenetic mechanisms act directly on the ribosome to advance oncogenesis is unclear. Here we find that trimethylation of the core ribosomal protein L40 (rpL40) at lysine 22 (rpL40K22me3) by the lysine methyltransferase SMYD5 regulates mRNA translation output to promote malignant progression of gastric adenocarcinoma (GAC) with lethal peritoneal ascites. A biochemical-proteomics strategy identifies the monoubiquitin fusion protein partner rpL40 (ref. 3) as the principal physiological substrate of SMYD5 across diverse samples. Inhibiting the SMYD5-rpL40K22me3 axis in GAC cell lines reprogrammes protein synthesis to attenuate oncogenic gene expression signatures. SMYD5 and rpL40K22me3 are upregulated in samples from patients with GAC and negatively correlate with clinical outcomes. SMYD5 ablation in vivo in familial and sporadic mouse models of malignant GAC blocks metastatic disease, including peritoneal carcinomatosis. Suppressing SMYD5 methylation of rpL40 inhibits human cancer cell and patient-derived GAC xenograft growth and renders them hypersensitive to inhibitors of PI3K and mTOR. Finally, combining SMYD5 depletion with PI3K-mTOR inhibition and chimeric antigen receptor T cell administration cures an otherwise lethal in vivo mouse model of aggressive GAC-derived peritoneal carcinomatosis. Together, our work uncovers a ribosome-based epigenetic mechanism that facilitates the evolution of malignant GAC and proposes SMYD5 targeting as part of a potential combination therapy to treat this cancer.

DOI: https://doi.org/10.1038/s41586-024-07718-0
Nat Commun. 2024 Jul 22. 15(1): 6172

Targeted degradation of extracellular mitochondrial aspartyl-tRNA synthetase modulates immune responses.

Benjamin S Johnson, Daniela Farkas, Rabab El-Mergawy, Jessica A Adair, Ajit Elhance, Moemen Eltobgy, Francesca M Coan, Lexie Chafin, Jessica A Joseph, Alex Cornwell, Finny J Johns, Lorena Rosas, Mauricio Rojas, Laszlo Farkas, Joseph S Bednash, James D Londino, Prabir Ray, Anuradha Ray, Valerian Kagan, Janet S Lee, Bill B Chen, Rama K Mallampalli.

The severity of bacterial pneumonia can be worsened by impaired innate immunity resulting in ineffective pathogen clearance. We describe a mitochondrial protein, aspartyl-tRNA synthetase (DARS2), which is released in circulation during bacterial pneumonia in humans and displays intrinsic innate immune properties and cellular repair properties. DARS2 interacts with a bacterial-induced ubiquitin E3 ligase subunit, FBXO24, which targets the synthetase for ubiquitylation and degradation, a process that is inhibited by DARS2 acetylation. During experimental pneumonia, Fbxo24 knockout mice exhibit elevated DARS2 levels with an increase in pulmonary cellular and cytokine levels. In silico modeling identified an FBXO24 inhibitory compound with immunostimulatory properties which extended DARS2 lifespan in cells. Here, we show a unique biological role for an extracellular, mitochondrially derived enzyme and its molecular control by the ubiquitin apparatus, which may serve as a mechanistic platform to enhance protective host immunity through small molecule discovery.

DOI: https://doi.org/10.1038/s41467-024-50031-7
FEBS Lett. 2024 Jul 26.

The COPII coat protein SEC24D is required for autophagosome closure in mammals.

Tianlong He, Cuicui Ji, Wenting Zhang, Xianghua Li, Yukun Liu, Xiaoli Wang, Haolin Zhang, Juan Wang.

  Macroautophagy involves the encapsulation of cellular components within double-membrane autophagosomes for subsequent degradation in vacuoles or lysosomes. Coat protein complex II (COPII) vesicles serve as a membrane source for autophagosome formation. However, the specific role of SEC24D, an isoform of the COPII coat protein SEC24, in the macroautophagy pathway remains unclear. In this study, we demonstrate that SEC24D is indispensable for macroautophagy and important for autophagosome closure. Depletion of SEC24D leads to the accumulation of unsealed isolation membranes. Furthermore, under conditions of starvation, SEC24D interacts with casein kinase1 delta (CK1δ), a member of the casein kinase 1 family, and autophagy-related 9A (ATG9A). Collectively, our findings unveil the indispensable role of SEC24D in starvation-induced autophagy in mammalian cells.

Keywords:  COPII; SEC24D; autophagosome closure; autophagy; isolation membrane

DOI:  https://doi.org/10.1002/1873-3468.14983
Cell Rep Med. 2024 Jul 18. pii: S2666-3791(24)00372-0. [Epub ahead of print] 101658

Myeloid cells coordinately induce glioma cell-intrinsic and cell-extrinsic pathways for chemoresistance via GP130 signaling.

Jiying Cheng, Min Li, Edyta Motta, Deivi Barci, Wangyang Song, Ding Zhou, Gen Li, Sihan Zhu, Anru Yang, Brian D Vaillant, Axel Imhof, Ignasi Forné, Sabine Spiegl-Kreinecker, Nu Zhang, Hiroshi Katayama, Krishna P L Bhat, Charlotte Flüh, Roland E Kälin, Rainer Glass.

  The DNA damage response (DDR) and the blood-tumor barrier (BTB) restrict chemotherapeutic success for primary brain tumors like glioblastomas (GBMs). Coherently, GBMs almost invariably relapse with fatal outcomes. Here, we show that the interaction of GBM and myeloid cells simultaneously induces chemoresistance on the genetic and vascular levels by activating GP130 receptor signaling, which can be addressed therapeutically. We provide data from transcriptomic and immunohistochemical screens with human brain material and pharmacological experiments with a humanized organotypic GBM model, proteomics, transcriptomics, and cell-based assays and report that nanomolar concentrations of the signaling peptide humanin promote temozolomide (TMZ) resistance through DDR activation. GBM mouse models recapitulating intratumoral humanin release show accelerated BTB formation. GP130 blockade attenuates both DDR activity and BTB formation, resulting in improved preclinical chemotherapeutic efficacy. Altogether, we describe an overarching mechanism for TMZ resistance and outline a translatable strategy with predictive markers to improve chemotherapy for GBMs.

Keywords:  DDR; DNA damage response; GP130; IL6ST; TAM; blood-tumor barrier; chemotherapy; glioblastoma; humanin; temozolomide; tumor-associated myeloid cells

DOI:  https://doi.org/10.1016/j.xcrm.2024.101658
J Cell Sci. 2024 Jul 26. pii: jcs.261952. [Epub ahead of print]

When less is more - A fast TurboID KI approach for high sensitivity endogenous interactome mapping.

Alexander Stockhammer, Carissa Spalt, Antonia Klemt, Laila S Benz, Shelly Harel, Vini Natalia, Lukas Wiench, Christian Freund, Benno Kuropka, Francesca Bottanelli.

  In recent years, proximity labeling has established itself as an unbiased and powerful approach to map the interactome of specific proteins. While physiological expression of labeling enzymes is beneficial for the mapping of interactors, generation of the desired cell lines remains time-consuming and challenging. Using our established pipeline for rapid generation of C- and N-terminal CRISPR-Cas9 knock-ins (KIs) based on antibiotic selection, we were able to compare the performance of commonly used labeling enzymes when endogenously expressed. Endogenous tagging of the µ subunit of the AP-1 complex with TurboID allowed identification of known interactors and cargo proteins that simple overexpression of a labeling enzyme fusion protein could not reveal. We used the KI-strategy to compare the interactome of the different adaptor protein (AP) complexes and clathrin and were able to assemble lists of potential interactors and cargo proteins that are specific for each sorting pathway. Our approach greatly simplifies the execution of proximity labeling experiments for proteins in their native cellular environment and allows going from CRISPR transfection to mass spectrometry analysis and interactome data in just over a month.

Keywords:  Gene editing; Membrane trafficking; TurboID

DOI:  https://doi.org/10.1242/jcs.261952
Mol Cell. 2024 Jul 17. pii: S1097-2765(24)00544-6. [Epub ahead of print]

Blending and separating dynamics of RNA-binding proteins develop architectural splicing networks spreading throughout the nucleus.

Akio Masuda, Takaaki Okamoto, Toshihiko Kawachi, Jun-Ichi Takeda, Tomonari Hamaguchi, Kinji Ohno.

  The eukaryotic nucleus has a highly organized structure. Although the spatiotemporal arrangement of spliceosomes on nascent RNA drives splicing, the nuclear architecture that directly supports this process remains unclear. Here, we show that RNA-binding proteins (RBPs) assembled on RNA form meshworks in human and mouse cells. Core and accessory RBPs in RNA splicing make two distinct meshworks adjacently but distinctly distributed throughout the nucleus. This is achieved by mutual exclusion dynamics between the charged and uncharged intrinsically disordered regions (IDRs) of RBPs. These two types of meshworks compete for spatial occupancy on pre-mRNA to regulate splicing. Furthermore, the optogenetic enhancement of the RBP meshwork causes aberrant splicing, particularly of genes involved in neurodegeneration. Genetic mutations associated with neurodegenerative diseases are often found in the IDRs of RBPs, and cells harboring these mutations exhibit impaired meshwork formation. Our results uncovered the spatial organization of RBP networks to drive RNA splicing.

Keywords:  CLIP; RNA-binding proteins; intrinsically disordered region; meshwork; neurodegeneration; phase separation; splicing

DOI:  https://doi.org/10.1016/j.molcel.2024.07.001
Neuropathol Appl Neurobiol. 2024 Aug;50(4): e12999

Unfolded protein response markers Grp78 and eIF2alpha are upregulated with increasing alpha-synuclein levels in Lewy body disease.

Dominik Hrabos, Ilaria Poggiolini, Livia Civitelli, Emilia Galli, Chris Esapa, Mart Saarma, Päivi Lindholm, Laura Parkkinen.

   AIMS: Endoplasmic reticulum stress followed by the unfolded protein response is one of the cellular mechanisms contributing to the progression of α-synuclein pathology in Parkinson's disease and other Lewy body diseases. We aimed to investigate the activation of endoplasmic reticulum stress and its correlation with α-synuclein pathology in human post-mortem brain tissue.
METHODS: We analysed brain tissue from 45 subjects-14 symptomatic patients with Lewy body disease, 19 subjects with incidental Lewy body disease, and 12 healthy controls. The analysed brain regions included the medulla, pons, midbrain, striatum, amygdala and entorhinal, temporal, frontal and occipital cortex. We analysed activation of endoplasmic reticulum stress via levels of the unfolded protein response-related proteins (Grp78, eIF2α) and endoplasmic reticulum stress-regulating neurotrophic factors (MANF, CDNF).
RESULTS: We showed that regional levels of two endoplasmic reticulum-localised neurotrophic factors, MANF and CDNF, did not change in response to accumulating α-synuclein pathology. The concentration of MANF negatively correlated with age in specific regions. eIF2α was upregulated in the striatum of Lewy body disease patients and correlated with increased α-synuclein levels. We found the upregulation of chaperone Grp78 in the amygdala and nigral dopaminergic neurons of Lewy body disease patients. Grp78 levels in the amygdala strongly correlated with soluble α-synuclein levels.
CONCLUSIONS: Our data suggest a strong but regionally specific change in Grp78 and eIF2α levels, which positively correlates with soluble α-synuclein levels. Additionally, MANF levels decreased in dopaminergic neurons in the substantia nigra. Our research suggests that endoplasmic reticulum stress activation is not associated with Lewy pathology but rather with soluble α-synuclein concentration and disease progression.

Keywords:  ER stress; Lewy body disease; Parkinson's disease; alpha‐synuclein; unfolded protein response

DOI:  https://doi.org/10.1111/nan.12999
NAR Cancer. 2024 Sep;6(3): zcae032

Decoding ribosome complexity: role of ribosomal proteins in cancer and disease.

Pedro Fuentes, Joffrey Pelletier, Antonio Gentilella.

The ribosome is a remarkably complex machinery, at the interface with diverse cellular functions and processes. Evolutionarily conserved, yet intricately regulated, ribosomes play pivotal roles in decoding genetic information into the synthesis of proteins and in the generation of biomass critical for cellular physiological functions. Recent insights have revealed the existence of ribosome heterogeneity at multiple levels. Such heterogeneity extends to cancer, where aberrant ribosome biogenesis and function contribute to oncogenesis. This led to the emergence of the concept of 'onco-ribosomes', specific ribosomal variants with altered structural dynamics, contributing to cancer initiation and progression. Ribosomal proteins (RPs) are involved in many of these alterations, acting as critical factors for the translational reprogramming of cancer cells. In this review article, we highlight the roles of RPs in ribosome biogenesis, how mutations in RPs and their paralogues reshape the translational landscape, driving clonal evolution and therapeutic resistance. Furthermore, we present recent evidence providing new insights into post-translational modifications of RPs, such as ubiquitylation, UFMylation and phosphorylation, and how they regulate ribosome recycling, translational fidelity and cellular stress responses. Understanding the intricate interplay between ribosome complexity, heterogeneity and RP-mediated regulatory mechanisms in pathology offers profound insights into cancer biology and unveils novel therapeutic avenues targeting the translational machinery in cancer.

DOI: https://doi.org/10.1093/narcan/zcae032
Brief Bioinform. 2024 Jul 25. pii: bbae359. [Epub ahead of print]25(5):

TUnA: an uncertainty-aware transformer model for sequence-based protein-protein interaction prediction.

Young Su Ko, Jonathan Parkinson, Cong Liu, Wei Wang.

  Protein-protein interactions (PPIs) are important for many biological processes, but predicting them from sequence data remains challenging. Existing deep learning models often cannot generalize to proteins not present in the training set and do not provide uncertainty estimates for their predictions. To address these limitations, we present TUnA, a Transformer-based uncertainty-aware model for PPI prediction. TUnA uses ESM-2 embeddings with Transformer encoders and incorporates a Spectral-normalized Neural Gaussian Process. TUnA achieves state-of-the-art performance and, importantly, evaluates uncertainty for unseen sequences. We demonstrate that TUnA's uncertainty estimates can effectively identify the most reliable predictions, significantly reducing false positives. This capability is crucial in bridging the gap between computational predictions and experimental validation.

Keywords:  deep learning; protein–protein interaction prediction; uncertainty awareness

DOI:  https://doi.org/10.1093/bib/bbae359
Nucleic Acids Res. 2024 Jul 23. pii: gkae630. [Epub ahead of print]

Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains.

Arka Banerjee, Meric Ataman, Maciej Jerzy Smialek, Debdatto Mookherjee, Julius Rabl, Aleksei Mironov, Lea Mues, Ludovic Enkler, Mairene Coto-Llerena, Alexander Schmidt, Daniel Boehringer, Salvatore Piscuoglio, Anne Spang, Nitish Mittal, Mihaela Zavolan.

Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated the expression pattern, structure within the ribosome and effect on protein synthesis of the ribosomal protein paralog 39L (RPL39L). With a novel mass spectrometric approach we revealed the expression of RPL39L protein beyond mouse germ cells, in human pluripotent cells, cancer cell lines and tissue samples. We generated RPL39L knock-out mouse embryonic stem cell (mESC) lines and demonstrated that RPL39L impacts the dynamics of translation, to support the pluripotency and differentiation, spontaneous and along the germ cell lineage. Most differences in protein abundance between WT and RPL39L KO lines were explained by widespread autophagy. By CryoEM analysis of purified RPL39 and RPL39L-containing ribosomes we found that, unlike RPL39, RPL39L has two distinct conformations in the exposed segment of the nascent peptide exit tunnel, creating a distinct hydrophobic patch that has been predicted to support the efficient co-translational folding of alpha helices. Our study shows that ribosomal protein paralogs provide switchable modular components that can tune translation to the protein production needs of individual cell types.

DOI: https://doi.org/10.1093/nar/gkae630