The EMBO Journal

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Hypertranscription and transcription-replication conflicts (TRCs) are frequent features of cancer cells. RAS oncogenes promote hypertranscription to allow cell growth and proliferation, which can the lead to TRCs. Here, we report that hyperactivation of the PI3K-AKT signalling pathway is required for TRCs induced by RAS oncogenes. Oncogenic HRAS causes more TRCs than oncogenic KRAS or BRAF, because HRAS hyperactivates PI3K. PI3K hyperactivation is associated with in glycogen synthase kinase-3{beta} (GSK3{beta}) inhibition, increased E2F and MYC transcription programmes, increased nascent transcription of ribosome biogenesis genes and small nucleolar RNAs (snoRNA) expression. Small molecule inhibition of PI3K signalling prevents RAS-induced replication stress, and small molecule PI3K activation promotes replication stress. RAS-induced TRCs require a cooperation of MAPK and Pi3K signalling, S phase entry and hypertranscription. Our findings suggest a mechanistic explanation for replication stress variability between RAS activation models and identify PI3K pathway activation as a potential new determinant of TRCs in cancer.

In bacteria, transcription and RNA degradation are physically separated via segregation of the main ribonucleolytic machinery - the RNA degradosome - into phase-separated or membrane-anchored molecular assemblies driven by RNase E. Despite the widespread conservation of an amphipathic membrane anchor (MTS) in RNase E, the regulatory information embedded within this sequence and its biological importance remain poorly understood. Here, we have studied the importance of the Pseudomonas aeruginosa RNase E MTS for bacterial fitness or virulence and assessed its interchangeability. We show that amphipathicity is dispensable for foci scaffolding but necessary for proper foci morphology, dynamics, and localisation, although sequence modulates foci behaviour. Loss of the MTS additionally causes a drastic sensitivity to high salinity and a consistent virulence defect in Galleria mellonella larvae. Moreover, transcriptomics and analysis of mRNA spatial organisation reveal that the MTS mutant has specific stabilisation of localised membrane protein-encoding transcripts, together with abnormal operon processing. Altogether, our study highlights the elegant MTS-mediated control of spatial organisation and target selection, shaping the transcriptome and bacterial stress response.

Most proteins synthesized in the endoplasmic reticulum (ER) are covalently modified upon addition of pre-assembled oligosaccharides to side chains of asparagine (N) residues. Processing of N-linked oligosaccharides by ER-resident glucosidases, mannosidases and glucosyltransferases determines the fate of the associated polypeptides. Terminally glucose residues are removed from N-glycans to hamper engagement of ER-resident glucose-binding chaperones and promote secretion of native polypeptides. Mannose residues are removed to target terminally misfolded proteins for dislocation across the ER membrane and clearance by the cytoplasmic ubiquitin proteasome system (ER-associated degradation, ERAD). Recent evidence highlights the role of persistent N-glycan glucosylation as a signal that promotes segregation of misfolded proteins in ER subdomains that are eventually delivered to endolysosomal compartments for ER-to-Lysosome-Associated Degradation (ERLAD). Here we show that the polymerization-prone Portland variant of Neuroserpin (NS_PL) associated with familial encephalopathy with NS inclusion bodies (FENIB) is a client of the ERLAD machinery. Its lysosomal clearance relies on the LC3-dependent delivery branch of ERLAD involving the lectin chaperone Calnexin (CNX), the ERphagy receptor FAM134B and the SNARE protein Syntaxin17 (STX17), which is engaged upon persistent glucosylation of the NS_PL oligosaccharide linked at the asparagine residue at position 321.

Lipid droplets (LDs) rapidly form in infected cells to participate in the defence against microbes. Here, we investigate the involvement of LD lipids in these immune responses. Comparative shotgun and targeted lipidomics demonstrate that in vivo host LDs accumulate polyunsaturated fatty acids (PUFAs). PUFAs arrive at cells from the bloodstream to be further metabolised into complex PUFAs accrued by LD-triglycerides and -phospholipids. Host lipid metabolism is transcriptionally controlled by rapid, transient, and intricate immune programs initiated by pathogen-associated molecular patterns and relayed by cytokines such as interferons (type I and II), interleukins (IL-1{beta}), and tumour necrosis factor. When this lipid and signalling environment is reproduced in cultured macrophages, newly formed LDs accumulate defensive proteins, coordinate the synthesis of complex PUFAs, and become PUFA reservoirs and suppliers. Among LD-PUFAs, the {omega}-6 arachidonic acid is the most actively metabolised during the initial phases of innate immunity. Released from LDs by adipose triglyceride lipase, arachidonic acid is used by macrophages for prostaglandin synthesis, bacterial phagocytosis, and elimination of microbes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=163 HEIGHT=200 SRC="FIGDIR/small/711356v2_ufig1.gif" ALT="Figure 1"> View larger version (107K): org.highwire.dtl.DTLVardef@14d65eorg.highwire.dtl.DTLVardef@5ecc1org.highwire.dtl.DTLVardef@fa99e5org.highwire.dtl.DTLVardef@8d9632_HPS_FORMAT_FIGEXP M_FIG C_FIG

The biogenesis of outer mitochondrial membrane {beta}-barrel proteins relies on the mitochondrial Sorting and Assembly Machinery (SAM) complex. In humans, the SAM complex contains SAM50 along with Metaxin (MTX) accessory subunits. MTX1 and MTX3 are homologous yet their functional similarities and differences have scarcely been investigated. Homozygous null mutations in the MTX2 gene are linked to a rare progeroid syndrome that causes severe depletion of MTX1. Here, we uncover unique phenotypes associated with the loss of MTX1 or MTX3 in human cells. Loss of MTX1 confers a deficiency in mitochondrial volume and causes network-wide mitochondrial morphology abnormalities. MTX3 loss resulted in negligible consequences for the biogenesis of {beta}-barrel proteins but resulted in increased mitochondrial mass. We also find that both MTX1 and MTX3 stability are dependent on the presence of MTX2, with MTX1 deficiency causing defective import and assembly. Collectively, our findings support the notion that MTX1 and MTX3 are functionally diverse homologs and are unlikely to be functionally redundant.

Signalling via the epidermal growth factor receptor (EGFR) is indispensable for morphogenesis and tissue homeostasis. It is activated by extracellular ligands, typically released from transmembrane precursors by proteolysis. Ligand shedding activity is provided by the conserved rhomboid intramembrane serine proteases in Drosophila, but by the unrelated ADAM family metalloproteases in mammals, leaving the functions of mammalian non-mitochondrial rhomboids underexplored. Using quantitative proteomics, we show that EGFR is the main endogenous substrate of the human rhomboid protease RHBDL2 in keratinocytes. By shedding the EGFR ectodomain, thus producing a decoy receptor, RHBDL2 suppresses EGFR signalling, limiting cell migration and invasion. Conspicuously, RHBDL2 activity is upregulated by elevated intracellular calcium concentration, a condition typical for keratinocyte differentiation. These effects are recapitulated in primary human keratinocytes, and human skin equivalents deficient in RHBDL2 display incomplete differentiation and are morphologically disordered compared to wild type cells. We propose that context-specific fine-tuning of EGFR signalling and sensitivity to cross-talk from other signalling pathways could be important and hitherto overlooked roles of rhomboid proteases in mammals.

Tau aggregates contribute to multiple neurodegenerative diseases including frontotemporal dementia and Alzheimers disease (AD). In models of tauopathy and in patient tissue, tau aggregates can form in the cytoplasm, perinuclear region, and nucleus. Using a HEK293T tau biosensor system, we identified that cytoplasmic tau aggregates formed first, followed by perinuclear-ring-like tau assemblies, and then nuclear tau aggregates formed in nuclear speckles. Nuclear tau aggregates only form in cells with pre-existing cytoplasmic tau aggregates and mostly form independently of cells traversing mitosis. Finally, nuclear tau aggregates do not contain exogenous tau seeds and arise by a secondary seeding event dependent on VCP. Nuclear tau aggregates inhibit mRNA export and show a twofold increase in poly-adenylated mRNAs in the nucleus. Together, these findings indicate that nuclear tau aggregation alters RNA biogenesis and occurs by a secondary seeding event from cytoplasmic tau aggregates, which could contribute to tau pathology.

The subcellular distribution of lysosomes, the main degradative organelles of mammalian cells, responds to metabolic cues in a highly dynamic way. While lysosomal positioning due to amino acid levels is well-characterized, cholesterol-dependent regulation of lysosomal motility is incompletely understood. We explored impaired lysosomal cholesterol export using a mass spectrometry-based multi-OMICs approach, identifying widespread reallocation of resources and signaling pathway modulation. We identified increased phosphorylation at LAMTOR1 serine 56 in response to cholesterol level perturbations. We demonstrate that this phosphorylation site is sufficient to disrupt Rag GTPases/SLC38A9 binding to the Ragulator complex, inhibiting canonical mTORC1 and facilitating binding of BORC, therefore promoting lysosomal retrograde movement. LAMTOR1 S56 phosphorylation responds exclusively to depletion of lysosomal limiting membrane cholesterol, is facilitated by mTOR, and presents a negative feedback loop for amino acid independent displacement of Ragulator bound Rag GTPases, limiting canonical mTORC1 activity. Mass spectrometry data are available via ProteomeXchange with identifier PXD073489. HighlightsO_LIPerturbation of lysosomal cholesterol homeostasis results in adaptation of cellular protein and lipid biosynthesis C_LIO_LILAMTOR1 is phosphorylated at serine 56 via mTORC1 C_LIO_LILAMTOR1 S56 phosphorylation is lysosomal membrane cholesterol dependent C_LIO_LILAMTOR1 S56 phosphorylation disrupts binding of Rag GTPases to the Ragulator complex C_LIO_LILAMTOR1 S56 phosphorylation promotes binding of Ragulator to BORC, facilitating lysosomal retrograde transport C_LI

Cancer metabolism rewiring is one of the hallmarks of cancer, enabling cancer cell survival in a nutrient deprived microenvironment. Key to this is nutrient scavenging where cancer cells rely on extracellular proteins, including extracellular matrix (ECM) components, to sustain their proliferation. ECM uptake is mediated by 2{beta}1 integrin, however it is not clear how this process is controlled by nutrient availability. Here we demonstrated that amino acid starvation promoted ECM internalisation, by inducing the expression of 2 integrin. Mechanistically, starvation-driven RAS/MAPK pathway activation in cells harbouring oncogenic RAS mutations and mTOR inhibition increased 2 integrin, while the GCN2-depedent integrated stress response was not required. Functionally, elevated 2 integrin levels promoted cell adhesion and migration in nutrient starved cells. Finally, 2 integrin was found upregulated in pancreatic tumours and correlated with poor prognosis in pancreatic adenocarcinoma patients. Together, these data indicate that the nutrient- starved pancreatic cancer microenvironment synergises with KRAS mutation to drive pancreatic cancer aggressiveness.

Amyloid aggregates of -Synuclein are hallmark of Parkinsons Disease (PD) and related neurodegenerative diseases. -Synuclein, being an non-canonical RNA-binding protein (RBP), associates with other RBPs within cytosolic RNA-protein granules to modulate mRNA-stability. Conversely, mRNA G-quadruplexes (rG4s) expedite -Synuclein amyloidogenesis. However, spatiotemporal control on -Synuclein amyloidogenesis by other RBPs remains unexplored. Here, we report that RNA-dependent cytosolic interaction with DEAD-box RNA-helicase DDX39A decelerates -Synuclein amyloidogenesis. Viral infections transiently elevate rG4s in cytoplasm. Perturbing interactions between Synuclein and DDX39A using viral rG4s from H1N1-influenza and SARS-CoV-2 genomes expedites intracellular amyloidogenesis. Conversely, DDX39A overexpression alleviates -Synuclein amyloidogenesis in mouse primary neurons triggered by SARS-CoV-2 infection. We demonstrate that while DDX39A unwinds viral rG4s to mitigate -Synuclein sol-gel transition, its reciprocal cooperative phase separation with -Synuclein enhances the helicases rG4-unwinding activity. We propose that accelerated -Synuclein amyloidogenesis represents a trade-off within this RNA-protein interaction equilibrium, contributing to the viral etiology of PD.

Naked mole-rats (NMRs, Heterocephalus glaber) display unusual longevity and resistance to age-related decline, and accumulating evidence suggests that their autophagy-lysosome pathway (ALP) is regulated differently from that of conventional mammalian models. However, most studies in NMR cells have relied on static biochemical or ultrastructural readouts, leaving the dynamic organisation of autophagy in living cells poorly defined. Here, we establish a stable tandem fluorescent autophagy reporter in NMR skin fibroblasts using an mCherry-EGFP-LC3NMR construct to enable live-cell, single-cell resolution analysis of ALP dynamics. Under basal conditions, NMR skin fibroblasts exhibit a greater abundance of LC3-positive structures than HeLa cells, together with a mixed population of autophagosomes and autolysosomes, indicating a distinct steady-state organisation of the ALP. Chloroquine (CQ)-induced lysosomal stress caused the expected accumulation of LC3-positive structures but also triggered the formation of large cytoplasmic vacuoles in NMR skin fibroblasts. Importantly, this vacuolation was not associated with acute cytotoxicity and progressively resolved following CQ removal, accompanied by reorganisation of LC3-positive compartments and recovery of lysosomal acidity. Electron microscopy showed that CQ-induced vacuoles are membrane-bound, containing internal material and co-existing with multiple ALP-related vesicular compartments. Primary NMR skin fibroblasts display a similar vacuolation phenotype, indicating that this response is not an artefact of immortalisation or reporter expression. Together, these findings establish a live-cell platform for analysing autophagy in NMR cells and identify a distinctive, reversible vacuolation response to lysosomal stress, consistent with dynamic remodelling of the lysosomal system within NMR skin fibroblasts.

The ubiquitin ligase HOIL-1 has a unique role in controlling quantity of Met1-linked/ linear ubiquitin chains in cells by coordinating action with the ubiquitin ligase HOIP. Both ligases are components of the Linear UBiquitin chain Assembly Complex (LUBAC), the only known ligase complex that is able to generate Met1-linked ubiquitin chains. Although importance of Met1-linked ubiquitin chains in inflammation and immunity is well established, physiological relevance of quantity of these chains remain unknown. Here, we demonstrate that cells expressing catalytically inactive HOIL-1 exhibited significantly higher numbers of -Synuclein, tau, and amyloid beta aggregates. This phenotype is associated with a disruption in late-stage autophagic flux, wherein p62-positive aggregates fail to colocalize with lysosomal markers, leading to impaired clearance. Additionally, a biophysical transition in aggregate properties was observed in vitro, with mutant cells forming more rigid solid-like inclusions, shifting from dynamic and liquid-like condensates. Elevated Met1-linked ubiquitin chains, either through HOIL-1 catalytic inactivation or knockdown of the Met1-linked chain-specific deubiquitinase OTULIN, phenocopied the defects in aggregate clearance. These findings reveal a critical role of HOIL-1 catalytic activity in modulating aggregate clearance through autophagy and maintaining the quantity of Met1-ubiquitin chains, highlighting HOIL-1 as a key factor in proteostasis in neurodegenerative diseases. HighlightsO_LIHOIL-1 catalytic activity prevents neurodegenerative protein aggregate accumulation C_LIO_LIInactive HOIL-1 impairs late-stage autophagic clearance of protein aggregates C_LIO_LILoss of HOIL-1 shifts aggregates to rigid, solid-like states C_LIO_LIExcess Met1-ubiquitin chains drive aggregate solidification C_LI

Autophagy is a recycling pathway that clears cellular constituents, supporting homeostasis. In primary murine neurons, autophagosome biogenesis declines during aging. Importantly, this decline can be restored by the ectopic expression of key autophagy component WIPI2B. The phosphorylation state of WIPI2B serine 395 is critical for this restoration, suggesting that WIPI2B S395 phosphorylation regulates autophagosome biogenesis. Here, we identified protein phosphatase 2A (PP2A) and CDK16 as regulators of WIPI2B S395 phosphorylation and neuronal autophagy. Using Caenorhabditis elegans, we showed that PP2A and CDK16 regulate neuronal autophagy through the same genetic pathway as WIPI2B in vivo. Further, purified mammalian PP2A and CDK16 directly modified WIPI2B S395 phosphorylation in vitro. In primary murine neurons, PP2A and CDK16 colocalized with WIPI2B at autophagosomes, and manipulation of PP2A and CDK16 expression altered WIPI2B puncta formation and rates of autophagosome biogenesis. Altogether, our data support the conclusion that PP2A and CDK16 regulate WIPI2B S395 phosphorylation, modulating autophagosome biogenesis in neurons.

RAD51 is targeted to single-stranded (ss)DNA for homologous recombination and DNA replication fork homeostasis. However, the physiological consequences of RAD51 binding to intact double-stranded (ds)DNA, which is tightly limited in vivo, remain elusive. Here we revealed an intrinsic property of RAD51 to bind chromosome axes where cohesin and condensin bind, which is actively suppressed by FIGNL1 AAA+ ATPase. In Fignl1-deficient mouse oocytes, an age-dependent RAD51 accumulation with little DNA damage leads to improper chromosomal localization of condensin II and topoisomerase II, failure in chromosome condensation with massive chromosome entanglement, and meiosis I arrest. We propose that promiscuous RAD51 binding to non-damaged chromosomes, which is prevented by a RAD51 remodeler, is a unique type of chromosomal pathology associated with genome instability.

Lipid droplets (LDs) accumulate in response to diverse cellular stresses. However, their regulation and physiological roles remain poorly understood in most contexts. Here, we show that, in budding yeast, chronic hyperosmotic stress induces sustained LD accumulation. Unlike the transient LD response observed during acute osmotic shock, chronic stress triggers prolonged, Dga1-dependent triacylglycerol synthesis. In the absence of triacylglycerol synthesis cellular fitness is severely affected. Lipidomic profiling reveals extensive membrane remodelling during chronic hyperosmotic stress, most notably a shift from phosphatidylethanolamine to phosphatidylcholine. In LD-deficient cells, the stress-induced PC increase is blunted and manipulation of PC synthesis modulates the fitness of triacylglycerol-deficient cells under hyperosmotic stress. Thus, LD accumulation and phospholipid remodelling underlie an adaptive response to chronic hyperosmotic stress. SummaryThis work demonstrates that membrane remodelling occurs in cells experiencing chronic hyperosmotic stress. Both triacylglycerol and phosphatidylcholine levels are increased. Cell fitness depends upon increased triacylglycerol synthesis and is further modulated by manipulating phosphatidylcholine levels.

Myelin turnover is essential for its structural and functional integrity, yet how this particularly lipid-rich membrane is renewed and why it deteriorates with ageing remain unresolved. Combining deuterium oxide administration in mice with high resolution lipidomics, we establish that brain lipid turnover rates are highly heterogeneous, differ by brain region, and depend primarily on lipid class. Half-lives of common glycerophospholipids in purified myelin were under 2 months whereas many sphingolipids exhibited half-lives exceeding 8 months, dependent on acyl chain length and saturation. Myelin sphingolipid and cholesterol replacement rates in the corpus callosum decreased markedly between 3 and 12 months of age, while disrupting lipid trafficking through ApoE ablation preferentially impaired cholesterol turnover and incorporation into myelin. Our results establish that myelin renewal occurs through continual replacement of individual lipid constituents in a manner that depends on lipid class, hydrophobicity, and ApoE-dependent trafficking, and that this process slows significantly with ageing.

Translational repression enables rapid adaptation to environmental changes. Under stress, translational repressed mRNA and mRNA decay factors accumulate in cytoplasmic processing bodies (PBs), implicated in mRNA storage and decay. PBs have been mostly studied under glucose starvation in yeast, yet, knowledge is limited under other stress conditions. Here, we identify a correlation between the level of translation attenuation and the number, brightness, fluidity and recruitment of PB core components. Stresses triggering strong translation attenuation caused the formation of few bright and more fluid PBs that recruit the decay factors en bloc. Conversely, weaker translation attenuation induced numerous, dim, more viscous PBs to which PB proteins were sequentially recruited. Importantly, increasing non-translated mRNA levels augmented the brightness of dim PBs and accelerated decay machinery recruitment. Finally, boosting RNA levels increased the size of Dhh1 helicase-containing droplets in vitro. Taken together, we propose a model in which the assembly pathway and biophysical properties of PBs are governed by non-translated mRNA abundance. TeaserBiophysical properties, protein composition and assembly pathways of processing bodies are dependent on available mRNA levels.

Meiotic prophase-I chromosomes are organized into linear arrays of chromatin loops anchored to proteinaceous axes that define the interaction interfaces for the pairing and synapsis of homologous chromosomes. Chromatin loop size and axial chromosome length are inversely correlated and vary widely both between and within species, including between the sexes. The molecular basis of this variation remains unclear. Here, we provide evidence that the small ubiquitin-like modifier, SUMO, regulates loop-axis organization in mouse meiosis. Our analysis shows that the longer axes of oocyte chromosomes contain more SUMO per unit length than the shorter axes of spermatocyte chromosomes. In mouse models, the loss of SUMO1 results in shorter axes and longer chromatin loops. Conversely, increased SUMO1 conjugation, caused by mutation of the SENP1 isopeptidase, produces longer axes with shorter loops. Axis length positively correlates with meiotic recombination. Accordingly, Sumo1 and Senp1 mutations respectively decrease and increase crossover frequency. These findings identify SUMO as a key regulator of meiotic chromosome architecture and suggest a molecular basis for the physiological variation in chromosome length and recombination rates seen among species, sexes, individuals, and individual meiocytes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/710713v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@145c465org.highwire.dtl.DTLVardef@160c8aborg.highwire.dtl.DTLVardef@1165b76org.highwire.dtl.DTLVardef@ced5e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

Macroautophagy/autophagy is a cellular process enabling degradation of intracellular components during starvation. In mammalian cells, autophagosomes can reach diameters of over 1000 nm within 30 min after triggering starvation, but how such substantial amounts of membranes can be synthesized within a brief time remains elusive. A protein complex central to the phagophore initiation is the lipid kinase PIK3C3-Complex 1 (PtdIns3K-C1), which produces phosphatidylinositol-3-phosphate (PtdIns3P). PtdIns3P recruits a variety of downstream proteins, among which is PtdIns3P-binding WIPI2 that facilitates lipidation of mammalian ATG8 (mATG8) family proteins on phagophores. Here we show that upon inhibition of mATG8 lipidation in cells, there is a decreased accumulation of WIPI2, suggesting a feedback loop between mATG8s and PtdIns3P production. The role of PtdIns3K-C1 in this feedback was demonstrated by in vitro experiments where recombinant membrane-coupled mATG8s bind to and potently activate PtdIns3K-C1, with GABARAP being the most potent activator among all mATG8s. By a combination of cryo-electron microscopy, structural mass spectrometry, activity assays and mutagenesis, we show that GABARAP binds two sites in PtdIns3K-C1, with one site showing an atypical bipartite interaction with the mATG8. We also confirm both sites are essential for GABARAP to activate PtdIns3K-C1. We propose that once GABARAP is indirectly recruited by PtdIns3P generated by basal activity of PtdIns3K-C1, a positive feedback loop is formed where PtdIns3K-C1 interacts with GABARAP and becomes activated to produce more PtdIns3P, thereby further stimulating GABARAP lipidation. This mechanism would be central for autophagosome biogenesis, where enlarged membranes need to be synthesized within a brief period. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/712327v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@15b116eorg.highwire.dtl.DTLVardef@1d55dddorg.highwire.dtl.DTLVardef@1058a58org.highwire.dtl.DTLVardef@bdd88e_HPS_FORMAT_FIGEXP M_FIG The GABARAP-PtdIns3K-C1 positive feedback loop. Model for the GABARAP-PtdIns3K-C1 positive feedback loop. GABARAP is indirectly recruited to the growing phagophore by PtdIns3P and activates PtdIns3K-C1, leading to an increased PtdIns3P production. The E1 (ATG7), E2 (ATG3) and E3 (ATG5-ATG12-ATG16L1) enzymes and WIPI2 are involved in the lipidation (covalent coupling) of GABARAP to membranes. C_FIG