Journal: The EMBO Journal

Abbreviation

EMBO J

Publisher

EMBO Press

Journal Volumes

ISSN

0261-4189
1460-2075

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2011 - 201942020 - 202633
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Publications1 - 10 of 37
  • Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective
    Item type: Review Article
    Karousis, Evangelos D.; Schubert, Katharina; Ban, Nenad (2024)
    The EMBO Journal
    Coronaviruses are a group of related RNA viruses that cause respiratory diseases in humans and animals. Understanding the mechanisms of translation regulation during coronaviral infections is critical for developing antiviral therapies and preventing viral spread. Translation of the viral single-stranded RNA genome in the host cell cytoplasm is an essential step in the life cycle of coronaviruses, which affects the cellular mRNA translation landscape in many ways. Here we discuss various viral strategies of translation control, including how members of the Betacoronavirus genus shut down host cell translation and suppress host innate immune functions, as well as the role of the viral non-structural protein 1 (Nsp1) in the process. We also outline the fate of viral RNA, considering stress response mechanisms triggered in infected cells, and describe how unique viral RNA features contribute to programmed ribosomal -1 frameshifting, RNA editing, and translation shutdown evasion.
  • Oligomers of the ATPase EHD2 confine caveolae to the plasma membrane through association with actin
    Item type: Journal Article
    Stoeber, Miriam; Stoeck, Ina Karen; Hänni, Christine; et al. (2012)
    The EMBO Journal
    Caveolae are specialized domains present in the plasma membrane (PM) of mostmammalian cell types. They function in signalling, membrane regulation, andendocytosis. We found that the Eps-15 homology domain-containing protein 2 (EHD2, anATPase) associated with the static population of PM caveolae. Recruitment to the PMinvolved ATP binding, interaction with anionic lipids, and oligomerization intolarge complexes (60–75S) via interaction of the EH domains with intrinsicNPF/KPF motifs. Hydrolysis of ATP was essential for binding of EHD2 complexes tocaveolae. EHD2 was found to undergo dynamic exchange at caveolae, a process thatdepended on a functional ATPase cycle. Depletion of EHD2 by siRNA or expression of adominant-negative mutant dramatically increased the fraction of mobile caveolarvesicles coming from the PM. Overexpression of EHD2, in turn, caused confinement ofcholera toxin B in caveolae. The confining role of EHD2 relied on its capacity tolink caveolae to actin filaments. Thus, EHD2 likely plays a key role in adjustingthe balance between PM functions of stationary caveolae and the role of caveolae asvesicular carriers.
  • Rewiring phospholipid biosynthesis reveals resilience to membrane perturbations and uncovers regulators of lipid homeostasis
    Item type: Journal Article
    Peter, Arun T. John; van Schie, Sabine N.S.; Cheung, Ngaam J.; et al. (2022)
    The EMBO Journal
    The organelles of eukaryotic cells differ in their membrane lipid composition. This heterogeneity is achieved by the localization of lipid synthesizing and modifying enzymes to specific compartments, as well as by intracellular lipid transport that utilizes vesicular and non-vesicular routes to ferry lipids from their place of synthesis to their destination. For instance, the major and essential phospholipids, phosphatidylethanolamine (PE) and phosphatidylcholine (PC), can be produced by multiple pathways and, in the case of PE, also at multiple locations. However, the molecular components that underlie lipid homeostasis as well as the routes allowing their distribution remain unclear. Here, we present an approach in which we simplify and rewire yeast phospholipid synthesis by redirecting PE and PC synthesis reactions to distinct subcellular locations using chimeric enzymes fused to specific organelle targeting motifs. In rewired conditions, viability is expected to depend on homeostatic adaptation to the ensuing lipostatic perturbations and on efficient interorganelle lipid transport. We therefore performed genetic screens to identify factors involved in both of these processes. Among the candidates identified, we find genes linked to transcriptional regulation of lipid homeostasis, lipid metabolism, and transport. In particular, we identify a requirement for Csf1 – an uncharacterized protein harboring a Chorein-N lipid transport motif – for survival under certain rewired conditions as well as lipidomic adaptation to cold, implicating Csf1 in interorganelle lipid transport and homeostatic adaptation.
  • Auxin-dependent regulation of cell division rates governs root thermomorphogenesis
    Item type: Journal Article
    Ai, Haiyue; Bellstaedt, Julia; Bartusch, Kai Steffen; et al. (2023)
    The EMBO Journal
    Roots are highly plastic organs enabling plants to adapt to a changing below-ground environment. In addition to abiotic factors like nutrients or mechanical resistance, plant roots also respond to temperature variation. Below the heat stress threshold, Arabidopsis thaliana seedlings react to elevated temperature by promoting primary root growth, possibly to reach deeper soil regions with potentially better water saturation. While above-ground thermomorphogenesis is enabled by thermo-sensitive cell elongation, it was unknown how temperature modulates root growth. We here show that roots are able to sense and respond to elevated temperature independently of shoot-derived signals. This response is mediated by a yet unknown root thermosensor that employs auxin as a messenger to relay temperature signals to the cell cycle. Growth promotion is achieved primarily by increasing cell division rates in the root apical meristem, depending on de novo local auxin biosynthesis and temperature-sensitive organization of the polar auxin transport system. Hence, the primary cellular target of elevated ambient temperature differs fundamentally between root and shoot tissues, while the messenger auxin remains the same.
  • The CUL4B-based E3 ubiquitin ligase regulates mitosis and brain development by recruiting phospho-specific DCAFs
    Item type: Journal Article
    Stier, Anna; Gilberto, Samuel; Mohamed, Weaam I.; et al. (2023)
    The EMBO Journal
    The paralogs CUL4A and CUL4B assemble cullin-RING E3 ubiquitin ligase (CRL) complexes regulating multiple chromatin-associated cellular functions. Although they are structurally similar, we found that the unique N-terminal extension of CUL4B is heavily phosphorylated during mitosis, and the phosphorylation pattern is perturbed in the CUL4B-P50L mutation causing X-linked intellectual disability (XLID). Phenotypic characterization and mutational analysis revealed that CUL4B phosphorylation is required for efficient progression through mitosis, controlling spindle positioning and cortical tension. While CUL4B phosphorylation triggers chromatin exclusion, it promotes binding to actin regulators and to two previously unrecognized CUL4B-specific substrate receptors (DCAFs), LIS1 and WDR1. Indeed, co-immunoprecipitation experiments and biochemical analysis revealed that LIS1 and WDR1 interact with DDB1, and their binding is enhanced by the phosphorylated N-terminal domain of CUL4B. Finally, a human forebrain organoid model demonstrated that CUL4B is required to develop stable ventricular structures that correlate with onset of forebrain differentiation. Together, our study uncovers previously unrecognized DCAFs relevant for mitosis and brain development that specifically bind CUL4B, but not the CUL4B-P50L patient mutant, by a phosphorylation-dependent mechanism.
  • Loss of TDP-43 oligomerization or RNA binding elicits distinct aggregation patterns
    Item type: Journal Article
    Pérez-Berlanga, Manuela; Wiersma, Vera I.; Zbinden, Aurélie; et al. (2023)
    The EMBO Journal
    Aggregation of the RNA-binding protein TAR DNA-binding protein 43 (TDP-43) is the key neuropathological feature of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). In physiological conditions, TDP-43 is predominantly nuclear, forms oligomers, and is contained in biomolecular condensates assembled by liquid-liquid phase separation (LLPS). In disease, TDP-43 forms cytoplasmic or intranuclear inclusions. How TDP-43 transitions from physiological to pathological states remains poorly understood. Using a variety of cellular systems to express structure-based TDP-43 variants, including human neurons and cell lines with near-physiological expression levels, we show that oligomerization and RNA binding govern TDP-43 stability, splicing functionality, LLPS, and subcellular localization. Importantly, our data reveal that TDP-43 oligomerization is modulated by RNA binding. By mimicking the impaired proteasomal activity observed in ALS/FTLD patients, we found that monomeric TDP-43 forms inclusions in the cytoplasm, whereas its RNA binding-deficient counterpart aggregated in the nucleus. These differentially localized aggregates emerged via distinct pathways: LLPS-driven aggregation in the nucleus and aggresome-dependent inclusion formation in the cytoplasm. Therefore, our work unravels the origins of heterogeneous pathological species reminiscent of those occurring in TDP-43 proteinopathy patients.
  • Loss of all three APP family members during development impairs synaptic function and plasticity, disrupts learning, and causes an autism-like phenotype
    Item type: Journal Article
    Steubler, Vicky; Erdinger, Susanne; Back, Michaela K.; et al. (2021)
    The EMBO Journal
    The key role of APP for Alzheimer pathogenesis is well established. However, perinatal lethality of germline knockout mice lacking the entire APP family has so far precluded the analysis of its physiological functions for the developing and adult brain. Here, we generated conditional APP/APLP1/APLP2 triple KO (cTKO) mice lacking the APP family in excitatory forebrain neurons from embryonic day 11.5 onwards. NexCre cTKO mice showed altered brain morphology with agenesis of the corpus callosum and disrupted hippocampal lamination. Further, NexCre cTKOs revealed reduced basal synaptic transmission and drastically reduced long-term potentiation that was associated with reduced dendritic length and reduced spine density of pyramidal cells. With regard to behavior, lack of the APP family leads not only to severe impairments in a panel of tests for learning and memory, but also to an autism-like phenotype including repetitive rearing and climbing, impaired social communication, and deficits in social interaction. Together, our study identifies essential functions of the APP family during development, for normal hippocampal function and circuits important for learning and social behavior.
  • MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays
    Item type: Journal Article
    Meurs, Romane; De Matos, Mara; Bothe, Adrian; et al. (2025)
    The EMBO Journal
    Ribosomes scanning from the mRNA 5 ' cap to the start codon may initiate at upstream open reading frames (uORFs), decreasing protein biosynthesis. Termination at a uORF can lead to re-initiation, where 40S subunits resume scanning and initiate another translation event downstream. The noncanonical translation factors MCTS1-DENR participate in re-initiation at specific uORFs, but knowledge of other trans-acting factors or uORF features influencing re-initiation is limited. Here, we establish a cell-free re-initiation assay using HeLa lysates to address this question. Comparing in vivo and in vitro re-initiation on uORF-containing reporters, we validate MCTS1-DENR-dependent re-initiation in vitro. Using this system and ribosome profiling in cells, we found that knockdown of the MCTS1-DENR homolog eIF2D causes widespread gene deregulation unrelated to uORF translation, and thus distinct to MCTS1-DENR-dependent re-initiation regulation. Additionally, we identified MCTS2, encoded by an Mcts1 retrogene, as a DENR partner promoting re-initiation in vitro, providing a plausible explanation for clinical differences associated with DENR vs. MCTS1 mutations in humans.
  • Control of flagellar gene expression by a chemotaxis receptor-like regulator in pathogenic Escherichia coli
    Item type: Journal Article
    Lee, Jae-Woo; Wang, Liyun; Comer, Sarah L.; et al. (2025)
    The EMBO Journal
    Chemoreceptors enable bacteria to modulate their swimming behavior in response to the perceived environmental cues. Despite the large diversity of stimuli sensed by bacterial chemoreceptors, their output to the chemotaxis pathway that controls the flagellar motor typically converges on a few conserved signaling proteins. Here, we characterize a unique chemoreceptor-like protein, Tls, which is found in the B2 phylogroup of Escherichia coli that includes many extraintestinal pathogenic (ExPEC) strains. Instead of mediating chemotactic signaling, Tls controls motility by repressing the expression of flagellar genes, and thus cell motility, through sequestration of the transcriptional master activator of flagellar genes, FlhDC. The subcellular localization of Tls, the sequestration of FlhDC, and the repression of flagellar gene expression and motility are all abolished during growth on porous medium, indicating that this regulation may be mechanosensitive. Deletion of tls in a uropathogenic E. coli strain leads to reduced attachment to the urinary tract cells and an increased migration to and/or proliferation in the murine gut, a pathogen reservoir niche, thus implicating Tls in the regulation of motility during infection.
  • Shared structural features of Miro binding control mitochondrial homeostasis
    Item type: Journal Article
    Covill-Cooke, Christian; Kwizera, Brian; López-Doménech, Guillermo; et al. (2024)
    The EMBO Journal
    Miro proteins are universally conserved mitochondrial calcium-binding GTPases that regulate a multitude of mitochondrial processes, including transport, clearance, and lipid trafficking. The exact role of Miro in these functions is unclear but involves binding to a variety of client proteins. How this binding is operated at the molecular level and whether and how it is important for mitochondrial health, however, remains unknown. Here, we show that known Miro interactors-namely, CENPF, Trak, and MYO19-all use a similar short motif to bind the same structural element: a highly conserved hydrophobic pocket in the first calcium-binding domain of Miro. Using these Miro-binding motifs, we identified direct interactors de novo, including MTFR1/2/1L, the lipid transporters Mdm34 and VPS13D, and the ubiquitin E3-ligase Parkin. Given the shared binding mechanism of these functionally diverse clients and its conservation across eukaryotes, we propose that Miro is a universal mitochondrial adaptor coordinating mitochondrial health.
Publications1 - 10 of 37