eLife最新文献

{"title":"Membrane binding properties of the cytoskeletal protein bactofilin.","authors":"Ying Liu, Rajani Karmakar, Maria Billini, Wieland Steinchen, Saumyak Mukherjee, Rogelio Hernandez-Tamayo, Thomas Heimerl, Gert Bange, Lars V Schäfer, Martin Thanbichler","doi":"10.7554/eLife.100749","DOIUrl":"10.7554/eLife.100749","url":null,"abstract":"<p><p>Bactofilins are a widespread family of cytoskeletal proteins that are essential for bacterial morphogenesis, chromosome organization, and motility. They assemble into non-polar filaments independently of nucleotides and typically associate with the cytoplasmic membrane. Their membrane interaction is thought to involve a short N-terminal peptide, but the underlying mechanism is unclear. Here, we clarify the complete membrane-targeting sequence (MTS) of the <i>Caulobacter crescentus</i> bactofilin BacA and identify residues critical for its function. Using molecular dynamics simulations, we show that its affinity for membranes arises from hydrophobic residue-driven water exclusion and electrostatic interactions with negatively charged phospholipid headgroups. Bioinformatic analysis suggests that this mode of membrane binding is conserved across diverse bacterial phyla. Importantly, we observe that BacA polymerization and membrane binding stimulate each other, and both of these processes are necessary for recruiting the membrane-bound client protein PbpC, a cell wall synthase that interacts with BacA via its N-terminal cytoplasmic region. PbpC can functionally replace the MTS of BacA when overproduced, demonstrating that client proteins contribute to the bactofilin-membrane association. Thus, bactofilin assembly and localization are determined by a complex interplay of different factors, thereby enabling the adaptation of these processes to the needs of the systems they control.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Maintenance of neuronal TDP-43 expression requires axonal lysosome transport.","authors":"Veronica H Ryan, Sydney Lawton, Joel F Reyes, James Hawrot, Ashley M Frankenfield, Sahba Seddighi, Daniel M Ramos, Jacob Epstein, Faraz Faghri, Nicholas L Johnson, Jizhong Zou, Martin Kampmann, John Replogle, Yue Andy Qi, Hebao Yuan, Kory Johnson, Dragan Maric, Ling Hao, Mike A Nalls, Michael Emmerson Ward","doi":"10.7554/eLife.104057","DOIUrl":"10.7554/eLife.104057","url":null,"abstract":"<p><p>TDP-43 mislocalization and pathology occurs across a range of neurodegenerative diseases, but the pathways that modulate TDP-43 in neurons are not well understood. We generated a Halo-TDP-43 knock-in human induced pluripotent stem cell (iPSC) line and performed a genome-wide CRISPR interference FACS-based screen to identify modifiers of TDP-43 levels in neurons. A meta-analysis of our screen and publicly available screens identified both specific hits and pathways present across multiple screens, the latter likely responsible for generic protein level maintenance. We identified BORC, a complex required for anterograde lysosome transport, as a specific modifier of TDP-43 protein, but not mRNA, levels in neurons. BORC loss led to longer half-life of TDP-43 and other proteins, suggesting lysosome location is required for proper protein turnover. As such, lysosome location and function are crucial for maintaining TDP-43 protein levels in neurons.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"14 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics.","authors":"Elena G Govorunova, Oleg A Sineshchekov, Hai Li, Yueyang Gou, Hongmei Chen, Shuyuan Yang, Yumei Wang, Stephen Mitchell, Alyssa Palmateer, Leonid S Brown, François St-Pierre, Mingshan Xue, John L Spudich","doi":"10.7554/eLife.106508","DOIUrl":"10.7554/eLife.106508","url":null,"abstract":"<p><p>Light-gated ion channels from protists (channelrhodopsins or ChRs) are optogenetic tools widely used for controlling neurons and cardiomyocytes. Multiplex optogenetic applications require spectrally separated molecules, which are difficult to engineer without disrupting channel function. Scanning numerous sequence databases, we identified three naturally blue-shifted ChRs from ancyromonads. They form a separate branch on the phylogenetic tree and contain residue motifs characteristic of anion ChRs (ACRs). However, only two conduct chloride, whereas the closely related <i>Nutomonas longa</i> homolog generates inward cation currents in mammalian cells under physiological conditions, significantly exceeding those by previously known tools with similar spectral maxima (peak absorption at ~440 nm). Measurements of transient absorption changes and pH titration of purified proteins combined with mutant analysis revealed the roles of the residues in the photoactive site. Ancyromonad ChRs could be activated by near-infrared two-photon illumination, a technique that enables the deeper-tissue optogenetic activation of specific neurons in three dimensions. Both ancyromonad ACRs allowed optogenetic silencing of mouse cortical neurons in brain slices. <i>Ancyromonas sigmoides</i> ACR (<i>Ans</i>ACR) expression in cholinergic neurons enabled photoinhibition of pharyngeal muscle contraction in live worms. Overall, our results deepen the mechanistic understanding of light-gated channel function and expand the optogenetic toolkit with potent, blue-shifted ChRs.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"14 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distinct functions of cardiac β-adrenergic receptors in the T-tubule vs. outer surface membrane.","authors":"George W P Madders, Marion Barthe, Flora Lefebvre, Emilie Langlois, Florence Lefebvre, Patrick Lechêne, Maya Dia, Xavier Iturrioz, Catherine Llorens-Cortes, Tap Ha-Duong, Laurence Moine, Nicolas Tsapis, Rodolphe Fischmeister","doi":"10.7554/eLife.84243","DOIUrl":"https://doi.org/10.7554/eLife.84243","url":null,"abstract":"<p><p>β-adrenoceptors (β-ARs) regulate cardiac function during sympathetic nerve stimulation. β-ARs are present in both the cardiac T-tubule (TTM) and outer surface membrane (OSM), but how their location impacts their function is unknown. Here, we developed a technology based on size exclusion to explore the function of β-ARs located in the OSM. We synthetized a PEG-Iso molecule by covalently linking isoprenaline (Iso) to a 5000 Da PolyEthylene-Glycol (PEG) chain to increase the size of the β-AR agonist and prevent it from accessing the T-tubule network. The affinity of PEG-Iso and Iso on β₁- and β₂-ARs was measured using radioligand binding. Molecular dynamics simulation was used to assess PEG-Iso conformation and visualise the accessibility of the Iso moiety to water. Using confocal microscopy, we show that PEGylation constrains molecules outside the T-tubule network of adult rat ventricular myocytes (ARVMs) due to the presence of the extracellular glycocalyx. β-AR activation in OSM with PEG-Iso produced a lower stimulation of [cAMP]_i than Iso but a larger stimulation of cytosolic PKA at equivalent levels of [cAMP]_I and similar effects on excitation-contraction coupling parameters. However, PEG-Iso produced a much lower stimulation of nuclear cAMP and PKA than Iso. Thus, OSM β-ARs in ARVMs control mainly cytosolic cAMP/PKA pathway and contractility, while TTM β-ARs control mainly nuclear cAMP, PKA and consequent nuclear protein phosphorylation. Size exclusion strategy using ligand PEGylation provides a unique approach to evaluate the respective contribution of T-tubule <i>vs.</i> outer surface membrane proteins in cardiac cells.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"14 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145080029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recovery of the full <i>in vivo</i> firing range in post-lesion surviving DA SN neurons associated with Kv4.3-mediated pacemaker plasticity.","authors":"Lora Kovacheva, Josef Shin, Josefa Zaldivar-Diez, Johanna Mankel, Navid Farassat, Kauê Machado Costa, Poonam Thakur, José A Obeso, Jochen Roeper","doi":"10.7554/eLife.104037","DOIUrl":"https://doi.org/10.7554/eLife.104037","url":null,"abstract":"<p><p>Dopamine (DA) neurons in the substantia nigra (SN) control several essential functions, including the voluntary movement, learning and motivated behavior. Healthy DA SN neurons show diverse firing patterns <i>in vivo</i>, ranging from slow pacemaker-like activity (1-10 Hz) to transient high frequency bursts (<100 Hz), interspersed with pauses that can last hundreds of milliseconds. Recent <i>in vivo</i> patch experiments have started to reveal the subthreshold mechanisms underlying this physiological diversity, but the impact of challenges like cell loss on the <i>in vivo</i> activity of adult DA SN neurons, and how these may relate to behavioral disturbances, are still largely unknown. We investigated the <i>in vivo</i> electrophysiological properties of surviving SN DA neurons after partial unilateral 6-OHDA lesions, a single-hit, non-progressive model of neuronal cell loss. We show that mice subjected to this model have an initial motor impairment, measured by asymmetrical rotations in the open field test, which recovered over time. At 3 weeks post-lesion, when open field locomotion was strongly impaired, surviving DA SN neurons showed a compressed <i>in vivo</i> dynamic firing range, characterized by a 10-fold reduction of <i>in vivo</i> burst firing compared to controls. This <i>in vivo</i> phenotype was accompanied by pronounced <i>in vitro</i> pacemaker instability. In contrast, in the chronic post-lesion phase (>2 months), where turning symmetry in open field locomotion had recovered, surviving SN DA neurons displayed the full dynamic range of <i>in vivo</i> firing, including <i>in vivo</i> bursting, similar to controls. The normalized <i>in vivo</i> firing pattern was associated with a 2-fold acceleration of stable <i>in vitro</i> pacemaking, mediated by Kv4.3 potassium channel downregulation. Our findings demonstrate the existence of a homeostatic pacemaker plasticity mechanism in surviving DA SN neurons after pronounced cell loss.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"14 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the origins of a signaling pathway.","authors":"Balaji Santhanam","doi":"10.7554/eLife.108735","DOIUrl":"10.7554/eLife.108735","url":null,"abstract":"<p><p>The 19 Wnt proteins found in humans are part of a larger superfamily of proteins that are also found in Archaea and Bacteria.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"14 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel mouse model for <i>LAMA2</i>-related muscular dystrophy with analysis of molecular pathogenesis and clinical phenotype.","authors":"Dandan Tan, Yidan Liu, Huaxia Luo, Qiang Shen, Xingbo Long, Luzheng Xu, Jieyu Liu, Nanbert A Zhong, Hong Zhang, Hui Xiong","doi":"10.7554/eLife.94288","DOIUrl":"10.7554/eLife.94288","url":null,"abstract":"<p><p>Our understanding of the molecular pathogenesis of <i>LAMA2</i>-related muscular dystrophy (<i>LAMA2</i>-MD) requires improving. Here, we report the phenotype, neuropathology, and transcriptomics data (scRNA-seq and bulk RNA-seq) of a new <i>Lama2</i> knockout mouse (dy^H/dy^H) which was created based on the human <i>LAMA2</i>-MD mutation hotspot region using CRISPR-Cas9. The dy^H/dy^H mice presented a severe phenotype with muscular dystrophy. Mouse brain scRNA-seq showed that <i>Lama2</i> gene was expressed predominantly and specifically in vascular and leptomeningeal fibroblasts and vascular smooth muscle cells, and weakly in astrocytes in wild-type mouse. Laminin α2 expression on the cortical surface was observed with immunofluorescence. In dy^H/dy^H, <i>Lama2</i> expression was decreased in those cell types, which might be associated with the disruption of gliovascular basal lamina assembly. Additionally, transcriptomic investigation of muscles showed 2020 differentially expressed genes, mainly associated with the impaired muscle cytoskeleton and development. In summary, this study provided potentially useful information for understanding the molecular pathogenesis of <i>LAMA2</i>-MD.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12443477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Monitoring circulating cell-free HPV DNA in metastatic or recurrent cervical cancer: clinical significance and treatment implications.","authors":"Zhuomin Yin, Tao Feng, Qing Xu, Wumin Dai, Maowei Ni, Juan Ni, Hanmei Lou","doi":"10.7554/eLife.101887","DOIUrl":"10.7554/eLife.101887","url":null,"abstract":"<p><strong>Background: </strong>Monitoring circulating HPV cell-free DNA (cfDNA) offers a minimally invasive method for surveillance in HPV-associated cancers, particularly cervical cancer. However, the role of dynamic HPV cfDNA monitoring in guiding clinical treatment decisions for recurrent or metastatic cervical cancer remains underexplored.</p><p><strong>Methods: </strong>In this prospective pilot observational study, levels of HPV cfDNA in serum samples from 28 patients with recurrent or metastatic HPV-positive cervical cancer were measured via digital droplet polymerase chain reaction. Results for HPV cfDNA levels were matched to clinical outcomes and to serum levels of squamous cell carcinoma antigen (SCC-Ag) to assess the clinical potential of HPV cfDNA as a tumor marker.</p><p><strong>Results: </strong>HPV cfDNA was detected in all 28 patients. Notably, median baseline HPV cfDNA levels varied according to the metastatic pattern observed in individual patients (p=0.019). All participants exhibited changes in HPV cfDNA levels over a median monitoring period of 2 months (range 0.3-16.9 months) prior to evaluations for treatment response or disease progression. Among 26 patients initially diagnosed with squamous cell cervical cancer, the positivity rate was 100% for HPV cfDNA and 69.2% for SCC-Ag (p=0.004, 95% confidence interval (CI), 0-0.391). Among 20 patients longitudinally monitored for squamous cell cervical cancer, the concordance with changes in disease status was 90% for HPV cfDNA and 50% for SCC-Ag (p=0.014, 95% CI, 0.022-0.621).</p><p><strong>Conclusions: </strong>Our study demonstrates that HPV cfDNA is a promising tumor marker for monitoring of recurrent or metastatic HPV-positive cervical cancer.</p><p><strong>Funding: </strong>This work was supported by the Key R&D Program of Zhejiang (2022C04001), the Zhejiang Province Medicine and Health Science and Technology Program (2020KY454), the Zhejiang Science and Technology Department Public Welfare Project (LGF22H160075).</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12443474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fast evolutionary turnover and overlapping variances of sex-biased gene expression patterns defy a simple binary sex classification of somatic tissues.","authors":"Chen Xie, Sven Künzel, Diethard Tautz","doi":"10.7554/eLife.99602","DOIUrl":"10.7554/eLife.99602","url":null,"abstract":"<p><p>Sexual dimorphism in phenotypes is largely driven by genes with sex-biased expression, spanning from key regulators to numerous organ-specific effectors. Current understanding is limited regarding the evolutionary dynamics of these genes in somatic tissues that generate the adult phenotype versus gonadal organs that are required for reproduction. Here, we investigate sex-biased gene expression and micro-evolutionary patterns of these genes in populations of subspecies and species of wild mice (genus <i>Mus</i>) that were raised under controlled conditions. We find a faster evolutionary turnover of sex-biased gene expression in somatic tissues, but not in the gonads, when compared to the turnover of non-sex-biased genes. We introduce a sex-biased gene expression index (SBI) to quantify individual variances. We find a range from binary to overlapping SBI patterns across individuals. SBI values do not correlate between organs of the same individuals, thus supporting a mosaic model of somatic sex determination. Comparison with data from humans shows mostly fewer sex-biased genes compared to mice and strongly overlapping SBI distributions between the somatic organs of the sexes. We conclude that adult individuals are composed of a mosaic spectrum of sex characteristics in their somatic tissues that should not be cumulated into a simple binary classification.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12443475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response.","authors":"C J San Felipe, Jyoti Batra, Monita Muralidharan, Shivali Malpotra, Durga Anand, Rachel Bauer, Kliment A Verba, Danielle L Swaney, Nevan J Krogan, Michael Grabe, James S Fraser","doi":"10.7554/eLife.106484","DOIUrl":"10.7554/eLife.106484","url":null,"abstract":"<p><p>Open Reading Frame 9b (Orf9b), an accessory protein of SARS-CoV and -2, is involved in innate immune suppression through its binding to the mitochondrial receptor Translocase of Outer Membrane 70 (Tom70). Previous structural studies of Orf9b in isolation revealed a β-sheet-rich homodimer; however, structures of Orf9b in complex with Tom70 revealed a monomeric helical fold. Here, we developed a biophysical model that quantifies how Orf9b switches between these conformations and binds to Tom70, a requirement for suppressing the type 1 interferon response. We used this model to characterize the effect of lipid binding and mutations in variants of concern to the Orf9b:Tom70 equilibrium. We found that the binding of a lipid to the Orf9b homodimer biases the Orf9b monomer:dimer equilibrium towards the dimer by reducing the dimer dissociation rate ~100 fold. We also found that mutations in variants of concern can alter different microscopic rate constants without significantly affecting binding to Tom70. Together, our results highlight how perturbations to different steps in these coupled equilibria can affect the apparent affinity of Orf9b to Tom70, with potential downstream implications for interferon signaling in coronavirus infection.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"14 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12443476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}