IF 6.4 1区生物学

eLife Pub Date : 2024-12-06 DOI: 10.7554/eLife.98450

Bikash Adhikari, Katharina Schneider, Mathias Diebold, Christoph Sotriffer, Elmar Wolf

{"title":"Identification of suitable target/E3 ligase pairs for PROTAC development using a rapamycin-induced proximity assay (RiPA).","authors":"Bikash Adhikari, Katharina Schneider, Mathias Diebold, Christoph Sotriffer, Elmar Wolf","doi":"10.7554/eLife.98450","DOIUrl":"10.7554/eLife.98450","url":null,"abstract":"The development of proteolysis targeting chimeras (PROTACs), which induce the degradation of target proteins by bringing them into proximity with cellular E3 ubiquitin ligases, has revolutionized drug development. While the human genome encodes more than 600 different E3 ligases, current PROTACs use only a handful of them, drastically limiting their full potential. Furthermore, many PROTAC development campaigns fail because the selected E3 ligase candidates are unable to induce degradation of the particular target of interest. As more and more ligands for novel E3 ligases are discovered, the chemical effort to identify the best E3 ligase for a given target is exploding. Therefore, a genetic system to identify degradation-causing E3 ligases and suitable target/E3 ligase pairs is urgently needed. Here, we used the well-established dimerization of the FKBP12 protein and FRB domain by rapamycin to bring the target protein WDR5 into proximity with candidate E3 ligases. Strikingly, this rapamycin-induced proximity assay (RiPA) revealed that VHL, but not Cereblon, is able to induce WDR5 degradation - a finding previously made by PROTACs, demonstrating its predictive power. By optimizing the steric arrangement of all components and fusing the target protein with a minimal luciferase, RiPA can identify the ideal E3 for any target protein of interest in living cells, significantly reducing and focusing the chemical effort in the early stages of PROTAC development.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784649","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}

引用次数: 0

Lineage-specific intersection of endothelin and GDNF signaling in enteric nervous system development.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-06 DOI: 10.7554/eLife.96424

Denise M Poltavski, Alexander T Cunha, Jaime Tan, Henry M Sucov, Takako Makita

{"title":"Lineage-specific intersection of endothelin and GDNF signaling in enteric nervous system development.","authors":"Denise M Poltavski, Alexander T Cunha, Jaime Tan, Henry M Sucov, Takako Makita","doi":"10.7554/eLife.96424","DOIUrl":"10.7554/eLife.96424","url":null,"abstract":"Two major ligand-receptor signaling axes - endothelin Edn3 and its receptor Ednrb, and glial-derived neurotrophic factor (GDNF) and its receptor Ret - are required for migration of enteric nervous system (ENS) progenitors to the hindgut. Mutations in either component cause colonic aganglionosis, also called Hirschsprung disease. Here, we have used Wnt1Cre and Pax2Cre in mice to show that these driver lines label distinct ENS lineages during progenitor migration and in their terminal hindgut fates. Both Cre lines result in Hirschsprung disease when combined with conditional Ednrb or conditional Ret alleles. In vitro explant assays and analysis of lineage-labeled mutant embryos show that GDNF but not Edn3 is a migration cue for cells of both lineages. Instead, Edn3-Ednrb function is required in both for GDNF responsiveness albeit in different ways: by expanding the Ret+ population in the Pax2Cre lineage, and by supporting Ret function in Wnt1Cre-derived cells. Our results demonstrate that two distinct lineages of progenitors give rise to the ENS, and that these divergently utilize endothelin signaling to support migration to the hindgut.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784653","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}

引用次数: 0

Reversing protonation of weakly basic drugs greatly enhances intracellular diffusion and decreases lysosomal sequestration.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-06 DOI: 10.7554/eLife.97255

Debabrata Dey, Shir Marciano, Anna Poryval, Ondřej Groborz, Lucie Wohlrabova, Tomás Slanina, Gideon Schreiber

{"title":"Reversing protonation of weakly basic drugs greatly enhances intracellular diffusion and decreases lysosomal sequestration.","authors":"Debabrata Dey, Shir Marciano, Anna Poryval, Ondřej Groborz, Lucie Wohlrabova, Tomás Slanina, Gideon Schreiber","doi":"10.7554/eLife.97255","DOIUrl":"10.7554/eLife.97255","url":null,"abstract":"For drugs to be active they have to reach their targets. Within cells this requires crossing the cell membrane, and then free diffusion, distribution, and availability. Here, we explored the in-cell diffusion rates and distribution of a series of small molecular fluorescent drugs, in comparison to proteins, by microscopy and fluorescence recovery after photobleaching (FRAP). While all proteins diffused freely, we found a strong correlation between pKa and the intracellular diffusion and distribution of small molecule drugs. Weakly basic, small-molecule drugs displayed lower fractional recovery after photobleaching and 10- to-20-fold slower diffusion rates in cells than in aqueous solutions. As, more than half of pharmaceutical drugs are weakly basic, they, are protonated in the cell cytoplasm. Protonation, facilitates the formation of membrane impermeable ionic form of the weak base small molecules. This results in ion trapping, further reducing diffusion rates of weakly basic small molecule drugs under macromolecular crowding conditions where other nonspecific interactions become more relevant and dominant. Our imaging studies showed that acidic organelles, particularly the lysosome, captured these molecules. Surprisingly, blocking lysosomal import only slightly increased diffusion rates and fractional recovery. Conversely, blocking protonation by N-acetylated analogues, greatly enhanced their diffusion and fractional recovery after FRAP. Based on these results, N-acetylation of small molecule drugs may improve the intracellular availability and distribution of weakly basic, small molecule drugs within cells.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784659","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}

引用次数: 0

When abstract becomes concrete, naturalistic encoding of concepts in the brain.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-05 DOI: 10.7554/eLife.91522

Viktor Nikolaus Kewenig, Gabriella Vigliocco, Jeremy I Skipper

{"title":"When abstract becomes concrete, naturalistic encoding of concepts in the brain.","authors":"Viktor Nikolaus Kewenig, Gabriella Vigliocco, Jeremy I Skipper","doi":"10.7554/eLife.91522","DOIUrl":"10.7554/eLife.91522","url":null,"abstract":"Language is acquired and processed in complex and dynamic naturalistic contexts, involving the simultaneous processing of connected speech, faces, bodies, objects, etc. How words and their associated concepts are encoded in the brain during real-world processing is still unknown. Here, the representational structure of concrete and abstract concepts was investigated during movie watching to address the extent to which brain responses dynamically change depending on visual context. First, across contexts, concrete and abstract concepts are shown to encode different experience-based information in separable sets of brain regions. However, these differences are reduced when multimodal context is considered. Specifically, the response profile of abstract words becomes more concrete-like when these are processed in visual scenes highly related to their meaning. Conversely, when the visual context is unrelated to a given concrete word, the activation pattern resembles more that of abstract conceptual processing. These results suggest that while concepts generally encode habitual experiences, the underlying neurobiological organisation is not fixed but depends dynamically on available contextual information.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784667","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}

引用次数: 0

β-1,6-Glucan plays a central role in the structure and remodeling of the bilaminate fungal cell wall.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-05 DOI: 10.7554/eLife.100569

Clara Bekirian, Isabel Valsecchi, Sophie Bachellier-Bassi, Cyril Scandola, J Inaki Guijarro, Murielle Chauvel, Thierry Mourer, Neil A R Gow, Vishu Kumar Aimanianda, Christophe d'Enfert, Thierry Fontaine

{"title":"β-1,6-Glucan plays a central role in the structure and remodeling of the bilaminate fungal cell wall.","authors":"Clara Bekirian, Isabel Valsecchi, Sophie Bachellier-Bassi, Cyril Scandola, J Inaki Guijarro, Murielle Chauvel, Thierry Mourer, Neil A R Gow, Vishu Kumar Aimanianda, Christophe d'Enfert, Thierry Fontaine","doi":"10.7554/eLife.100569","DOIUrl":"10.7554/eLife.100569","url":null,"abstract":"The cell wall of human fungal pathogens plays critical roles as an architectural scaffold and as a target and modulator of the host immune response. Although the cell wall of the pathogenic yeast Candida albicans is intensively studied, one of the major fibrillar components in its cell wall, β-1,6-glucan, has been largely neglected. Here, we show that β-1,6-glucan is essential for bilayered cell wall organization, cell wall integrity, and filamentous growth. For the first time, we show that β-1,6-glucan production compensates the defect in mannan elongation in the outer layer of the cell wall. In addition, β-1,6-glucan dynamics are also coordinated by host environmental stimuli and stresses with wall remodeling, where the regulation of β-1,6-glucan structure and chain length is a crucial process. As we point out that β-1,6-glucan is exposed at the yeast surface and modulate immune response, β-1,6-glucan must be considered a key factor in host-pathogen interactions.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784669","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}

引用次数: 0

A conserved cell-pole determinant organizes proper polar flagellum formation.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-05 DOI: 10.7554/eLife.93004

Erick E Arroyo-Pérez, John C Hook, Alejandra Alvarado, Stephan Wimmi, Timo Glatter, Kai Thormann, Simon Ringgaard

{"title":"A conserved cell-pole determinant organizes proper polar flagellum formation.","authors":"Erick E Arroyo-Pérez, John C Hook, Alejandra Alvarado, Stephan Wimmi, Timo Glatter, Kai Thormann, Simon Ringgaard","doi":"10.7554/eLife.93004","DOIUrl":"10.7554/eLife.93004","url":null,"abstract":"The coordination of cell cycle progression and flagellar synthesis is a complex process in motile bacteria. In γ-proteobacteria, the localization of the flagellum to the cell pole is mediated by the SRP-type GTPase FlhF. However, the mechanism of action of FlhF, and its relationship with the cell pole landmark protein HubP remain unclear. In this study, we discovered a novel protein called FipA that is required for normal FlhF activity and function in polar flagellar synthesis. We demonstrated that membrane-localized FipA interacts with FlhF and is required for normal flagellar synthesis in Vibrio parahaemolyticus, Pseudomonas putida, and Shewanella putrefaciens, and it does so independently of the polar localization mediated by HubP. FipA exhibits a dynamic localization pattern and is present at the designated pole before flagellar synthesis begins, suggesting its role in licensing flagellar formation. This discovery provides insight into a new pathway for regulating flagellum synthesis and coordinating cellular organization in bacteria that rely on polar flagellation and FlhF-dependent localization.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784582","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}

引用次数: 0

Parallel mechanisms signal a hierarchy of sequence structure violations in the auditory cortex.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-05 DOI: 10.7554/eLife.102702

Sara Jamali, Sophie Bagur, Enora Bremont, Timo Van Kerkoerle, Stanislas Dehaene, Brice Bathellier

{"title":"Parallel mechanisms signal a hierarchy of sequence structure violations in the auditory cortex.","authors":"Sara Jamali, Sophie Bagur, Enora Bremont, Timo Van Kerkoerle, Stanislas Dehaene, Brice Bathellier","doi":"10.7554/eLife.102702","DOIUrl":"10.7554/eLife.102702","url":null,"abstract":"The brain predicts regularities in sensory inputs at multiple complexity levels, with neuronal mechanisms that remain elusive. Here, we monitored auditory cortex activity during the local-global paradigm, a protocol nesting different regularity levels in sound sequences. We observed that mice encode local predictions based on stimulus occurrence and stimulus transition probabilities, because auditory responses are boosted upon prediction violation. This boosting was due to both short-term adaptation and an adaptation-independent surprise mechanism resisting anesthesia. In parallel, and only in wakefulness, VIP interneurons responded to the omission of the locally expected sound repeat at the sequence ending, thus providing a chunking signal potentially useful for establishing global sequence structure. When this global structure was violated, by either shortening the sequence or ending it with a locally expected but globally unexpected sound transition, activity slightly increased in VIP and PV neurons, respectively. Hence, distinct cellular mechanisms predict different regularity levels in sound sequences.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784657","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}

引用次数: 0

Unravelling hidden hearing loss.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-05 DOI: 10.7554/eLife.104936

Emmanuel Ponsot

引用次数: 0

Dynamic tracking of native precursors in adult mice.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-05 DOI: 10.7554/eLife.97504

Suying Liu, Sarah E Adams, Haotian Zheng, Juliana Ehnot, Seul K Jung, Greer Jeffrey, Theresa Menna, Louise Purton, Hongzhe Lee, Peter Kurre

{"title":"Dynamic tracking of native precursors in adult mice.","authors":"Suying Liu, Sarah E Adams, Haotian Zheng, Juliana Ehnot, Seul K Jung, Greer Jeffrey, Theresa Menna, Louise Purton, Hongzhe Lee, Peter Kurre","doi":"10.7554/eLife.97504","DOIUrl":"10.7554/eLife.97504","url":null,"abstract":"Hematopoietic dysfunction has been associated with a reduction in the number of active precursors. However, precursor quantification at homeostasis and under diseased conditions is constrained by the scarcity of available methods. To address this issue, we optimized a method for quantifying a wide range of hematopoietic precursors. Assuming the random induction of a stable label in precursors following a binomial distribution, estimates depend on the inverse correlation between precursor numbers and the variance of precursor labeling among independent samples. Experimentally validated to cover the full dynamic range of hematopoietic precursors in mice (1-105), we utilized this approach to demonstrate that thousands of precursors, which emerge after modest expansion during fetal-to-adult transition, contribute to native and perturbed hematopoiesis. We further estimated the number of precursors in a mouse model of Fanconi Anemia, showcasing how repopulation deficits can be classified as autologous (cell proliferation) and non-autologous (lack of precursor). Our results support an accessible and reliable approach for precursor quantification, emphasizing the contemporary perspective that native hematopoiesis is highly polyclonal.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784619","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}

引用次数: 0

Endogenous hydrogen peroxide positively regulates secretion of a gut-derived peptide in neuroendocrine potentiation of the oxidative stress response in Caenorhabditis elegans.

IF 6.4 1区生物学

eLife Pub Date : 2024-12-05 DOI: 10.7554/eLife.97503

Qi Jia, Drew Young, Qixin Zhang, Derek Sieburth

{"title":"Endogenous hydrogen peroxide positively regulates secretion of a gut-derived peptide in neuroendocrine potentiation of the oxidative stress response in Caenorhabditis elegans.","authors":"Qi Jia, Drew Young, Qixin Zhang, Derek Sieburth","doi":"10.7554/eLife.97503","DOIUrl":"10.7554/eLife.97503","url":null,"abstract":"The gut-brain axis mediates bidirectional signaling between the intestine and the nervous system and is critical for organism-wide homeostasis. Here, we report the identification of a peptidergic endocrine circuit in which bidirectional signaling between neurons and the intestine potentiates the activation of the antioxidant response in Caenorhabditis elegans in the intestine. We identify an FMRF-amide-like peptide, FLP-2, whose release from the intestine is necessary and sufficient to activate the intestinal oxidative stress response by promoting the release of the antioxidant FLP-1 neuropeptide from neurons. FLP-2 secretion from the intestine is positively regulated by endogenous hydrogen peroxide (H2O2) produced in the mitochondrial matrix by sod-3/superoxide dismutase, and is negatively regulated by prdx-2/peroxiredoxin, which depletes H2O2 in both the mitochondria and cytosol. H2O2 promotes FLP-2 secretion through the DAG and calcium-dependent protein kinase C family member pkc-2 and by the SNAP25 family member aex-4 in the intestine. Together, our data demonstrate a role for intestinal H2O2 in promoting inter-tissue antioxidant signaling through regulated neuropeptide-like protein exocytosis in a gut-brain axis to activate the oxidative stress response.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784646","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}

引用次数: 0

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