eLife最新文献 - Book学术

A VgrG2b fragment cleaved by caspase-11/4 promotes Pseudomonas aeruginosa infection through suppressing the NLRP3 inflammasome.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-25 DOI: 10.7554/eLife.99939

Yan Qian, Qiannv Liu, Xiangyun Cheng, Chunlei Wang, Chun Kong, Mengqian Li, Chao Ren, Dong Jiang, Shuo Wang, Pengyan Xia

引用次数: 0

A statistical framework for quantifying the nuclear export rate of influenza viral mRNAs.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-25 DOI: 10.7554/eLife.88468

Michi Miura, Naho Kiuchi, Siu-Ying Lau, Bobo Wing-Yee Mok, Hiroshi Ushirogawa, Tadasuke Naito, Honglin Chen, Mineki Saito

引用次数: 0

Aeromonas hydrophila CobQ is a new type of NAD⁺- and Zn²⁺-independent protein lysine deacetylase.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-25 DOI: 10.7554/eLife.97511

Yuqian Wang, Guibin Wang, Lishan Zhang, Qilan Cai, Meizhen Lin, Dongping Huang, Yuyue Xie, Wenxiong Lin, Xiangmin Lin

{"title":"Aeromonas hydrophila CobQ is a new type of NAD+- and Zn2+-independent protein lysine deacetylase.","authors":"Yuqian Wang, Guibin Wang, Lishan Zhang, Qilan Cai, Meizhen Lin, Dongping Huang, Yuyue Xie, Wenxiong Lin, Xiangmin Lin","doi":"10.7554/eLife.97511","DOIUrl":"https://doi.org/10.7554/eLife.97511","url":null,"abstract":"Protein NƐ-lysine acetylation (Kac) modifications play crucial roles in diverse physiological and pathological functions in cells. In prokaryotic cells, there are only two types of lysine deacetylases (KDACs) that are Zn2+- or NAD+-dependent. In this study, we reported a protein, AhCobQ, in Aeromonas hydrophila ATCC 7966 that presents NAD+- and Zn2+-independent KDAC activity. Furthermore, its KDAC activity is located in an unidentified domain (from 195 to 245 aa). Interestingly, AhCobQ has no homology with current known KDACs, and no homologous protein was found in eukaryotic cells. A protein substrate analysis showed that AhCobQ has specific protein substrates in common with other known KDACs, indicating that these KDACs can dynamically co-regulate the states of Kac proteins. Microbiological methods employed in this study affirmed AhCobQ's positive regulation of isocitrate dehydrogenase (ICD) enzymatic activity at the K388 site, implicating AhCobQ in the modulation of bacterial enzymatic activities. In summary, our findings present compelling evidence that AhCobQ represents a distinctive type of KDAC with significant roles in bacterial biological functions.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491332","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}

引用次数: 0

Multidimensionality of tree communities structure host-parasitoid networks and their phylogenetic composition.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-25 DOI: 10.7554/eLife.100202

Ming-Qiang Wang, Shi-Kun Guo, Peng-Fei Guo, Juan-Juan Yang, Guo-Ai Chen, Douglas Chesters, Michael C Orr, Ze-Qing Niu, Michael Staab, Jing-Ting Chen, Yi Li, Qing-Song Zhou, Felix Fornoff, Xiaoyu Shi, Shan Li, Massimo Martini, Alexandra-Maria Klein, Andreas Schuldt, Xiaojuan Liu, Keping Ma, Helge Bruelheide, Arong Luo, Chao-Dong Zhu

{"title":"Multidimensionality of tree communities structure host-parasitoid networks and their phylogenetic composition.","authors":"Ming-Qiang Wang, Shi-Kun Guo, Peng-Fei Guo, Juan-Juan Yang, Guo-Ai Chen, Douglas Chesters, Michael C Orr, Ze-Qing Niu, Michael Staab, Jing-Ting Chen, Yi Li, Qing-Song Zhou, Felix Fornoff, Xiaoyu Shi, Shan Li, Massimo Martini, Alexandra-Maria Klein, Andreas Schuldt, Xiaojuan Liu, Keping Ma, Helge Bruelheide, Arong Luo, Chao-Dong Zhu","doi":"10.7554/eLife.100202","DOIUrl":"https://doi.org/10.7554/eLife.100202","url":null,"abstract":"Environmental factors can influence ecological networks, but these effects are poorly understood in the realm of the phylogeny of host-parasitoid interactions. Especially, we lack a comprehensive understanding of the ways that biotic factors, including plant species richness, overall community phylogenetic and functional composition of consumers, and abiotic factors such as microclimate, determine host-parasitoid network structure and host-parasitoid community dynamics. To address this, we leveraged a 5-year dataset of trap-nesting bees and wasps and their parasitoids collected in a highly controlled, large-scale subtropical tree biodiversity experiment. We tested for effects of tree species richness, tree phylogenetic, and functional diversity, and species and phylogenetic composition on species and phylogenetic diversity of both host and parasitoid communities and the composition of their interaction networks. We show that multiple components of tree diversity and canopy cover impacted both, species and phylogenetic composition of hosts and parasitoids. Generally, phylogenetic associations between hosts and parasitoids reflected nonrandomly structured interactions between phylogenetic trees of hosts and parasitoids. Further, host-parasitoid network structure was influenced by tree species richness, tree phylogenetic diversity, and canopy cover. Our study indicates that the composition of higher trophic levels and corresponding interaction networks are determined by plant diversity and canopy cover, especially via trophic links in species-rich ecosystems.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491338","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}

引用次数: 0

Precision-based causal inference modulates audiovisual temporal recalibration.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-25 DOI: 10.7554/eLife.97765

Luhe Li, Fangfang Hong, Stephanie Badde, Michael S Landy

{"title":"Precision-based causal inference modulates audiovisual temporal recalibration.","authors":"Luhe Li, Fangfang Hong, Stephanie Badde, Michael S Landy","doi":"10.7554/eLife.97765","DOIUrl":"https://doi.org/10.7554/eLife.97765","url":null,"abstract":"Cross-modal temporal recalibration guarantees stable temporal perception across ever-changing environments. Yet, the mechanisms of cross-modal temporal recalibration remain unknown. Here, we conducted an experiment to measure how participants' temporal perception was affected by exposure to audiovisual stimuli with constant temporal delays that we varied across sessions. Consistent with previous findings, recalibration effects plateaued with increasing audiovisual asynchrony (nonlinearity) and varied by which modality led during the exposure phase (asymmetry). We compared six observer models that differed in how they update the audiovisual temporal bias during the exposure phase and in whether they assume a modality-specific or modality-independent precision of arrival latency. The causal-inference observer shifts the audiovisual temporal bias to compensate for perceived asynchrony, which is inferred by considering two causal scenarios: when the audiovisual stimuli have a common cause or separate causes. The asynchrony-contingent observer updates the bias to achieve simultaneity of auditory and visual measurements, modulating the update rate by the likelihood of the audiovisual stimuli originating from a simultaneous event. In the asynchrony-correction model, the observer first assesses whether the sensory measurement is asynchronous; if so, she adjusts the bias proportionally to the magnitude of the measured asynchrony. Each model was paired with either modality-specific or modality-independent precision of arrival latency. A Bayesian model comparison revealed that both the causal-inference process and modality-specific precision in arrival latency are required to capture the nonlinearity and asymmetry observed in audiovisual temporal recalibration. Our findings support the hypothesis that audiovisual temporal recalibration relies on the same causal-inference processes that govern cross-modal perception.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491340","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}

引用次数: 0

DNA methylome regulates virulence and metabolism in Pseudomonas syringae.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-24 DOI: 10.7554/eLife.96290

Jiadai Huang, Fang Chen, Beifang Lu, Yue Sun, Youyue Li, Canfeng Hua, Xin Deng

{"title":"DNA methylome regulates virulence and metabolism in Pseudomonas syringae.","authors":"Jiadai Huang, Fang Chen, Beifang Lu, Yue Sun, Youyue Li, Canfeng Hua, Xin Deng","doi":"10.7554/eLife.96290","DOIUrl":"https://doi.org/10.7554/eLife.96290","url":null,"abstract":"Bacterial pathogens employ epigenetic mechanisms, including DNA methylation, to adapt to environmental changes, and these mechanisms play important roles in various biological processes. Pseudomonas syringae is a model phytopathogenic bacterium, but its methylome is less well known than that of other species. In this study, we conducted single-molecule real-time sequencing to profile the DNA methylation landscape in three model pathovars of P. syringae. We identified one Type I restriction-modification system (HsdMSR), including the conserved sequence motif associated with N6-methyladenine (6mA). About 25-40% of the genes involved in DNA methylation were conserved in two or more of the strains, revealing the functional conservation of methylation in P. syringae. Subsequent transcriptomic analysis highlighted the involvement of HsdMSR in virulent and metabolic pathways, including the Type III secretion system, biofilm formation, and translational efficiency. The regulatory effect of HsdMSR on transcription was dependent on both strands being fully 6mA methylated. Overall, this work illustrated the methylation profile in P. syringae and the critical involvement of DNA methylation in regulating virulence and metabolism. Thus, this work contributes to a deeper understanding of epigenetic transcriptional control in P. syringae and related bacteria.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491336","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}

引用次数: 0

Axon-specific microtubule regulation drives asymmetric regeneration of sensory neuron axons.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-24 DOI: 10.7554/eLife.104069

Ana Catarina Costa, Blanca R Murillo, Rita Bessa, Ricardo Ribeiro, Tiago Ferreira da Silva, Patrícia Porfírio-Rodrigues, Gabriel G Martins, Pedro Brites, Matthias Kneussel, Thomas Misgeld, Monika S Brill, Monica M Sousa

{"title":"Axon-specific microtubule regulation drives asymmetric regeneration of sensory neuron axons.","authors":"Ana Catarina Costa, Blanca R Murillo, Rita Bessa, Ricardo Ribeiro, Tiago Ferreira da Silva, Patrícia Porfírio-Rodrigues, Gabriel G Martins, Pedro Brites, Matthias Kneussel, Thomas Misgeld, Monika S Brill, Monica M Sousa","doi":"10.7554/eLife.104069","DOIUrl":"10.7554/eLife.104069","url":null,"abstract":"Sensory dorsal root ganglion (DRG) neurons have a unique pseudo-unipolar morphology in which a stem axon bifurcates into a peripheral and a central axon, with different regenerative abilities. Whereas peripheral DRG axons regenerate, central axons are unable to regrow. Central axon regeneration can however be elicited by a prior conditioning lesion to the peripheral axon. How DRG axon asymmetry is established remains unknown. Here we developed a rodent in vitro system replicating DRG pseudo-unipolarization and asymmetric axon regeneration. Using this model, we observed that from early development, central DRG axons have a higher density of growing microtubules. This asymmetry was also present in vivo and was abolished by a conditioning lesion that decreased microtubule polymerization of central DRG axons. An axon-specific microtubule-associated protein (MAP) signature, including the severases spastin and katanin and the microtubule regulators CRMP5 and tau, was found and shown to adapt upon conditioning lesion. Supporting its significance, interfering with the DRG MAP signature either in vitro or in vivo readily abolished central-peripheral asymmetries in microtubule dynamics and regenerative ability. In summary, our data unveil that axon-specific microtubule regulation drives asymmetric regeneration of sensory neuron axons.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482417","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}

引用次数: 0

Chronic RNA G-quadruplex accumulation in aging and Alzheimer's disease.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-24 DOI: 10.7554/eLife.105446

Lena Kallweit, Eric Daniel Hamlett, Hannah Saternos, Anah Gilmore, Ann-Charlotte Granholm, Scott Horowitz

引用次数: 0

Altered hepatic metabolism mediates sepsis preventive effects of reduced glucose supply in infected preterm newborns.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-24 DOI: 10.7554/eLife.97830

Ole Bæk, Tik Muk, Ziyuan Wu, Yongxin Ye, Bekzod Khakimov, Alessandra Maria Casano, Bagirath Gangadharan, Ivan Bilic, Anders Brunse, Per Torp Sangild, Duc Ninh Nguyen

{"title":"Altered hepatic metabolism mediates sepsis preventive effects of reduced glucose supply in infected preterm newborns.","authors":"Ole Bæk, Tik Muk, Ziyuan Wu, Yongxin Ye, Bekzod Khakimov, Alessandra Maria Casano, Bagirath Gangadharan, Ivan Bilic, Anders Brunse, Per Torp Sangild, Duc Ninh Nguyen","doi":"10.7554/eLife.97830","DOIUrl":"10.7554/eLife.97830","url":null,"abstract":"Preterm infants are susceptible to neonatal sepsis, a syndrome of pro-inflammatory activity, organ damage, and altered metabolism following infection. Given the unique metabolic challenges and poor glucose regulatory capacity of preterm infants, their glucose intake during infection may have a high impact on the degree of metabolism dysregulation and organ damage. Using a preterm pig model of neonatal sepsis, we previously showed that a drastic restriction in glucose supply during infection protects against sepsis via suppression of glycolysis-induced inflammation, but results in severe hypoglycemia. Now we explored clinically relevant options for reducing glucose intake to decrease sepsis risk, without causing hypoglycemia and further explore the involvement of the liver in these protective effects. We found that a reduced glucose regime during infection increased survival via reduced pro-inflammatory response, while maintaining normoglycemia. Mechanistically, this intervention enhanced hepatic oxidative phosphorylation and possibly gluconeogenesis, and dampened both circulating and hepatic inflammation. However, switching from a high to a reduced glucose supply after the debut of clinical symptoms did not prevent sepsis, suggesting metabolic conditions at the start of infection are key in driving the outcome. Finally, an early therapy with purified human inter-alpha inhibitor protein, a liver-derived anti-inflammatory protein, partially reversed the effects of low parenteral glucose provision, likely by inhibiting neutrophil functions that mediate pathogen clearance. Our findings suggest a clinically relevant regime of reduced glucose supply for infected preterm infants could prevent or delay the development of sepsis in vulnerable neonates.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482416","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}

引用次数: 0

Improved base editing and functional screening in Leishmania via co-expression of the AsCas12a ultra variant, a T7 RNA polymerase, and a cytosine base editor.

IF 6.4 1区生物学

eLife Pub Date : 2025-02-24 DOI: 10.7554/eLife.97437

Nicole Herrmann May, Anh Cao, Annika Schmid, Fabian Link, Jorge Arias-Del-Angel, Elisabeth Meiser, Tom Beneke

{"title":"Improved base editing and functional screening in Leishmania via co-expression of the AsCas12a ultra variant, a T7 RNA polymerase, and a cytosine base editor.","authors":"Nicole Herrmann May, Anh Cao, Annika Schmid, Fabian Link, Jorge Arias-Del-Angel, Elisabeth Meiser, Tom Beneke","doi":"10.7554/eLife.97437","DOIUrl":"10.7554/eLife.97437","url":null,"abstract":"The ability to analyze the function of all genes in a genome is highly desirable, yet challenging in Leishmania due to a repetitive genome, limited DNA repair mechanisms, and lack of RNA interference in most species. While our introduction of a cytosine base editor (CBE) demonstrated potential to overcome these limitations (Engstler and Beneke, 2023), challenges remained, including low transfection efficiency, variable editing rates across species, parasite growth effects, and competition between deleterious and non-deleterious mutations. Here, we present an optimized approach addressing these issues. We identified a T7 RNAP promoter variant ensuring high editing rates across Leishmania species without compromising growth. A revised CBE single-guide RNAs (sgRNAs) scoring system was developed to prioritize STOP codon generation. Additionally, a triple-expression construct was created for stable integration of CBE sgRNA expression cassettes into a Leishmania safe harbor locus using AsCas12a ultra-mediated DNA double-strand breaks, increasing transfection efficiency by ~400-fold to 1 transfectant per 70 transfected cells. Using this improved system for a small-scale proof-of-principle pooled screen, we successfully confirmed the essential and fitness-associated functions of CK1.2, CRK2, CRK3, AUK1/AIRK, TOR1, IFT88, IFT139, IFT140, and RAB5A in Leishmania mexicana, demonstrating a significant improvement over our previous method. Lastly, we show the utility of co-expressing AsCas12a ultra, T7 RNAP, and CBE for hybrid CRISPR gene replacement and base editing within the same cell line. Overall, these improvements will broaden the range of possible gene editing applications in Leishmania species and will enable a variety of loss-of-function screens in the near future.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482523","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}

引用次数: 0