IF 6.4 1区生物学

eLife Pub Date : 2024-11-12 DOI: 10.7554/eLife.96266

Nyasha Charura, Ernesto Llamas, Concetta De Quattro, David Vilchez, Moritz K Nowack, Alga Zuccaro

{"title":"Root cap cell corpse clearance limits microbial colonization in Arabidopsis thaliana.","authors":"Nyasha Charura, Ernesto Llamas, Concetta De Quattro, David Vilchez, Moritz K Nowack, Alga Zuccaro","doi":"10.7554/eLife.96266","DOIUrl":"10.7554/eLife.96266","url":null,"abstract":"Programmed cell death occurring during plant development (dPCD) is a fundamental process integral for plant growth and reproduction. Here, we investigate the connection between developmentally controlled PCD and fungal accommodation in Arabidopsis thaliana roots, focusing on the root cap-specific transcription factor ANAC033/SOMBRERO (SMB) and the senescence-associated nuclease BFN1. Mutations of both dPCD regulators increase colonization by the beneficial fungus Serendipita indica, primarily in the differentiation zone. smb-3 mutants additionally exhibit hypercolonization around the meristematic zone and a delay of S. indica-induced root-growth promotion. This demonstrates that root cap dPCD and rapid post-mortem clearance of cellular corpses represent a physical defense mechanism restricting microbial invasion of the root. Additionally, reporter lines and transcriptional analysis revealed that BFN1 expression is downregulated during S. indica colonization in mature root epidermal cells, suggesting a transcriptional control mechanism that facilitates the accommodation of beneficial microbes in the roots.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11556792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617124","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

Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function. 镜像毛细胞定向对小鼠耳石器官和斑马鱼神经嵴功能的贡献

IF 6.4 1区生物学

eLife Pub Date : 2024-11-12 DOI: 10.7554/eLife.97674

Kazuya Ono, Amandine Jarysta, Natasha C Hughes, Alma Jukic, Hui Ho Vanessa Chang, Michael R Deans, Ruth Anne Eatock, Kathleen E Cullen, Katie S Kindt, Basile Tarchini

{"title":"Contributions of mirror-image hair cell orientation to mouse otolith organ and zebrafish neuromast function.","authors":"Kazuya Ono, Amandine Jarysta, Natasha C Hughes, Alma Jukic, Hui Ho Vanessa Chang, Michael R Deans, Ruth Anne Eatock, Kathleen E Cullen, Katie S Kindt, Basile Tarchini","doi":"10.7554/eLife.97674","DOIUrl":"10.7554/eLife.97674","url":null,"abstract":"Otolith organs in the inner ear and neuromasts in the fish lateral-line harbor two populations of hair cells oriented to detect stimuli in opposing directions. The underlying mechanism is highly conserved: the transcription factor EMX2 is regionally expressed in just one hair cell population and acts through the receptor GPR156 to reverse cell orientation relative to the other population. In mouse and zebrafish, loss of Emx2 results in sensory organs that harbor only one hair cell orientation and are not innervated properly. In zebrafish, Emx2 also confers hair cells with reduced mechanosensory properties. Here, we leverage mouse and zebrafish models lacking GPR156 to determine how detecting stimuli of opposing directions serves vestibular function, and whether GPR156 has other roles besides orienting hair cells. We find that otolith organs in Gpr156 mouse mutants have normal zonal organization and normal type I-II hair cell distribution and mechano-electrical transduction properties. In contrast, gpr156 zebrafish mutants lack the smaller mechanically evoked signals that characterize Emx2-positive hair cells. Loss of GPR156 does not affect orientation-selectivity of afferents in mouse utricle or zebrafish neuromasts. Consistent with normal otolith organ anatomy and afferent selectivity, Gpr156 mutant mice do not show overt vestibular dysfunction. Instead, performance on two tests that engage otolith organs is significantly altered - swimming and off-vertical-axis rotation. We conclude that GPR156 relays hair cell orientation and transduction information downstream of EMX2, but not selectivity for direction-specific afferents. These results clarify how molecular mechanisms that confer bi-directionality to sensory organs contribute to function, from single hair cell physiology to animal behavior.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11556791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617101","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

Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a poxvirus substrate mimic. 人类 PKR 激酶结构域的系统遗传特征突显了其在逃避痘病毒底物模拟物时的功能可塑性。

IF 6.4 1区生物学

eLife Pub Date : 2024-11-12 DOI: 10.7554/eLife.99575

Michael James Chambers, Sophia B Scobell, Meru J Sadhu

{"title":"Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a poxvirus substrate mimic.","authors":"Michael James Chambers, Sophia B Scobell, Meru J Sadhu","doi":"10.7554/eLife.99575","DOIUrl":"10.7554/eLife.99575","url":null,"abstract":"Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued.  However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that mimic the natural substrate, eIF2α, and inhibit PKR activity. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface's critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3, encoded by the vaccinia virus gene K3L. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11556786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617130","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

The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression patterns through regulation of WDR5 stability. E3泛素连接酶RNF220通过调节WDR5的稳定性维持后脑Hox表达模式。

IF 6.4 1区生物学

eLife Pub Date : 2024-11-11 DOI: 10.7554/eLife.94657

Huishan Wang, Xingyan Liu, Yamin Liu, Chencheng Yang, Yaxin Ye, Xiaomei Yu, Nengyin Sheng, Shihua Zhang, Bingyu Mao, Pengcheng Ma

{"title":"The E3 ubiquitin ligase RNF220 maintains hindbrain Hox expression patterns through regulation of WDR5 stability.","authors":"Huishan Wang, Xingyan Liu, Yamin Liu, Chencheng Yang, Yaxin Ye, Xiaomei Yu, Nengyin Sheng, Shihua Zhang, Bingyu Mao, Pengcheng Ma","doi":"10.7554/eLife.94657","DOIUrl":"10.7554/eLife.94657","url":null,"abstract":"The spatial and temporal linear expression of Hox genes establishes a regional Hox code, which is crucial for the antero-posterior (A-P) patterning, segmentation, and neuronal circuit development of the hindbrain. RNF220, an E3 ubiquitin ligase, is widely involved in neural development via targeting of multiple substrates. Here, we found that the expression of Hox genes in the pons was markedly up-regulated at the late developmental stage (post-embryonic day E15.5) in Rnf220-/- and Rnf220+/- mouse embryos. Single-nucleus RNA sequencing (RNA-seq) analysis revealed different Hox de-repression profiles in different groups of neurons, including the pontine nuclei (PN). The Hox pattern was disrupted and the neural circuits were affected in the PN of Rnf220+/- mice. We showed that this phenomenon was mediated by WDR5, a key component of the TrxG complex, which can be polyubiquitinated and degraded by RNF220. Intrauterine injection of WDR5 inhibitor (WDR5-IN-4) and genetic ablation of Wdr5 in Rnf220+/- mice largely recovered the de-repressed Hox expression pattern in the hindbrain. In P19 embryonal carcinoma cells, the retinoic acid-induced Hox expression was further stimulated by Rnf220 knockdown, which can also be rescued by Wdr5 knockdown. In short, our data suggest a new role of RNF220/WDR5 in Hox pattern maintenance and pons development in mice.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617132","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

Body mass and growth rates predict protein intake across animals. 体重和生长速度可预测动物的蛋白质摄入量。

IF 6.4 1区生物学

eLife Pub Date : 2024-11-11 DOI: 10.7554/eLife.88933

Stav Talal, Jon F Harrison, Ruth Farington, Jacob P Youngblood, Hector E Medina, Rick Overson, Arianne J Cease

{"title":"Body mass and growth rates predict protein intake across animals.","authors":"Stav Talal, Jon F Harrison, Ruth Farington, Jacob P Youngblood, Hector E Medina, Rick Overson, Arianne J Cease","doi":"10.7554/eLife.88933","DOIUrl":"https://doi.org/10.7554/eLife.88933","url":null,"abstract":"Organisms require dietary macronutrients in specific ratios to maximize performance, and variation in macronutrient requirements plays a central role in niche determination. Although it is well recognized that development and body size can have strong and predictable effects on many aspects of organismal function, we lack a predictive understanding of ontogenetic or scaling effects on macronutrient intake. We determined protein and carbohydrate intake throughout development on lab populations of locusts and compared to late instars of field populations. Self-selected protein:carbohydrate targets declined dramatically through ontogeny, due primarily to declines in mass-specific protein consumption rates which were highly correlated with declines in specific growth rates. Lab results for protein consumption rates partly matched results from field-collected locusts. However, field locusts consumed nearly double the carbohydrate, likely due to higher activity and metabolic rates. Combining our results with the available data for animals, both across species and during ontogeny, protein consumption scaled predictably and hypometrically, demonstrating a new scaling rule key for understanding nutritional ecology.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617099","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

Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays. 利用全蛋白质组热转移测定法大规模鉴定药物的作用机制。

IF 6.4 1区生物学

eLife Pub Date : 2024-11-11 DOI: 10.7554/eLife.95595

Jonathan G Van Vranken, Jiaming Li, Julian Mintseris, Ting-Yu Wei, Catherine M Sniezek, Meagan Gadzuk-Shea, Steven P Gygi, Devin K Schweppe

{"title":"Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays.","authors":"Jonathan G Van Vranken, Jiaming Li, Julian Mintseris, Ting-Yu Wei, Catherine M Sniezek, Meagan Gadzuk-Shea, Steven P Gygi, Devin K Schweppe","doi":"10.7554/eLife.95595","DOIUrl":"10.7554/eLife.95595","url":null,"abstract":"In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent changes in thermal stability, the proteome-wide thermal shift assay has emerged as a powerful tool in this arsenal. The most recent iterations have drastically improved the overall efficiency of these assays, providing an opportunity to screen compounds at a previously unprecedented rate. Taking advantage of this advance, we quantified more than one million thermal stability measurements in response to multiple classes of therapeutic and tool compounds (96 compounds in living cells and 70 compounds in lysates). When interrogating the dataset as a whole, approximately 80% of compounds (with quantifiable targets) caused a significant change in the thermal stability of an annotated target. There was also a wealth of evidence portending off-target engagement despite the extensive use of the compounds in the laboratory and/or clinic. Finally, the combined application of cell- and lysate-based assays, aided in the classification of primary (direct ligand binding) and secondary (indirect) changes in thermal stability. Overall, this study highlights the value of these assays in the drug development process by affording an unbiased and reliable assessment of compound mechanism of action.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617112","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

Regulating uric acid. 调节尿酸

IF 6.4 1区生物学

eLife Pub Date : 2024-11-11 DOI: 10.7554/eLife.104493

Caihong Hu

引用次数: 0

Derivation and internal validation of prediction models for pulmonary hypertension risk assessment in a cohort inhabiting Tibet, China. 中国西藏队列肺动脉高压风险评估预测模型的推导和内部验证。

IF 6.4 1区生物学

eLife Pub Date : 2024-11-11 DOI: 10.7554/eLife.98169

Junhui Tang, Rui Yang, Hui Li, Xiaodong Wei, Zhen Yang, Wenbin Cai, Yao Jiang, Ga Zhuo, Li Meng, Yali Xu

{"title":"Derivation and internal validation of prediction models for pulmonary hypertension risk assessment in a cohort inhabiting Tibet, China.","authors":"Junhui Tang, Rui Yang, Hui Li, Xiaodong Wei, Zhen Yang, Wenbin Cai, Yao Jiang, Ga Zhuo, Li Meng, Yali Xu","doi":"10.7554/eLife.98169","DOIUrl":"10.7554/eLife.98169","url":null,"abstract":"Individuals residing in plateau regions are susceptible to pulmonary hypertension (PH) and there is an urgent need for a prediction nomogram to assess the risk of PH in this population. A total of 6603 subjects were randomly divided into a derivation set and a validation set at a ratio of 7:3. Optimal predictive features were identified through the least absolute shrinkage and selection operator regression technique, and nomograms were constructed using multivariate logistic regression. The performance of these nomograms was evaluated and validated using the area under the curve (AUC), calibration curves, the Hosmer-Lemeshow test, and decision curve analysis. Comparisons between nomograms were conducted using the net reclassification improvement (NRI) and integrated discrimination improvement (IDI) indices. NomogramI was established based on independent risk factors, including gender, Tibetan ethnicity, age, incomplete right bundle branch block (IRBBB), atrial fibrillation (AF), sinus tachycardia (ST), and T wave changes (TC). The AUCs for NomogramI were 0.716 in the derivation set and 0.718 in the validation set. NomogramII was established based on independent risk factors, including Tibetan ethnicity, age, right axis deviation, high voltage in the right ventricle, IRBBB, AF, pulmonary P waves, ST, and TC. The AUCs for NomogramII were 0.844 in the derivation set and 0.801 in the validation set. Both nomograms demonstrated satisfactory clinical consistency. The IDI and NRI indices confirmed that NomogramII outperformed NomogramI. Therefore, the online dynamic NomogramII was established to predict the risks of PH in the plateau population.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617104","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

Shortcutting from self-motion signals reveals a cognitive map in mice. 自我运动信号捷径揭示了小鼠的认知图谱

IF 6.4 1区生物学

eLife Pub Date : 2024-11-11 DOI: 10.7554/eLife.95764

Jiayun Xu, Mauricio Girardi-Schappo, Jean-Claude Beique, André Longtin, Leonard Maler

引用次数: 0

Exposure to live saprophytic Leptospira before challenge with a pathogenic serovar prevents severe leptospirosis and promotes kidney homeostasis. 在接触致病性血清前接触活的钩端螺旋体可预防严重的钩端螺旋体病，并促进肾脏平衡。

IF 6.4 1区生物学

eLife Pub Date : 2024-11-11 DOI: 10.7554/eLife.96470

Suman Kundu, Advait Shetty, Maria Gomes-Solecki

{"title":"Exposure to live saprophytic Leptospira before challenge with a pathogenic serovar prevents severe leptospirosis and promotes kidney homeostasis.","authors":"Suman Kundu, Advait Shetty, Maria Gomes-Solecki","doi":"10.7554/eLife.96470","DOIUrl":"10.7554/eLife.96470","url":null,"abstract":"Previous studies demonstrated that Leptospira biflexa, a saprophytic species, triggers innate immune responses in the host during early infection. This raised the question of whether these responses could suppress a subsequent challenge with pathogenic Leptospira. We inoculated C3H/HeJ mice with a single or a double dose of L. biflexa before challenge with a pathogenic serovar, Leptospira interrogans serovar Copenhageni FioCruz (LIC). Pre-challenge exposure to L. biflexa did not prevent LIC dissemination and colonization of the kidney. However, it rescued weight loss and mouse survival thereby mitigating disease severity. Unexpectedly, there was correlation between rescue of overall health (weight gain, higher survival, lower kidney fibrosis marker ColA1) and higher shedding of LIC in urine. This stood in contrast to the L. biflexa unexposed LIC challenged control. Immune responses were dominated by increased frequency of effector T helper (CD4+) cells in spleen, as well as significant increases in serologic IgG2a. Our findings suggest that exposure to live saprophytic Leptospira primes the host to develop Th1 biased immune responses that prevent severe disease induced by a subsequent challenge with a pathogenic species. Thus, mice exposed to live saprophytic Leptospira before facing a pathogenic serovar may withstand infection with far better outcomes. Furthermore, a status of homeostasis may have been reached after kidney colonization that helps LIC complete its enzootic cycle.","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635941","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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