RESUMEN
Angiogenin (ANG) is a secreted ribonuclease (RNase) with cell-type- and context-specific roles in growth, survival, and regeneration. Although these functions require receptor-mediated endocytosis and appropriate subcellular localization, the identity of the cell surface receptor remains undefined. Here, we show that plexin-B2 (PLXNB2) is the functional receptor for ANG in endothelial, cancer, neuronal, and normal hematopoietic and leukemic stem and progenitor cells. Mechanistically, PLXNB2 mediates intracellular RNA processing that contribute to cell growth, survival, and regenerative capabilities of ANG. Antibodies generated against the ANG-binding site on PLXNB2 restricts ANG activity in vitro and in vivo, resulting in inhibition of established xenograft tumors, ANG-induced neurogenesis and neuroprotection, levels of pro-self-renewal transcripts in hematopoietic and patient-derived leukemic stem and progenitor cells, and reduced progression of leukemia in vivo. PLXNB2 is therefore required for the physiological and pathological functions of ANG and has significant therapeutic potential in solid and hematopoietic cancers and neurodegenerative diseases.
Asunto(s)
Proteínas del Tejido Nervioso/metabolismo , Ribonucleasa Pancreática/metabolismo , Animales , Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/patología , Proliferación Celular , Femenino , Glioblastoma/metabolismo , Glioblastoma/patología , Células Madre Hematopoyéticas/metabolismo , Xenoinjertos , Humanos , Leucemia Mielógena Crónica BCR-ABL Positiva/tratamiento farmacológico , Leucemia Mielógena Crónica BCR-ABL Positiva/metabolismo , Leucemia Mielógena Crónica BCR-ABL Positiva/patología , Masculino , Ratones , Ratones Endogámicos C57BL , Trasplante de Neoplasias , Proteínas del Tejido Nervioso/antagonistas & inhibidores , Neurogénesis , Ribonucleasa Pancreática/químicaRESUMEN
As the stimulus-responsive mediator of actin dynamics, actin-depolymerizing factor (ADF)/cofilin is subject to tight regulation. It is well known that kinase-mediated phosphorylation inactivates ADF/cofilin. Here, however, we found that the activity of Arabidopsis ADF7 is enhanced by CDPK16-mediated phosphorylation. We found that CDPK16 interacts with ADF7 both in vitro and in vivo, and it enhances ADF7-mediated actin depolymerization and severing in vitro in a calcium-dependent manner. Accordingly, the rate of actin turnover is reduced in cdpk16 pollen and the amount of actin filaments increases significantly at the tip of cdpk16 pollen tubes. CDPK16 phosphorylates ADF7 at Serine128 both in vitro and in vivo, and the phospho-mimetic mutant ADF7S128D has enhanced actin-depolymerizing activity compared to ADF7. Strikingly, we found that failure in the phosphorylation of ADF7 at Ser128 impairs its function in promoting actin turnover in vivo, which suggests that this phospho-regulation mechanism is biologically significant. Thus, we reveal that CDPK16-mediated phosphorylation up-regulates ADF7 to promote actin turnover in pollen.
Asunto(s)
Actinas , Arabidopsis , Citoesqueleto de Actina/metabolismo , Factores Despolimerizantes de la Actina/metabolismo , Actinas/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Destrina/metabolismo , Fosforilación , Tubo Polínico/metabolismoRESUMEN
The bilateral-to-radial symmetry transition occurring during the development of the Arabidopsis thaliana female reproductive organ (gynoecium) is a crucial biological process linked to plant fertilization and seed production. Despite its significance, the cellular mechanisms governing the establishment and breaking of radial symmetry at the gynoecium apex (style) remain unknown. To fill this gap, we employed quantitative confocal imaging coupled with MorphoGraphX analysis, in vivo and in vitro transcriptional experiments, and genetic analysis encompassing mutants in two bHLH transcription factors necessary and sufficient to promote transition to radial symmetry, SPATULA (SPT) and INDEHISCENT (IND). Here, we show that defects in style morphogenesis correlate with defects in cell-division orientation and rate. We showed that the SPT-mediated accumulation of auxin in the medial-apical cells undergoing symmetry transition is required to maintain cell-division-oriented perpendicular to the direction of organ growth (anticlinal, transversal cell division). In addition, SPT and IND promote the expression of specific core cell-cycle regulators, CYCLIN-D1;1 (CYC-D1;1) and CYC-D3;3, to support progression through the G1 phase of the cell cycle. This transcriptional regulation is repressed by auxin, thus forming an incoherent feed-forward loop mechanism. We propose that this mechanism fine-tunes cell division rate and orientation with the morphogenic signal provided by auxin, during patterning of radial symmetry at the style.
RESUMEN
The formation of the branched actin networks is essential for cell polarity, but it remains unclear how the debranching activity of actin filaments contributes to this process. Here, we showed that an evolutionarily conserved coronin family protein, the Caenorhabditis elegans POD-1, debranched the Arp2/3-nucleated actin filaments in vitro. By fluorescence live imaging analysis of the endogenous POD-1 protein, we found that POD-1 colocalized with Arp2/3 at the leading edge of the migrating C. elegans neuroblasts. Conditional mutations of POD-1 in neuroblasts caused aberrant actin assembly, disrupted cell polarity, and impaired cell migration. In C. elegans one-cell-stage embryos, POD-1 and Arp2/3, moved together during cell polarity establishment, and inhibition of POD-1 blocked Arp2/3 motility and affected the polarized cortical flow, leading to symmetric segregation of cell fate determinants. Together, these results indicate that F-actin debranching organizes actin network and cell polarity in migrating neuroblasts and asymmetrically dividing embryos.
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Citoesqueleto de Actina/metabolismo , Proteínas de Caenorhabditis elegans/metabolismo , Polaridad Celular/fisiología , Proteínas de Microfilamentos/metabolismo , Citoesqueleto de Actina/fisiología , Complejo 2-3 Proteico Relacionado con la Actina/metabolismo , Actinas/metabolismo , Animales , División Celular Asimétrica/fisiología , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/fisiología , Movimiento Celular/fisiología , Proteínas de Microfilamentos/fisiología , Células-Madre Neurales/metabolismoRESUMEN
ADF/cofilin is a central regulator of actin dynamics. We previously demonstrated that two closely related Arabidopsis class IIa ADF isovariants, ADF7 and ADF10, are involved in the enhancement of actin turnover in pollen, but whether they have distinct functions remains unknown. Here, we further demonstrate that they exhibit distinct functions in regulating actin turnover both in vitro and in vivo. We found that ADF7 binds to ADP-G-actin with lower affinity, and severs and depolymerizes actin filaments less efficiently in vitro than ADF10. Accordingly, in pollen grains, ADF7 more extensively decorates actin filaments and is less freely distributed in the cytoplasm compared to ADF10. We further demonstrate that ADF7 and ADF10 show distinct intracellular localizations during pollen germination, and they have non-equivalent functions in promoting actin turnover in pollen. We thus propose that cooperation and labor division of ADF7 and ADF10 enable pollen cells to achieve exquisite control of the turnover of different actin structures to meet different cellular needs.
Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Citoesqueleto de Actina/metabolismo , Actinas/metabolismo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Polen/metabolismo , Tubo Polínico/metabolismoRESUMEN
In this report, red-emissive carbon dots (C-dots) were facilely prepared from o-phenylenediamine via microwave-assisted hydrothermal treatment. The C-dots demonstrated excitation wavelength-independent emission with maximums at 621 nm that could be effectively quenched by Ag+ via static quenching. This phenomenon was exploited to establish a sensitive fluorescence assay with a low detection limit (0.37 µM) and wide linear range (0-50 µM). In addition, this assay demonstrated excellent selectivity toward Ag+, free from the interference of 16 commonly seen metal ions. Most importantly, the assay demonstrated high reliability toward samples in deionized water, mineral water, lake water, and serum, which could indicate potential applications for Ag+ monitoring in complicated natural and biological environments.
Asunto(s)
Colorantes Fluorescentes , Puntos Cuánticos , Carbono , Agua , Reproducibilidad de los Resultados , Espectrometría de FluorescenciaRESUMEN
BACKGROUND: Angiogenin is a multifunctional secreted ribonuclease that is upregulated in human cancers and downregulated or mutationally inactivated in neurodegenerative diseases. A role for angiogenin in glioblastoma was inferred from the inverse correlation of angiogenin expression with patient survival but had not been experimentally investigated. METHODS: Angiogenin knockout mice were generated and the effect of angiogenin deficiency on glioblastoma progression was examined. Angiogenin and plexin-B2 genes were knocked down in glioblastoma cells and the changes in cell proliferation, invasion and vascular association were examined. Monoclonal antibodies of angiogenin and small molecules were used to assess the therapeutic activity of the angiogenin-plexin-B2 pathway in both genetic and xenograft animal models. RESULTS: Deletion of Ang1 gene prolonged survival of PDGF-induced glioblastoma in mice in the Ink4a/Arf-/-:Pten-/- background, accompanied by decreased invasion, vascular association and proliferation. Angiogenin upregulated MMP9 and CD24 leading to enhanced invasion and vascular association. Inhibition of angiogenin or plexin-B2, either by shRNA, monoclonal antibody or small molecule inhibitor, decreases sphere formation of patient-derived glioma stem cells, reduces glioblastoma proliferation and invasion and inhibits glioblastoma growth in both genetic and xenograft animal models. CONCLUSIONS: Angiogenin and its receptor, plexin-B2, are a pair of novel regulators that mediate invasion, vascular association and proliferation of glioblastoma cells. Inhibitors of the angiogenin-plexin-B2 axis have therapeutic potential against glioblastoma.
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Glioblastoma , Proteínas del Tejido Nervioso , Ribonucleasa Pancreática , Animales , Línea Celular Tumoral , Proliferación Celular , Glioblastoma/tratamiento farmacológico , Humanos , Ratones , Proteínas del Tejido Nervioso/genética , Proteínas del Tejido Nervioso/metabolismoRESUMEN
Whole-exome and whole-genome sequencing studies in autism spectrum disorder (ASD) have identified hundreds of thousands of exonic variants. Only a handful of them, primarily loss-of-function variants, have been shown to increase the risk for ASD, while the contributory roles of other variants, including most missense variants, remain unknown. New approaches that combine tissue-specific molecular profiles with patients' genetic data can thus play an important role in elucidating the functional impact of exonic variation and improve understanding of ASD pathogenesis. Here, we integrate spatio-temporal gene co-expression networks from the developing human brain and protein-protein interaction networks to first reach accurate prioritization of ASD risk genes based on their connectivity patterns with previously known high-confidence ASD risk genes. We subsequently integrate these gene scores with variant pathogenicity predictions to further prioritize individual exonic variants based on the positive-unlabeled learning framework with gene- and variant-score calibration. We demonstrate that this approach discriminates among variants between cases and controls at the high end of the prediction range. Finally, we experimentally validate our top-scoring de novo mutation NP_001243143.1:p.Phe309Ser in the sodium/potassium-transporting ATPase ATP1A3 to disrupt protein binding with different partners.
Asunto(s)
Trastorno del Espectro Autista , Trastorno Autístico , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Trastorno del Espectro Autista/genética , Trastorno Autístico/genética , Predisposición Genética a la Enfermedad , Humanos , Mutación , Potasio/metabolismo , Sodio/metabolismo , ATPasa Intercambiadora de Sodio-Potasio/genéticaRESUMEN
Srv2p/CAP1 is an essential regulator of actin turnover, but its exact function in regulating actin polymerization, particularly the contribution of its actin nucleotide exchange activity, remains incompletely understood. We found that, although Arabidopsis CAP1 is distributed uniformly in the cytoplasm, its loss of function has differential effects on the actin cytoskeleton within different regions of the pollen tube. Specifically, the F-actin level increases in the shank but decreases in the apical region of cap1 pollen tubes. The reduction in apical F-actin results mainly from impaired polymerization of membrane-originated actin within cap1 pollen tubes. The actin nucleotide exchange activity of CAP1 is involved in apical actin polymerization. CAP1 acts synergistically with pollen ADF and profilin to promote actin turnover in vitro, and it can overcome the inhibitory effects of ADF and synergize with profilin to promote actin nucleotide exchange. Consistent with its role as a shuttle molecule between ADF and profilin, the cytosolic concentration of CAP1 is much lower than that of ADF and profilin in pollen. Thus, CAP1 synergizes with ADF and profilin to drive actin turnover in pollen and promote apical actin polymerization in pollen tubes in a manner that involves its actin nucleotide exchange activity.
Asunto(s)
Actinas/metabolismo , Proteínas de Arabidopsis/metabolismo , Oligopéptidos/metabolismo , Tubo Polínico/metabolismo , Citoesqueleto de Actina/metabolismo , Arabidopsis/metabolismo , Regulación de la Expresión Génica de las Plantas/fisiología , Proteínas de Microfilamentos/metabolismo , Polen/metabolismo , Polimerizacion , Profilinas/metabolismoRESUMEN
Stomatal movement is essential for plant growth. This process is precisely regulated by various cellular activities in guard cells. F-actin dynamics and vacuole morphology are both involved in stomatal movement. The sorting of cargoes by clathrin adaptor protein (AP) complexes from the Golgi to the vacuole is critical for establishing a normal vacuole morphology. In this study, we demonstrate that the medium subunit of the AP3 complex (AP3M) binds to and severs actin filaments in vitro and that it participates in the sorting of cargoes (such as the sucrose exporter SUC4) to the tonoplast, and thereby regulates stomatal closure in Arabidopsis thaliana Defects in AP3 or SUC4 led to more rapid water loss and delayed stomatal closure, as well as hypersensitivity to drought stress. In ap3m mutants, the F-actin status was altered compared to the wild type, and the sorted cargoes failed to localize to the tonoplast. AP3M contains a previously unidentified F-actin binding domain that is conserved in AP3M homologs in both plants and animals. Mutations in the F-actin binding domain of AP3M abolished its F-actin binding activity in vitro, leading to an aberrant vacuole morphology and reduced levels of SUC4 on the tonoplast in guard cells. Our findings indicate that the F-actin binding activity of AP3M is required for the precise localization of AP3-dependent cargoes to the tonoplast and for the regulation of vacuole morphology in guard cells during stomatal closure.
Asunto(s)
Citoesqueleto de Actina/metabolismo , Complejo 3 de Proteína Adaptadora/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Estomas de Plantas/metabolismo , Vacuolas/metabolismo , Citoesqueleto de Actina/genética , Complejo 3 de Proteína Adaptadora/genética , Arabidopsis/citología , Proteínas de Arabidopsis/genética , Estomas de Plantas/citología , Estomas de Plantas/genética , Vacuolas/genéticaRESUMEN
In this study, C-dots were facilely synthesized via microwave irradiation using citric acid and ethylenediamine as carbon precursors. The fluorescence emissions of the C-dots could be selectively quenched by Fe3+, and the degree of quenching was linearly related to the concentrations of Fe3+ presented. This phenomenon was utilized to develop a sensitive fluorescence assay for Fe3+ detection with broad linear range (0-250, 250-1200 µmol/L) and low detection limit (1.68 µmol/L). Most importantly, the assay demonstrated high reliability towards samples in deionized water, tap water and lake water, which should find potential applications for Fe3+ monitoring in complicated environments.
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Carbono , Puntos Cuánticos , Ácido Cítrico , Etilenodiaminas , Colorantes Fluorescentes , Lagos , Límite de Detección , Reproducibilidad de los Resultados , Espectrometría de Fluorescencia , AguaRESUMEN
The Critical Assessment of Genome Interpretation-5 intellectual disability challenge asked to use computational methods to predict patient clinical phenotypes and the causal variant(s) based on an analysis of their gene panel sequence data. Sequence data for 74 genes associated with intellectual disability (ID) and/or autism spectrum disorders (ASD) from a cohort of 150 patients with a range of neurodevelopmental manifestations (i.e. ID, autism, epilepsy, microcephaly, macrocephaly, hypotonia, ataxia) have been made available for this challenge. For each patient, predictors had to report the causative variants and which of the seven phenotypes were present. Since neurodevelopmental disorders are characterized by strong comorbidity, tested individuals often present more than one pathological condition. Considering the overall clinical manifestation of each patient, the correct phenotype has been predicted by at least one group for 93 individuals (62%). ID and ASD were the best predicted among the seven phenotypic traits. Also, causative or potentially pathogenic variants were predicted correctly by at least one group. However, the prediction of the correct causative variant seems to be insufficient to predict the correct phenotype. In some cases, the correct prediction has been supported by rare or common variants in genes different from the causative one.
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Trastorno del Espectro Autista/genética , Biología Computacional/métodos , Discapacidad Intelectual/genética , Análisis de Secuencia de ADN/métodos , Femenino , Predisposición Genética a la Enfermedad , Humanos , Masculino , Fenotipo , Sitios de Carácter CuantitativoRESUMEN
Genetics play a key role in venous thromboembolism (VTE) risk, however established risk factors in European populations do not translate to individuals of African descent because of the differences in allele frequencies between populations. As part of the fifth iteration of the Critical Assessment of Genome Interpretation, participants were asked to predict VTE status in exome data from African American subjects. Participants were provided with 103 unlabeled exomes from patients treated with warfarin for non-VTE causes or VTE and asked to predict which disease each subject had been treated for. Given the lack of training data, many participants opted to use unsupervised machine learning methods, clustering the exomes by variation in genes known to be associated with VTE. The best performing method using only VTE related genes achieved an area under the ROC curve of 0.65. Here, we discuss the range of methods used in the prediction of VTE from sequence data and explore some of the difficulties of conducting a challenge with known confounders. In addition, we show that an existing genetic risk score for VTE that was developed in European subjects works well in African Americans.
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Secuenciación del Exoma/métodos , Tromboembolia Venosa/genética , Warfarina/administración & dosificación , Análisis por Conglomerados , Biología Computacional/métodos , Congresos como Asunto , Femenino , Predisposición Genética a la Enfermedad , Humanos , Masculino , Curva ROC , Aprendizaje Automático no Supervisado , Tromboembolia Venosa/tratamiento farmacológico , Warfarina/uso terapéuticoRESUMEN
Whole-genome sequencing (WGS) holds great potential as a diagnostic test. However, the majority of patients currently undergoing WGS lack a molecular diagnosis, largely due to the vast number of undiscovered disease genes and our inability to assess the pathogenicity of most genomic variants. The CAGI SickKids challenges attempted to address this knowledge gap by assessing state-of-the-art methods for clinical phenotype prediction from genomes. CAGI4 and CAGI5 participants were provided with WGS data and clinical descriptions of 25 and 24 undiagnosed patients from the SickKids Genome Clinic Project, respectively. Predictors were asked to identify primary and secondary causal variants. In addition, for CAGI5, groups had to match each genome to one of three disorder categories (neurologic, ophthalmologic, and connective), and separately to each patient. The performance of matching genomes to categories was no better than random but two groups performed significantly better than chance in matching genomes to patients. Two of the ten variants proposed by two groups in CAGI4 were deemed to be diagnostic, and several proposed pathogenic variants in CAGI5 are good candidates for phenotype expansion. We discuss implications for improving in silico assessment of genomic variants and identifying new disease genes.
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Biología Computacional/métodos , Variación Genética , Enfermedades no Diagnosticadas/diagnóstico , Adolescente , Niño , Preescolar , Simulación por Computador , Bases de Datos Genéticas , Femenino , Predisposición Genética a la Enfermedad , Humanos , Masculino , Fenotipo , Enfermedades no Diagnosticadas/genética , Secuenciación Completa del GenomaRESUMEN
Here, we show that Arabidopsis ADF10 plays an important role in shaping the overall organization of apical actin filaments by promoting their turnover and ordering. ADF10 severs and depolymerizes actin filaments in vitro and is distributed throughout the entire pollen tube. In adf10 mutants, severing and monomer dissociation events for apical actin filaments are reduced, and the apical actin structure extends further toward the tube base than in wild-type tubes. In particular, the percentage of apical actin filaments that form large angles to the tube growth axis is much higher in adf10 pollen tubes, and the actin filaments are more randomly distributed, implying that ADF10 promotes their ordering. Consistent with the role of apical actin filaments in physically restricting the movement of vesicles, the region in which apical vesicles accumulate is enlarged at the tip of adf10 pollen tubes. Both tipward and backward movements of small vesicles are altered within the growth domain of adf10 pollen tubes. Thus, our study suggests that ADF10 shapes the organization of apical actin filaments to regulate vesicle trafficking and pollen tube growth.
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Citoesqueleto de Actina/metabolismo , Factores Despolimerizantes de la Actina/genética , Proteínas de Arabidopsis/genética , Regulación de la Expresión Génica de las Plantas , Tubo Polínico/metabolismo , Transporte de Proteínas/genética , Actinas/metabolismo , Arabidopsis/metabolismo , Polen/genética , Polen/metabolismoRESUMEN
Motivation: Modern problems of concept annotation associate an object of interest (gene, individual, text document) with a set of interrelated textual descriptors (functions, diseases, topics), often organized in concept hierarchies or ontologies. Most ontology can be seen as directed acyclic graphs (DAGs), where nodes represent concepts and edges represent relational ties between these concepts. Given an ontology graph, each object can only be annotated by a consistent sub-graph; that is, a sub-graph such that if an object is annotated by a particular concept, it must also be annotated by all other concepts that generalize it. Ontologies therefore provide a compact representation of a large space of possible consistent sub-graphs; however, until now we have not been aware of a practical algorithm that can enumerate such annotation spaces for a given ontology. Results: We propose an algorithm for enumerating consistent sub-graphs of DAGs. The algorithm recursively partitions the graph into strictly smaller graphs until the resulting graph becomes a rooted tree (forest), for which a linear-time solution is computed. It then combines the tallies from graphs created in the recursion to obtain the final count. We prove the correctness of this algorithm, propose several practical accelerations, evaluate it on random graphs and then apply it to characterize four major biomedical ontologies. We believe this work provides valuable insights into the complexity of concept annotation spaces and its potential influence on the predictability of ontological annotation. Availability and implementation: https://github.com/shawn-peng/counting-consistent-sub-DAG. Supplementary information: Supplementary data are available at Bioinformatics online.
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Algoritmos , Ontologías Biológicas , Curaduría de Datos , Curaduría de Datos/métodosRESUMEN
The opening and closing of stomata are crucial for plant photosynthesis and transpiration. Actin filaments undergo dynamic reorganization during stomatal closure, but the underlying mechanism for this cytoskeletal reorganization remains largely unclear. In this study, we identified and characterized Arabidopsis thaliana casein kinase 1-like protein 2 (CKL2), which responds to abscisic acid (ABA) treatment and participates in ABA- and drought-induced stomatal closure. Although CKL2 does not bind to actin filaments directly and has no effect on actin assembly in vitro, it colocalizes with and stabilizes actin filaments in guard cells. Further investigation revealed that CKL2 physically interacts with and phosphorylates actin depolymerizing factor 4 (ADF4) and inhibits its activity in actin filament disassembly. During ABA-induced stomatal closure, deletion of CKL2 in Arabidopsis alters actin reorganization in stomata and renders stomatal closure less sensitive to ABA, whereas deletion of ADF4 impairs the disassembly of actin filaments and causes stomatal closure to be more sensitive to ABA Deletion of ADF4 in the ckl2 mutant partially recues its ABA-insensitive stomatal closure phenotype. Moreover, Arabidopsis ADFs from subclass I are targets of CKL2 in vitro. Thus, our results suggest that CKL2 regulates actin filament reorganization and stomatal closure mainly through phosphorylation of ADF.
Asunto(s)
Citoesqueleto de Actina/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Estomas de Plantas/metabolismo , Ácido Abscísico/farmacología , Citoesqueleto de Actina/efectos de los fármacos , Factores Despolimerizantes de la Actina/genética , Factores Despolimerizantes de la Actina/metabolismo , Arabidopsis/efectos de los fármacos , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Sequías , Fosforilación/efectos de los fármacos , Fosforilación/genética , Estomas de Plantas/efectos de los fármacos , Transducción de Señal/efectos de los fármacos , Transducción de Señal/genéticaRESUMEN
Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT-associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus.
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Actinas/química , Núcleo Celular/química , Proteínas Cromosómicas no Histona/química , Proteínas de Unión al ADN/química , Adenosina Trifosfato/química , Ensamble y Desensamble de Cromatina , Cristalización , Células HEK293 , Células HeLa , Humanos , Dominios ProteicosRESUMEN
Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype-phenotype relationships.
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Trastorno Bipolar/genética , Enfermedad de Crohn/genética , Secuenciación del Exoma/métodos , Medicina de Precisión/métodos , Warfarina/uso terapéutico , Biología Computacional/métodos , Bases de Datos Genéticas , Predisposición Genética a la Enfermedad , Humanos , Difusión de la Información , Variantes Farmacogenómicas , Fenotipo , Warfarina/farmacologíaRESUMEN
Actin filaments are often arranged into higher-order structures, such as the longitudinal actin cables that generate the reverse fountain cytoplasmic streaming pattern present in pollen tubes. While several actin binding proteins have been implicated in the generation of these cables, the mechanisms that regulate their dynamic turnover remain largely unknown. Here, we show that Arabidopsis thaliana actin-depolymerizing factor7 (ADF7) is required for turnover of longitudinal actin cables. In vitro biochemical analyses revealed that ADF7 is a typical ADF that prefers ADP-G-actin over ATP-G-actin. ADF7 inhibits nucleotide exchange on actin and severs filaments, but its filament severing and depolymerizing activities are less potent than those of the vegetative ADF1. ADF7 primarily decorates longitudinal actin cables in the shanks of pollen tubes. Consistent with this localization pattern, the severing frequency and depolymerization rate of filaments significantly decreased, while their maximum lifetime significantly increased, in adf7 pollen tube shanks. Furthermore, an ADF7-enhanced green fluorescent protein fusion with defective severing activity but normal G-actin binding activity could not complement adf7, providing compelling evidence that the severing activity of ADF7 is vital for its in vivo functions. These observations suggest that ADF7 evolved to promote turnover of longitudinal actin cables by severing actin filaments in pollen tubes.