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1.
Cell ; 183(2): 474-489.e17, 2020 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-33035451

RESUMEN

Mg2+ is the most abundant divalent cation in metazoans and an essential cofactor for ATP, nucleic acids, and countless metabolic enzymes. To understand how the spatio-temporal dynamics of intracellular Mg2+ (iMg2+) are integrated into cellular signaling, we implemented a comprehensive screen to discover regulators of iMg2+ dynamics. Lactate emerged as an activator of rapid release of Mg2+ from endoplasmic reticulum (ER) stores, which facilitates mitochondrial Mg2+ (mMg2+) uptake in multiple cell types. We demonstrate that this process is remarkably temperature sensitive and mediated through intracellular but not extracellular signals. The ER-mitochondrial Mg2+ dynamics is selectively stimulated by L-lactate. Further, we show that lactate-mediated mMg2+ entry is facilitated by Mrs2, and point mutations in the intermembrane space loop limits mMg2+ uptake. Intriguingly, suppression of mMg2+ surge alleviates inflammation-induced multi-organ failure. Together, these findings reveal that lactate mobilizes iMg2+ and links the mMg2+ transport machinery with major metabolic feedback circuits and mitochondrial bioenergetics.


Asunto(s)
Retículo Endoplásmico/metabolismo , Ácido Láctico/metabolismo , Magnesio/metabolismo , Animales , Células COS , Calcio/metabolismo , Señalización del Calcio/fisiología , Chlorocebus aethiops , Retículo Endoplásmico/fisiología , Femenino , Células HeLa , Células Hep G2 , Humanos , Masculino , Ratones Endogámicos C57BL , Ratones Noqueados , Mitocondrias/metabolismo
2.
Plant Cell ; 35(6): 1936-1955, 2023 05 29.
Artículo en Inglés | MEDLINE | ID: mdl-37070465

RESUMEN

In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and nonsense-mediated mRNA decay (NMD). There is limited information on the functional role of DNE1 in RNA turnover, and the identities of its endogenous targets are unknown. In this study, we utilized RNA degradome approaches to globally investigate DNE1 substrates. Monophosphorylated 5' ends, produced by DNE1, should accumulate in mutants lacking the cytoplasmic exoribonuclease XRN4, but be absent from DNE1 and XRN4 double mutants. In seedlings, we identified over 200 such transcripts, most of which reflect cleavage within coding regions. While most DNE1 targets were NMD-insensitive, some were upstream ORF (uORF)-containing and NMD-sensitive transcripts, indicating that this endoribonuclease is required for turnover of a diverse set of mRNAs. Transgenic plants expressing DNE1 cDNA with an active-site mutation in the endoribonuclease domain abolished the in planta cleavage of transcripts, demonstrating that DNE1 endoribonuclease activity is required for cleavage. Our work provides key insights into the identity of DNE1 substrates and enhances our understanding of DNE1-mediated mRNA decay.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Endorribonucleasas/genética , Endorribonucleasas/metabolismo , Degradación de ARNm Mediada por Codón sin Sentido/genética , ARN Helicasas/genética , Estabilidad del ARN/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo
3.
Plant Physiol ; 194(3): 1481-1497, 2024 Feb 29.
Artículo en Inglés | MEDLINE | ID: mdl-38048422

RESUMEN

Plant extracellular vesicles (EVs) are membrane-bound organelles involved mainly in intercellular communications and defense responses against pathogens. Recent studies have demonstrated the presence of proteins, nucleic acids including small RNAs, and lipids along with other metabolites in plant EVs. Here, we describe the isolation and characterization of EVs from sorghum (Sorghum bicolor). Nanoparticle tracking analysis, dynamic light scattering, and cryo-electron tomography showed the presence of a heterogeneous population of EVs isolated from the apoplastic wash of sorghum leaves. Cryo-electron microscopy revealed that EVs had a median size of 110 nm and distinct populations of vesicles with single or multiple lipid bilayers and low or high amounts of contents. The heterogeneity was further supported by data showing that only a subset of EVs that were stained with a membrane dye, Potomac Gold, were also stained with the membrane-permeant esterase-dependent dye, calcein acetoxymethyl ester. Proteomic analysis identified 437 proteins that were enriched in multiple EV isolations, with the majority of these also found in the EV proteome of Arabidopsis (Arabidopsis thaliana). These data suggest a partial conservation of EV contents and function between the monocot, sorghum, and a distantly related eudicot, Arabidopsis.


Asunto(s)
Arabidopsis , Vesículas Extracelulares , Sorghum , Proteoma , Arabidopsis/genética , Sorghum/genética , Microscopía por Crioelectrón , Proteómica , Grano Comestible
4.
Nature ; 574(7780): 658-662, 2019 10.
Artículo en Inglés | MEDLINE | ID: mdl-31666724

RESUMEN

The engineering of biological molecules is a key concept in the design of highly functional, sophisticated soft materials. Biomolecules exhibit a wide range of functions and structures, including chemical recognition (of enzyme substrates or adhesive ligands1, for instance), exquisite nanostructures (composed of peptides2, proteins3 or nucleic acids4), and unusual mechanical properties (such as silk-like strength3, stiffness5, viscoelasticity6 and resiliency7). Here we combine the computational design of physical (noncovalent) interactions with pathway-dependent, hierarchical 'click' covalent assembly to produce hybrid synthetic peptide-based polymers. The nanometre-scale monomeric units of these polymers are homotetrameric, α-helical bundles of low-molecular-weight peptides. These bundled monomers, or 'bundlemers', can be designed to provide complete control of the stability, size and spatial display of chemical functionalities. The protein-like structure of the bundle allows precise positioning of covalent linkages between the ends of distinct bundlemers, resulting in polymers with interesting and controllable physical characteristics, such as rigid rods, semiflexible or kinked chains, and thermally responsive hydrogel networks. Chain stiffness can be controlled by varying only the linkage. Furthermore, by controlling the amino acid sequence along the bundlemer periphery, we use specific amino acid side chains, including non-natural 'click' chemistry functionalities, to conjugate moieties into a desired pattern, enabling the creation of a wide variety of hybrid nanomaterials.


Asunto(s)
Nanoestructuras/química , Péptidos/química , Polímeros/química , Secuencia de Aminoácidos , Diseño de Fármacos , Proteínas/química
5.
Mol Cell ; 65(6): 1014-1028.e7, 2017 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-28262504

RESUMEN

Ca2+ dynamics and oxidative signaling are fundamental mechanisms for mitochondrial bioenergetics and cell function. The MCU complex is the major pathway by which these signals are integrated in mitochondria. Whether and how these coactive elements interact with MCU have not been established. As an approach toward understanding the regulation of MCU channel by oxidative milieu, we adapted inflammatory and hypoxia models. We identified the conserved cysteine 97 (Cys-97) to be the only reactive thiol in human MCU that undergoes S-glutathionylation. Furthermore, biochemical, structural, and superresolution imaging analysis revealed that MCU oxidation promotes MCU higher order oligomer formation. Both oxidation and mutation of MCU Cys-97 exhibited persistent MCU channel activity with higher [Ca2+]m uptake rate, elevated mROS, and enhanced [Ca2+]m overload-induced cell death. In contrast, these effects were largely independent of MCU interaction with its regulators. These findings reveal a distinct functional role for Cys-97 in ROS sensing and regulation of MCU activity.


Asunto(s)
Canales de Calcio/metabolismo , Señalización del Calcio , Calcio/metabolismo , Células Endoteliales/metabolismo , Activación del Canal Iónico , Mitocondrias/metabolismo , Membranas Mitocondriales/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Animales , Células COS , Canales de Calcio/química , Canales de Calcio/genética , Señalización del Calcio/efectos de los fármacos , Muerte Celular , Hipoxia de la Célula , Chlorocebus aethiops , Cisteína , Células Endoteliales/efectos de los fármacos , Células Endoteliales/patología , Metabolismo Energético , Glutatión/metabolismo , Células HEK293 , Células HeLa , Humanos , Activación del Canal Iónico/efectos de los fármacos , Lipopolisacáridos/farmacología , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Mitocondrias/efectos de los fármacos , Mitocondrias/patología , Membranas Mitocondriales/efectos de los fármacos , Membranas Mitocondriales/patología , Mutación , Oxidación-Reducción , Multimerización de Proteína , Procesamiento Proteico-Postraduccional , Estructura Cuaternaria de Proteína , Relación Estructura-Actividad , Trombina/farmacología , Factores de Tiempo , Transfección
6.
Plant Cell ; 32(6): 1790-1796, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32220850

RESUMEN

The origin and early evolution of sex chromosomes have been hypothesized to involve the linkage of factors with antagonistic effects on male and female function. Garden asparagus (Asparagus officinalis) is an ideal species to investigate this hypothesis, as the X and Y chromosomes are cytologically homomorphic and evolved from an ancestral autosome pair in association with a shift from hermaphroditism to dioecy. Mutagenesis screens paired with single-molecule fluorescence in situ hybridization directly implicate Y-specific genes that respectively suppress female (pistil) development and are necessary for male (anther) development. Comparison of contiguous X and Y chromosome assemblies shows that hemizygosity underlies the loss of recombination between the genes suppressing female organogenesis (SUPPRESSOR OF FEMALE FUNCTION) and promoting male function (TAPETAL DEVELOPMENT AND FUNCTION1 [aspTDF1]). We also experimentally demonstrate the function of aspTDF1. These findings provide direct evidence that sex chromosomes can function through linkage of two sex determination genes.


Asunto(s)
Asparagus/genética , Cromosomas de las Plantas/genética , Proteínas de Plantas/metabolismo , Hemicigoto , Mutagénesis , Proteínas de Plantas/genética
7.
Cell ; 132(3): 449-62, 2008 Feb 08.
Artículo en Inglés | MEDLINE | ID: mdl-18267075

RESUMEN

Plant innate immunity relies on the recognition of pathogen effector molecules by nucleotide-binding-leucine-rich repeat (NB-LRR) immune receptor families. Previously we have shown the N immune receptor, a member of TIR-NB-LRR family, indirectly recognizes the 50 kDa helicase (p50) domain of Tobacco mosaic virus (TMV) through its TIR domain. We have identified an N receptor-interacting protein, NRIP1, that directly interacts with both N's TIR domain and p50. NRIP1 is a functional rhodanese sulfurtransferase and is required for N to provide complete resistance to TMV. Interestingly, NRIP1 that normally localizes to the chloroplasts is recruited to the cytoplasm and nucleus by the p50 effector. As a consequence, NRIP1 interacts with N only in the presence of the p50 effector. Our findings show that a chloroplastic protein is intimately involved in pathogen recognition. We propose that N's activation requires a prerecognition complex containing the p50 effector and NRIP1.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/inmunología , Nicotiana/inmunología , Proteínas Nucleares/inmunología , Enfermedades de las Plantas/inmunología , Proteínas de Plantas/inmunología , Receptores Virales/inmunología , Virus del Mosaico del Tabaco/inmunología , Proteínas Adaptadoras Transductoras de Señales/análisis , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Antígenos Virales/inmunología , Núcleo Celular/química , Cloroplastos/química , Citoplasma/química , Inmunidad Innata , Proteínas Nucleares/análisis , Proteínas Nucleares/metabolismo , Proteína de Interacción con Receptores Nucleares 1 , Proteínas de Plantas/análisis , Proteínas de Plantas/metabolismo , Estructura Terciaria de Proteína , Receptores Virales/análisis , Receptores Virales/metabolismo , Tiosulfato Azufretransferasa/metabolismo , Nicotiana/virología , Técnicas del Sistema de Dos Híbridos
8.
J Am Chem Soc ; 144(4): 1647-1662, 2022 02 02.
Artículo en Inglés | MEDLINE | ID: mdl-35072462

RESUMEN

Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as "CABL". Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dienophile. 6-(2-Pyridyl)dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation produce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 of 106 M-1 s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin, or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore were demonstrated. CABL is light-dose dependent, and two-photon excitation promotes CABL at the suborganelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous protein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small molecule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of "ordinary" tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.


Asunto(s)
Colorantes Fluorescentes/química , Luz , Catálisis , Reacción de Cicloadición , Ciclooctanos/química , Escherichia coli/metabolismo , Colorantes Fluorescentes/síntesis química , Células HeLa , Compuestos Heterocíclicos con 1 Anillo/síntesis química , Compuestos Heterocíclicos con 1 Anillo/química , Humanos , Cinética , Proteínas Luminiscentes/química , Microscopía Fluorescente , Oxidación-Reducción
9.
Nucleic Acids Res ; 48(16): e96, 2020 09 18.
Artículo en Inglés | MEDLINE | ID: mdl-32716042

RESUMEN

Small RNAs are non-coding RNAs that play important roles in the lives of both animals and plants. They are 21- to 24-nt in length and ∼10 nm in size. Their small size and high diversity have made it challenging to develop detection methods that have sufficient resolution and specificity to multiplex and quantify. We created a method, sRNA-PAINT, for the detection of small RNAs with 20 nm resolution by combining the super-resolution method, DNA-based points accumulation in nanoscale topography (DNA-PAINT), and the specificity of locked nucleic acid (LNA) probes for the in situ detection of multiple small RNAs. The method relies on designing probes to target small RNAs that combine DNA oligonucleotides (oligos) for PAINT with LNA-containing oligos for hybridization; therefore, we developed an online tool called 'Vetting & Analysis of RNA for in situ Hybridization probes' (VARNISH) for probe design. Our method utilizes advances in DNA-PAINT methodologies, including qPAINT for quantification, and Exchange-PAINT for multiplexing. We demonstrated these capabilities of sRNA-PAINT by detecting and quantifying small RNAs in different cell layers of early developmental stage maize anthers that are important for male sexual reproduction.


Asunto(s)
Flores/genética , Hibridación Fluorescente in Situ/métodos , Microscopía Fluorescente/métodos , ARN de Planta/genética , ARN Pequeño no Traducido/genética , Zea mays/genética , Oligonucleótidos/genética
10.
Mol Plant Microbe Interact ; 34(10): 1209-1211, 2021 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-34662144

RESUMEN

Colletotrichum species are globally distributed and well known as members of a destructive phytopathogenic genus, causing the anthracnose disease in a wide variety of crops and fruits. Colletotrichum sublineola is the causal agent of the anthracnose disease in sorghum, causing losses of up to 50% in yield. Here, we used PacBio sequencing combined with RNA-seq to generate a chromosome-level assembly and annotation of the Colletotrichum sublineola strain CsGL1.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.


Asunto(s)
Colletotrichum , Sorghum , Colletotrichum/genética , Enfermedades de las Plantas , Sorghum/genética , Transcriptoma/genética
11.
Exp Eye Res ; 203: 108371, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33248069

RESUMEN

Congenital aniridia is caused by heterozygous mutations in the PAX6 gene. In this disease, congenital iris and foveal hypoplasia is associated with juvenile onset cataract, glaucoma, and corneal keratopathy. In rodents, Pax6 mutations result in a congenital reduction in ocular size that is not typically described in human aniridia. Here, the ocular morphometry of aniridia patients is compared with the lens phenotype of Pax6+/tm1/Pgr mice to reveal whether there are species differences in Pax6 regulation of lens development and homeostasis. Ultrasound biometry (UBM) revealed that eleven percent of aniridia patients exhibited mild microphthalmia while the anterior chamber depth of aniridic eyes was significantly reduced from 6 months of age onward. Although aniridic lens thickness was normal from birth, it was significantly decreased in aniridic lenses older than 30. Notably, 86% of aniridic lenses exhibited cataractous changes in this cohort. In addition, a significant proportion of aniridia patients develop lens subluxation as they age associated with reduced lens diameter as measured by anterior segment optical coherence tomography (AS-OCT). Analysis of young adult Pax6+/tm1/Pgr mouse lenses by micro-computed tomography (microCT), bright field and dark field imaging revealed that they are reduced in size but did not exhibit overt cataracts at this age. Overall, this study reveals that congenital microphthalmia as assessed by axial length, or microphakia, as assessed by lens thickness, are not typical in human aniridia, although these are primary manifestations of Pax6 mutations in mice, suggesting that PAX6 regulates some aspects of lens development differently between these species.


Asunto(s)
Aniridia/patología , Catarata/patología , Cristalino/patología , Microftalmía/patología , Adolescente , Adulto , Anciano , Animales , Aniridia/genética , Cámara Anterior/patología , Longitud Axial del Ojo/patología , Catarata/genética , Niño , Preescolar , Modelos Animales de Enfermedad , Femenino , Humanos , Lactante , Masculino , Ratones , Ratones Mutantes , Microftalmía/genética , Microscopía Acústica , Persona de Mediana Edad , Factor de Transcripción PAX6/genética , Fenotipo , Microscopía con Lámpara de Hendidura , Tomografía de Coherencia Óptica , Adulto Joven
12.
J Biol Chem ; 294(16): 6405-6415, 2019 04 19.
Artículo en Inglés | MEDLINE | ID: mdl-30733336

RESUMEN

Upon phagocytosis into macrophages, the intracellular bacterial pathogen Legionella pneumophila secretes effector proteins that manipulate host cell components, enabling it to evade lysosomal degradation. However, the bacterial proteins involved in this evasion are incompletely characterized. Here we show that the L. pneumophila effector protein RavD targets host membrane compartments and contributes to the molecular mechanism the pathogen uses to prevent encounters with lysosomes. Protein-lipid binding assays revealed that RavD selectively binds phosphatidylinositol-3-phosphate (PI(3)P) in vitro We further determined that a C-terminal RavD region mediates the interaction with PI(3)P and that this interaction requires Arg-292. In transiently transfected mammalian cells, mCherry-RavD colocalized with the early endosome marker EGFP-Rab5 as well as the PI(3)P biosensor EGFP-2×FYVE. However, treatment with the phosphoinositide 3-kinase inhibitor wortmannin did not disrupt localization of mCherry-RavD to endosomal compartments, suggesting that RavD's interaction with PI(3)P is not necessary to anchor RavD to endosomal membranes. Using superresolution and immunogold transmission EM, we observed that, upon translocation into macrophages, RavD was retained onto the Legionella-containing vacuole and was also present on small vesicles adjacent to the vacuole. We also report that despite no detectable effects on intracellular growth of L. pneumophila within macrophages or amebae, the lack of RavD significantly increased the number of vacuoles that accumulate the late endosome/lysosome marker LAMP-1 during macrophage infection. Together, our findings suggest that, although not required for intracellular replication of L. pneumophila, RavD is a part of the molecular mechanism that steers the Legionella-containing vacuole away from endolysosomal maturation pathways.


Asunto(s)
Proteínas Bacterianas/metabolismo , Endosomas/metabolismo , Legionella pneumophila/metabolismo , Enfermedad de los Legionarios/metabolismo , Lisosomas/metabolismo , Macrófagos/metabolismo , Vacuolas/metabolismo , Proteínas Bacterianas/genética , Endosomas/genética , Endosomas/ultraestructura , Células HEK293 , Células HeLa , Humanos , Legionella pneumophila/genética , Legionella pneumophila/patogenicidad , Enfermedad de los Legionarios/genética , Enfermedad de los Legionarios/patología , Proteínas de Membrana de los Lisosomas/genética , Proteínas de Membrana de los Lisosomas/metabolismo , Lisosomas/genética , Lisosomas/ultraestructura , Macrófagos/microbiología , Macrófagos/ultraestructura , Fosfatidilinositol 3-Quinasas/genética , Fosfatidilinositol 3-Quinasas/metabolismo , Fosfatos de Fosfatidilinositol/antagonistas & inhibidores , Fosfatos de Fosfatidilinositol/genética , Fosfatos de Fosfatidilinositol/metabolismo , Células U937 , Vacuolas/genética , Vacuolas/microbiología , Vacuolas/ultraestructura , Wortmanina/farmacología , Proteínas de Unión al GTP rab5/genética , Proteínas de Unión al GTP rab5/metabolismo
13.
Plant J ; 98(2): 359-369, 2019 04.
Artículo en Inglés | MEDLINE | ID: mdl-30577085

RESUMEN

Localization of mRNA and small RNAs (sRNAs) is important for understanding their function. Fluorescent in situ hybridization (FISH) has been used extensively in animal systems to study the localization and expression of sRNAs. However, current methods for fluorescent in situ detection of sRNA in plant tissues are less developed. Here we report a protocol (sRNA-FISH) for efficient fluorescent detection of sRNAs in plants. This protocol is suitable for application in diverse plant species and tissue types. The use of locked nucleic acid probes and antibodies conjugated with different fluorophores allows the detection of two sRNAs in the same sample. Using this method, we have successfully detected the co-localization of miR2275 and a 24-nucleotide phased small interfering RNA in maize anther tapetal and archesporial cells. We describe how to overcome the common problem of the wide range of autofluorescence in embedded plant tissue using linear spectral unmixing on a laser scanning confocal microscope. For highly autofluorescent samples, we show that multi-photon fluorescence excitation microscopy can be used to separate the target sRNA-FISH signal from background autofluorescence. In contrast to colorimetric in situ hybridization, sRNA-FISH signals can be imaged using super-resolution microscopy to examine the subcellular localization of sRNAs. We detected maize miR2275 by super-resolution structured illumination microscopy and direct stochastic optical reconstruction microscopy. In this study, we describe how we overcame the challenges of adapting FISH for imaging in plant tissue and provide a step-by-step sRNA-FISH protocol for studying sRNAs at the cellular and even subcellular level.


Asunto(s)
Hibridación Fluorescente in Situ/métodos , ARN Interferente Pequeño/aislamiento & purificación , Zea mays/genética , Técnica del Anticuerpo Fluorescente , Litchi/genética , MicroARNs , Sondas de Oligonucleótidos , Oryza/genética , ARN Mensajero , ARN Interferente Pequeño/genética , ARN Pequeño no Traducido/genética , Coloración y Etiquetado/métodos
14.
PLoS Biol ; 14(1): e1002374, 2016 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-26807877

RESUMEN

[This corrects the article DOI: 10.1371/journal.pbio.0050068.].

15.
Nucleic Acids Res ; 45(14): e130, 2017 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-28586459

RESUMEN

Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play a variety of important regulatory roles in many eukaryotes. Their small size has made it challenging to study them directly in live cells. Here we describe an RNA-based fluorescent sensor for small RNA detection both in vitro and in vivo, adaptable for any small RNA. It utilizes an sxRNA switch for detection of miRNA-mRNA interactions combined with a fluorophore-binding sequence 'Spinach', a GFP-like RNA aptamer for which the RNA-fluorophore complex exhibits strong and consistent fluorescence under an excitation wavelength. Two example sensors, FASTmiR171 and FASTmiR122, can rapidly detect and quantify the levels of miR171 and miR122 in vitro. The sensors can determine relative levels of miRNAs in total RNA extracts with sensitivity similar to small RNA sequencing and northern blots. FASTmiR sensors were also used to estimate the copy number range of miRNAs in total RNA extracts. To localize and analyze the spatial distribution of small RNAs in live, single cells, tandem copies of FASTmiR122 were expressed in different cell lines. FASTmiR122 was able to quantitatively detect the differences in miR122 levels in Huh7 and HEK293T cells demonstrating its potential for tracking miRNA expression and localization in vivo.


Asunto(s)
Técnicas Biosensibles/métodos , MicroARNs/genética , ARN de Planta/genética , Spinacia oleracea/genética , Secuencia de Bases , Northern Blotting , Línea Celular Tumoral , Núcleo Celular/metabolismo , Citoplasma/metabolismo , Colorantes Fluorescentes/química , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Células HEK293 , Humanos , Hibridación Fluorescente in Situ , MicroARNs/metabolismo , Microscopía Fluorescente , ARN de Planta/metabolismo , Reproducibilidad de los Resultados , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Spinacia oleracea/citología , Spinacia oleracea/metabolismo
16.
Biochemistry ; 57(7): 1178-1189, 2018 02 20.
Artículo en Inglés | MEDLINE | ID: mdl-29341594

RESUMEN

The development of genetically encoded fluorescent probes for analyte-specific imaging has revolutionized our understanding of intracellular processes. Current classes of intracellular probes depend on the selection of binding domains that either undergo conformational changes on analyte binding or can be linked to thiol redox chemistry. Here we have designed novel probes by fusing a flavoenzyme, whose fluorescence is quenched on reduction by the analyte of interest, with a GFP domain to allow for rapid and specific ratiometric sensing. Two flavoproteins, Escherichia coli thioredoxin reductase and Saccharomyces cerevisiae lipoamide dehydrogenase, were successfully developed into thioredoxin and NAD+/NADH specific probes, respectively, and their performance was evaluated in vitro and in vivo. A flow cell format, which allowed dynamic measurements, was utilized in both bacterial and mammalian systems. In E. coli the first reported intracellular steady-state of the cytoplasmic thioredoxin pool was measured. In HEK293T mammalian cells, the steady-state cytosolic ratio of NAD+/NADH induced by glucose was determined. These genetically encoded fluorescent constructs represent a modular approach to intracellular probe design that should extend the range of metabolites that can be quantitated in live cells.


Asunto(s)
Escherichia coli/enzimología , Flavoproteínas/metabolismo , Sustancias Luminiscentes/metabolismo , Imagen Óptica/métodos , Saccharomyces cerevisiae/enzimología , Dihidrolipoamida Deshidrogenasa/análisis , Dihidrolipoamida Deshidrogenasa/metabolismo , Proteínas Fluorescentes Verdes/metabolismo , Células HEK293 , Humanos , Modelos Moleculares , NADP/análisis , NADP/metabolismo , Oxidación-Reducción , Proteínas Recombinantes de Fusión/metabolismo , Reductasa de Tiorredoxina-Disulfuro/análisis , Reductasa de Tiorredoxina-Disulfuro/metabolismo , Tiorredoxinas/análisis , Tiorredoxinas/metabolismo
17.
BMC Microbiol ; 18(1): 5, 2018 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-29433439

RESUMEN

BACKGROUND: The intracellular bacterial pathogen Legionella pneumophila proliferates in human alveolar macrophages, resulting in a severe pneumonia termed Legionnaires' disease. Throughout the course of infection, L. pneumophila remains enclosed in a specialized membrane compartment that evades fusion with lysosomes. The pathogen delivers over 300 effector proteins into the host cell, altering host pathways in a manner that sets the stage for efficient pathogen replication. The L. pneumophila effector protein AnkX targets host Rab GTPases and functions in preventing fusion of the Legionella-containing vacuole with lysosomes. However, the current understanding of AnkX's interaction with host proteins and the means through which it exerts its cellular function is limited. RESULTS: Here, we investigated the protein interaction network of AnkX by using the nucleic acid programmable protein array (NAPPA), a high-density platform comprising 10,000 unique human ORFs. This approach facilitated the discovery of PLEKHN1 as a novel interaction partner of AnkX. We confirmed this interaction through multiple independent in vitro pull-down, co-immunoprecipitation, and cell-based assays. Structured illumination microscopy revealed that endogenous PLEKHN1 is found in the nucleus and on vesicular compartments, whereas ectopically produced AnkX co-localized with lipid rafts at the plasma membrane. In mammalian cells, HaloTag-AnkX co-localized with endogenous PLEKHN1 on vesicular compartments. A central fragment of AnkX (amino acids 491-809), containing eight ankyrin repeats, extensively co-localized with endogenous PLEKHN1, indicating that this region may harbor a new function. Further, we found that PLEKHN1 associated with multiple proteins involved in the inflammatory response. CONCLUSIONS: Altogether, our study provides evidence that in addition to Rab GTPases, the L. pneumophila effector AnkX targets nuclear host proteins and suggests that AnkX may have novel functions related to manipulating the inflammatory response.


Asunto(s)
Repetición de Anquirina/fisiología , Proteínas Bacterianas/metabolismo , Interacciones Huésped-Patógeno/fisiología , Legionella pneumophila/metabolismo , Enfermedad de los Legionarios/metabolismo , Proteínas Ligadas a Lípidos/metabolismo , Repetición de Anquirina/genética , Membrana Celular/metabolismo , Endocitosis/fisiología , Células HEK293 , Células HeLa , Humanos , Legionella pneumophila/patogenicidad , Lisosomas/metabolismo , Macrófagos/microbiología , Proteínas Nucleares , Proteínas Recombinantes , Vacuolas/metabolismo , Proteínas de Unión al GTP rab/metabolismo
18.
New Phytol ; 217(3): 1012-1028, 2018 02.
Artículo en Inglés | MEDLINE | ID: mdl-29250789

RESUMEN

Contents Summary 1012 I. Introduction 1012 II. The endomembrane system in plant-microbe interactions 1013 III. The cytoskeleton in plant-microbe interactions 1017 IV. Organelles in plant-microbe interactions 1019 V. Inter-organellar communication in plant-microbe interactions 1022 VI. Conclusions and prospects 1023 Acknowledgements 1024 References 1024 SUMMARY: Plants have evolved a multilayered immune system with well-orchestrated defense strategies against pathogen attack. Multiple immune signaling pathways, coordinated by several subcellular compartments and interactions between these compartments, play important roles in a successful immune response. Pathogens use various strategies to either directly attack the plant's immune system or to indirectly manipulate the physiological status of the plant to inhibit an immune response. Microscopy-based approaches have allowed the direct visualization of membrane trafficking events, cytoskeleton reorganization, subcellular dynamics and inter-organellar communication during the immune response. Here, we discuss the contributions of organelles and the cytoskeleton to the plant's defense response against microbial pathogens, as well as the mechanisms used by pathogens to target these compartments to overcome the plant's defense barrier.


Asunto(s)
Citoesqueleto/metabolismo , Interacciones Huésped-Patógeno , Orgánulos/metabolismo , Pared Celular/metabolismo , Modelos Biológicos , Inmunidad de la Planta
19.
J Biol Chem ; 290(29): 17710-17723, 2015 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-26023236

RESUMEN

Oviductosomes ((OVS), exosomes/microvesicles), which deliver the Ca(2+) efflux pump, plasma membrane Ca(2+)ATPase 4 (PMCA4), to sperm are likely to play an important role in sperm fertilizing ability (Al-Dossary, A. A., Strehler, E. E., and Martin-DeLeon, P. A. (2013) PloS one 8, e80181). It is unknown how exosomes/microvesicles deliver transmembrane proteins such as PMCA4 to sperm. Here we define a novel experimental approach for the assessment of the interaction of OVS with sperm at a nanoscale level, using a lipophilic dye (FM4-64FX) and three-dimensional SR/SIM, which has an 8-fold increase in volumetric resolution, compared with conventional confocal microscopy. Coincubation assays detected fusion of prelabeled OVS with sperm, primarily over the head and midpiece. Immunofluorescence revealed oviductosomal delivery of PMCA4a to WT and Pmca4 KO sperm, and also endogenous PMCA4a on the inner acrosomal membrane. Fusion was confirmed by transmission immunoelectron microscopy, showing immunogold particles in OVS, and fusion stalks on sperm membrane. Immunofluorescence colocalized OVS with the αv integrin subunit which, along with CD9, resides primarily on the sperm head and midpiece. In capacitated and acrosome reacted sperm, fusion was significantly (p < 0.001) inhibited by blocking integrin/ligand interactions via antibodies, exogenous ligands (vitronectin and fibronectin), and their RGD recognition motif. Our results provide evidence that receptor/ligand interactions, involving αvß3 and α5ß1integrins on sperm and OVS, facilitate fusion of OVS in the delivery of transmembrane proteins to sperm. The mechanism uncovered is likely to be also involved in cargo delivery of prostasomes, epididymosomes, and uterosomes.


Asunto(s)
Exosomas/metabolismo , Trompas Uterinas/metabolismo , Integrinas/metabolismo , Fusión de Membrana , ATPasas Transportadoras de Calcio de la Membrana Plasmática/metabolismo , Espermatozoides/metabolismo , Animales , Células Cultivadas , Trompas Uterinas/citología , Trompas Uterinas/ultraestructura , Femenino , Fertilización , Técnica del Anticuerpo Fluorescente , Colorantes Fluorescentes/análisis , Integrinas/análisis , Masculino , Ratones , Microscopía Electrónica de Transmisión , Microscopía Inmunoelectrónica , ATPasas Transportadoras de Calcio de la Membrana Plasmática/análisis , Transporte de Proteínas , Espermatozoides/ultraestructura
20.
Biochim Biophys Acta ; 1854(5): 469-75, 2015 May.
Artículo en Inglés | MEDLINE | ID: mdl-25707358

RESUMEN

The intracellular enzyme platelet-activating factor acetylhydrolase type-II (PAFAH-II) hydrolyzes platelet-activating factor and oxidatively fragmented phospholipids. PAFAH-II in its resting state is mainly cytoplasmic, and it responds to oxidative stress by becoming increasingly bound to endoplasmic reticulum and Golgi membranes. Numerous studies have indicated that this enzyme is essential for protecting cells from oxidative stress induced apoptosis. However, the regulatory mechanism of the oxidative stress response by PAFAH-II has not been fully resolved. Here, changes to the oligomeric state of human PAFAH-II were investigated as a potential regulatory mechanism toward enzyme trafficking. Native PAGE analysis in vitro and photon counting histogram within live cells showed that PAFAH-II is both monomeric and dimeric. A Gly-2-Ala site-directed mutation of PAFAH-II demonstrated that the N-terminal myristoyl group is required for homodimerization. Additionally, the distribution of oligomeric PAFAH-II is distinct within the cell; homodimers of PAFAH-II were localized to the cytoplasm while monomers were associated to the membranes of the endoplasmic reticulum and Golgi. We propose that the oligomeric state of PAFAH-II drives functional protein trafficking. PAFAH-II localization to the membrane is critical for substrate acquisition and effective oxidative stress protection. It is hypothesized that the balance between monomer and dimer serves as a regulatory mechanism of a PAFAH-II oxidative stress response.


Asunto(s)
1-Alquil-2-acetilglicerofosfocolina Esterasa/metabolismo , Multimerización de Proteína/fisiología , 1-Alquil-2-acetilglicerofosfocolina Esterasa/química , Citoplasma/metabolismo , Células HEK293 , Humanos , Modelos Moleculares , Estrés Oxidativo , Transporte de Proteínas , Distribución Tisular
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