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1.
J Physiol ; 602(9): 1967-1986, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38564214

RESUMEN

Mitochondria within skeletal muscle cells are located either between the muscle contractile apparatus (interfibrillar mitochondria, IFM) or beneath the cell membrane (subsarcolemmal mitochondria, SSM), with several structural and functional differences reported between IFM and SSM. However, recent 3D imaging studies demonstrate that mitochondria are particularly concentrated in the proximity of capillaries embedded in sarcolemmal grooves rather than in proximity to the sarcolemma itself (paravascular mitochondria, PVM). To evaluate the impact of capillary vs. sarcolemmal proximity, we compared the structure and function of skeletal muscle mitochondria located either lateral to embedded capillaries (PVM), adjacent to the sarcolemma but not in PVM pools (SSM) or interspersed between sarcomeres (IFM). Mitochondrial morphology and interactions were assessed by 3D electron microscopy coupled with machine learning segmentation, whereas mitochondrial energy conversion was assessed by two-photon microscopy of mitochondrial membrane potential, content, calcium, NADH redox and flux in live, intact cells. Structurally, although PVM and SSM were similarly larger than IFM, PVM were larger, rounder and had more physical connections to neighbouring mitochondria compared to both IFM and SSM. Functionally, PVM had similar or greater basal NADH flux compared to SSM and IFM, respectively, despite a more oxidized NADH pool and a greater membrane potential, signifying a greater activation of the electron transport chain in PVM. Together, these data indicate that proximity to capillaries has a greater impact on resting mitochondrial energy conversion and distribution in skeletal muscle than the sarcolemma alone. KEY POINTS: Capillaries have a greater impact on mitochondrial energy conversion in skeletal muscle than the sarcolemma. Paravascular mitochondria are larger, and the outer mitochondrial membrane is more connected with neighbouring mitochondria. Interfibrillar mitochondria are longer and have greater contact sites with other organelles (i.e. sarcoplasmic reticulum and lipid droplets). Paravascular mitochondria have greater activation of oxidative phosphorylation than interfibrillar mitochondria at rest, although this is not regulated by calcium.


Asunto(s)
Capilares , Mitocondrias Musculares , Músculo Esquelético , Sarcolema , Sarcolema/metabolismo , Sarcolema/ultraestructura , Sarcolema/fisiología , Animales , Capilares/fisiología , Capilares/metabolismo , Mitocondrias Musculares/metabolismo , Mitocondrias Musculares/ultraestructura , Músculo Esquelético/fisiología , Músculo Esquelético/metabolismo , Músculo Esquelético/irrigación sanguínea , Ratones , Metabolismo Energético/fisiología , Masculino , Ratones Endogámicos C57BL , Potencial de la Membrana Mitocondrial/fisiología
2.
J Physiol ; 602(5): 891-912, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38429930

RESUMEN

Skeletal muscle cellular development requires the integrated assembly of mitochondria and other organelles adjacent to the sarcomere in support of muscle contractile performance. However, it remains unclear how interactions among organelles and with the sarcomere relates to the development of muscle cell function. Here, we combine 3D volume electron microscopy, proteomic analyses, and live cell functional imaging to investigate the postnatal reorganization of mitochondria-organelle interactions in skeletal muscle. We show that while mitochondrial networks are disorganized and loosely associated with the contractile apparatus at birth, contact sites among mitochondria, lipid droplets and the sarcoplasmic reticulum are highly abundant in neonatal muscles. The maturation process is characterized by a transition to highly organized mitochondrial networks wrapped tightly around the muscle sarcomere but also to less frequent interactions with both lipid droplets and the sarcoplasmic reticulum. Concomitantly, expression of proteins involved in mitochondria-organelle membrane contact sites decreases during postnatal development in tandem with a decrease in abundance of proteins associated with sarcomere assembly despite an overall increase in contractile protein abundance. Functionally, parallel measures of mitochondrial membrane potential, NADH redox status, and NADH flux within intact cells revealed that mitochondria in adult skeletal muscle fibres maintain a more activated electron transport chain compared with neonatal muscle mitochondria. These data demonstrate a developmental redesign reflecting a shift from muscle cell assembly and frequent inter-organelle communication toward a muscle fibre with mitochondrial structure, interactions, composition and function specialized to support contractile function. KEY POINTS: Mitochondrial network organization is remodelled during skeletal muscle postnatal development. The mitochondrial outer membrane is in frequent contact with other organelles at birth and transitions to more close associations with the contractile apparatus in mature muscles. Mitochondrial energy metabolism becomes more activated during postnatal development. Understanding the developmental redesign process within skeletal muscle cells may help pinpoint specific areas of deficit in muscles with developmental disorders.


Asunto(s)
NAD , Proteómica , Humanos , Adulto , Recién Nacido , NAD/metabolismo , Mitocondrias/metabolismo , Músculo Esquelético/metabolismo , Mitocondrias Musculares/metabolismo , Gotas Lipídicas/metabolismo
3.
bioRxiv ; 2023 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-37781589

RESUMEN

Molecular oxygen (O 2 ) is one of the most functionally relevant metabolites. O 2 is essential for mito-chondrial aerobic respiration. Changes in O 2 affect muscle metabolism and play a critical role in the maintenance of skeletal muscle mass, with lack of sufficient O 2 resulting in detrimental loss of muscle mass and function. How exactly O 2 is used by muscle cells is less known, mainly due to the lack of tools to address O 2 dynamics at the cellular level. Here we discuss a new imaging method for the real time quantification of intracellular O 2 in muscle cells based on a genetically encoded O 2 -responsive sensor, Myoglobin-mCherry. We show that we can spatially resolve and quantify intracellular O 2 concentration in single muscle cells and that the spatiotemporal O 2 gradient measured by the sensor is linked to, and reflects, functional metabolic changes occurring during the process of muscle differentiation. Highlights: Real time quantitation of intracellular oxygen with spatial resolutionIdentification of metabolically active sites in single cellsOxygen metabolism is linked to muscle differentiation.

4.
Dev Cell ; 58(21): 2249-2260.e9, 2023 11 06.
Artículo en Inglés | MEDLINE | ID: mdl-37647895

RESUMEN

In multicellular lives, the differentiation of stem cells and progenitor cells is often accompanied by a transition from glycolysis to mitochondrial oxidative phosphorylation (OXPHOS). However, the underlying mechanism of this metabolic transition remains largely unknown. In this study, we investigate the role of mechanical stress in activating OXPHOS during differentiation of the female germline cyst in Drosophila. We demonstrate that the surrounding somatic cells flatten the 16-cell differentiating cyst, resulting in an increase of the membrane tension of germ cells inside the cyst. This mechanical stress is necessary to maintain cytosolic Ca2+ concentration in germ cells through a mechanically activated channel, transmembrane channel-like. The sustained cytosolic Ca2+ triggers a CaMKI-Fray-JNK signaling relay, leading to the transcriptional activation of OXPHOS in differentiating cysts. Our findings demonstrate a molecular link between cell mechanics and mitochondrial energy metabolism, with implications for other developmentally orchestrated metabolic transitions in mammals.


Asunto(s)
Proteínas de Drosophila , Drosophila , Animales , Drosophila/metabolismo , Células Germinativas/metabolismo , Metabolismo Energético , Diferenciación Celular , Proteínas de Drosophila/metabolismo , Mamíferos/metabolismo
5.
Nat Commun ; 14(1): 2969, 2023 05 23.
Artículo en Inglés | MEDLINE | ID: mdl-37221204

RESUMEN

Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.


Asunto(s)
Ingeniería , Colorantes Fluorescentes , Dimerización , Fluorescencia , Ionóforos , Oligonucleótidos , ARN , Verduras , Zea mays
6.
Phys Chem Chem Phys ; 25(10): 7239-7250, 2023 Mar 08.
Artículo en Inglés | MEDLINE | ID: mdl-36853740

RESUMEN

Ultrafast Förster Resonance Energy Transfer (FRET) between tyrosine (Tyr) and tryptophan (Trp) residues in the protein monellin has been investigated using picosecond and femtosecond time-resolved fluorescence spectroscopy. Decay associated spectra (DAS) and time-resolved emission spectra (TRES) taken with the different excitation wavelengths of 275, 290 and 295 nm were constructed via global analysis. At two of those three excitation loci (275 and 290 nm), earmarks of energy transfer from Tyr to Trp in monellin are seen, and particularly when the excitation is 275 nm, the energy transfer between Tyr and Trp clearly changes the signature emission DAS shape to that indicating excited state reaction (especially on the red side of fluorescence emission, near 380 nm). Those FRET signatures may overlap with the conventional signatory DAS in heterogeneous systems. When overlap and addition occur between FRET type DAS and "full positive" QSSQ (quasi-static self-quenching), mixed DAS shapes will emerge that still show "positive blue side and negative red sides", just with zero crossing shifted. In addition, excitation decay associated spectra (EDAS) taken with the different emission wavelengths of 330, 350 and 370 nm were constructed. In the study of protein dynamics, ultrafast FRET between Tyr and Trp could provide a basis for an intrinsic (non-perturbing) "spectroscopic ruler", potentially a powerful tool to detect even slight changes in protein structures.


Asunto(s)
Transferencia Resonante de Energía de Fluorescencia , Tirosina , Triptófano , Espectrometría de Fluorescencia
7.
J Biol Chem ; 299(3): 103018, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36796514

RESUMEN

The endosymbiotic theory posits that ancient eukaryotic cells engulfed O2-consuming prokaryotes, which protected them against O2 toxicity. Previous studies have shown that cells lacking cytochrome c oxidase (COX), required for respiration, have increased DNA damage and reduced proliferation, which could be improved by reducing O2 exposure. With recently developed fluorescence lifetime microscopy-based probes demonstrating that the mitochondrion has lower [O2] than the cytosol, we hypothesized that the perinuclear distribution of mitochondria in cells may create a barrier for O2 to access the nuclear core, potentially affecting cellular physiology and maintaining genomic integrity. To test this hypothesis, we utilized myoglobin-mCherry fluorescence lifetime microscopy O2 sensors without subcellular targeting ("cytosol") or with targeting to the mitochondrion or nucleus for measuring their localized O2 homeostasis. Our results showed that, similar to the mitochondria, the nuclear [O2] was reduced by ∼20 to 40% compared with the cytosol under imposed O2 levels of ∼0.5 to 18.6%. Pharmacologically inhibiting respiration increased nuclear O2 levels, and reconstituting O2 consumption by COX reversed this increase. Similarly, genetic disruption of respiration by deleting SCO2, a gene essential for COX assembly, or restoring COX activity in SCO2-/- cells by transducing with SCO2 cDNA replicated these changes in nuclear O2 levels. The results were further supported by the expression of genes known to be affected by cellular O2 availability. Our study reveals the potential for dynamic regulation of nuclear O2 levels by mitochondrial respiratory activity, which in turn could affect oxidative stress and cellular processes such as neurodegeneration and aging.


Asunto(s)
Mitocondrias , Oxígeno , Oxígeno/metabolismo , Mitocondrias/metabolismo , Respiración , Complejo IV de Transporte de Electrones/genética , Complejo IV de Transporte de Electrones/metabolismo , Núcleo Celular/metabolismo , Consumo de Oxígeno , Respiración de la Célula
8.
Methods Mol Biol ; 2568: 25-36, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36227560

RESUMEN

Fluorescent RNA aptamers are tools for studying RNA localization and interactions in vivo. The photophysical properties of these in vitro selected RNAs should be characterized prior to cellular imaging experiments. Here, we describe the process of determining the fluorophore affinity, fluorescence enhancement, and fluorescence lifetime(s) of the Mango-III fluorescence turn-on aptamer. Parameters determined through these protocols will aid in establishing conditions for live-cell imaging.


Asunto(s)
Aptámeros de Nucleótidos , Aptámeros de Nucleótidos/genética , Fluorescencia , Colorantes Fluorescentes , ARN
9.
Int J Mol Sci ; 23(20)2022 Oct 20.
Artículo en Inglés | MEDLINE | ID: mdl-36293452

RESUMEN

Computational modeling can provide a mechanistic and quantitative framework for describing intracellular spatial heterogeneity of solutes such as oxygen partial pressure (pO2). This study develops and evaluates a finite-element model of oxygen-consuming mitochondrial bioenergetics using the COMSOL Multiphysics program. The model derives steady-state oxygen (O2) distributions from Fickian diffusion and Michaelis-Menten consumption kinetics in the mitochondria and cytoplasm. Intrinsic model parameters such as diffusivity and maximum consumption rate were estimated from previously published values for isolated and intact mitochondria. The model was compared with experimental data collected for the intracellular and mitochondrial pO2 levels in human cervical cancer cells (HeLa) in different respiratory states and under different levels of imposed pO2. Experimental pO2 gradients were measured using lifetime imaging of a Förster resonance energy transfer (FRET)-based O2 sensor, Myoglobin-mCherry, which offers in situ real-time and noninvasive measurements of subcellular pO2 in living cells. On the basis of these results, the model qualitatively predicted (1) the integrated experimental data from mitochondria under diverse experimental conditions, and (2) the impact of changes in one or more mitochondrial processes on overall bioenergetics.


Asunto(s)
Consumo de Oxígeno , Oxígeno , Humanos , Mioglobina/metabolismo , Simulación por Computador , Metabolismo Energético
10.
Phys Chem Chem Phys ; 24(30): 18055-18066, 2022 Aug 03.
Artículo en Inglés | MEDLINE | ID: mdl-35861343

RESUMEN

Ultrafast Förster Resonance Energy Transfer (FRET) between Tyrosine (Tyr, Y) and Tryptophan (Trp, W) in the model peptides Trp-(Pro)n-Tyr (WPnY) has been investigated using a femtosecond up-conversion spectrophotofluorometer. The ultrafast energy transfer process (<100 ps) in short peptides (WY, WPY and WP2Y) has been resolved. In fact, this FRET rate is found to be mixed with the rates of solvent relaxation (SR), ultrafast population decay (QSSQ) and other lifetime components. To further dissect and analyze the FRET, a spectral working model is constructed, and the contribution of a FRET lifetime is separated by reconciling the shapes of decay associated spectra (DAS). Surprisingly, FRET efficiency did not decrease monotonically with the growth of the peptide chain (as expected) but increased first and then decreased. The highest FRET efficiency occurred in peptide WPY. The kinetic results have been accompanied with molecular dynamics simulations that reconcile and explain this strange phenomenon: due to the strong interaction between amino acids, the distance between the donor and receptor in peptide WPY is actually closest, resulting in the fastest FRET. In addition, the FRET lifetimes (τcal) were estimated within the molecular dynamics simulations, and they were consistent with the lifetimes (τexp) separated out by the experimental measurements and the DAS working model. This benchmark study has implications for both previous and future studies of protein ultrafast dynamics. The approach taken can be generalized for the study of proximate tyrosine and tryptophan in proteins and it suggests spectral strategies for extracting mixed rates in other complex FRET problems.


Asunto(s)
Transferencia Resonante de Energía de Fluorescencia , Triptófano , Péptidos , Triptófano/química , Tirosina , Agua/química
11.
Artículo en Inglés | MEDLINE | ID: mdl-35463920

RESUMEN

Myoglobin is a protein that is expressed quite unevenly among different cell types. Nevertheless, it has been widely acknowledged that the Fe3+ state of myoglobin, metmyoglobin (metMb) has a broad functional role in metabolism, oxidative/nitrative regulation and gene networks. Accordingly, real-time monitoring of oxygenated, deoxygenated and metMb proportions- or, more broadly, of the mechanisms by which metMb is formed, presents a promising line of research. We had previously introduced a Förster resonance energy transfer (FRET) method to read out the deoxygenation/oxygenation states of myoglobin, by creating the targetable oxygen (O2) sensor Myoglobin-mCherry. In this sensor, changes in myoglobin absorbance features that occur with lost O2 occupancy -or upon metMb production- control the FRET rate from the fluorescent protein to myoglobin. When O2 is bound, mCherry fluorescence is only slightly quenched, but if either O2 is released or met is produced, FRET will increase- and this rate competing with emission reduces both emission yield and lifetime. Nitric oxide (NO) is an important signal (but also a toxic molecule) that can oxidize myoglobin to metMb with absorbance increases in the red visible range. mCherry thus senses both met and deoxygenated myoglobin, which cannot be easily separated at hypoxia. In order to dissect this, we treat cells with NO and investigate how the Myoglobin-mCherry lifetime is affected by generating metMb. More discriminatory power is then achieved when the fluorescent protein EYFP is added to Myoglobin-mCherry, creating a sandwich probe whose lifetime can selectively respond to metMb while being indifferent to O2 occupancy.

12.
Chem Phys ; 5532022 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-35465176

RESUMEN

Thiazole orange (TO), an asymmetric cyanine dye, has been widely used in biomolecular detection and imaging of DNA/ RNA in gels, due to its unique fluorogenic behavior: fluorescence of free dye in aqueous solution is very weak but emission can be significantly enhanced in nucleic-acid-bound dye. Herein we describe the ultrafast excited-state dynamics of free TO in aqueous solution by exploiting both a femtosecond upconversion spectrophotofluorometer and a picosecond time-correlated single-photon counting (TCSPC) apparatus. For the first time, the fluorescence lifetime of TO monomer in water was found to be ∼1 ps, mixed with concurrent solvent relaxation (which was confirmed by the experimental results of TO in DMSO). Even at moderate concentration, this lifetime has an amplitude (a measure of molecular fraction) that significantly dominates other lifetimes, and this is the origin of weak steady state fluorescence of free TO in water. We also found a novel slower decay component around 34 ps. Interestingly and in addition, the lifetime component on the 30-40 ps timescale was also found in TO-γ-Cyclodextrin (CD) complexes. The fraction of this component increased with the addition of γ-CD. Cyclodextrin has been reported to promote the aggregation of TO. Thus, although a very coincidental match of this time constant by one for a torsional process within the cavity can not be ruled out, we ascribe the shared 30-40 ps component to the lifetime of a highly quenched TO dimer experiencing intra-and inter-molecular rearrangement.

13.
J Biophotonics ; 15(3): e202100166, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-34689421

RESUMEN

The biological relevance of nitric oxide (NO) and reactive oxygen species (ROS) in signaling, metabolic regulation, and disease treatment has become abundantly clear. The dramatic change in NO/ROS processing that accompanies a changing oxygen landscape calls for new imaging tools that can provide cellular details about both [O2 ] and the production of reactive species. Myoglobin oxidation to the met state by NO/ROS is a known sensor with absorbance changes in the visible range. We previously employed Förster resonance energy transfer to read out the deoxygenation/oxygenation of myoglobin, creating the subcellular [O2 ] sensor Myoglobin-mCherry. We now add the fluorescent protein EYFP to this sensor to create a novel probe that senses both met formation, a proxy for ROS/NO exposure, and [O2 ]. Since both proteins are present in the construct, it can also relieve users from the need to measure fluorescence lifetime, making [O2 ] sensing available to a wider group of laboratories.


Asunto(s)
Metamioglobina , Mioglobina , Transferencia Resonante de Energía de Fluorescencia , Metamioglobina/metabolismo , Mioglobina/metabolismo , Óxido Nítrico/metabolismo , Oxidación-Reducción , Oxígeno/metabolismo , Especies Reactivas de Oxígeno
14.
FEBS J ; 289(22): 6959-6968, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-34235856

RESUMEN

Molecular oxygen possesses a dual nature due to its highly reactive free radical property: it is capable of oxidizing metabolic substrates to generate cellular energy, but can also serve as a substrate for genotoxic reactive oxygen species generation. As a labile substance upon which aerobic life depends, the mechanisms for handling cellular oxygen have been fine-tuned and orchestrated in evolution. Protection from atmospheric oxygen toxicity as originally posited by the Endosymbiotic Theory of the Mitochondrion is likely to be one basic principle underlying oxygen homeostasis. We briefly review the literature on oxygen homeostasis both in vitro and in vivo with a focus on the role of the mitochondrion where the majority of cellular oxygen is consumed. The insights gleaned from these basic mechanisms are likely to be important for understanding disease pathogenesis and developing strategies for maintaining health.


Asunto(s)
Mitocondrias , Oxígeno , Mitocondrias/metabolismo , Radicales Libres/metabolismo , Oxígeno/metabolismo , Homeostasis , Especies Reactivas de Oxígeno/metabolismo , Estrés Oxidativo
15.
Methods Mol Biol ; 2304: 315-337, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34028725

RESUMEN

Oxygen (O2) is a critical metabolite for cellular function as it fuels aerobic cellular metabolism; further, it is a known regulator of gene expression. Monitoring oxygenation within cells and organelles can provide valuable insights into how O2, or lack thereof, both influences and responds to cell processes. In recent years, fluorescence lifetime imaging microscopy (FLIM) has been used to track several probe concentration independent intracellular phenomena, such as pH, viscosity, and, in conjunction with Förster resonance energy transfer (FRET), protein-protein interactions. Here, we describe methods for synthesizing and expressing the novel FLIM-FRET intracellular O2 probe Myoglobin-mCherry (Myo-mCherry) in cultured cell lines, as well as acquiring FLIM images using a laser scanning confocal microscope configured for two-photon excitation and a time-correlated single photon counting (TCSPC) module. Finally, we provide step-by-step protocols for FLIM analysis of Myo-mCherry using the commercial software SPCImage and conversion of fluorescence lifetime values in each pixel to apparent intracellular oxygen partial pressures (pO2).


Asunto(s)
Proteínas Luminiscentes/metabolismo , Mioglobina/metabolismo , Oxígeno/análisis , Transferencia Resonante de Energía de Fluorescencia , Regulación Neoplásica de la Expresión Génica , Células HeLa , Humanos , Proteínas Luminiscentes/química , Microscopía de Fluorescencia por Excitación Multifotónica , Modelos Moleculares , Mioglobina/química , Proteínas Recombinantes/metabolismo , Programas Informáticos , Proteína Fluorescente Roja
16.
Molecules ; 26(1)2021 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-33401638

RESUMEN

In this review, the experimental set-up and functional characteristics of single-wavelength and broad-band femtosecond upconversion spectrophotofluorometers developed in our laboratory are described. We discuss applications of this technique to biophysical problems, such as ultrafast fluorescence quenching and solvation dynamics of tryptophan, peptides, proteins, reduced nicotinamide adenine dinucleotide (NADH), and nucleic acids. In the tryptophan dynamics field, especially for proteins, two types of solvation dynamics on different time scales have been well explored: ~1 ps for bulk water, and tens of picoseconds for "biological water", a term that combines effects of water and macromolecule dynamics. In addition, some proteins also show quasi-static self-quenching (QSSQ) phenomena. Interestingly, in our more recent work, we also find that similar mixtures of quenching and solvation dynamics occur for the metabolic cofactor NADH. In this review, we add a brief overview of the emerging development of fluorescent RNA aptamers and their potential application to live cell imaging, while noting how ultrafast measurement may speed their optimization.


Asunto(s)
Fluorescencia , Ácidos Nucleicos/química , Péptidos/química , Proteínas/química , Biofisica , Espectrometría de Fluorescencia , Triptófano/química
17.
RNA ; 27(4): 433-444, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33376189

RESUMEN

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.


Asunto(s)
Aptámeros de Nucleótidos/química , Transferencia Resonante de Energía de Fluorescencia/métodos , ARN/química , Riboswitch , Aptámeros de Nucleótidos/metabolismo , Fluorescencia , Colorantes Fluorescentes/química , Modelos Moleculares , Conformación de Ácido Nucleico , ARN/metabolismo
18.
J Phys Chem B ; 124(31): 6721-6727, 2020 08 06.
Artículo en Inglés | MEDLINE | ID: mdl-32660250

RESUMEN

The fluorescence of dinucleotide NADH has been exploited for decades to determine the redox state of cells and tissues in vivo and in vitro. Particularly, nanosecond (ns) fluorescence lifetime imaging microscopy (FLIM) of NADH (in free vs bound forms) has recently offered a label-free readout of mitochondrial function and allowed the different "pools" of NADH to be distinguished in living cells. In this study, the ultrafast fluorescence dynamics of NADH-dehydrogenase (MDH/LDH) complexes have been investigated by using both a femtosecond (fs) upconversion spectrophotofluorometer and a picosecond (ps) time-correlated single photon counting (TCSPC) apparatus. With these enhanced time-resolved tools, a few-picosecond decay process with a signatory spectrum was indeed found for bound NADH, and it can best be ascribed to the solvent relaxation originating in "bulk water". However, it is quite unlike our previously discovered ultrafast "dark" component (∼26 ps) that is prominent in free NADH (Chemical Physics Letters 2019, 726, 18-21). For these two critical protein-bound NADH exemplars, the decay transients lack the ultrafast quenching that creates the "dark" subpopulation of free NADH. Therefore, we infer that the apparent ratio of free to bound NADH recovered by ordinary (>50 ps) FLIM methods may be low, since the "dark" molecule subpopulation (lifetime too short for conventional FLIM), which effectively hides about a quarter of free molecules, is not present in the dehydrogenase-bound state.


Asunto(s)
Fosfatos de Dinucleósidos , NAD , Sitios de Unión , Microscopía Fluorescente , Oxidorreductasas
19.
Redox Biol ; 34: 101549, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32403080

RESUMEN

Oxidation-reduction chemistry is fundamental to the metabolism of all living organisms, and hence quantifying the principal redox players is important for a comprehensive understanding of cell metabolism in normal and pathological states. In mammalian cells, this is accomplished by measuring oxygen partial pressure (pO2) in parallel with free and enzyme-bound reduced nicotinamide adenine dinucleotide (phosphate) [H] (NAD(P)H) and flavin adenine dinucleotide (FAD, a proxy for NAD+). Previous optical methods for these measurements had accompanying problems of cytotoxicity, slow speed, population averaging, and inability to measure all redox parameters simultaneously. Herein we present a Förster resonance energy transfer (FRET)-based oxygen sensor, Myoglobin-mCherry, compatible with fluorescence lifetime imaging (FLIM)-based measurement of nicotinamide coenzyme state. This offers a contemporaneous reading of metabolic activity through real-time, non-invasive, cell-by-cell intracellular pO2 and coenzyme status monitoring in living cells. Additionally, this method reveals intracellular spatial heterogeneity and cell-to-cell variation in oxygenation and coenzyme states.


Asunto(s)
Flavina-Adenina Dinucleótido , Imagen Óptica , Animales , Flavina-Adenina Dinucleótido/metabolismo , NAD/metabolismo , NADP/metabolismo , Oxidación-Reducción
20.
J Phys Chem B ; 124(5): 771-776, 2020 02 06.
Artículo en Inglés | MEDLINE | ID: mdl-31941277

RESUMEN

The ultrafast solvation dynamics of reduced nicotinamide adenine dinucleotide (NADH) free in solution has been investigated, using both a femtosecond upconversion spectrophotofluorometer and a picosecond time-correlated single-photon counting (TCSPC) apparatus. The familiar time constant of solvent relaxation originating in "bulk water" was found to be ∼1.4 ps, revealing ultrafast solvent reorientation upon excitation. We also found a slower spectral relaxation process with an apparent time of 27 ps, suggesting there could either be dissociable "biological water" hydration sites on the surface of NADH or internal dielectric rearrangements of the flexible solvated molecule on that timescale. In contrast, the femtosecond fluorescence anisotropy measurement revealed that rotational diffusion happened on two different timescales (3.6 ps (local) and 141 ps (tumbling)); thus, any dielectric rearrangement scenario for the 27 ps relaxation must occur without significant chromophore oscillator rotation. The coexistence of quasi-static self quenching (QSSQ) with the slower relaxation is also discussed.


Asunto(s)
NAD/química , Agua/química , Solventes/química , Espectrometría de Fluorescencia
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