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1.
Opt Express ; 32(5): 8189-8204, 2024 Feb 26.
Artículo en Inglés | MEDLINE | ID: mdl-38439482

RESUMEN

Lidar has emerged as a promising technique for vertically profiling optical parameters in water. The application of single-photon technology has enabled the development of compact oceanic lidar systems, facilitating their deployment underwater. This is crucial for conducting ocean observations that are free from interference at the air-sea interface. However, simultaneous inversion of the volume scattering function at 180° at 532 nm (ßm) and the lidar attenuation coefficient at 532 nm (K l i d a r m) from the elastic backscattered signals remains challenging, especially in the case of near-field signals affected by the geometric overlap factor (GOF). To address this challenge, this work proposes adding a Raman channel, obtaining Raman backscattered profiles using single-photon detection. By normalizing the elastic backscattered signals with the Raman signals, the sensitivity of the normalized signal to variations in the lidar attenuation coefficient is significantly reduced. This allows for the application of a perturbation method to invert ßm and subsequently obtain the K l i d a r m. Moreover, the influence of GOF and fluctuations in laser power on the inversion can be reduced. To further improve the accuracy of the inversion algorithm for stratified water bodies, an iterative algorithm is proposed. Additionally, since the optical telescope of the lidar adopts a small aperture and narrow field of view design, K l i d a r m tends to the beam attenuation coefficient at 532 nm (cm). Using Monte Carlo simulation, a relationship between cm and K l i d a r m is established, allowing cm derivation from K l i d a r m. Finally, the feasibility of the algorithm is verified through inversion error analysis. The robustness of the lidar system and the effectiveness of the algorithm are validated through a preliminary experiment conducted in a water tank. These results demonstrate that the lidar can accurately profile optical parameters of water, contributing to the study of particulate organic carbon (POC) in the ocean.

2.
Opt Express ; 32(6): 10204-10218, 2024 Mar 11.
Artículo en Inglés | MEDLINE | ID: mdl-38571237

RESUMEN

Laser-induced fluorescence (LIF) technology has been widely applied in remote sensing of aquatic phytoplankton. However, due to the weak fluorescence signal induced by laser excitation and the significant attenuation of laser in water, profiling detection becomes challenging. Moreover, it remains difficult to simultaneously retrieve the attenuation coefficient (K l i d a r m f) and the fluorescence volume scattering function at 180° (ßf) through a single fluorescence lidar. To address these issues, a novel all-fiber fluorescence oceanic lidar is proposed, characterized by: 1) obtaining subsurface fluorescence profiles using single-photon detection technology, and 2) introducing the Klett inversion method for fluorescence lidar to simultaneously retrieve K l i d a r m f and ßf. According to theoretical analysis, the maximum relative error of ßf for the chlorophyll concentration ranging from 0.01 mg/m3 to 10 mg/m3 within a water depth of 10 m is less than 20%, while the maximum relative error of K l i d a r m f is less than 10%. Finally, the shipborne single-photon fluorescence lidar was deployed on the experimental vessel for continuous experiments of over 9 hours at fixed stations in the offshore area, validating its profiling detection capability. These results demonstrate the potential of lidar in profiling detection of aquatic phytoplankton, providing support for studying the dynamic changes and environmental responses of subsurface phytoplankton.

3.
J Struct Biol ; 215(2): 107945, 2023 06.
Artículo en Inglés | MEDLINE | ID: mdl-36889560

RESUMEN

Single particle reconstruction (SPR) in cryoEM is an image processing task with an elaborate hierarchy that starts with many very noisy multi-frame images. Efficient representation of the intermediary image structures is critical for keeping the calculations manageable. One such intermediary structure is called a particle stack and contains cut-out images of particles in square boxes of predefined size. The micrograph that is the source of the boxed images is usually corrected for motion between frames prior to particle stack creation. However, the contrast transfer function (CTF) or its Fourier Transform point spread function (PSF) are not considered at this step. Historically, the particle stack was intended for large particles and for a tighter PSF, which is characteristic of lower resolution data. The field now performs analyses of smaller particles and to higher resolution, and these conditions result in a broader PSF that requires larger padding and slower calculations to integrate information for each particle. Consequently, the approach to handling structures such as the particle stack should be reexamined to optimize data processing. Here we propose to use as a source image for the particle stack a complex-valued image, in which CTF correction is implicitly applied as a real component of the image. We can achieve it by applying an initial CTF correction to the entire micrograph first and perform box cutouts as a subsequent step. The final CTF correction that we refine and apply later has a very narrow PSF, and so cutting out particles from micrographs that were approximately corrected for CTF does not require extended buffering, i.e. the boxes during the analysis only have to be large enough to encompass the particle. The Fourier Transform of an exit-wave reconstruction creates an image that has complex values. This is a complex value image considered in real space, opposed to standard SPR data processing where complex numbers appear only in Fourier space. This extension of the micrograph concept provides multiple advantages because the particle box size can be small and calculations crucial for high resolution reconstruction such as Ewald sphere correction, aberration refinement, and particle-specific defocus refinement can be performed on the small box data.


Asunto(s)
Algoritmos , Procesamiento de Imagen Asistido por Computador , Microscopía por Crioelectrón/métodos , Procesamiento de Imagen Asistido por Computador/métodos , Tamaño de la Partícula
4.
BMC Plant Biol ; 23(1): 292, 2023 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-37264351

RESUMEN

BACKGROUND: Quinoa (Chenopodium quinoa Willd.) originates in high altitude areas, such as the Andes, and has some inherent characteristics of cold, drought, and salinity tolerance, but is sensitive to high temperature. RESULTS: To gain insight into the response mechanism of quinoa to high temperature stress, we conducted an extensive targeted metabolomic study of two cultivars, Dianli-3101 and Dianli-3051, along with a combined transcriptome analysis. A total of 794 metabolites and 54,200 genes were detected, in which the genes related to photosynthesis were found down-regulated at high temperatures, and two metabolites, lipids and flavonoids, showed the largest changes in differential accumulation. Further analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and transcription factors revealed that quinoa inhibits photosynthesis at high temperatures, and the possible strategies being used for high temperature stress management are regulation of heat stress transcription factors (HSFs) to obtain heat tolerance, and regulation of purine metabolism to enhance stress signals for rapid response to high temperature stress. The tolerant genotype could have an enhanced response through lower purine levels. The induction of the stress response could be mediated by HSF transcription factors. The results of this study may provide theoretical references for understanding the response mechanism of quinoa to high temperature stress, and for screening potential high temperature tolerant target genes and high temperature tolerant strains. CONCLUSIONS: These findings reveal the regulation of the transcription factor family HSF and the purinergic pathway in response to high temperature stress to improve quinoa varieties with high temperature tolerance.


Asunto(s)
Chenopodium quinoa , Plantones , Plantones/genética , Chenopodium quinoa/fisiología , Temperatura , Transcriptoma , Perfilación de la Expresión Génica , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
5.
Opt Express ; 31(16): 25398-25414, 2023 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-37710428

RESUMEN

A lidar technique has been proposed and demonstrated for remotely sensing particulate beam attenuation coefficient (cp) profiles using the Raman backscattered signal from water. In Raman lidar, the backscatter coefficient at 180° can be considered constant, allowing for the determination of the lidar attenuation coefficient (Klidar) from the Raman backscattered signal. This scheme has these features. 1) The bandwidth of the filter that used to extract the Raman component from the backscattered signal of the lidar was optimized to ensure sufficient lidar signal strength while minimizing the influence of chlorophyll fluorescence on inversion. 2) A receiving telescope with narrow field of view (FOV) and small aperture was utilized to suppress multi-scattering components in the backscattered signal. 3) A relationship between the beam attenuation coefficient (c) and Klidar was established after simulations via a semi-analytic Monto Carlo. 4) The value of cp was obtained by subtracting the attenuation coefficient of pure seawater (cw) from c. According to the theoretical analysis, the maximum relative error of cp is less than 15% for chlorophyll concentrations up to 10 mg/m3. Due to the water Raman backscattered signal being several orders of magnitude lower than the elastic backscattered signal, a single-photon detector is required to significantly improve the detection sensitivity to the single-photon level. To validate this approach, a field experiment was conducted aboard the R/V Tan Kah Kee in the South China Sea from September 4th to September 5th, 2022, and continuous subsurface profiles of cp were obtained. These measurements confirm the robustness and reliability of the oceanic single-photon Raman lidar system and the inversion method.

6.
Opt Express ; 31(24): 40393-40410, 2023 Nov 20.
Artículo en Inglés | MEDLINE | ID: mdl-38041342

RESUMEN

A novel oceanic fluorescence lidar technique has been proposed and demonstrated for remotely sensing the volume scattering function at 180° (ßf), which can be used to further retrieve the profiles of the absorption coefficient of phytoplankton (aph) at 532 nm and chlorophyll concentration (Chl). This scheme has these features. 1) The single-photon detection technology is employed to enhance the detection sensitivity to the single-photon level, enabling the oceanic lidar to obtain fluorescence backscatter profiles. 2) In terms of algorithms, the Raman backscattered signals of the water are utilized to normalize the backscattered signals of chlorophyll fluorescence, effectively minimizing the depth-dependent variation of the differential lidar attenuation coefficient (Δ K l i d a r f r). To reduce the contamination of fluorescence signals in the Raman backscatter signals, a Raman filter with a bandwidth of 6 nm was chosen. Subsequently, a perturbation method is utilized to invert the ßf of the fluorescence lidar. Finally, aph and Chl profiles can be inverted based on empirical models. 3) The value of Δ K l i d a r f r used in inversion is obtained through a semi-analytic Monte Carlo simulation. According to theoretical analysis, the maximum relative error of ßf for Chl ranging from 0.01 mg/m3 to 10 mg/m3 is less than 13 %. To validate this approach, a field experiment was conducted aboard the R/V Tan Kah Kee in the South China Sea from September 4th to September 5th, 2022, resulting in continuous subsurface profiles of ßf, aph, and Chl. These measurements confirm the robustness and reliability of the oceanic single-photon fluorescence lidar system and the inversion algorithm.

7.
Appl Opt ; 62(19): 5301-5305, 2023 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-37707235

RESUMEN

The detection of oil in water is of great importance for maintaining subsurface infrastructures such as oil pipelines. As a potential technology for oceanic application, an oceanic lidar has proved its advantages for remote sensing of optical properties and subsea materials. However, current oceanic lidar systems are highly power-consuming and bulky, making them difficult to deploy underwater to monitor oil in water. To address this issue, we have developed a compact single-photon Raman lidar by using a single-photon detector with high quantum efficiency and low dark noise. Due to the single-photon sensitivity, the detection of the relatively weak Raman backscattered signal from underwater oil was realized with a laser with a pulse energy of 1 µJ and a telescope with a diameter of 22.4 mm. An experimental demonstration was conducted to obtain the distance-resolved Raman backscatter of underwater oil of different thicknesses up to a distance of 12 m. The results indicate the single-photon Raman lidar's potential for inspecting underwater oil pipelines.

8.
Genomics ; 114(1): 138-148, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34863898

RESUMEN

Quinoa (Chenopodium quinoa Willd.) is an herb of the genus Chenopodiaceae that is native to the Andes Mountains of South America. To understand the metabolic differences between various quinoa strains, we selected quinoa strains of four colors (black, red, yellow, and white) and we subjected seeds to extensive targeted metabolomics analysis using liquid chromatography-tandem mass spectrometry and transcriptomics analysis. In total, 90 flavonoid-related metabolites were detected in quinoa seeds of the four colors. We elucida ted the regulatory mechanisms of flavonoid biosynthesis in the different quinoa varieties, and thus identified key genes for flavonoid biosynthesis. The results showed that 18 flavone metabolites and 25 flavonoid-related genes were key contributors to flavonoid biosynthesis in quinoa seeds. The results of this study may provide a basis for the breeding and identification of new quinoa strains and for the screening of potential target genes in flavonoid biosynthesis regulation in quinoa.


Asunto(s)
Chenopodium quinoa , Chenopodium quinoa/genética , Flavonoides , Metabolómica , Fitomejoramiento , Semillas/genética , Transcriptoma
9.
J Am Chem Soc ; 144(50): 23061-23072, 2022 12 21.
Artículo en Inglés | MEDLINE | ID: mdl-36503221

RESUMEN

RNA interference (RNAi) has proved to be a promising modality for disease treatment. However, the promise of conventional RNA therapeutics for clinical application is severely impeded by low delivery efficiency and susceptibility of RNAs to serum RNases. Therefore, developing advanced RNAi technology is an increasing demand for achieving precise medicine. Herein, for the first time, we propose an alkaline phosphatase (ALP)-controllable and red light-activated RNA modification (ALARM) approach for anti-tumor therapeutic application. An ALP-responsive NIR fluorogenic probe f-RCP consisting of a tumor-targeting cyclic RGD peptide, an ALP-activated photosensitizer CyOP, and an 1O2-susceptible furan module for RNA modification was rationally designed and synthesized. Studies have demonstrated that f-RCP can specifically target to liver carcinoma HepG2 cells and spontaneously emit activated NIR/photoacoustic signals upon cleavage by the ALP enzyme, allowing for sensitive detection of ALP-positive tumors. More notably, we surprisingly found that the capability of f-RCP producing singlet oxygen (1O2) under red light irradiation could be simultaneously unlocked, which can ignite the covalent cyclization reaction between furan and nucleobases of intracellular RNA molecules, leading to significant mitochondrial damage and severe apoptosis of tumor cells, in consequence realizing efficient tumor suppression. Most importantly, the potential therapeutic mechanism was first explored on the transcriptomic level. This delicate ALARM strategy may open up new insights into cancer gene therapy.


Asunto(s)
Fosfatasa Alcalina , Neoplasias , Humanos , Luz , Colorantes Fluorescentes/química , ARN
10.
BMC Plant Biol ; 22(1): 604, 2022 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-36539684

RESUMEN

BACKGROUND: Quinoa (Chenopodium quinoa Willd.) is a herb within the Quinoa subfamily of Amaranthaceae, with remarkable environmental adaptability. Its edible young leaves and grains are rich in protein, amino acids, microorganisms, and minerals. Although assessing the effects of fertilization on quinoa yield and quality has become an intensive area of research focus, the associated underlying mechanisms remain unclear. As one of the three macro nutrients in plants, potassium has an important impact on plant growth and development. In this study, extensive metabolome and transcriptome analyses were conducted in quinoa seedlings 30 days after fertilizer application to characterize the growth response mechanism to potassium.  RESULTS: The differential metabolites and genes present in the seedlings of white and red quinoa cultivars were significantly enriched in the photosynthetic pathway. Moreover, the PsbQ enzyme on photosystem II and delta enzyme on ATP synthase were significantly down regulated in quinoa seedlings under potassium deficiency. Additionally, the differential metabolites and genes of red quinoa seedlings were significantly enriched in the arginine biosynthetic pathway. CONCLUSIONS: These findings provide a more thorough understanding of the molecular changes in quinoa seedlings that occur under deficient, relative to normal, potassium levels. Furthermore, this study provides a theoretical basis regarding the importance of potassium fertilizers, as well as their efficient utilization by growing quinoa seedlings.


Asunto(s)
Chenopodium quinoa , Chenopodium quinoa/química , Plantones/genética , Transcriptoma , Potasio/metabolismo , Metaboloma
11.
Org Biomol Chem ; 20(4): 790-795, 2022 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-34994749

RESUMEN

Herein, a protocol that combines heterogeneous catalysis and solar photocatalysis for the regioselective α-substitution of asymmetric ketones with quinoxalinones has been reported. The result indicates that the reaction is more likely to occur on the α-carbon. This strategy provides a green and efficient way for the α-functionalization of ketones. A singlet oxygen involved mechanism is suggested for the transformation.

12.
Urol Int ; 106(11): 1107-1125, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-34818225

RESUMEN

PURPOSE: The aim of this study was to explore the diagnostic value of different fluorine-18 (18F)-labeled tracers for lymph node/bone metastasis and biochemical recurrence detection in advanced prostate cancer (PCa). METHODS: PubMed, Embase, Web of Science, Cochrane databases, and the WHO International Clinical Trial Center were searched. The inclusion criteria were determined based on the Preferred Report Items of the Systematic Review and Meta-Analysis Guidelines. The Quality Assessment of Diagnostic Accuracy Studies-2 was used to assess the quality assessment of the included studies. The quantitative analysis of the included literature was performed on the patient and lesion basis, and the equivocal findings were considered negative or positive results, respectively. RESULTS: Thirty-seven articles were included. On the patient basis, the pooled sensitivity and specificity of [18F]-labeled tracers were 0.80 (95% confidence interval [CI]: 0.78-0.83) and 0.89 (95% CI: 0.87-0.90) when equivocal results were considered to be positive and 0.80 (95% CI: 0.77-0.82) and 0.87 (95% CI: 0.85-0.89) when equivocal results were considered to be negative. On the lesion basis, the pooled sensitivity and specificity of [18F]-labeled tracers were 0.82 (95% CI: 0.80-0.83) and 0.91 (95% CI: 0.90-0.92) when equivocal lesions were regarded as positive and 0.81 (95% CI: 0.80-0.82) and 0.91 (95% CI: 0.90-0.92) when equivocal lesions were considered to be negative. CONCLUSION: [18F]-labeled tracers have high diagnostic efficacy for lymph node/bone metastasis and biochemical recurrence in advanced PCa.


Asunto(s)
Tomografía Computarizada por Tomografía de Emisión de Positrones , Neoplasias de la Próstata , Masculino , Humanos , Tomografía Computarizada por Tomografía de Emisión de Positrones/métodos , Radioisótopos de Flúor , Neoplasias de la Próstata/diagnóstico por imagen , Neoplasias de la Próstata/patología , Metástasis Linfática , Ganglios Linfáticos/patología
13.
Int J Mol Sci ; 23(9)2022 Apr 24.
Artículo en Inglés | MEDLINE | ID: mdl-35563095

RESUMEN

Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual herb of Family Amaranthaceae and Subfamily Chenopodiaceae. It has high nutritional and economic value. Phosphorus (P) is an essential plant macronutrient, a component of many biomolecules, and vital to growth, development, and metabolism. We analyzed the transcriptomes and metabolomes of Dianli-1299 and Dianli-71 quinoa seedlings, compared their phenotypes, and elucidated the mechanisms of their responses to the phosphorus treatments. Phenotypes significantly varied with phosphorus level. The plants responded to changes in available phosphorus by modulating metabolites and genes implicated in glycerophospholipid, glycerolipid and glycolysis, and glyconeogenesis metabolism. We detected 1057 metabolites, of which 149 were differentially expressed (DEMs) and common to the control (CK) vs. the low-phosphorus (LP) treatment samples, while two DEMs were common to CK vs. the high-phosphorus (HP) treatment samples. The Kyoto Encyclopedia of genes and genomes (KEGG) annotated 29,232 genes, of which 231 were differentially expressed (DEGs) and common to CK vs. LP, while one was common to CK vs. HP. A total of 15 DEMs and 11 DEGs might account for the observed differences in the responses of the quinoa seedlings to the various phosphorus levels. The foregoing results may provide a theoretical basis for improving the phosphorus utilization efficiency in quinoa.


Asunto(s)
Chenopodium quinoa , Chenopodium quinoa/genética , Chenopodium quinoa/metabolismo , Metaboloma , Fósforo/metabolismo , Plantones/genética , Plantones/metabolismo , Transcriptoma
14.
Int J Mol Sci ; 23(9)2022 May 06.
Artículo en Inglés | MEDLINE | ID: mdl-35563578

RESUMEN

Spot blotch (SB) is a fungal disease that threatens wheat yield and quality. Presently, the molecular mechanism against SB is unclear. In this study, the resistant variety Zhenkang iron shell wheat (Yunmai 0030) and susceptible variety Lincang iron shell wheat (Yunmai 0608) were selected by identifying SB of Yunnan iron shell wheat. The metabolome and transcriptome of leaves of two varieties at different positions were detected using the systemic acquired resistance theory to investigate the molecular and physiological changes in Yunnan iron shell wheat under SB stress. We found that the genes and metabolites related to benzoxazinoid biosynthesis and arginine and proline metabolism were highly enriched after infection with leaf blight. The enriched differential metabolites mainly included phenolic acids, alkaloids, and flavonoids. We further observed that DIBOA- and DIMBOA-glucoside positively affected iron shell wheat resistance to leaf blight and proline and its derivatives were important for plant self-defense. Furthermore, we confirmed that the related metabolites in benzoxazinoid biosynthesis and arginine and proline metabolism positively affected Triticum aestivum ssp. resistance to SB. This study provides new insights into the dynamic physiological changes of wheat in response to SB, helps us better understand the mechanism of resistance to SB, and contributes to the breeding and utilization of resistant varieties.


Asunto(s)
Ascomicetos , Triticum , Arginina/genética , Ascomicetos/genética , Benzoxazinas , China , Resistencia a la Enfermedad/genética , Hierro , Metaboloma , Fitomejoramiento , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Prolina/genética , Transcriptoma , Triticum/genética , Triticum/microbiología
15.
BMC Endocr Disord ; 21(1): 247, 2021 Dec 24.
Artículo en Inglés | MEDLINE | ID: mdl-34952580

RESUMEN

BACKGROUND: The relationship between sleep duration and anthropometric indices are still unclear. This study aimed to explore the association between sleep duration and body mass index (BMI), percentage of body fat (PBF) and visceral fat area (VFA) among Chinese adults, further to explore gender difference in it. METHODS: We analyzed part of the baseline data of a cohort study among adult attendees at two health-screening centers in China. Sleep duration was self-reported and categorized into short (< 7 h/day), optimal (7-9 h/day) and long sleep (≥ 9 h/day). BMI, PBF and VFA were assessed by bioelectric impedance analysis. Demographic characteristics, chronic diseases and medication history, physical activity, smoking and alcohol drinking behaviors were measured by an investigator-administrated questionnaire. RESULTS: A total of 9059 adult participants (63.08% were females) were included in the analysis. The participants aged from 19 to 91 years with the mean age of 45.0 ± 14.6 years. Short sleep was independently associated with elevated odds of general obesity (defined using BMI) and visceral obesity (defined using VFA) among the total study population, and gender differences were observed in these associations. Among women, short sleep was associated with 62% increased odds of general obesity (OR = 1.62, 95% CI: 1.24-2.12) and 22% increased odds of visceral obesity (OR = 1.22, 95% CI: 1.02-1.45). Among men, long sleep duration was associated with 21% decreased odds of visceral obesity (OR = 0.79, 95% CI: 0.64-0.99). No association was observed between sleep duration and PBF in both sexes. CONCLUSIONS: Sleep duration was associated with increased odds of general and visceral obesity, and this association differed between men and women. No association was observed between sleep duration and PBF among either males or females.


Asunto(s)
Tejido Adiposo/metabolismo , Índice de Masa Corporal , Obesidad/epidemiología , Sueño/fisiología , Adulto , Anciano , Anciano de 80 o más Años , China/epidemiología , Estudios Transversales , Femenino , Humanos , Grasa Intraabdominal/metabolismo , Masculino , Persona de Mediana Edad , Obesidad Abdominal/epidemiología , Factores Sexuales , Factores de Tiempo , Adulto Joven
16.
Chembiochem ; 20(1): 7-19, 2019 01 02.
Artículo en Inglés | MEDLINE | ID: mdl-30320963

RESUMEN

Heme-nitric oxide/oxygen binding (H-NOX) proteins are a family of gas-binding hemoproteins that bind diatomic gas ligands such as nitric oxide (NO) and oxygen (O2 ). In bacteria, H-NOXs are often associated with signaling partners, including histidine kinases (HKs), diguanylate cyclases (DGCs) or methyl-accepting chemotaxis proteins (MCPs), either as a stand-alone protein or as a domain of a larger polypeptide. H-NOXs regulate the activity of cognate signaling proteins through ligand-induced conformational changes in the H-NOX domain and protein/protein interactions between the H-NOX and the cognate signaling partner. This review summarizes recent progress toward deciphering the molecular mechanism of bacterial H-NOX activation and the subsequent regulation of H-NOX-associated cognate sensor proteins from a structural and biochemical point of view.


Asunto(s)
Proteínas Bacterianas/metabolismo , Hemoproteínas/metabolismo , Óxido Nítrico/metabolismo , Oxígeno/metabolismo , Bacterias/metabolismo , Proteínas de Escherichia coli/metabolismo , Histidina Quinasa/metabolismo , Liasas de Fósforo-Oxígeno/metabolismo , Unión Proteica , Dominios Proteicos , Transducción de Señal/fisiología
17.
Nat Chem Biol ; 13(12): 1216-1221, 2017 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-28967923

RESUMEN

The binding of nitric oxide (NO) to the heme cofactor of heme-nitric oxide/oxygen binding (H-NOX) proteins can lead to the dissociation of the heme-ligating histidine residue and yield a five-coordinate nitrosyl complex, an important step for NO-dependent signaling. In the five-coordinate nitrosyl complex, NO can reside on either the distal or proximal side of the heme, which could have a profound influence over the lifetime of the in vivo signal. To investigate this central molecular question, we characterized the Shewanella oneidensis H-NOX (So H-NOX)-NO complex biophysically under limiting and excess NO conditions. The results show that So H-NOX preferably forms a distal NO species with both limiting and excess NO. Therefore, signal strength and complex lifetime in vivo will be dictated by the dissociation rate of NO from the distal complex and the rebinding of the histidine ligand to the heme.


Asunto(s)
Proteínas Bacterianas/metabolismo , Óxido Nítrico/metabolismo , Shewanella/metabolismo , Transducción de Señal , Proteínas Bacterianas/química , Proteínas Bacterianas/aislamiento & purificación , Histidina Quinasa/antagonistas & inhibidores , Histidina Quinasa/metabolismo , Ligandos , Modelos Moleculares , Óxido Nítrico/química
18.
Biochemistry ; 57(47): 6570-6580, 2018 11 27.
Artículo en Inglés | MEDLINE | ID: mdl-30398342

RESUMEN

Nitric oxide (NO) is a critical signaling molecule involved in the regulation of a wide variety of physiological processes across every domain of life. In most aerobic and facultative anaerobic bacteria, heme-nitric oxide/oxygen binding (H-NOX) proteins selectively sense NO and inhibit the activity of a histidine kinase (HK) located on the same operon. This NO-dependent inhibition of the cognate HK alters the phosphorylation of the downstream response regulators. In the marine bacterium Saccharophagus degradans ( Sde), in addition to a typical H-NOX ( Sde 3804)/HK ( Sde 3803) pair, an orphan H-NOX ( Sde 3557) with no associated signaling protein has been identified distant from the H-NOX/HK pair in the genome. The characterization reported here elucidates the function of both H-NOX proteins. Sde 3557 exhibits a weaker binding affinity with the kinase, yet both Sde 3804 and Sde 3557 are functional H-NOXs with proper gas binding properties and kinase inhibition activity. Additionally, Sde 3557 has an NO dissociation rate that is significantly slower than that of Sde 3804, which may confer prolonged kinase inhibition in vivo. While it is still unclear whether Sde 3557 has another signaling partner or shares the histidine kinase with Sde 3804, Sde 3557 is the only orphan H-NOX characterized to date. S. degradans is likely using a dual-H-NOX system to fine-tune the downstream response of NO signaling.


Asunto(s)
Proteínas Bacterianas/metabolismo , Gammaproteobacteria/metabolismo , Hemoproteínas/metabolismo , Histidina Quinasa/antagonistas & inhibidores , Óxido Nítrico/metabolismo , Proteínas Bacterianas/química , Hemoproteínas/química , Filogenia
19.
Biochemistry ; 57(11): 1779-1789, 2018 03 20.
Artículo en Inglés | MEDLINE | ID: mdl-29457883

RESUMEN

Heme-nitric oxide/oxygen binding (H-NOX) proteins are a group of hemoproteins that bind diatomic gas ligands such as nitric oxide (NO) and oxygen (O2). H-NOX proteins typically regulate histidine kinases (HK) located within the same operon. It has been reported that NO-bound H-NOXs inhibit cognate histidine kinase autophosphorylation in bacterial H-NOX/HK complexes; however, a detailed mechanism of NO-mediated regulation of the H-NOX/HK activity remains unknown. In this study, the binding interface of Vibrio cholerae ( Vc) H-NOX/HK complex was characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) and further validated by mutagenesis, leading to a new model for NO-dependent kinase inhibition. A conformational change in Vc H-NOX introduced by NO generates a new kinase-binding interface, thus locking the kinase in an inhibitory conformation.


Asunto(s)
Proteínas Bacterianas/química , Hemoproteínas/química , Histidina Quinasa/química , Óxido Nítrico/química , Vibrio cholerae/química , Proteínas Bacterianas/metabolismo , Medición de Intercambio de Deuterio , Hemoproteínas/metabolismo , Histidina Quinasa/metabolismo , Espectrometría de Masas , Óxido Nítrico/metabolismo , Vibrio cholerae/metabolismo
20.
J Biol Chem ; 290(12): 7707-21, 2015 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-25627682

RESUMEN

The hypoxia-inducible factor complex (HIF-α·aryl hydrocarbon receptor nuclear translocator (ARNT)) requires association with several transcription coactivators for a successful cellular response to hypoxic stress. In addition to the conventional global transcription coactivator CREB-binding protein/p300 (CBP/p300) that binds to the HIF-α transactivation domain, a new group of transcription coactivators called the coiled-coil coactivators (CCCs) interact directly with the second PER-ARNT-SIM (PAS) domain of ARNT (ARNT PAS-B). These less studied transcription coactivators play essential roles in the HIF-dependent hypoxia response, and CCC misregulation is associated with several forms of cancer. To better understand CCC protein recruitment by the heterodimeric HIF transcription factor, we used x-ray crystallography, NMR spectroscopy, and biochemical methods to investigate the structure of the ARNT PAS-B domain in complex with the C-terminal fragment of a coiled-coil coactivator protein, transforming acidic coiled-coil coactivator 3 (TACC3). We found that the HIF-2α PAS-B domain also directly interacts with TACC3, motivating an NMR data-derived model suggesting a means by which TACC3 could form a ternary complex with HIF-2α PAS-B and ARNT PAS-B via ß-sheet/coiled-coil interactions. These findings suggest that TACC3 could be recruited as a bridge to cooperatively mediate between the HIF-2α PAS-B·ARNT PAS-B complex, thereby participating more directly in HIF-dependent gene transcription than previously anticipated.


Asunto(s)
Translocador Nuclear del Receptor de Aril Hidrocarburo/metabolismo , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Proteínas Asociadas a Microtúbulos/metabolismo , Transactivadores/fisiología , Translocador Nuclear del Receptor de Aril Hidrocarburo/química , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/química , Cristalografía por Rayos X , Dimerización , Humanos , Proteínas Asociadas a Microtúbulos/química , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular
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