Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation

2021 ◽  
Vol 118 (47) ◽  
pp. e2109026118
Author(s):  
Adrien Chauvier ◽  
Pujan Ajmera ◽  
Rajeev Yadav ◽  
Nils G. Walter
Keyword(s):  
Transcription Factor ◽  
Transcription Regulation ◽  
Single Molecule ◽  
Transcriptional Control ◽  
Response Times ◽  
Fast Response ◽  
Control Element ◽  
Order Structure ◽  
Control Of Gene Expression ◽  
Bacterial Transcription

Cotranscriptional RNA folding is widely assumed to influence the timely control of gene expression, but our understanding remains limited. In bacteria, the fluoride (F−)-sensing riboswitch is a transcriptional control element essential to defend against toxic F− levels. Using this model riboswitch, we find that its ligand F− and essential bacterial transcription factor NusA compete to bind the cotranscriptionally folding RNA, opposing each other’s modulation of downstream pausing and termination by RNA polymerase. Single-molecule fluorescence assays probing active transcription elongation complexes discover that NusA unexpectedly binds highly reversibly, frequently interrogating the complex for emerging, cotranscriptionally folding RNA duplexes. NusA thus fine-tunes the transcription rate in dependence of the ligand-responsive higher-order structure of the riboswitch. At the high NusA concentrations found intracellularly, this dynamic modulation is expected to lead to adaptive bacterial transcription regulation with fast response times.

scholarly journals Transcription factor IIIA gene expression in Xenopus oocytes utilizes a transcription factor similar to the major late transcription factor.

1989 ◽  
Vol 9 (11) ◽  
pp. 5003-5011 ◽  
Author(s):  
R K Hall ◽  
W L Taylor
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Control ◽  
Somatic Cells ◽  
State Level ◽  
Control Element ◽  
Transcription Factor Iiia ◽  
Shift Analysis ◽  
Late Transcription ◽  
Upstream Element

Xenopus transcription factor IIIA (TFIIIA) gene expression is stringently regulated during development. The steady-state level of TFIIIA mRNA in a somatic cell is approximately 10(6) times less than in an immature oocyte. We have undertaken studies designed to identify differences in how the TFIIIA gene is transcribed in oocytes and somatic cells. In this regard, we have localized an upstream transcriptional control element in the TFIIIA promoter that stimulates transcription from the TFIIIA promoter approximately threefold in microinjected oocytes. The upstream element, in cis. does not stimulate transcription from the TFIIIA promoter in somatic cells. Thus, the element appears to be oocyte specific in the context of the TFIIIA promoter. However, both oocytes and somatic cells contain a protein (or a related protein) that binds the upstream element. We have termed this protein from oocytes the TFIIIA distal element factor. The sequence of the upstream element is similar to the sequence of the upstream element found in the adenovirus major late promoter that is a binding site for the major late transcription factor. By gel shift analysis, chemical footprinting, methylation intereference, and point mutation analysis, we demonstrate that the TFIIIA distal element factor and major late transcription factor have similar DNA-binding properties.

Transcription factor IIIA gene expression in Xenopus oocytes utilizes a transcription factor similar to the major late transcription factor

1989 ◽  
Vol 9 (11) ◽  
pp. 5003-5011
Author(s):  
R K Hall ◽  
W L Taylor
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Control ◽  
Somatic Cells ◽  
State Level ◽  
Control Element ◽  
Transcription Factor Iiia ◽  
Shift Analysis ◽  
Late Transcription ◽  
Upstream Element

Xenopus transcription factor IIIA (TFIIIA) gene expression is stringently regulated during development. The steady-state level of TFIIIA mRNA in a somatic cell is approximately 10(6) times less than in an immature oocyte. We have undertaken studies designed to identify differences in how the TFIIIA gene is transcribed in oocytes and somatic cells. In this regard, we have localized an upstream transcriptional control element in the TFIIIA promoter that stimulates transcription from the TFIIIA promoter approximately threefold in microinjected oocytes. The upstream element, in cis. does not stimulate transcription from the TFIIIA promoter in somatic cells. Thus, the element appears to be oocyte specific in the context of the TFIIIA promoter. However, both oocytes and somatic cells contain a protein (or a related protein) that binds the upstream element. We have termed this protein from oocytes the TFIIIA distal element factor. The sequence of the upstream element is similar to the sequence of the upstream element found in the adenovirus major late promoter that is a binding site for the major late transcription factor. By gel shift analysis, chemical footprinting, methylation intereference, and point mutation analysis, we demonstrate that the TFIIIA distal element factor and major late transcription factor have similar DNA-binding properties.

Nanostructure of semiconductor quantum dots in a borosilicate glass matrix by complementary use of HREM and AEM

1990 ◽  
Vol 48 (4) ◽  
pp. 728-729
Author(s):  
M.J. Kim ◽  
L.C. Liu ◽  
S.H. Risbud ◽  
R.W. Carpenter
Keyword(s):  
Quantum Dots ◽  
Borosilicate Glass ◽  
Glass Matrix ◽  
Optical Switching ◽  
Response Times ◽  
Fast Response ◽  
Processing Technique ◽  
Internal Stresses ◽  
Electron Hole ◽  
Spatial Dimensions

When the size of a semiconductor is reduced by an appropriate materials processing technique to a dimension less than about twice the radius of an exciton in the bulk crystal, the band like structure of the semiconductor gives way to discrete molecular orbital electronic states. Clusters of semiconductors in a size regime lower than 2R {where R is the exciton Bohr radius; e.g. 3 nm for CdS and 7.3 nm for CdTe) are called Quantum Dots (QD) because they confine optically excited electron- hole pairs (excitons) in all three spatial dimensions. Structures based on QD are of great interest because of fast response times and non-linearity in optical switching applications.In this paper we report the first HREM analysis of the size and structure of CdTe and CdS QD formed by precipitation from a modified borosilicate glass matrix. The glass melts were quenched by pouring on brass plates, and then annealed to relieve internal stresses. QD precipitate particles were formed during subsequent "striking" heat treatments above the glass crystallization temperature, which was determined by differential thermal analysis.

Compact and efficient gas diffusion electrodes based on nanoporous alumina membranes for microfuel cells and gas sensors

The Analyst ◽  
2020 ◽  
Vol 145 (1) ◽  
pp. 122-131 ◽  
Author(s):  
Wanda V. Fernandez ◽  
Rocío T. Tosello ◽  
José L. Fernández
Keyword(s):  
Response Times ◽  
Hydrogen Oxidation ◽  
Fast Response ◽  
Gas Diffusion ◽  
Limiting Current ◽  
Gas Diffusion Electrodes ◽  
Nanoporous Alumina ◽  
Alumina Membranes ◽  
Current Densities ◽  
Microfuel Cells

Gas diffusion electrodes based on nanoporous alumina membranes electrocatalyze hydrogen oxidation at high diffusion-limiting current densities with fast response times.

scholarly journals MiRNAs and Muscle Regeneration: Therapeutic Targets in Duchenne Muscular Dystrophy

2021 ◽  
Vol 22 (8) ◽  
pp. 4236
Author(s):  
Amelia Eva Aránega ◽  
Estefanía Lozano-Velasco ◽  
Lara Rodriguez-Outeiriño ◽  
Felicitas Ramírez de Acuña ◽  
Diego Franco ◽  
...  
Keyword(s):  
Stem Cell ◽  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Muscle Regeneration ◽  
Transcriptional Control ◽  
Neuromuscular Disorders ◽  
Critical Role ◽  
Gene Replacement ◽  
Control Of Gene Expression ◽  
Muscle Disorders

microRNAs (miRNAs) are small non-coding RNAs required for the post-transcriptional control of gene expression. MicroRNAs play a critical role in modulating muscle regeneration and stem cell behavior. Muscle regeneration is affected in muscular dystrophies, and a critical point for the development of effective strategies for treating muscle disorders is optimizing approaches to target muscle stem cells in order to increase the ability to regenerate lost tissue. Within this framework, miRNAs are emerging as implicated in muscle stem cell response in neuromuscular disorders and new methodologies to regulate the expression of key microRNAs are coming up. In this review, we summarize recent advances highlighting the potential of miRNAs to be used in conjunction with gene replacement therapies, in order to improve muscle regeneration in the context of Duchenne Muscular Dystrophy (DMD).

scholarly journals Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model

2021 ◽  
Author(s):  
David A Garcia ◽  
Gregory Fettweis ◽  
Diego M Presman ◽  
Ville Paakinaho ◽  
Christopher Jarzynski ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Power Law ◽  
Dwell Time ◽  
Specific Binding ◽  
Power Law Distribution ◽  
Single Molecule Level ◽  
Binding Behavior ◽  
Chromatin Template ◽  
Nuclear Domains

Abstract Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs—one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.

scholarly journals Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

2021 ◽  
Vol 22 (5) ◽  
pp. 2398
Author(s):  
Wooyoung Kang ◽  
Seungha Hwang ◽  
Jin Young Kang ◽  
Changwon Kang ◽  
Sungchul Hohng
Keyword(s):  
Single Molecule ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Facilitated Diffusion ◽  
One Dimensional ◽  
Bacterial Transcription ◽  
Fluorescence Measurements ◽  
Dimensional Diffusion ◽  
Single Molecule Studies ◽  
Hopping Diffusion

Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion.

scholarly journals FEM Simulation of Frequency-Selective Surface Based on Thermoelectric Bi-Sb Thin Films for THz Detection

Photonics ◽  
2021 ◽  
Vol 8 (4) ◽  
pp. 119
Author(s):  
Anastasiia Tukmakova ◽  
Ivan Tkhorzhevskiy ◽  
Artyom Sedinin ◽  
Aleksei Asach ◽  
Anna Novotelnova ◽  
...  
Keyword(s):  
Thin Films ◽  
Response Times ◽  
Fem Simulation ◽  
Film Surface ◽  
Frequency Selective Surface ◽  
Fast Response ◽  
Radiation Absorption ◽  
Thz Radiation ◽  
Frequency Filter ◽  
Frequency Selective

Terahertz (THz) filters and detectors can find a wide application in such fields as: sensing, imaging, security systems, medicine, wireless connection, and detection of substances. Thermoelectric materials are promising basis for THz detectors’ development due to their sensitivity to the THz radiation, possibility to be heated under the THz radiation and produce voltage due to Seebeck effect. Thermoelectric thin films of Bi-Sb solid solutions are semimetals/semiconductors with the band gap comparable with THz energy and with high thermoelectric conversion efficiency at room temperature. Detecting film surface can be transformed into a periodic frequency selective surface (FSS) that can operate as a frequency filter and increases the absorption of THz radiation. We report for the first time about the simulation of THz detector based on thermoelectric Bi-Sb thin-filmed frequency-selective surface. We show that such structure can be both detector and frequency filter. Moreover, it was shown that FSS design increases not only a heating due to absorption but a temperature gradient in Bi-Sb film by two orders of magnitude in comparison with continuous films. Local temperature gradients can reach the values of the order of 100 K·mm−1. That opens new perspectives for thin-filmed thermoelectric detectors’ efficiency increase. Temperature difference formed due to THz radiation absorption can reach values on the order of 1 degree. Frequency-transient calculations show the power dependence of film temperature on time with characteristic saturation at times around several ms. That points to the perspective of reaching fast response times on such structures.

Novel optical oxygen sensing by phosphorescence quenching of palladium porphyrin self-assembled film on alumina plate

2000 ◽  
Vol 04 (02) ◽  
pp. 179-184 ◽  
Author(s):  
YUTAKA AMAO ◽  
KEISUKE ASAI ◽  
ICHIRO OKURA
Keyword(s):  
Oxygen Pressure ◽  
Oxygen Sensor ◽  
Response Times ◽  
Oxygen Sensing ◽  
Fast Response ◽  
Phosphorescence Quenching ◽  
Highly Sensitive ◽  
Optical Oxygen Sensor ◽  
Self Assembled ◽  
Quenching By Oxygen

An optical oxygen sensor based on the phosphorescence quenching of palladium tetrakis(4-carboxyphenyl)porphyrin (PdTCPP) self-assembled film (SAM) on alumina plate was developed. The phosphorescence intensity of PdTCPP film decreased with increasing oxygen pressure, indicating that the film can be used as an optical oxygen-sensing device based on phosphorescence quenching by oxygen. The ratio I0/I100 as a sensitivity measure of the sensing film is estimated to be 17.7, showing that the film is a highly sensitive device for oxygen pressure. The film obeyed Stern–Volmer plots with a multisite model and possessed good operational stability and a fast response. Response times are 36 s for deoxygenated to oxygenated conditions and 148 s for the reverse conditions.

Sign in / Sign up

Export Citation Format

Share Document