The structural basis for release factor activation during translation termination revealed by time-resolved cryogenic electron microscopy

2018 ◽  
Author(s):  
David Wright
Keyword(s):  
Electron Microscopy ◽  
Translation Termination ◽  
Structural Basis ◽  
Release Factor ◽  
Time Resolved

scholarly journals The Structural Basis for Release Factor Activation during Translation Termination Revealed by Time-Resolved Cryogenic Electron Microscopy

2019 ◽  
Vol 116 (3) ◽  
pp. 574a-575a ◽  
Author(s):  
Ziao Fu ◽  
Gabriele Indrisiunaite ◽  
Sandip Kaledhonkar ◽  
Binita Shah ◽  
Ming Sun ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Translation Termination ◽  
Structural Basis ◽  
Release Factor ◽  
Time Resolved

scholarly journals The structural basis for release factor activation during translation termination revealed by time-resolved cryogenic electron microscopy

2018 ◽  
Author(s):  
Ziao Fu ◽  
Gabriele Indrisiunaite ◽  
Sandip Kaledhonkar ◽  
Binita Shah ◽  
Ming Sun ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
High Speed ◽  
Stop Codon ◽  
Structural Basis ◽  
Ester Bond ◽  
Dependent Manner ◽  
Release Factor ◽  
Accuracy Class ◽  
Time Resolved ◽  
Class 1

AbstractWhen the mRNA translating ribosome encounters a stop codon in its aminoacyl site (A site), it recruits a class-1 release factor (RF) to induce hydrolysis of the ester bond between peptide chain and peptidyl-site (P-site) tRNA. This process, called termination of translation, is under strong selection pressure for high speed and accuracy. Class-1 RFs (RF1, RF2 in bacteria, eRF1 in eukarya and aRF1 in archaea), have structural motifs that recognize stop codons in the decoding center (DC) and a universal GGQ motif for induction of ester bond hydrolysis in the peptidyl transfer center (PTC) 70 Å away from the DC. The finding that free RF2 is compact with only 20 Å between its codon reading and GGQ motifs came therefore as a surprise1. Cryo-electron microscopy (cryo-EM) then showed that ribosome-bound RF1 and RF2 have extended structures2,3, suggesting that bacterial RFs are compact when entering the ribosome and switch to the extended form in a stop signal-dependent manner3. FRET4, cryo-EM5,6 and X-ray crystallography7, along with a rapid kinetics study suggesting a pre-termination conformational change on the millisecond time-scale of ribosome-bound RF1 and RF28, have lent indirect support to this proposal. However, direct experimental evidence for such a short-lived compact conformation on the native pathway to RF-dependent termination is missing due to its transient nature. Here we use time-resolved cryo-EM9,10,11,12,13 to visualize compact and extended forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing complex on the pathway to termination. About 25% of ribosomal complexes have RFs in the compact state at 24 ms reaction time after mixing RF and ribosomes, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.

Microtubule nucleation sequence studied by time-resolved x-ray scattering and electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 766-767
Author(s):  
Eva-Maria Mandelkow ◽  
Eckhard Mandelkow ◽  
Joan Bordas
Keyword(s):  
Electron Microscopy ◽  
Dynamic Equilibrium ◽  
Time Resolved ◽  
X Ray ◽  
Additional Information ◽  
X Ray Scattering ◽  
Low Concentrations ◽  
Microtubule Growth ◽  
Ray Patterns ◽  
Ray Scattering

When a solution of microtubule protein is changed from non-polymerising to polymerising conditions (e.g. by temperature jump or mixing with GTP) there is a series of structural transitions preceding microtubule growth. These have been detected by time-resolved X-ray scattering using synchrotron radiation, and they may be classified into pre-nucleation and nucleation events. X-ray patterns are good indicators for the average behavior of the particles in solution, but they are difficult to interpret unless additional information on their structure is available. We therefore studied the assembly process by electron microscopy under conditions approaching those of the X-ray experiment. There are two difficulties in the EM approach: One is that the particles important for assembly are usually small and not very regular and therefore tend to be overlooked. Secondly EM specimens require low concentrations which favor disassembly of the particles one wants to observe since there is a dynamic equilibrium between polymers and subunits.

Electron Microscopy and image reconstruction reveal the structural basis for spectrin's elastic properties

1992 ◽  
Vol 50 (1) ◽  
pp. 510-511
Author(s):  
Amy M. McGough ◽  
Robert Josephs
Keyword(s):  
Electron Microscopy ◽  
Elastic Properties ◽  
Conformational Changes ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Membrane Skeleton ◽  
Projection Algorithm ◽  
Structural Basis ◽  
Iterative Approximation ◽  
Membrane Skeletons

The remarkable deformability of the erythrocyte derives in large part from the elastic properties of spectrin, the major component of the membrane skeleton. It is generally accepted that spectrin's elasticity arises from marked conformational changes which include variations in its overall length (1). In this work the structure of spectrin in partially expanded membrane skeletons was studied by electron microscopy to determine the molecular basis for spectrin's elastic properties. Spectrin molecules were analysed with respect to three features: length, conformation, and quaternary structure. The results of these studies lead to a model of how spectrin mediates the elastic deformation of the erythrocyte.Membrane skeletons were isolated from erythrocyte membrane ghosts, negatively stained, and examined by transmission electron microscopy (2). Particle lengths and end-to-end distances were measured from enlarged prints using the computer program MACMEASURE. Spectrin conformation (straightness) was assessed by calculating the particles’ correlation length by iterative approximation (3). Digitised spectrin images were correlation averaged or Fourier filtered to improve their signal-to-noise ratios. Three-dimensional reconstructions were performed using a suite of programs which were based on the filtered back-projection algorithm and executed on a cluster of Microvax 3200 workstations (4).

Time-resolved high-resolution electron microscopy of structural stability in mgo clusters

1996 ◽  
Vol 54 ◽  
pp. 672-673
Author(s):  
T. Kizuka ◽  
N. Tanaka
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Magnesium Oxide ◽  
Structural Stability ◽  
High Resolution Electron Microscopy ◽  
Video Tape ◽  
Solid State Physics ◽  
Time Resolved ◽  
Resolution Electron ◽  
Structural And Functional Properties

Structure and stability of atomic clusters have been studied by time-resolved high-resolution electron microscopy (TRHREM). Typical examples are observations of structural fluctuation in gold (Au) clusters supported on silicon oxide films, graphtized carbon films and magnesium oxide (MgO) films. All the observations have been performed on the clusters consisted of single metal element. Structural stability of ceramics clusters, such as metal-oxide, metal-nitride and metal-carbide clusters, has not been observed by TRHREM although the clusters show anomalous structural and functional properties concerning to solid state physics and materials science.In the present study, the behavior of ceramic, magnesium oxide (MgO) clusters is for the first time observed by TRHREM at 1/60 s time resolution and at atomic resolution down to 0.2 nm.MgO and gold were subsequently deposited on sodium chloride (001) substrates. The specimens, single crystalline MgO films on which Au particles were dispersed were separated in distilled water and observed by using a 200-kV high-resolution electron microscope (JEOL, JEM2010) equipped with a high sensitive TV camera and a video tape recorder system.

Time-Resolved Cryo-Electron Microscopy of Oscillating Microtubules

1990 ◽  
Vol 48 (1) ◽  
pp. 502-503
Author(s):  
Eva-Maria Mandelkow ◽  
Ron Milligan
Keyword(s):  
Electron Microscopy ◽  
Dynamic Instability ◽  
Entire Solution ◽  
Reaction Scheme ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
A Chain ◽  
Ray Scattering

Microtubules form part of the cytoskeleton of eukaryotic cells. They are hollow libers of about 25 nm diameter made up of 13 protofilaments, each of which consists of a chain of heterodimers of α-and β-tubulin. Microtubules can be assembled in vitro at 37°C in the presence of GTP which is hydrolyzed during the reaction, and they are disassembled at 4°C. In contrast to most other polymers microtubules show the behavior of “dynamic instability”, i.e. they can switch between phases of growth and phases of shrinkage, even at an overall steady state [1]. In certain conditions an entire solution can be synchronized, leading to autonomous oscillations in the degree of assembly which can be observed by X-ray scattering (Fig. 1), light scattering, or electron microscopy [2-5]. In addition such solutions are capable of generating spontaneous spatial patterns [6].In an earlier study we have analyzed the structure of microtubules and their cold-induced disassembly by cryo-EM [7]. One result was that disassembly takes place by loss of protofilament fragments (tubulin oligomers) which fray apart at the microtubule ends. We also looked at microtubule oscillations by time-resolved X-ray scattering and proposed a reaction scheme [4] which involves a cyclic interconversion of tubulin, microtubules, and oligomers (Fig. 2). The present study was undertaken to answer two questions: (a) What is the nature of the oscillations as seen by time-resolved cryo-EM? (b) Do microtubules disassemble by fraying protofilament fragments during oscillations at 37°C?

Femtosecond Time-resolved Electron Microscopy

2014 ◽  
Vol 134 (4) ◽  
pp. 515-520
Author(s):  
Jinfeng Yang ◽  
Yoichi Yoshida ◽  
Hiromi Shibata
Keyword(s):  
Electron Microscopy ◽  
Time Resolved

scholarly journals A data reduction and compression description for high throughput time-resolved electron microscopy

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Abhik Datta ◽  
Kian Fong Ng ◽  
Deepan Balakrishnan ◽  
Melissa Ding ◽  
See Wee Chee ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Temporal Resolution ◽  
Data Reduction ◽  
Accurate Estimation ◽  
Data Streaming ◽  
Compression Scheme ◽  
Raw Data ◽  
Time Resolved ◽  
Detection And Counting ◽  
Spatio Temporal

AbstractFast, direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies. Preserving both spatial and temporal resolution in extended observations, however, requires storing prohibitively large amounts of data. Here, we describe an efficient and flexible data reduction and compression scheme (ReCoDe) that retains both spatial and temporal resolution by preserving individual electron events. Running ReCoDe on a workstation we demonstrate on-the-fly reduction and compression of raw data streaming off a detector at 3 GB/s, for hours of uninterrupted data collection. The output was 100-fold smaller than the raw data and saved directly onto network-attached storage drives over a 10 GbE connection. We discuss calibration techniques that support electron detection and counting (e.g., estimate electron backscattering rates, false positive rates, and data compressibility), and novel data analysis methods enabled by ReCoDe (e.g., recalibration of data post acquisition, and accurate estimation of coincidence loss).

Gene Overexpression as a Tool for Identifying New trans-Acting Factors Involved in Translation Termination in Saccharomyces cerevisiae

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 585-594
Author(s):  
Olivier Namy ◽  
Isabelle Hatin ◽  
Guillaume Stahl ◽  
Hongmei Liu ◽  
Stephanie Barnay ◽  
...  
Keyword(s):  
Protein Transport ◽  
Stop Codon ◽  
Translation Termination ◽  
Spindle Pole Body ◽  
Spindle Pole ◽  
Release Factor ◽  
Lacz Reporter Gene ◽  
Pole Body ◽  
Secondary Phenotypes ◽  
Termination Process

Abstract In eukaryotes, translation termination is dependent on the availability of both release factors, eRF1 and eRF3; however, the precise mechanisms involved remain poorly understood. In particular, the fact that the phenotype of release factor mutants is pleiotropic could imply that other factors and interactions are involved in translation termination. To identify unknown elements involved in this process, we performed a genetic screen using a reporter strain in which a leaky stop codon is inserted in the lacZ reporter gene, attempting to isolate factors modifying termination efficiency when overexpressed. Twelve suppressors and 11 antisuppressors, increasing or decreasing termination readthrough, respectively, were identified and analyzed for three secondary phenotypes often associated with translation mutations: thermosensitivity, G418 sensitivity, and sensitivity to osmotic pressure. Interestingly, among these candidates, we identified two genes, SSO1 and STU2, involved in protein transport and spindle pole body formation, respectively, suggesting puzzling connections with the translation termination process.

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