scholarly journals A novel structural mechanism of ribosomal stop codon readthrough in VEGF-A

2021 ◽  
Author(s):  
Nico O. Wagner ◽  
Jerome M. Edwards ◽  
Juliana Abramovich ◽  
Paromita Gupta ◽  
Harish Swaminathan ◽  
...  
Keyword(s):  
Structural Organization ◽  
Closed Loop ◽  
Stop Codon ◽  
Structural Studies ◽  
Range Interaction ◽  
Structural Mechanism ◽  
Coding Sequence ◽  
Long Range Interaction ◽  
Functional Relevance ◽  
Stop Codon Readthrough

Abstract The process of ribosomal recoding is generally regulated by an autonomous mRNA signal downstream of stop-codons. While structural studies have provided mechanistic insights into viral systems, no such studies exist in mammalian systems. Here we define a novel structural mechanism for the VEGF-A readthrough system and show that regulation is multifaceted and complex, requiring a multipartite set of RNA elements located at long distances that interact with each other and with hnRNP A2/B1 to synergistically enhance readthrough levels. The Ax-element downstream of the stop codon adopts a unique multistem (SL-Ax1-3) architecture: SL-Ax1 interacts with hnRNP A2/B1, while SL-Ax2 interacts with an RNA element (SL-Au1) located ~500 nt upstream at the start of the coding sequence. SL-Au1 also independently binds to hnRNP A2/B1, which manipulates an equilibrium between alternate structures— from a sequestered bulge towards one that allows for the long-range interaction with SL-Ax2. Overall, our study not only highlights the significance of structural organization of elements within the coding sequence of mRNA, but also provides a functional relevance of the closed-loop mRNA organization in non-canonical translation and suggests complex mechanisms allow for finer integration of many signals for a required output.

Ribosome Structural Organization

1974 ◽  
Vol 32 ◽  
pp. 332-333
Author(s):  
James A. Lake
Keyword(s):  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Small Subunit ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Specific Antibodies ◽  
X Ray ◽  
E Coli ◽  
Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

Phase transformation and Raman spectra in BaTiO3 nanocrystals

2002 ◽  
Vol 718 ◽  
Author(s):  
Jian Yu ◽  
X. J. Meng ◽  
J.L. Sun ◽  
G.S. Wang ◽  
J.H. Chu
Keyword(s):  
Particle Size ◽  
Phase Transformation ◽  
Low Temperature ◽  
Long Range ◽  
Lattice Expansion ◽  
Inversion Symmetry ◽  
Range Interaction ◽  
Cooperative Phenomena ◽  
Long Range Interaction ◽  
Hydrothermal Methods

AbstractIn this paper, size-induced ferroelectricit yweakening, phase transformation, and anomalous lattice expansion are observed in nanocrystalline BaTiO3 (nc-BaTiO3) deriv ed b y low temperature hydrothermal methods, and they are w ellunderstood using the terms of the long-range interaction and its cooperative phenomena altered by particle size in covalen t ionic nanocrystals. In cubic nc-BaTiO3, five modes centerd at 186, 254, 308, 512 and 716 cm-1 are observed Raman active in cubic nanophase, and they are attributed to local rhombohedral distortion breaking inversion-symmetry in cubic nanophase. The254 and 308 cm-1 modes are significantly affected not only by the concentration of hydroxyl defects, but also their particular configuration. And the 806 cm-1 modes found to be closely associated with OH - absorbed on grain boundaries.

scholarly journals L-MPZ, a Novel Isoform of Myelin P0, Is Produced by Stop Codon Readthrough

2012 ◽  
Vol 287 (21) ◽  
pp. 17765-17776 ◽  
Author(s):  
Yoshihide Yamaguchi ◽  
Akiko Hayashi ◽  
Celia W. Campagnoni ◽  
Akio Kimura ◽  
Takashi Inuzuka ◽  
...  
Keyword(s):  
Stop Codon ◽  
Stop Codon Readthrough

scholarly journals Inverse Problem for Ising Connection Matrix with Long-Range Interaction

Mathematics ◽  
2021 ◽  
Vol 9 (14) ◽  
pp. 1624
Author(s):  
Leonid Litinskii ◽  
Boris Kryzhanovsky
Keyword(s):  
Inverse Problem ◽  
Long Range ◽  
Random Number ◽  
Connection Matrix ◽  
Range Interaction ◽  
Connection Matrices ◽  
Ising Systems ◽  
Long Range Interaction ◽  
Matrix Spectrum ◽  
Analytical Expressions

In the present paper, we examine Ising systems on d-dimensional hypercube lattices and solve an inverse problem where we have to determine interaction constants of an Ising connection matrix when we know a spectrum of its eigenvalues. In addition, we define restrictions allowing a random number sequence to be a connection matrix spectrum. We use the previously obtained analytical expressions for the eigenvalues of Ising connection matrices accounting for an arbitrary long-range interaction and supposing periodic boundary conditions.

scholarly journals Modulation of Viral Programmed Ribosomal Frameshifting and Stop Codon Readthrough by the Host Restriction Factor Shiftless

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1230
Author(s):  
Sawsan Napthine ◽  
Chris H. Hill ◽  
Holly C. M. Nugent ◽  
Ian Brierley
Keyword(s):  
Rna Binding ◽  
Mutational Analysis ◽  
Stop Codon ◽  
Leukemia Virus ◽  
Size Exclusion ◽  
Human Immunodeficiency Virus Replication ◽  
Mobility Shift ◽  
Ribosomal Frameshifting ◽  
Stop Codon Readthrough

The product of the interferon-stimulated gene C19orf66, Shiftless (SHFL), restricts human immunodeficiency virus replication through downregulation of the efficiency of the viral gag/pol frameshifting signal. In this study, we demonstrate that bacterially expressed, purified SHFL can decrease the efficiency of programmed ribosomal frameshifting in vitro at a variety of sites, including the RNA pseudoknot-dependent signals of the coronaviruses IBV, SARS-CoV and SARS-CoV-2, and the protein-dependent stimulators of the cardioviruses EMCV and TMEV. SHFL also reduced the efficiency of stop-codon readthrough at the murine leukemia virus gag/pol signal. Using size-exclusion chromatography, we confirm the binding of the purified protein to mammalian ribosomes in vitro. Finally, through electrophoretic mobility shift assays and mutational analysis, we show that expressed SHFL has strong RNA binding activity that is necessary for full activity in the inhibition of frameshifting, but shows no clear specificity for stimulatory RNA structures.

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