scholarly journals From Recoding to Peptides for MHC Class I Immune Display: Enriching Viral Expression, Virus Vulnerability and Virus Evasion

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1251
Author(s):  
John F. Atkins ◽  
Kate M. O’Connor ◽  
Pramod R. Bhatt ◽  
Gary Loughran
Keyword(s):  
Deep Level ◽  
Stop Codon ◽  
Level Structure ◽  
Translation Speed ◽  
Viral Expression ◽  
Persistent Viruses ◽  
Selection For ◽  
High Level ◽  
Stop Codon Readthrough ◽  
Coding Capacity

Many viruses, especially RNA viruses, utilize programmed ribosomal frameshifting and/or stop codon readthrough in their expression, and in the decoding of a few a UGA is dynamically redefined to specify selenocysteine. This recoding can effectively increase viral coding capacity and generate a set ratio of products with the same N-terminal domain(s) but different C-terminal domains. Recoding can also be regulatory or generate a product with the non-universal 21st directly encoded amino acid. Selection for translation speed in the expression of many viruses at the expense of fidelity creates host immune defensive opportunities. In contrast to host opportunism, certain viruses, including some persistent viruses, utilize recoding or adventitious frameshifting as part of their strategy to evade an immune response or specific drugs. Several instances of recoding in small intensively studied viruses escaped detection for many years and their identification resolved dilemmas. The fundamental importance of ribosome ratcheting is consistent with the initial strong view of invariant triplet decoding which however did not foresee the possibility of transitory anticodon:codon dissociation. Deep level dynamics and structural understanding of recoding is underway, and a high level structure relevant to the frameshifting required for expression of the SARS CoV-2 genome has just been determined.

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 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.

scholarly journals The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code

Open Biology ◽  
2016 ◽  
Vol 6 (11) ◽  
pp. 160246 ◽  
Author(s):  
Julia Hofhuis ◽  
Fabian Schueren ◽  
Christopher Nötzel ◽  
Thomas Lingner ◽  
Jutta Gärtner ◽  
...  
Keyword(s):  
Malate Dehydrogenase ◽  
Stop Codon ◽  
Protein Isoforms ◽  
Translational Readthrough ◽  
Peroxisomal Targeting ◽  
Codon Context ◽  
Targeting Signal ◽  
Stop Codon Readthrough ◽  
Insight Into ◽  
Actual Ratio

Translational readthrough gives rise to C-terminally extended proteins, thereby providing the cell with new protein isoforms. These may have different properties from the parental proteins if the extensions contain functional domains. While for most genes amino acid incorporation at the stop codon is far lower than 0.1%, about 4% of malate dehydrogenase (MDH1) is physiologically extended by translational readthrough and the actual ratio of MDH1x (e x tended protein) to ‘normal' MDH1 is dependent on the cell type. In human cells, arginine and tryptophan are co-encoded by the MDH1x UGA stop codon. Readthrough is controlled by the 7-nucleotide high-readthrough stop codon context without contribution of the subsequent 50 nucleotides encoding the extension. All vertebrate MDH1x is directed to peroxisomes via a hidden peroxisomal targeting signal (PTS) in the readthrough extension, which is more highly conserved than the extension of lactate dehydrogenase B. The hidden PTS of non-mammalian MDH1x evolved to be more efficient than the PTS of mammalian MDH1x. These results provide insight into the genetic and functional co-evolution of these dually localized dehydrogenases.

Deep Level Centers in Carbon-Doped High Resistivity GaN

2014 ◽  
Vol 997 ◽  
pp. 492-495
Author(s):  
Huan Cui ◽  
Li Wu Lu ◽  
Ling Sang ◽  
Bai He Chen ◽  
Zhi Wei He ◽  
...  
Keyword(s):  
Deep Level ◽  
Chemical Vapor ◽  
Deep Levels ◽  
Hall Measurement ◽  
High Resistivity ◽  
Organic Chemical ◽  
Carbon Doped ◽  
Metal Organic ◽  
High Level ◽  
Organic Chemical Vapor Deposition

The deep levels of carbon doped high resistivity (HR) GaN samples grown by metal-organic chemical vapor deposition (MOCVD) has been investigated using thermally stimulated current (TSC) spectroscopy and high temperature (HT) Hall measurement. Two different thickness of 100 and 300 nm were used to be compared. It was found that four distinct deep levels by TSC and one deep level by HT Hall measurement were observed in both samples, which means great help for the decrease of leakage current and lifetime limitations of device utilizing the structure. The activation energy of these levels was calculated and their possible origins were also proposed. The low temperature traps, might be related to VN, 0.50 and 0.52eV related to incorporate a high level carbon, 0.57eV related to VGa, 0.59eV related to CGaor NGa, 0.91 and 0.97eV related to interstitial N1.

scholarly journals Evaluation of Resistance Development in Bemisia tabaci Genn. (Homoptera: Aleyrodidae) in Cotton against Different Insecticides

Insects ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 996
Author(s):  
Muhammad Zaryab Khalid ◽  
Sohail Ahmed ◽  
Ibrahim Al-ashkar ◽  
Ayman EL Sabagh ◽  
Liyun Liu ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
The Other ◽  
Resistance Development ◽  
Susceptible Population ◽  
Low Level ◽  
Development Of Resistance ◽  
Major Pest ◽  
Selection For ◽  
High Level ◽  
Very High

Cotton is a major crop of Pakistan, and Bemisia tabaci (Homoptera: Aleyrodidae) is a major pest of cotton. Due to the unwise and indiscriminate use of insecticides, resistance develops more readily in the whitefly. The present study was conducted to evaluate the resistance development in the whitefly against the different insecticides that are still in use. For this purpose, the whitefly population was selected with five concentrations of each insecticide, for five generations. At G1, compared with the laboratory susceptible population, a very low level of resistance was observed against bifenthrin, cypermethrin, acetamiprid, imidacloprid, thiamethoxam, nitenpyram, chlorfenapyr, and buprofezin with a resistance ratio of 3-fold, 2-fold, 1-fold, 4-fold, 3-fold, 3-fold, 3-fold, and 3-fold, respectively. However, the selection for five generations increased the resistance to a very high level against buprofezin (127-fold), and to a high level against imidacloprid (86-fold) compared with the laboratory susceptible population. While, a moderate level of resistance was observed against cypermethrin (34-fold), thiamethoxam (34-fold), nitenpyram (30-fold), chlorfenapyr (29-fold), and acetamiprid (21-fold). On the other hand, the resistance was low against bifenthrin (18-fold) after selection for five generations. A very low level of resistance against the field population of B. tabaci, at G1, showed that these insecticides are still effective, and thus can be used under the field conditions for the management of B. tabaci. However, the proper rotation of insecticides among different groups can help to reduce the development of resistance against insecticides.

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