Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning (Q38563962)

4 September 2017

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title

Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning (English)

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4 September 2017

1

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4 September 2017

2

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author name string

Martina M Yordanova

series ordinal

3

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4 September 2017

11 August 2015

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4 September 2017

13

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inferred from page(s)

published in

Nature Reviews Genetics

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4 September 2017

16

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4 September 2017

9

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4 September 2017

517-529

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https://scigraph.springernature.com/pub.10.1038/nrg3963

4 September 2017

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cites work

The origin of the genetic code

1 reference

External suppression of a frameshift mutant in salmonella.

21 January 2018

1 reference

A different genetic code in human mitochondria

21 January 2018

1 reference

UGA is read as tryptophan in Mycoplasma capricolum

21 January 2018

1 reference

An unusual genetic code in nuclear genes of Tetrahymena

21 January 2018

1 reference

Deviation from the universal code shown by the gene for surface protein 51A in Paramecium.

21 January 2018

1 reference

Nucleotide sequence of a yeast Ty element: evidence for an unusual mechanism of gene expression

21 January 2018

1 reference

Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting

21 January 2018

1 reference

A retrovirus-like strategy for expression of a fusion protein encoded by yeast transposon Ty1.

21 January 2018

1 reference

Expression of peptide chain release factor 2 requires high-efficiency frameshift.

21 January 2018

1 reference

A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60.

21 January 2018

1 reference

Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme

21 January 2018

1 reference

Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA

21 January 2018

1 reference

Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA.

21 January 2018

1 reference

Evidence of abundant stop codon readthrough in Drosophila and other metazoa

21 January 2018

1 reference

Carbon source-dependent expansion of the genetic code in bacteria

21 January 2018

1 reference

Massive programmed translational jumping in mitochondria.

21 January 2018

1 reference

Rewiring the keyboard: evolvability of the genetic code

21 January 2018

1 reference

Natural expansion of the genetic code

21 January 2018

1 reference

A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment

21 January 2018

1 reference

Identification of the nature of reading frame transitions observed in prokaryotic genomes

21 January 2018

1 reference

GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences

21 January 2018

1 reference

Stop codon reassignments in the wild

21 January 2018

1 reference

Non-universal decoding of the leucine codon CUG in several Candida species

21 January 2018

1 reference

Evolution and diversification of the organellar release factor family.

21 January 2018

1 reference

Molecular features of mollicutes

21 January 2018

1 reference

Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont

21 January 2018

1 reference

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

21 January 2018

1 reference

Codon reassignment (codon capture) in evolution.

21 January 2018

1 reference

The use of the rare UUA codon to define "expression space" for genes involved in secondary metabolism, development and environmental adaptation in streptomyces.

21 January 2018

1 reference

The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella

21 January 2018

1 reference

The 'polysemous' codon--a codon with multiple amino acid assignment caused by dual specificity of tRNA identity

21 January 2018

1 reference

The non-standard genetic code of Candida spp.: an evolving genetic code or a novel mechanism for adaptation?

21 January 2018

1 reference

Innate immune and chemically triggered oxidative stress modifies translational fidelity.

21 January 2018

1 reference

Promiscuous methionyl-tRNA synthetase mediates adaptive mistranslation to protect cells against oxidative stress

21 January 2018

1 reference

Adding pyrrolysine to the Escherichia coli genetic code.

21 January 2018

1 reference

In vivo contextual requirements for UAG translation as pyrrolysine

21 January 2018

1 reference

Pyrrolysine and selenocysteine use dissimilar decoding strategies

21 January 2018

1 reference

The distinction between recoding and codon reassignment

21 January 2018

1 reference

Non-canonical translation in RNA viruses

21 January 2018

1 reference

Translational control in positive strand RNA plant viruses

21 January 2018

1 reference

A novel stop codon readthrough mechanism produces functional Headcase protein in Drosophila trachea

21 January 2018

1 reference

Identification of stop codon readthrough genes in Saccharomyces cerevisiae.

21 January 2018

1 reference

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

21 January 2018

1 reference

Evidence of efficient stop codon readthrough in four mammalian genes

21 January 2018

1 reference

Programmed translational readthrough generates antiangiogenic VEGF-Ax

21 January 2018

1 reference

Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals

21 January 2018

1 reference

Ribosomal readthrough at a short UGA stop codon context triggers dual localization of metabolic enzymes in Fungi and animals.

21 January 2018

1 reference

A direct estimation of the context effect on the efficiency of termination

21 January 2018

1 reference

The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae.

21 January 2018

1 reference

Impact of the six nucleotides downstream of the stop codon on translation termination

21 January 2018

1 reference

The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons

21 January 2018

1 reference

Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element

21 January 2018

1 reference

Mammalian thioredoxin reductase: oxidation of the C-terminal cysteine/selenocysteine active site forms a thioselenide, and replacement of selenium with sulfur markedly reduces catalytic activity

21 January 2018

1 reference

Structure and mechanism of mammalian thioredoxin reductase: the active site is a redox-active selenolthiol/selenenylsulfide formed from the conserved cysteine-selenocysteine sequence

21 January 2018

1 reference

Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons.

21 January 2018

1 reference

A recoding element that stimulates decoding of UGA codons by Sec tRNA[Ser]Sec

21 January 2018

1 reference

Eukaryotic selenoprotein synthesis: mechanistic insight incorporating new factors and new functions for old factors

21 January 2018

1 reference

Mechanism and regulation of selenoprotein synthesis

21 January 2018

1 reference

Selenoproteins: molecular pathways and physiological roles.

21 January 2018

1 reference

The many levels of control on bacterial selenoprotein synthesis.

21 January 2018

1 reference

Selenoprotein synthesis in archaea

21 January 2018

1 reference

A selDABC cluster for selenocysteine incorporation in Eubacterium acidaminophilum

21 January 2018

1 reference

Adjustments, extinction, and remains of selenocysteine incorporation machinery in the nematode lineage.

21 January 2018

1 reference

Relaxation of Selective Constraints Causes Independent Selenoprotein Extinction in Insect Genomes

21 January 2018

1 reference

Reduced reliance on the trace element selenium during evolution of mammals

21 January 2018

1 reference

Targeted insertion of cysteine by decoding UGA codons with mammalian selenocysteine machinery

21 January 2018

1 reference

Macronuclear gene-sized molecules of hypotrichs

21 January 2018

1 reference

Genetic code supports targeted insertion of two amino acids by one codon

21 January 2018

1 reference

Is there a twenty third amino acid in the genetic code?

21 January 2018

1 reference

Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach

21 January 2018

1 reference

Release factor 2 frameshifting sites in different bacteria.

21 January 2018

1 reference

ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting.

21 January 2018

1 reference

Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation

21 January 2018

1 reference

Regulation of gene expression by macrolide-induced ribosomal frameshifting

21 January 2018

1 reference

Translational recoding in archaea

21 January 2018

1 reference

Control of gene expression by translational recoding.

21 January 2018

1 reference

Recoding: translational bifurcations in gene expression.

21 January 2018

1 reference

Recoding in bacteriophages and bacterial IS elements.

21 January 2018

1 reference

Reprogrammed genetic decoding in cellular gene expression.

21 January 2018

1 reference

Orsay virus utilizes ribosomal frameshifting to express a novel protein that is incorporated into virions

21 January 2018

1 reference

Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein

21 January 2018

1 reference

Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome

21 January 2018

1 reference

Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses

21 January 2018

1 reference

NS1' of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness

21 January 2018

1 reference

A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting

21 January 2018

1 reference

Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma

21 January 2018

1 reference

An overlapping protein-coding region in influenza A virus segment 3 modulates the host response

21 January 2018

1 reference

Translational recoding signals between gag and pol in diverse LTR retrotransposons.

21 January 2018

1 reference

A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene

21 January 2018

1 reference

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes

21 January 2018

1 reference

Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC).

21 January 2018

1 reference

Ribosome profiling: new views of translation, from single codons to genome scale

21 January 2018

1 reference

Observation of dually decoded regions of the human genome using ribosome profiling data

21 January 2018

1 reference

Computational identification of putative programmed translational frameshift sites

21 January 2018

1 reference

Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli.

21 January 2018

1 reference

Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae

21 January 2018

1 reference

Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli

21 January 2018

1 reference

PRFdb: a database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals

21 January 2018

1 reference

Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast

21 January 2018

1 reference

Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

21 January 2018

1 reference

rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift

21 January 2018

1 reference

The interplay of mRNA stimulatory signals required for AUU-mediated initiation and programmed -1 ribosomal frameshifting in decoding of transposable element IS911.

21 January 2018

1 reference

Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL.

21 January 2018

1 reference

A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation

21 January 2018

1 reference

Stem-loop structures can effectively substitute for an RNA pseudoknot in -1 ribosomal frameshifting.

21 January 2018

1 reference

Apical loop-internal loop RNA pseudoknots: a new type of stimulator of -1 translational frameshifting in bacteria

21 January 2018

1 reference

Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot

21 January 2018

1 reference

Programmed ribosomal frameshifting in decoding the SARS-CoV genome

21 January 2018

1 reference

A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal

21 January 2018

1 reference

An atypical RNA pseudoknot stimulator and an upstream attenuation signal for -1 ribosomal frameshifting of SARS coronavirus

21 January 2018

1 reference

An intermolecular RNA triplex provides insight into structural determinants for the pseudoknot stimulator of -1 ribosomal frameshifting

21 January 2018

1 reference

Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting

21 January 2018

1 reference

An 'elaborated' pseudoknot is required for high frequency frameshifting during translation of HCV 229E polymerase mRNA.

21 January 2018

1 reference

Unusual -1 ribosomal frameshift caused by stable RNA G-quadruplex in open reading frame

21 January 2018

1 reference

Stimulation of ribosomal frameshifting by RNA G-quadruplex structures

21 January 2018

1 reference

A long-distance RNA-RNA interaction plays an important role in programmed -1 ribosomal frameshifting in the translation of p88 replicase protein of Red clover necrotic mosaic virus

21 January 2018

1 reference

A -1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA

21 January 2018

1 reference

Frameshifting RNA pseudoknots: structure and mechanism

21 January 2018

1 reference

Frameshifting in alphaviruses: a diversity of 3' stimulatory structures

21 January 2018

1 reference

RNA pseudoknots and the regulation of protein synthesis

21 January 2018

1 reference

Transactivation of programmed ribosomal frameshifting by a viral protein

21 January 2018

1 reference

Efficient stimulation of site-specific ribosome frameshifting by antisense oligonucleotides

21 January 2018

1 reference

Novel application of sRNA: stimulation of ribosomal frameshifting

21 January 2018

1 reference

Polyamine sensing by nascent ornithine decarboxylase antizyme stimulates decoding of its mRNA.

21 January 2018

1 reference

Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins

21 January 2018

1 reference

Expanded ATXN3 frameshifting events are toxic in Drosophila and mammalian neuron models.

21 January 2018

1 reference

The potential role of ribosomal frameshifting in generating aberrant proteins implicated in neurodegenerative diseases

21 January 2018

1 reference

Ribosomal frameshifting on MJD-1 transcripts with long CAG tracts

21 January 2018

1 reference

Depletion of cognate charged transfer RNA causes translational frameshifting within the expanded CAG stretch in huntingtin

21 January 2018

1 reference

P-site tRNA is a crucial initiator of ribosomal frameshifting.

21 January 2018

1 reference

Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon

21 January 2018

1 reference

Isolation and characterization of a novel actin filament-binding protein from Saccharomyces cerevisiae

21 January 2018

1 reference

Special peptidyl-tRNA molecules can promote translational frameshifting without slippage.

21 January 2018

1 reference

Hungry codons promote frameshifting in human mitochondrial ribosomes

21 January 2018

1 reference

Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria

21 January 2018

1 reference

Ribosome rescue and translation termination at non-standard stop codons by ICT1 in mammalian mitochondria.

21 January 2018

1 reference

Shifty ciliates: frequent programmed translational frameshifting in euplotids

21 January 2018

1 reference

Connection between stop codon reassignment and frequent use of shifty stop frameshifting

21 January 2018

1 reference

Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA

21 January 2018

1 reference

One protein from two open reading frames: mechanism of a 50 nt translational bypass.

21 January 2018

1 reference

Coupling of open reading frames by translational bypassing

21 January 2018

1 reference

A nascent peptide is required for ribosomal bypass of the coding gap in bacteriophage T4 gene 60.

21 January 2018

1 reference

High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide

21 January 2018

1 reference

Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp

21 January 2018

1 reference

Bifunctional transfer-messenger RNA.

21 January 2018

1 reference

tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell

21 January 2018

1 reference

21 January 2018

1 reference

Ends of the line for tmRNA-SmpB.

21 January 2018

1 reference

The 'cleavage' activities of foot-and-mouth disease virus 2A site-directed mutants and naturally occurring '2A-like' sequences

21 January 2018

1 reference

Expanding and reprogramming the genetic code of cells and animals

21 January 2018

1 reference

Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes

21 January 2018

1 reference

Deleterious mutations and the evolution of sexual reproduction

21 January 2018

1 reference

Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria

21 January 2018

1 reference

Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance

21 January 2018

1 reference

Posttranscriptional recoding by RNA editing

21 January 2018

1 reference

Identification of A-to-I RNA editing: dotting the i's in the human transcriptome.

21 January 2018

1 reference

A-to-I editing of protein coding and noncoding RNAs

21 January 2018

1 reference

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

21 January 2018

1 reference

Converting nonsense codons into sense codons by targeted pseudouridylation

21 January 2018

1 reference

Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting

21 January 2018

1 reference

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

21 January 2018

1 reference

RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders

21 January 2018

1 reference

Repeat-associated non-AUG translation and its impact in neurodegenerative disease

21 January 2018

1 reference

Repeat-associated non-ATG (RAN) translation in neurological disease

21 January 2018

1 reference

Natural Read-through at the UGA Termination Signal of Qβ Coat Protein Cistron

21 January 2018

1 reference

On malleability in the genetic code

31 March 2020

1 reference

Translational readthrough of the PDE2 stop codon modulates cAMP levels in Saccharomyces cerevisiae

31 March 2020

1 reference

Invertebrate synapsins: a single gene codes for several isoforms in Drosophila.

31 March 2020

1 reference

Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons

31 March 2020

1 reference

Computational Resources for Studying Recoding

31 March 2020

1 reference

Ribosomal frameshifting used in influenza A virus expression occurs within the sequence UCC_UUU_CGU and is in the +1 direction

31 March 2020

1 reference

Identification and characterisation of a developmentally regulated mammalian gene that utilises -1 programmed ribosomal frameshifting

31 March 2020

1 reference

A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA

31 March 2020

1 reference

Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site

31 March 2020

1 reference

Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast

31 March 2020

1 reference

Analysis of the aphthovirus 2A/2B polyprotein ‘cleavage’ mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal ‘skip’

31 March 2020

1 reference

31 March 2020

1 reference

Reading frame switch caused by base-pair formation between the 3' end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli

31 March 2020

1 reference

12 December 2020

Methanogenesis from Methylated Amines in a Hypersaline Algal Mat

1 reference

12 December 2020

Examination of the function of two kelch proteins generated by stop codon suppression

1 reference

12 December 2020

The structure of the mouse glutathione peroxidase gene: the selenocysteine in the active site is encoded by the 'termination' codon, TGA

1 reference

12 December 2020

The cDNA for rat selenoprotein P contains 10 TGA codons in the open reading frame

1 reference

12 December 2020

Coding from a distance: dissection of the mRNA determinants required for the incorporation of selenocysteine into protein

1 reference

12 December 2020

Identifiers

DOI

10.1038/NRG3963

1 reference

PubMed ID

26260261

Dimensions Publication ID

4 September 2017

0 references

1 reference

PubMed ID

26260261