(Q35423038)

English

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

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scholarly article

1 reference

Europe PubMed Central

8 August 2017

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

1 reference

Europe PubMed Central

8 August 2017

object named as

Virag Sharma

1

0 references

object named as

Ivan Antonov

3

0 references

object named as

Pavel V Baranov

7

0 references

Andrew E. Firth

object named as

Andrew E Firth

2

0 references

object named as

John F Atkins

5

0 references

author name string

Olivier Fayet

4

1 reference

Europe PubMed Central

8 August 2017

Mark Borodovsky

6

1 reference

Europe PubMed Central

8 August 2017

publication date

14 June 2011

1 reference

Europe PubMed Central

8 August 2017

Molecular Biology and Evolution

1 reference

Europe PubMed Central

8 August 2017

28

1 reference

Europe PubMed Central

8 August 2017

3195-3211

1 reference

Europe PubMed Central

8 August 2017

11

1 reference

Europe PubMed Central

8 August 2017

Regulation of gene expression by reiterative transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Bacillus anthracis genome organization in light of whole transcriptome sequencing

1 reference

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12 July 2018

Functions and regulation of RNA editing by ADAR deaminases

1 reference

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12 July 2018

Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

The Pfam protein families database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Recode-2: new design, new search tools, and many more genes

1 reference

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12 July 2018

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

1 reference

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12 July 2018

AmiGO: online access to ontology and annotation data

1 reference

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12 July 2018

Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts.

1 reference

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12 July 2018

A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting

1 reference

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12 July 2018

Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses

1 reference

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12 July 2018

Argyrophilic grain disease

1 reference

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12 July 2018

Programmed Ribosomal Frameshifting Goes Beyond Viruses: Organisms from all three kingdoms use frameshifting to regulate gene expression, perhaps signaling a paradigm shift

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

PAML 4: phylogenetic analysis by maximum likelihood

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Recoding in bacteriophages and bacterial IS elements.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Transcriptional slippage in mxiE controls transcription and translation of the downstream mxiD gene, which encodes a component of the Shigella flexneri type III secretion apparatus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Paramyxovirus mRNA editing, the "rule of six" and error catastrophe: a hypothesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Frameshifting by transcriptional slippage is involved in production of MxiE, the transcription activator regulated by the activity of the type III secretion apparatus in Shigella flexneri.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

The origin and evolution of human pathogens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Complex management: RNA editing in trypanosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Conserved translational frameshift in dsDNA bacteriophage tail assembly genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Phase and antigenic variation in bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

WebLogo: A Sequence Logo Generator

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

-1 frameshifting at a CGA AAG hexanucleotide site is required for transposition of insertion sequence IS1222

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

MUSCLE: multiple sequence alignment with high accuracy and high throughput

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Reprogrammed genetic decoding in cellular gene expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed + 1 translational frameshifting in structural protein synthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Deoxyribo ucleic acid-directed synthesis of ribonucleic acid by an enzyme from Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

A-to-I RNA editing: recent news and residual mysteries

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Escherichia coli insertion sequence IS150: transposition via circular and linear intermediates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Chemical modification of nucleotide bases and mRNA editing depend on hexamer or nucleoprotein phase in Sendai virus nucleocapsids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Computational identification of putative programmed translational frameshift sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

The Ka/Ks ratio: diagnosing the form of sequence evolution

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

https://pubmed.ncbi.nlm.nih.gov/21673094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

RNA editing by adenosine deaminases that act on RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Recoding: translational bifurcations in gene expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Release factor 2 frameshifting sites in different bacteria.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

The many roles of an RNA editor.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

The versatility of paramyxovirus RNA polymerase stuttering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Ribosomal -1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Detection of an IS2-encoded 46-kilodalton protein capable of binding terminal repeats of IS2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Phosphoglycerate kinase and triosephosphate isomerase from the hyperthermophilic bacterium Thermotoga maritima form a covalent bifunctional enzyme complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Competition between frameshifting, termination and suppression at the frameshift site in the Escherichia coli release factor-2 mRNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Ribosomal frameshifting from -2 to +50 nucleotides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Sequence logos: a new way to display consensus sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Programmed translational frameshifting and initiation at an AUU codon in gene expression of bacterial insertion sequence IS911

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

High-level ribosomal frameshifting directs the synthesis of IS150gene products

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

Identification of the site of translational frameshifting required for production of the transposase encoded by insertion sequence IS 1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

12 July 2018

The distinction between recoding and codon reassignment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

26 September 2018

Functional characterization and high-throughput proteomic analysis of interrupted genes in the archaeon Sulfolobus solfataricus.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

26 September 2018

Gene conversion maintains nonfunctional transposable elements in an obligate mutualistic endosymbiont

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

26 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

26 September 2018

DNA sequence error rates in Genbank records estimated using the mouse genome as a reference.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3199440

26 September 2018

Recoding: reprogrammed genetic decoding

1 reference

https://pubmed.ncbi.nlm.nih.gov/21673094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent

1 reference

https://pubmed.ncbi.nlm.nih.gov/21673094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computing multiple sequence/structure alignments with the T-coffee package

1 reference

https://pubmed.ncbi.nlm.nih.gov/21673094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting

1 reference

https://pubmed.ncbi.nlm.nih.gov/21673094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Transcriptional slippage controls production of type III secretion apparatus components in Shigella flexneri

1 reference

https://pubmed.ncbi.nlm.nih.gov/21673094

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/MOLBEV/MSR155

1 reference

Europe PubMed Central

8 August 2017

1 reference

Europe PubMed Central

8 August 2017

1 reference

Europe PubMed Central

8 August 2017

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