ArticleNucleic acids research2013
Identification of the nature of reading frame transitions observed in prokaryotic genomes.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 36 citations in OpenAlex.
- Compensatory evolution facilitates loss of prfB autoregulation in Pseudomonas fluorescens SBW25.Molecular biology and evolution · 2026Article
- Pervasive genome structure heterogeneity iniScience · 2026Article
- Translational Frameshifting in theMicroorganisms · 2022Article
- Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance.BMC genomics · 2022Article
- "Pseudo-pseudogenes" in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica.Nucleic acids research · 2022Article
- Transcript Regulation of the Recoded Archaeal α-l-Fucosidase In Vivo.Molecules (Basel, Switzerland) · 2021Article
- Programmed Deviations of Ribosomes From Standard Decoding in Archaea.Frontiers in microbiology · 2021Review
- The energy landscape of -1 ribosomal frameshifting.Science advances · 2020Article
- Processive Recoding and Metazoan Evolution of Selenoprotein P: Up to 132 UGAs in Molluscs.Journal of molecular biology · 2019Article
- Natural Strain Variation Reveals Diverse Biofilm Regulation in Squid-ColonizingJournal of bacteriology · 2019Article
- Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes.BMC genomics · 2019Article
- Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis.Nucleic acids research · 2017Article
- Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage.Nucleic acids research · 2017Article
- Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.Nucleic acids research · 2016Review
- N-Methylation as a Strategy for Enhancing the Affinity and Selectivity of RNA-binding Peptides: Application to the HIV-1 Frameshift-Stimulating RNA.ACS chemical biology · 2016Article
- Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning.Nature reviews. Genetics · 2015Review
- Identification of protein coding regions in RNA transcripts.Nucleic acids research · 2015Article
- Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
Our goal was to identify evolutionary conserved frame transitions in protein coding regions and to uncover an underlying functional role of these structural aberrations. We used the ab initio frameshift prediction program, GeneTack, to detect reading frame transitions in 206 991 genes (fs-genes) from 1106 complete prokaryotic genomes. We grouped 102 731 fs-genes into 19 430 clusters based on sequence similarity between protein products (fs-proteins) as well as conservation of predicted position of the frameshift and its direction. We identified 4010 pseudogene clusters and 146 clusters of fs-genes apparently using recoding (local deviation from using standard genetic code) due to possessing specific sequence motifs near frameshift positions. Particularly interesting was finding of a novel type of organization of the dnaX gene, where recoding is required for synthesis of the longer subunit, τ. We selected 20 clusters of predicted recoding candidates and designed a series of genetic constructs with a reporter gene or affinity tag whose expression would require a frameshift event. Expression of the constructs in Escherichia coli demonstrated enrichment of the set of candidates with sequences that trigger genuine programmed ribosomal frameshifting; we have experimentally confirmed four new families of programmed frameshifts.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.