ArticleMolecular biology and evolution2011
A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.
Article in Molecular biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 47 citations in OpenAlex.
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- Transaldolase in Bacillus methanolicus: biochemical characterization and biological role in ribulose monophosphate cycle.BMC microbiology · 2020Article
- Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences.BMC evolutionary biology · 2019Article
- Non-programmed transcriptional frameshifting is common and highly RNA polymerase type-dependent.Microbial cell factories · 2018Article
- Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.Genome research · 2018Article
- A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting.BMC evolutionary biology · 2018Article
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- Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage.Nucleic acids research · 2017Article
- Position-dependent termination and widespread obligatory frameshifting in Euplotes translation.Nature structural & molecular biology · 2017Article
- Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.Nucleic acids research · 2016Review
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- Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges.BMC genomics · 2015Article
- Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning.Nature reviews. Genetics · 2015Review
- RNA editing by T7 RNA polymerase bypasses InDel mutations causing unexpected phenotypic changes.Nucleic acids research · 2015Article
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Authors and funding
7 authors at 6 institutions in 4 countries.
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Abstract
Bacterial genome annotations contain a number of coding sequences (CDSs) that, in spite of reading frame disruptions, encode a single continuous polypeptide. Such disruptions have different origins: sequencing errors, frameshift, or stop codon mutations, as well as instances of utilization of nontriplet decoding. We have extracted over 1,000 CDSs with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. Analysis of the clusters revealed deep phylogenetic conservation of open reading frame organization as well as the presence of conserved sequence patterns that indicate likely utilization of the nonstandard decoding mechanisms: programmed ribosomal frameshifting (PRF) and programmed transcriptional realignment (PTR). Further enrichment of these clusters with additional homologous nucleotide sequences revealed over 6,000 candidate genes utilizing PRF or PTR. Analysis of the patterns of conservation apparently associated with nontriplet decoding revealed the presence of both previously characterized frameshift-prone sequences and a few novel ones. Since the starting point of our analysis was a set of genes with already annotated disruptions, it is highly plausible that in this study, we have identified only a fraction of all bacterial genes that utilize PRF or PTR. In addition to the identification of a large number of recoded genes, a surprising observation is that nearly half of them are expressed via PTR-a mechanism that, in contrast to PRF, has not yet received substantial attention.
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