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Cited by 67RNA and protein synthesis mechanismsGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

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

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Baranov, Pavel V, Hammer, Andrew W, Zhou, Jiadong, Gesteland, Raymond F, Atkins, John F·2005·Genome Biology
DOI 10.1186/gb-2005-6-3-r25PMC PMC1088944
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Abstract

Background: Transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mRNAs. Individual mRNA molecules within this population differ in the number of nucleotides they contain that are not specified by the template. When transcriptional slippage occurs in a coding sequence, translation of the resulting mRNAs yields more than one protein product. Except where the products of the resulting mRNAs have distinct functions, transcription slippage occurring in a coding region is expected to be disadvantageous. This probably leads to selection against most slippage-prone sequences in coding regions. Results: To find a length at which such selection is evident, we analyzed the distribution of repetitive runs of A and T of different lengths in 108 bacterial genomes. This length varies significantly among different bacteria, but in a large proportion of available genomes corresponds to nine nucleotides. Comparative sequence analysis of these genomes was used to identify occurrences of 9A and 9T transcriptional slippage-prone sequences used for gene expression. Conclusions: IS element genes are the largest group found to exploit this phenomenon. A number of genes with disrupted open reading frames (ORFs) have slippage-prone sequences at which transcriptional slippage would result in uninterrupted ORF restoration at the mRNA level. The ability of such genes to encode functional full-length protein products brings into question their annotation as pseudogenes and in these cases is pertinent to the significance of the term 'authentic frameshift' frequently assigned to such genes.

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  • Mononucleotide repeats, especially poly(A) and poly(U) tracts, cause transcriptional and translational frameshifting.

    “Mononucleotide repeats, especially poly(A) and poly(U) tracts, are also known to cause transcriptional and translational frameshifting [8-10].”

    From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [8]

    The Background describes transcriptional slippage at a run of nine As, producing mRNAs with different reading frames. It also describes ribosomal frameshifting in E. coli, but does not establish that poly(A) or poly(U) tracts cause that translational frameshifting. The Discussion likewise supports transcriptional slippage on A and T runs, not both mechanisms. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Codon pair preferences can be shaped by decrease of frameshifting errors through avoidance of mononucleotide repeats.

    “One is the possible decrease of frameshifting errors through avoidance of mononucleotide repeats [8-10].”

    From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [8]

    The Results section reports that A/T runs are avoided in some prokaryotic coding regions, and the Discussion links their underrepresentation to slippage and possible frameshift errors. The paper does not establish that this avoidance shapes codon-pair preferences specifically; it also says it cannot distinguish transcriptional from replication-level slippage. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Codons in combination with surrounding nucleotides can form mononucleotide repeats, which may cause transcriptional or translational slippage.

    “In addition, codons in combination with surrounding nucleotides can form mononucleotide repeats, which may cause transcriptional [8,9] or translational [10] slippage.”

    From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [8]

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Cited by

Sorted by citations

Authors
Baranov, P. V., Hammer, A. W., Zhou, J., Gesteland, R. F., & Atkins, J. F.
Affiliations
University of Utah (US)
Corresponding author
Atkins, John F
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2005-02-15
Volume
6
Issue
3
Pages
R25-R25
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/gb-2005-6-3-r25
PMC
PMC1088944
OpenAlex
W2107534434
Cited by
67
References
0
Citations by year
2026: 1 · 2025: 2 · 2024: 4 · 2022: 1 · 2021: 4 · 2020: 2 · 2019: 2 · 2018: 3 · 2017: 2 · 2016: 4 · 2015: 6 · 2014: 5 · 2013: 2 · 2012: 3
FWCI
1.76
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders
  • U.S. Department of Energy (FG0301ER63132)
  • Science Foundation Ireland
  • National Institutes of Health
  • National Institute of General Medical Sciences (R01GM048152, GM48152)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
transcriptional slippage, ribosomal frameshifting, insertion sequences, pseudogenes, bacterial genomes, comparative genomics, mRNA heterogeneity
MeSH terms
Adenosine, Bacteria, Base Sequence, DNA Transposable Elements, Genes, Bacterial, Models, Biological, Molecular Sequence Data, RNA, Bacterial, Selection, Genetic, Thymidine, Transcription, Genetic, Open Reading Frames, Sequence Alignment, Genome, Bacterial, Computational Biology, Genomics

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