Global analysis of genomic texts: The distribution of AGCT tetranucleotides in the <i>Escherichia coli</i> and <i>Bacillus subtilis</i> genomes predicts translational frameshifting and ribosomal hopping in several genes

Hénaut, Alain; Lisacek, Frédérique; Nitschké, Patrick; Moszer, Ivan; Danchin, Antoine

doi:10.1002/elps.1150190411

Cited by 13 publications

(11 citation statements)

References 59 publications

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“…The present results also address a suggestion made by Danchin and colleagues (9). They found some association between the tetranucleotide AGCT and sites of translational initiation, frameshifting, or potential ''hopping'' (i.e., bypassing) in the genomes of Escherichia coli and Bacillus subtilis.…”

supporting

confidence: 91%

“…Our results demonstrate that the complex does scan through the coding gap sequence, although in a mode that precludes normal translation. We have also examined the effect near the landing site of the tetranucleotide AGCT, hypothesized to be a framekeeping motif (9), and found that it has no effect on bypassing efficiency in our example. Further consideration of the bypassing phenomenon leads to the hypothesis that codon::anticodon matching in the P-site strongly influences the ability of the adjacent A-site to accept aminoacyl-tRNA.…”

mentioning

confidence: 88%

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Evidence that the bypassing ribosome travels through the coding gap

Gallant¹,

Bonthuis²,

Lindsley³

2003

Proc. Natl. Acad. Sci. U.S.A.

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In translational bypassing, a peptidyl-tRNA::ribosome complex skips over a number of nucleotides in a messenger sequence and resumes protein chain elongation after a ''landing site'' downstream of the bypassed region. The present experiments demonstrate that the complex ''scans'' processively through the bypassed region. This conclusion rests on three observations. (i) When two potential ''landing sites'' are present, the protein sequence of the product shows that virtually all ribosomes land at the first and virtually none at the second. (ii) In such a sequence with two landing sites, the presence of a terminator triplet in phase in the coding region immediately after the first landing site drastically reduces the efficiency of bypassing. (iii) Internally complementary sequences that can form a stable stem͞loop in the bypassed region significantly reduce the efficiency of bypassing. We analyze bypassing from a given ''takeoff'' site to ''landing sites'' at different distances downstream so as to derive estimates of the frequency of ribosome takeoff and of the stability of the bypassing complex.I n ''translational bypassing,'' a ribosome skips over a number of nucleotides in a messenger sequence so as to join the information from two noncontiguous ORFs into the sequence of a single, continuous polypeptide chain (reviewed in ref. 1). The prototypical case has been the translation of the phage T4 gene 60 mRNA coding for a topoisomerase subunit, which involves the bypassing of a 50-nt untranslated segment (or ''coding gap'') between a GGA ''takeoff'' triplet and a GGA ''landing site'' triplet. (In the text, we use boldface to show RNA triplets and normal type for triplets or other sequences in DNA.) This case of bypassing depends on very specific features of the sequence (1-3): (i) identity of the takeoff and landing site triplets, implying that peptidyl-tRNA is what makes the trip; (ii) optimum spacing of the takeoff and landing sites; (iii) a terminator triplet immediately 3Ј of the takeoff triplet; (iv) a stem-loop of optimal stability and placement in the region after the takeoff site; and (v) a particular amino acid sequence of the peptide encoded in a region 5Ј of the takeoff site. The role of these sequence elements and of participating factors has been investigated in detail (1, 4-6).The sequence rules governing this kind of bypass event seem very constraining. We have reported on a type of bypass event that seems to be subject to more relaxed rules and may therefore occur on a wide variety of sequences. This is a bypass induced by ribosome pausing at a ''hungry'' codon calling for an aminoacyltRNA in short supply (7,8). We showed that this kind of bypass shared with the gene 60 case only the requirement for synonymous takeoff and landing sites. Otherwise, it could be demonstrated over various coding gap distances (from 7 to at least 40 nt), and seemed largely independent of the sequence in the coding gap and upstream of it (7). In those experiments and the present ones, we inhibited the activation of isole...

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supporting

confidence: 91%

mentioning

confidence: 88%

Evidence that the bypassing ribosome travels through the coding gap

Gallant¹,

Bonthuis²,

Lindsley³

2003

Proc. Natl. Acad. Sci. U.S.A.

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“…However, we have mapped short Illumina reads to the genome on several occasions for other purposes and have not seen evidence of sequencing errors. It is therefore more likely that the single insertion/deletion events may be tolerated due to translational hopping [42], [43] or some similar phenomenon.…”

Section: Resultsmentioning

confidence: 99%

Candidate Genes That May Be Responsible for the Unusual Resistances Exhibited by Bacillus pumilus SAFR-032 Spores

et al. 2013

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The spores of several Bacillus species, including Bacillus pumilus SAFR-032 and B. safensis FO-36b, which were isolated from the spacecraft assembly facility at NASA's Jet Propulsion Laboratory, are unusually resistant to UV radiation and hydrogen peroxide. In order to identify candidate genes that might be associated with these resistances, the whole genome of B. pumilus SAFR-032, and the draft genome of B. safensis FO-36b were compared in detail with the very closely related type strain B. pumilus ATCC7061T. 170 genes are considered characteristic of SAFR-032, because they are absent from both FO-36b and ATCC7061T. Forty of these SAFR-032 characteristic genes are entirely unique open reading frames. In addition, four genes are unique to the genomes of the resistant SAFR-032 and FO-36b. Fifty three genes involved in spore coat formation, regulation and germination, DNA repair, and peroxide resistance, are missing from all three genomes. The vast majority of these are cleanly deleted from their usual genomic context without any obvious replacement. Several DNA repair and peroxide resistance genes earlier reported to be unique to SAFR-032 are in fact shared with ATCC7061T and no longer considered to be promising candidates for association with the elevated resistances. Instead, several SAFR-032 characteristic genes were identified, which along with one or more of the unique SAFR-032 genes may be responsible for the elevated resistances. These new candidates include five genes associated with DNA repair, namely, BPUM_0608 a helicase, BPUM_0652 an ATP binding protein, BPUM_0653 an endonuclease, BPUM_0656 a DNA cytosine-5- methyltransferase, and BPUM_3674 a DNA helicase. Three of these candidate genes are in immediate proximity of two conserved hypothetical proteins, BPUM_0654 and BPUM_0655 that are also absent from both FO-36b and ATCC7061T. This cluster of five genes is considered to be an especially promising target for future experimental work.

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“…This deconvolution step was performed by subtracting the correlation function of a model genome constructed so as to contain only the trivial bias. The concept of model genome has been developed in [53,54]. This is performed here as follows:…”

Section: Methodsmentioning

confidence: 99%

Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"

Larsabal

Danchin

2005

BMC Bioinformatics

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BackgroundThe genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin.ResultsUsing a technique for analysis of auto-correlations based on linear projection, we identified the sequences responsible for the bias. Prokaryotic and lower eukaryotic genomes are covered with ubiquitous patterns that we termed "class A flexible patterns". Each pattern is composed of up to ten conserved nucleotides or dinucleotides distributed into a discontinuous motif. Each occurrence spans a region up to 50 bp in length. They belong to what we named the "flexible pattern" type, in that there is some limited fluctuation in the distances between the nucleotides composing each occurrence of a given pattern. When taken together, these patterns cover up to half of the genome in the majority of prokaryotes. They generate the previously recognized 11 bp periodic bias.ConclusionJudging from the structure of the patterns, we suggest that they may define a dense network of protein interaction sites in chromosomes.

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Global analysis of genomic texts: The distribution of AGCT tetranucleotides in the Escherichia coli and Bacillus subtilis genomes predicts translational frameshifting and ribosomal hopping in several genes

Cited by 13 publications

References 59 publications

Evidence that the bypassing ribosome travels through the coding gap

Evidence that the bypassing ribosome travels through the coding gap

Candidate Genes That May Be Responsible for the Unusual Resistances Exhibited by Bacillus pumilus SAFR-032 Spores

Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"

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