Enterobacterial Repetitive Intergenic Consensus Sequence Repeats in Yersiniae: Genomic Organization and Functional Properties

Gregorio, Eliana De; Silvestro, Giustina De; Petrillo, Mauro; Carlomagno, Maria Stella; Nocera, Pier Paolo Di

doi:10.1128/jb.187.23.7945-7954.2005

Cited by 54 publications

(64 citation statements)

References 46 publications

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“…It has been suggested that ERIC sequences would in all likelihood have some functional role in the bacterial cell (Asinmov et al, 2005;De Gregorio et al, 2005) although this has not yet been demonstrated.…”

Section: Discussionmentioning

confidence: 99%

ERIC-PCR genotyping of field isolates ofSalmonella entericasubsp.entericaserovar Gallinarum biovars Gallinarum and Pullorum

et al. 2015

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Salmonella Gallinarum (SG) and Salmonella Pullorum (SP) have been classified as biovars belonging to Salmonella enterica subsp. enterica serovar Gallinarum. Genetic diversity among isolates of the same biovar can be detected by DNA fingerprinting techniques which are useful in epidemiological investigations. In this study, we applied the PCR amplification of Enterobacterial Repetitive Intergenic Consensus sequences (ERIC-PCR) to analyse 45 strains of SG and SP, most of which were isolated from diseased poultry of different Brazilian regions over a period of 27 years until 2014. The ERIC-genotypes obtained were used to describe the epidemiological relationship amongst the strains. Our findings showed that there were six ERIC-patterns for SG strains at 80% similarity. In addition, some of the SG isolates recovered from different regions and years clustered with 100% similarity, suggesting that transfer of genotypes between these regions has taken place. The commercial rough vaccine strain 9R showed a unique profile. Meanwhile, more genetic diversity was observed among SP strains where ten ERICpatterns were also formed at 80% similarity.

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Section: Discussionmentioning

confidence: 99%

ERIC-PCR genotyping of field isolates ofSalmonella entericasubsp.entericaserovar Gallinarum biovars Gallinarum and Pullorum

et al. 2015

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“…Unlike SDR elements, the previously described ERIC/IRU (De Gregario et al 2005;Wilson and Sharp 2006), RSA (Bachellier et al 1999), and BoxC (Bachellier et al 1999) elements in enteric bacteria, RUP (Oggioni and Claverys 1999) and boxAB n C (Martin et al 1992;Knutson et al 2006) elements in Streptococcus, and NEMIS (Mazzone et al 2001) and SRE/Correia (Buisine et al 2002) elements in Neisseria are all relatively long, imperfect palindromes possibly derived from transposons.…”

Section: Do Sdr Elements Function As Rna?mentioning

confidence: 99%

“…Copies of retroposons (and degenerate retroposons, such as Alu sequences) are made through RNA intermediates, catalyzed by reverse transcriptase (Ostertag and Kazazian 2001). Minitransposons (also called MITEs), a category that may include the well-studied ERIC sequences (De Gregario et al 2005), are thought to rely on transposases encoded outside of the mobile element (Siguier et al 2006). The 8-nt highly iterated palindromic (HIP1) sequences observed in the genomes of many related cyanobacteria are thought not to be mobile but rather to form through mutation from pre-existing sequences (Robinson et al 1997), The mechanisms by which small dispersed repeats are generated are otherwise unknown.…”

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confidence: 99%

Very small mobile repeated elements in cyanobacterial genomes

Elhai

Kato²,

Cousins³

et al. 2008

Genome Res.

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Mobile DNA elements play a major role in genome plasticity and other evolutionary processes, an insight gained primarily through the study of transposons and retrotransposons (generally ∼1000 nt or longer). These elements spawn smaller parasitic versions (generally >100 nt) that propagate through proteins encoded by the full elements. Highly repeated sequences smaller than 100 nt have been described, but they are either nonmobile or their origins are not known. We have surveyed the genome of the multicellular cyanobacterium, Nostoc punctiforme, and its relatives for small dispersed repeat (SDR) sequences and have identified eight families in the range of from 21 to 27 nucleotides. Three of the families (SDR4, SDR5, and SDR6), despite little sequence similarity, share a common predicted secondary structure, a conclusion supported by patterns of compensatory mutations. The SDR elements are found in a diverse set of contexts, often embedded within tandemly repeated heptameric sequences or within minitransposons. One element (SDR5) is found exclusively within instances of an octamer, HIP1, that is highly over-represented in the genomes of many cyanobacteria. Two elements (SDR1 and SDR4) often are found within copies of themselves, producing complex nested insertions. An analysis of SDR elements within cyanobacterial genomes indicate that they are essentially confined to a coherent subgroup. The evidence indicates that some of the SDR elements, probably working through RNA intermediates, have been mobile in recent evolutionary time, making them perhaps the smallest known mobile elements.[Supplemental material is available online at www.genome.org.] The mechanisms by which new copies of dispersed repeats are generated are well understood in some, but by no means, all cases. Transposon copies arise through DNA intermediates, catalyzed by transposases (Gueguen et al. 2005). Copies of retroposons (and degenerate retroposons, such as Alu sequences) are made through RNA intermediates, catalyzed by reverse transcriptase (Ostertag and Kazazian 2001). Minitransposons (also called MITEs), a category that may include the well-studied ERIC sequences (De Gregario et al. 2005), are thought to rely on transposases encoded outside of the mobile element (Siguier et al. 2006). The 8-nt highly iterated palindromic (HIP1) sequences observed in the genomes of many related cyanobacteria are thought not to be mobile but rather to form through mutation from pre-existing sequences (Robinson et al. 1997), The mechanisms by which small dispersed repeats are generated are otherwise unknown.The genomes of the cyanobacterium Nostoc punctiforme ATCC 29,133 and its relatives are unusual in that about 1.5% (∼7.5% of intergenic sequences) is taken up by tandem repeats at least 20 nt in length (Meeks et al. 2001; J. Elhai, T. Katayama, R. Narikawa, S. Okamoto, C. Friedland, R. Nayak, M. Ikeuchi, and M. Kanehisa, unpubl.). Repeating units of 7 nt (Mazel et al. 1990;Meeks et al. 2001) are by far the most common, with only a few of the possible families ...

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“…These elements, which measure 69 to 127 bp, are moderately abundant (20 to 25 copies) in the genomes of several enterobacteria (19) but are overrepresented in the genomes of yersiniae (15). In Yersinia species, most ERIC sequences are inserted immediately downstream from open reading frames (ORFs) and hence are cotranscribed into mRNAs with upstream genes.…”

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confidence: 99%

Structural Organization and Functional Properties of Miniature DNA Insertion Sequences in Yersiniae

et al. 2006

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YPALs (Yersinia palindromic sequences) are miniature DNA insertions scattered along the chromosomes of yersiniae. The spread of these intergenic repeats likely occurred via transposition, as suggested by the presence of target site duplications at their termini and the identification of syntenic chromosomal regions which differ in the presence/absence of YPAL DNA among Yersinia strains. YPALs tend to be inserted closely downstream from the stop codon of flanking genes, and many YPAL targets overlap rho-independent transcriptional terminator-like sequences. This peculiar pattern of insertion supports the hypothesis that most of these repeats are cotranscribed with upstream sequences into mRNAs. YPAL RNAs fold into stable hairpins which may modulate mRNA decay. Accordingly, we found that YPAL-positive transcripts accumulate in Yersinia enterocolitica cells at significantly higher levels than homologous transcripts lacking YPAL sequences in their 3 untranslated region.Bacterial insertion sequences (ISs) are mobile genetic elements ranging in size from 800 to 2,500 bp which are widely distributed among bacteria (21, 5). Typically, ISs encode a transposase which mediates their movement and feature terminal inverted repeats (TIRs) 10 to 50 bp long, which serve as recognition sites for the transposase. Most ISs generate short direct repeats (target site duplications [TSDs]) at the point of insertion. For each element, the length of the TSD is fixed and ranges from 2 to 13 bp. Differences in the structural organization, coding capacity, and transposition properties make it possible to sort ISs into approximately 20 major subfamilies (21).In recent years, it has emerged that small IS-like sequences called MITEs (for miniature transposable elements) may be a relevant genome component in several eukaryotic species (16,20). These elements characteristically measure 150 to 400 bp, carry long TIRs, and are flanked by TSDs of variable lengths. MITEs likely represent deletion derivatives of longer, autonomous ISs, which have been mobilized by tranposases encoded by partly related mobile donor elements (20). Several MITE families have also been identified in archaeabacteria (5). Three families of MITEs have been described for eubacteria. RUP (repeat unit of pneumococcus) elements are spread in ϳ100 copies in the genome of the Streptococcus pneumoniae 4 strain, and it has been proposed that their mobilization is mediated by the IS630-Spn1 element (24). NEMIS (Neisseria miniature insertion sequences) are 108-to 158-bp-long repeats which make up ϳ2% of the Neisseria meningitidis genome. In contrast to RUP elements, which are mostly interspersed with other repeated DNA sequences, NEMIS sequences are frequently located next to Neisseria genes and are transcribed into mRNAs. Hairpins formed by the pairing of NEMIS TIRs are targeted by RNase III, and this interaction regulates sets of N. meningitidis genes at the posttranscriptional level (12, 13).A different type of eubacterial MITE is represented by ERIC (enterobacterial repetitive i...

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Enterobacterial Repetitive Intergenic Consensus Sequence Repeats in Yersiniae: Genomic Organization and Functional Properties

Cited by 54 publications

References 46 publications

ERIC-PCR genotyping of field isolates ofSalmonella entericasubsp.entericaserovar Gallinarum biovars Gallinarum and Pullorum

ERIC-PCR genotyping of field isolates ofSalmonella entericasubsp.entericaserovar Gallinarum biovars Gallinarum and Pullorum

Very small mobile repeated elements in cyanobacterial genomes

Structural Organization and Functional Properties of Miniature DNA Insertion Sequences in Yersiniae

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