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GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes.

Di Nocera PP, De Gregorio E, Rocco F - BMC Genomics (2013)

Bottom Line: We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus.It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases).CGTC REPs apparently lack a dedicated transposase.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Via S, Pansini 5 80131, Naples, Italy. dinocera@unina.it

ABSTRACT

Background: REPs (Repetitive Extragenic Palindromes) are small (20-40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization.

Results: We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in multiple species.

Conclusions: CGTC REPs apparently lack a dedicated transposase. Future work will clarify whether these elements may be mobilized by RAYTs or other transposases, and assess if de-novo formation of either GTAG or CGTC repeats type still occurs.

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Strain variations of REP families. For GTAG-1 and GTAG-3 families, the relative abundance of major sequence types (ST) in the indicated strains are shown. For clarity, of each ST only left-hand, stem sequences are reported. Abundant sequence-subfamilies are highlighted.
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Figure 3: Strain variations of REP families. For GTAG-1 and GTAG-3 families, the relative abundance of major sequence types (ST) in the indicated strains are shown. For clarity, of each ST only left-hand, stem sequences are reported. Abundant sequence-subfamilies are highlighted.

Mentions: The organization of abundant REP families was analyzed in genomes of the same or related species. We monitored the relative abundance of the predominant sequence types (STs), as changes in the distribution of singletons, dimers and grouped elements. Data on species containing one or more REP families are reported in Figure 3. No significative variations were found in families of repeats residing in P. aeruginosa, H. infuenzae, S. maltophilia, N. meningitidis, N. gonhorroeae, C. burnetii.


GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes.

Di Nocera PP, De Gregorio E, Rocco F - BMC Genomics (2013)

Strain variations of REP families. For GTAG-1 and GTAG-3 families, the relative abundance of major sequence types (ST) in the indicated strains are shown. For clarity, of each ST only left-hand, stem sequences are reported. Abundant sequence-subfamilies are highlighted.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3733652&req=5

Figure 3: Strain variations of REP families. For GTAG-1 and GTAG-3 families, the relative abundance of major sequence types (ST) in the indicated strains are shown. For clarity, of each ST only left-hand, stem sequences are reported. Abundant sequence-subfamilies are highlighted.
Mentions: The organization of abundant REP families was analyzed in genomes of the same or related species. We monitored the relative abundance of the predominant sequence types (STs), as changes in the distribution of singletons, dimers and grouped elements. Data on species containing one or more REP families are reported in Figure 3. No significative variations were found in families of repeats residing in P. aeruginosa, H. infuenzae, S. maltophilia, N. meningitidis, N. gonhorroeae, C. burnetii.

Bottom Line: We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus.It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases).CGTC REPs apparently lack a dedicated transposase.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Via S, Pansini 5 80131, Naples, Italy. dinocera@unina.it

ABSTRACT

Background: REPs (Repetitive Extragenic Palindromes) are small (20-40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization.

Results: We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in multiple species.

Conclusions: CGTC REPs apparently lack a dedicated transposase. Future work will clarify whether these elements may be mobilized by RAYTs or other transposases, and assess if de-novo formation of either GTAG or CGTC repeats type still occurs.

Show MeSH
Related in: MedlinePlus