Limits...
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.

Show MeSH

Related in: MedlinePlus

Distances between REPs and flanking ORFs. Dots denote the relative distances from flanking ORFs of uni- and conv-REPs of the P. entomophila GTAG-1 and S. wittichi CGTC-1 families. In the uni-REP graphs, upstream and downstream located ORFs are marked as black and gray, respectively. In the conv-REP graphs, the two upstream ORFs are arbitrarily distinguished by the two color code. Single elements and dimers have been separately analyzed. Distances have been sorted by length to facilitate data visualization.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3733652&req=5

Figure 6: Distances between REPs and flanking ORFs. Dots denote the relative distances from flanking ORFs of uni- and conv-REPs of the P. entomophila GTAG-1 and S. wittichi CGTC-1 families. In the uni-REP graphs, upstream and downstream located ORFs are marked as black and gray, respectively. In the conv-REP graphs, the two upstream ORFs are arbitrarily distinguished by the two color code. Single elements and dimers have been separately analyzed. Distances have been sorted by length to facilitate data visualization.

Mentions: Most REPs are located in the intergenic space. Relative to the orientation of flanking ORFs, repeats may be located between either convergently (conv-REPs), or divergently (div-REPs), or unidirectionally (uni-REP) transcribed ORFs. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs (Figure 5). This finding reinforces the notion that most REPs are transcribed, and may function as RNA sequences. The distances separating P. entomophila GTAG-1 and S. wittichi CGTC-1 elements from flanking ORFs are diagrammed in Figure 6. The pattern of interspersion of singletons and dimers, separately analyzed, is similar. In P. entomophila as in S. wittichi, most conv-REPs are next (<20 bp) to the 3′ end of both flanking ORFs. Uni-REPs are also located close to the 3′ end of upstream ORFs, but are at varying distances from downstream ORFs. This suggests that the fraction of readthrough transcripts spanning REPs, that may influence the expression of both flanking ORFs, may be limited. The pattern of interspersion of GTAG-1 and CGTC-1 elements and flanking ORFs did not vary in other REP-rich genomes analyzed (Additional file 2).


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

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

Distances between REPs and flanking ORFs. Dots denote the relative distances from flanking ORFs of uni- and conv-REPs of the P. entomophila GTAG-1 and S. wittichi CGTC-1 families. In the uni-REP graphs, upstream and downstream located ORFs are marked as black and gray, respectively. In the conv-REP graphs, the two upstream ORFs are arbitrarily distinguished by the two color code. Single elements and dimers have been separately analyzed. Distances have been sorted by length to facilitate data visualization.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Distances between REPs and flanking ORFs. Dots denote the relative distances from flanking ORFs of uni- and conv-REPs of the P. entomophila GTAG-1 and S. wittichi CGTC-1 families. In the uni-REP graphs, upstream and downstream located ORFs are marked as black and gray, respectively. In the conv-REP graphs, the two upstream ORFs are arbitrarily distinguished by the two color code. Single elements and dimers have been separately analyzed. Distances have been sorted by length to facilitate data visualization.
Mentions: Most REPs are located in the intergenic space. Relative to the orientation of flanking ORFs, repeats may be located between either convergently (conv-REPs), or divergently (div-REPs), or unidirectionally (uni-REP) transcribed ORFs. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs (Figure 5). This finding reinforces the notion that most REPs are transcribed, and may function as RNA sequences. The distances separating P. entomophila GTAG-1 and S. wittichi CGTC-1 elements from flanking ORFs are diagrammed in Figure 6. The pattern of interspersion of singletons and dimers, separately analyzed, is similar. In P. entomophila as in S. wittichi, most conv-REPs are next (<20 bp) to the 3′ end of both flanking ORFs. Uni-REPs are also located close to the 3′ end of upstream ORFs, but are at varying distances from downstream ORFs. This suggests that the fraction of readthrough transcripts spanning REPs, that may influence the expression of both flanking ORFs, may be limited. The pattern of interspersion of GTAG-1 and CGTC-1 elements and flanking ORFs did not vary in other REP-rich genomes analyzed (Additional file 2).

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