title: GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes.
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.
authors.affiliation: Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Via S, Pansini 5 80131, Naples, Italy. dinocera@unina.it
authors.forename: Pier Paolo
authors.initials: PP
authors.lastname: Di Nocera
authors.forename: Eliana
authors.initials: E
authors.lastname: De Gregorio
authors.forename: Francesco
authors.initials: F
authors.lastname: Rocco
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics*; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004269:DNA, Bacterial
references.citation: Nat Rev Genet. 2010 Mar;11(3):181-90
references.pmid: 20125085
references.citation: BMC Microbiol. 2008 Nov 24;8:202
references.pmid: 19025624
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D80-7
references.pmid: 17175540
references.citation: J Bacteriol. 2005 Dec;187(23):7945-54
references.pmid: 16291667
references.citation: J Bacteriol. 1990 Feb;172(2):1051-61
references.pmid: 2298692
references.citation: Annu Rev Microbiol. 2011;65:111-28
references.pmid: 21639786
references.citation: BMC Genomics. 2008 Jan 17;9:20
references.pmid: 18201379
references.citation: Nature. 2000 Mar 30;404(6777):502-6
references.pmid: 10761919
references.citation: Chem Biol. 2006 Nov;13(11):1125-35
references.pmid: 17113994
references.citation: Gene. 2001 Oct 31;278(1-2):211-22
references.pmid: 11707339
references.citation: FEMS Microbiol Lett. 2010 Jul;308(2):185-92
references.pmid: 20528935
references.citation: PLoS One. 2011;6(10):e25773
references.pmid: 22016774
references.citation: Genome Biol. 2009;10(5):R51
references.pmid: 19432983
references.citation: Mol Plant Microbe Interact. 2006 Nov;19(11):1151-8
references.pmid: 17073298
references.citation: Mol Microbiol. 2005 Jan;55(2):601-10
references.pmid: 15659173
references.citation: Genome Res. 2008 Sep;18(9):1484-99
references.pmid: 18599681
references.citation: BMC Genomics. 2010 Jan 19;11:44
references.pmid: 20085626
references.citation: Mol Microbiol. 2008 Feb;67(3):475-81
references.pmid: 18086200
references.citation: Nature. 2002 May 16;417(6886):244
references.pmid: 12015592
references.citation: PLoS Genet. 2011 Jun;7(6):e1002132
references.pmid: 21698139
references.citation: Nucleic Acids Res. 2006 Jan 10;34(1):66-77
references.pmid: 16407325
references.citation: Genome Biol Evol. 2011;3:959-73
references.pmid: 21803768
references.citation: Trends Biochem Sci. 2003 Feb;28(2):75-80
references.pmid: 12575994
references.citation: Microbiology (Reading). 1999 Oct;145 ( Pt 10):2647-53
references.pmid: 10537186
references.citation: FEMS Microbiol Rev. 2011 Mar;35(2):299-323
references.pmid: 20796030
references.citation: BMC Genomics. 2006 Mar 24;7:62
references.pmid: 16563168
references.citation: BMC Microbiol. 2007 Nov 28;7:106
references.pmid: 18045498
references.citation: Nucleic Acids Res. 2012 Apr;40(8):3596-609
references.pmid: 22199259
references.citation: J Bacteriol. 2004 Nov;186(22):7714-25
references.pmid: 15516586
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8319-25
references.pmid: 11459970
references.citation: J Bacteriol. 2004 Sep;186(17):5842-55
references.pmid: 15317790
references.citation: Bioinform Biol Insights. 2011;5:115-29
references.pmid: 22084572
references.citation: BMC Genomics. 2011 Sep 21;12:453
references.pmid: 21936919
references.citation: Biochem Biophys Res Commun. 2008 Jan 25;365(4):790-4
references.pmid: 18035045
references.citation: Crit Rev Microbiol. 2000;26(2):111-31
references.pmid: 10890353
references.citation: Curr Opin Biotechnol. 2006 Jun;17(3):241-9
references.pmid: 16704931
references.citation: Nucleic Acids Res. 1999 Feb 15;27(4):1039-46
references.pmid: 9927737
references.citation: Res Microbiol. 1999 Nov-Dec;150(9-10):627-39
references.pmid: 10673002
references.citation: Gene. 1988 Dec 10;72(1-2):3-14
references.pmid: 3072249
references.citation: Curr Opin Microbiol. 2006 Oct;9(5):526-31
references.pmid: 16935554
references.citation: EMBO J. 1993 Dec 15;12(13):5019-27
references.pmid: 8262044
references.citation: Int J Med Microbiol. 2007 Nov;297(7-8):601-13
references.pmid: 17572149
references.citation: Nucleic Acids Res. 2012 Oct;40(19):9964-79
references.pmid: 22885300
references.citation: J Bacteriol. 2006 Nov;188(22):7876-84
references.pmid: 16963573
references.citation: BMC Evol Biol. 2011 Feb 14;11:45
references.pmid: 21320320
references.citation: Science. 2007 Jun 1;316(5829):1307-12
references.pmid: 17540897
references.citation: Nucleic Acids Res. 2008 Dec;36(21):6688-719
references.pmid: 18948295
references.citation: PLoS One. 2010 Feb 08;5(2):e9109
references.pmid: 20174598
references.citation: Res Microbiol. 2005 Apr;156(3):424-33
references.pmid: 15808947
references.citation: Environ Microbiol. 2005 Feb;7(2):225-8
references.pmid: 15658989
references.citation: FEMS Microbiol Lett. 2009 Mar;292(1):7-12
references.pmid: 19222577
references.citation: Int Microbiol. 2004 Mar;7(1):3-12
references.pmid: 15179601
references.citation: mBio. 2011 Oct 04;2(5):
references.pmid: 21972240
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11064-9
references.pmid: 16043691
references.citation: Genome Res. 2002 May;12(5):808-16
references.pmid: 11997347
references.citation: RNA. 2010 Jan;16(1):106-17
references.pmid: 19952116
references.citation: Mol Biol Evol. 2007 Apr;24(4):969-81
references.pmid: 17251179
references.citation: BMC Genomics. 2006 Jul 04;7:170
references.pmid: 16820051
references.citation: Mol Biol Evol. 2006 Nov;23(11):2112-22
references.pmid: 16891376
references.citation: Nucleic Acids Res. 2002 Apr 15;30(8):1826-33
references.pmid: 11937637
references.citation: Genetics. 1991 Dec;129(4):991-1005
references.pmid: 1783300
references.citation: Trends Microbiol. 2005 Jun;13(6):253-5
references.pmid: 15936655
references.citation: Biochem J. 2003 Sep 15;374(Pt 3):799-805
references.pmid: 12826014
references.citation: J Mol Biol. 2001 Nov 30;314(3):375-86
references.pmid: 11846552