title: A novel class of small repetitive DNA sequences in Enterococcus faecalis.
abstract: The structural organization of Enterococcus faecalis repeats (EFAR) is described, palindromic DNA sequences identified in the genome of the Enterococcus faecalis V583 strain by in silico analyses. EFAR are a novel type of miniature insertion sequences, which vary in size from 42 to 650 bp. Length heterogeneity results from the variable assembly of 16 different sequence types. Most elements measure 170 bp, and can fold into peculiar L-shaped structures resulting from the folding of two independent stem-loop structures (SLSs). Homologous chromosomal regions lacking or containing EFAR sequences were identified by PCR among 20 E. faecalis clinical isolates of different genotypes. Sequencing of a representative set of 'empty' sites revealed that 24-37 bp-long sequences, unrelated to each other but all able to fold into SLSs, functioned as targets for the integration of EFAR. In the process, most of the SLS had been deleted, but part of the targeted stems had been retained at EFAR termini.
authors.affiliation: Dipartimento di Biologia e Patologia Cellulare e Molecolare, Facoltà di Medicina, Università Federico II, Napoli, Italy.
authors.forename: Rossella
authors.initials: R
authors.lastname: Venditti
authors.forename: Eliana
authors.initials: E
authors.lastname: De Gregorio
authors.forename: Giustina
authors.initials: G
authors.lastname: Silvestro
authors.forename: Tullia
authors.initials: T
authors.lastname: Bertocco
authors.forename: Maria Francesca
authors.initials: MF
authors.lastname: Salza
authors.forename: Raffaele
authors.initials: R
authors.lastname: Zarrilli
authors.forename: Pier Paolo
authors.initials: PP
authors.lastname: Di Nocera
mesh_terms: D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D013293:Enterococcus faecalis / Q000235:genetics*; D016680:Genome, Bacterial; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004269:DNA, Bacterial