Open AccessA novel class of small repetitive DNA sequences in Enterococcus faecalis
Author(s) -
Venditti Rossella,
De Gregorio Eliana,
Silvestro Giustina,
Bertocco Tullia,
Salza Maria Francesca,
Zarrilli Raffaele,
Di Nocera Pier Paolo
Publication year - 2007
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1111/j.1574-6968.2007.00717.x
Subject(s) - enterococcus faecalis , in silico , biology , genetics , palindrome , genome , enterococcus , inverted repeat , dna sequencing , dna , computational biology , palindromic sequence , sequence (biology) , gene , bacteria , escherichia coli
The structural organization of E nterococcus fa ecalis r epeats (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.