ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria

Abstract

We describe a family of highly conserved, Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences, 14 of which have been identified in Escherichia coli and Salmonella typhimurium and a further three in other enterobacterial species (Yersinia pseudotuberculosis, Klebsiella pneumoniae and Vibrio cholerae). ERIC sequences are 126 bp long and appear to be restricted to transcribed regions of the genome, either in intergenic regions of polycistronic operons or in untranslated regions upstream or downstream of open reading frames. ERIC sequences are highly conserved at the nucleotide sequence level but their chromosomal locations differ between species. Several features of ERIC sequences resemble those of REP sequences (Stern et al., 1984) although the nucleotide sequence is entirely different. The question of whether ERICs have a specific function, or represent a form of 'selfish' DNA, is discussed.

Inter-species transplantation of gut microbiota from human to pigs

“…PCR was performed in a 25-ml reaction containing 80 ng of fecal genomic DNA, 200 mM (each) deoxynucleoside triphosphates, 2.5 U Taq DNA polymerase (Promega, Madison, WI, USA), 1 Â reaction buffer, 2 mM MgCl 2 , and 0.4 mM of each primer (E1 and E2; Hulton et al, 1991;Versalovic et al, 1991). The amplification conditions were as follows: 7 min at 951C, 30 cycles consisting of 30 s at 951C, 1 min at 521C, 8 min at 651C and a final cycle of 16 min at 651C (Versalovic et al, 1991).…”

Fluorescent in situ hybridization and flow cytometry as tools to evaluate the treatments for the control of slime-forming enterobacteria in paper mills

“…The accessibility of these probes to the 16S rRNA molecule by FISH was also checked according to the ARB software (http,//www.arb-home.de; Kumar et al, 2005). The ERIC-1 probe used in this work (5´-ATGTAAGCTCCTGGGGATTCAC-3´) targets from 42 to 63 bp position of ERIC consensus sequence present in all Enterobacteriaceae (Bachelier et al, 1999;Hulton et al, 1991;Wilson & Sharp, 2006). These probes were covalently labelled at their 5´end with the isothiocyanate derivative (CY3) or with fluorescein isothiocyanate (FITC), and purified by reverse-phase liquid chromatography.…”

“…The aim of this work was to develop new probes to detect the main enterobacteria in microbial populations present in the paper mills, in order to evaluate the efficiency of different treatments to eliminate them. Bacterial detection and identification have been carried out by a FISH method that includes two new probes targeted to 16S rRNA and a probe based on the conserved central region of the Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences, which are located at a high copy number in extragenic regions of the Enterobacteriaceae genome (Bachelier et al, 1999;Hulton et al, 1991;Wilson & Sharp, 2006). The viability of these enterobacteria after the chemical treatments was measured by FC.…”

A PCR technique based on the Hipl interspersed repetitive sequence distinguishes cyanobacterial species and strains

“…The primers permit amplification of the DNA sequences between those adjacent repeated sequences which are present in a suitable orientation and distance apart. A number of different examples of the technique have been published, including ERIC (Enterobacterial Repetitive Interspersed Consensus) (Hulton et al, 1991) and REP (Repetitive Extragenic Palindrome) (Versalovic et al, 1991 ;Giesendorf et al, 1993;Georghiou et al, 1995).…”