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Journal of Bacteriology, December 2005, p. 7945-7954, Vol. 187, No. 23
0021-9193/05/$08.00+0     doi:10.1128/JB.187.23.7945-7954.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Enterobacterial Repetitive Intergenic Consensus Sequence Repeats in Yersiniae: Genomic Organization and Functional Properties

Eliana De Gregorio,1 Giustina Silvestro,1 Mauro Petrillo,2 Maria Stella Carlomagno,1 and Pier Paolo Di Nocera1*

Dipartimento di Biologia e Patologia Cellulare e Molecolare, Facoltà di Medicina, Università Federico II, Via S. Pansini 5, 80131 Napoli, Italy,1 CEINGE Biotecnologie Avanzate s.c.a.r.l., Via Comunale Margherita n. 482, 80131 Napoli, Italy2

Received 29 July 2005/ Accepted 21 September 2005

Genome-wide analyses carried out in silico revealed that the DNA repeats called enterobacterial repetitive intergenic consensus sequences (ERICs), which are present in several Enterobacteriaceae, are overrepresented in yersiniae. From the alignment of DNA regions from the wholly sequenced Yersinia enterocolitica 8081 and Yersinia pestis CO92 strains, we could establish that ERICs are miniature mobile elements whose insertion leads to duplication of the dinucleotide TA. ERICs feature long terminal inverted repeats (TIRs) and can fold as RNA into hairpin structures. The proximity to coding regions suggests that most Y. enterocolitica ERICs are cotranscribed with flanking genes. Elements which either overlap or are located next to stop codons are preferentially inserted in the same (or B) orientation. In contrast, ERICs located far apart from open reading frames are inserted in the opposite (or A) orientation. The expression of genes cotranscribed with A- and B-oriented ERICs has been monitored in vivo. In mRNAs spanning B-oriented ERICs, upstream gene transcripts accumulated at lower levels than downstream gene transcripts. This difference was abolished by treating cells with chloramphenicol. We hypothesize that folding of B-oriented elements is impeded by translating ribosomes. Consequently, upstream RNA degradation is triggered by the unmasking of a site for the RNase E located in the right-hand TIR of ERIC. A-oriented ERICs may act in contrast as upstream RNA stabilizers or may have other functions. The hypothesis that ERICs act as regulatory RNA elements is supported by analyses carried out in Yersinia strains which either lack ERIC sequences or carry alternatively oriented ERICs at specific loci.

* Corresponding author. Mailing address: Dipartimento di Biologia e Patologia Cellulare e Molecolare, Facoltà di Medicina, Università Federico II, Via S. Pansini 5, 80131 Napoli, Italy. Phone: 0039-81-7462059. Fax: 0039-81-7703285. E-mail: dinocera{at}unina.it.

Journal of Bacteriology, December 2005, p. 7945-7954, Vol. 187, No. 23
0021-9193/05/$08.00+0     doi:10.1128/JB.187.23.7945-7954.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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