Open Access Research article

Differential regulation of two closely related integrative and conjugative elements from Streptococcus thermophilus

Nicolas Carraro12, Virginie Libante12*, Catherine Morel12, Bernard Decaris12, Florence Charron-Bourgoin12, Pierre Leblond12 and Gérard Guédon12

Author Affiliations

1 Nancy-Université, UMR1128, Génétique et Microbiologie, F-54506 Vandœuvre-lès-Nancy, France

2 INRA, UMR1128, Génétique et Microbiologie, F-54506 Vandœuvre-lès-Nancy, France

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BMC Microbiology 2011, 11:238  doi:10.1186/1471-2180-11-238

Published: 24 October 2011

Additional files

Additional file 1:

Fig. S1: Determination of transcriptional units of the ICE core region in stationary phase. ICESt1 (A, B) and ICESt3 (C, D). For (A) and (B), location and orientation of ORFs and a truncated IS are indicated by arrowed boxes and rectangle, respectively. Above, ORF names beginning with "orf" are abbreviated with the corresponding letter or number. The pattern of the arrowed boxes depicts the putative function and/or relationships of each ORF deduced from functional analyses or from BLAST comparisons. White arrowed boxes correspond to unrelated ORFs of the two elements. Black arrowed box is the chromosomal fda gene. Star represents the putative origin of transfer. Horizontal lines delimitate functional modules with their names above. Arrows below each ICE represent transcripts deduced from the results given in B and D. For (B) and (D), RT-PCR amplification was used to determine if RNA spans the ORF end and the beginning of the following or next ORF. For each amplifications, the positive control performed on genomic DNA is presented on the left and the amplification obtained on cDNA is showed on the right. ORFs named above indicate the examined region and numbers below indicate the calculated amplicon size. Similar results were generated with RNA from three independent biological replicates and cells in exponential growth phase. A PCR was performed without reverse transcriptase step, in order to control for the absence of DNA contamination (not shown).

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Additional file 2:

Fig. S2: Multiple alignment of the four promoter regions of the seven closely related streptococcal ICEs. (A) PorfQ, (B) Pcr, (C) Parp2 and (D). Parp2s. Spara_15912, S. parasanguinis ATCC15912; Sinf_700779, S. infantis ATCC 700779; ICESpn8140 from S. pneumoniae 8140; Saus_700641, S. australis ATCC700641; Spara_F0405, S. parasanguinis F0405. The -10 and -35 boxes of the promoters are grey coloured and the transcriptional start sites (+1) are in boldface. For PorfQ region (A), the change in free energy (ΔG) of the underlined terminator is indicated on the right. For Parp2 region (C), horizontal lines below the sequences delimitate the putative stems regions and dashed lines the loop parts, which might be involved in mRNA cleavage.

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Additional file 3:

Table S1. Main primers used in this study.

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