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

Abstract

BackgroundTwo closely related ICEs, ICESt1 and ICESt3, have been identified in the lactic acid bacterium Streptococcus thermophilus. While their conjugation and recombination modules are almost identical (95% nucleotide identity) and their regulation modules related, previous work has demonstrated that transconjugants carrying ICESt3 were generated at rate exceeding by a 1000 factor that of ICESt1.ResultsThe functional regulation of ICESt1 and ICESt3 transcription, excision and replication were investigated under different conditions (exponential growth or stationary phase, DNA damage by exposition to mitomycin C). Analysis revealed an identical transcriptional organization of their recombination and conjugation modules (long unique transcript) whereas the transcriptional organization of their regulation modules were found to be different (two operons in ICESt1 but only one in ICESt3) and to depend on the conditions (promoter specific of stationary phase in ICESt3). For both elements, stationary phase and DNA damage lead to the rise of transcript levels of the conjugation-recombination and regulation modules. Whatever the growth culture conditions, excision of ICESt1 was found to be lower than that of ICESt3, which is consistent with weaker transfer frequencies. Furthermore, for both elements, excision increases in stationary phase (8.9-fold for ICESt1 and 1.31-fold for ICESt3) and is strongly enhanced by DNA damage (38-fold for ICESt1 and 18-fold for ICESt3). Although ICEs are generally not described as replicative elements, the copy number of ICESt3 exhibited a sharp increase (9.6-fold) after mitomycin C exposure of its harboring strain CNRZ385. This result was not observed when ICESt3 was introduced in a strain deriving ICESt1 host strain CNRZ368, deleted for this element. This finding suggests an impact of the host cell on ICE behavior.ConclusionsAll together, these results suggest a novel mechanism of regulation shared by ICESt1, ICESt3 and closely related ICEs, which we identified by analysis of recently sequenced genomes of firmicutes. This is the first report of a partial shutdown of the activity of an ICE executed by a strain belonging to its primary host species. The sharp increase of ICESt3 copy number suggests an induction of replication; such conditional intracellular replication may be common among ICEs.

Plasmid-like replication of a minimal streptococcal integrative and conjugative element

“…Sequencing reactions were performed by Cogenics. Quantitative PCR (qPCR) experiments were performed as described previously (Carraro et al, 2011). Experiments were performed in duplicate and repeated at least three times using three independently derived clones.…”

“…This module encodes two regulatory systems related to lambdoid prophage cI repressor (Beaber et al, 2004) and related to ImmA/ImmR regulatory systems (Bose & Grossman, 2011), suggesting a particularly complex regulation (Carraro & Burrus, 2014). Exposure of S. thermophilus to the DNA-damaging agent mitomycin C was found to promote not only excision and transfer of ICESt3 (Bellanger et al, 2009;Carraro et al, 2011), but also its adoption of a multicopy state, suggesting its capacity to replicate (Carraro et al, 2011). Moreover, the recombination and the conjugation modules of the ICESt3-like elements are co-transcribed, which coordinates excision and transfer (Carraro et al, 2011).…”

“…Exposure of S. thermophilus to the DNA-damaging agent mitomycin C was found to promote not only excision and transfer of ICESt3 (Bellanger et al, 2009;Carraro et al, 2011), but also its adoption of a multicopy state, suggesting its capacity to replicate (Carraro et al, 2011). Moreover, the recombination and the conjugation modules of the ICESt3-like elements are co-transcribed, which coordinates excision and transfer (Carraro et al, 2011).…”

“…The modules needed for transfer, integration and regulation ensure the basic biology of ICEs, and thus can be defined as the 'core region' (Carraro et al, 2011;Gaillard et al, 2010). The recombination module catalyses the site-specific integration of the ICE into the host genome, as well as the reverse reaction that leads to its excision as a circular form.…”

“…The conjugation module encodes the relaxase, which recognizes its origin of transfer (oriT) and nicks a specific site (nic) to initiate the ssDNA transfer (for review, see Bellanger et al, 2014) using its type IV secretion system (Cabezó n et al, 2015;Goessweiner-Mohr et al, 2013). Finally, the regulation module controls ICE excision and transfer (Carraro et al, 2011;Pradervand et al, 2014;see Wozniak & Waldor, 2010, for review).…”