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!. Zielenkiewicz, ! Mechanisms! of! plasmid! stable! maintenance!with!special!focus!on!plasmid!addiction!systems, 1003D1023.! ! ! 193! Communications orales, 2001.

. Carraro-)-nicolas, !. Libante, . Virginie, !. Morel, . Catherine et al., ! Regulation! of! Streptococcus) thermophilus! Genomic! ICElands, 2011.

!. Genomic, therefore!in!the!evolution!of!bacterial! species.! Bacterial! genomes! analyses! suggest! that! numbers! of! these! islands! are! Integrative! and! Conjugative! Elements!(ICE)!They!characteristically!share!a!modular!organization!as!genes!and!sequences!involved!in!the! same!biological!process!are!located!in!the!same!region.! Two!closely!related!integrative!and!conjugative!elements,!ICESt1!and!ICESt3,!have!been!identified!in!the!Gram! positive!bacteria!Streptococcus!thermophilus.!While!conjugation!and!recombination!modules!(core!region)

!. Rice-!-for-!-replicative, !. Integrative, !. , !. Conjugative, and !. Elements, excision! and! probably! transfer! are! regulated! at! the! transcriptional! level.! Unlike! in! other! characterized! elements,! the! transcript! levels! of! the! regulation! module! of! ICEs! from! S! thermophilus! rises! by! stationary! phase! and! DNA! damage.!These!results!strongly!suggest!an!original!mechanism!of!S.)thermophilus!ICEs!regulation;!which!would! implicate!complex!interactions!of!various!regulators.!As!homologs!of!the!regulation!modules!from!ICESt1!and! ICESt3!were!identified!on!several!other!ICEs,!this!regulation!strategy!may!be!conserved.!Although!ICEs!are!not! known! as! replicative! elements,! exposure! to! DNA! damaging! agents! resulted! in! increased! number! of! ICESt3! copies,!suggesting!its!amplification.!Therefore,!ICESt3!is!able!of!replicating!with!higher!spreading!efficiency!in! bacteria! population

!. La, !. , and !. , ADN)! sont! connus! pour! provoquer! l'activation!d'ICE!déjà!étudiés!comme!SXT!de!Vibrio)cholerae!(4)!et!ICEBs1!de!Bacillus)subtilis)(1,!2).!L'activation! transcriptionnelle!des!modules!de!conjugaison!et!de!recombinaison!résulte!alors!de!la!répression!du!module! ! 194! de!régulation!codant!le!répresseur!unique!du!transfert

!. La, !. , !. , !. , and !. Rtdpcr-!-et-!-5-'race-!, que! les! modules! de! régulation!des!deux!éléments!présentent!des!organisations!opéroniques!différentes.!De!plus,!ICESt3!possède! un!promoteur!spécifique!de!la!phase!stationnaire!en!amont!du!module!de!régulation.!Chez!les!deux!éléments

!. Florence, !. Libante, and !. Virginie, ! Regulation! of! ICESt1! and! ICESt3,! two! closely! related!

!. Les, !. Ice-!-de, . Streptococcus-)-thermophilus, !. Icest1, !. Icest3 et al., ! Ces! deux! ICE! sont! les! seuls! éléments! connus,! parmi! les! prophages! ou! ICE,! qui! posséderaient! simultanément! les! deux! types! de! répresseurs!:!cI!autoprotéolytique!(arp1)!et!cIDlike!(arp2)!clivable!par!une!protéase!associée!(orfQ)!! Les!quantités!de!transcrit!des!modules!de!conjugaison!et!de!recombinaison!des!deux!éléments!augmentent!en! phase!stationnaire!et!en!présence!de!mitomycine!C,!agent!endommageant!l'ADN,!ce!qui!est!en!accord!avec! l'augmentation!Ces!stimuli! sont! connus! pour! provoquer! la!,!y!compris!le!module!de!régulation.!! ICESt3!s'excise!et!se!transfère!beaucoup!plus!efficacement!(facteur!1000)!(3)

!. Leblond, !. Pierre, !. Guédon, !. Gérard, !. Charron et al., ! Dynamics! and! maintenance! of! ICEs! of! Streptococcus! thermophilus, 2011.

!. Comparative, !. Integrative, and !. Conjugative, These!elements!excise!from!donor!cell!chromosomes!by!siteDspecific! recombination,!transfer!through!conjugation!to!recipient!cell!and!integrate!into!specific!genomic!sites.! Previous! analysis! demonstrated! that! ICESt3,! an! ICE! from! Streptococcus) thermophilus,! is! activated! during! stationary! phase! and! upon! DNA! damage.! Its! activation! results! from! transcriptional! activation! of! the! core! region,!which!encodes!functions!involved!in!transfer.!While!ICEs!are!not!thought!to!be!replicative,!ICESt3!was! recently! found! to! replicate! under! DNA! damaging! conditions! reaching! from! one! copy! to10! copies! per! chromosome,!while!its!excision!rose!by!90%.!! Sequences! analyses! within! the! ICESt3! family! lead! us! to! specify! a! variable! region.! It! includes! a! restriction! modification!system,!which!is!postulated!to!regulate!maintenance!of!the!element.!In!order!to!investigate!the! involvement! of! the! variable! region! in! the! behavior! of! ICESt3,! a! MiniICESt3! lacking! this! region! has! been! genetically!engineered.!Surprisingly,!this!element!is!stable!among!generations.!! Normalized! copy! number! quantification! of! MiniICESt3! shows! a! threefold! replication! rate! in! all! growth! conditions! compare! to! ICESt3

!. Les, !. , !. , !. , !. et al., transfert! peut! permettre! l'acquisition! rapide! de! nouvelles!fonctions!biologiques.!L'analyse!des!génomes!bactériens!suggère!que!de!nombreux!îlots!génomiques! sont! des! éléments! intégratifs! conjugatifs! (ICE).! Ces! éléments! s'excisent,! se! transfèrent! par! conjugaison! et! s'intègrent

!. Les, !. Ice-!-de, . Streptococcus-)-thermophilus, and !. Icest1, ! possèdent! des! modules! de! conjugaison! et! de! recombinaison! ! qui! présentent! 95%! d'identité! nucléotidique! et! des! modules! de! régulation! apparentés.! Néanmoins,! ICESt3! s'excise! et! se! transfère! beaucoup! plus! efficacement! (facteur! 1000)! qu'ICESt1

!. La, !. , and !. , ADN)! sont! connus! pour! provoquer! l'activation!d'ICE!déjà!étudiés!comme!SXT!de!Vibrio)cholerae!et!ICEBs1!de!Bacillus)subtilis.!Chez!ces!éléments,! l'activation

!. Alors, !. , !. Ice-!-sont, !. , and !. , !des!études!quantitatives!ont!permis!de!mettre!en! évidence!qu'ICESt3)se!réplique!en!présence!de!dommages!à!l'ADN.!La!nomenclature!des!ICE!pourrait!ainsi!se! voir!complétée!par!une!nouvelle!classe!d'éléments!intégratifs!conjugatifs!et!réplicatifs!:!les!RICE

!. Le, !. , and !. , ! L'analyse! des! génomes!bactériens!suggère!que!de!nombreux!îlots!seraient!des!éléments!intégratifs!conjugatifs!(ICE).!Lors!de! leur!dissémination,!ces!éléments!s'excisent,!se!transfèrent!par!conjugaison!et!s'intègrent

!. Deux, !. Streptococcus-)-thermophilus-!-sont-!-porteuses-!-d-'icest1, !. Icest3, !. Ice-!-présentant, !. et al., ! ! ICESt3! se! transfère!bien!plus!efficacement!(facteur!1000),!probablement!en!raison!de!la!présence!de!gènes!de!régulation! spécifiques!à!un!élément!et

!. Les, !. , !. , and !. , ! d'une! part! entre! ICESt1! et! ICESt3! et! d'autre! part! lors! de! stimuli! connus! pour! induire! d'autres! éléments! transférables! (phase!de!croissance!et/ou!dommages!à!l'ADN).!Les!résultats!montrent!une!induction!en!phase!stationnaire!et! en!présence!de!mitomycine!C

!. Deux, !. Icest1, . Icest3, and . Streptococcus, Ces!éléments!présentent!une!organisation!modulaire,!l'ensemble!des!gènes!et!des!séquences!impliqués!dans! une!même!fonction!biologique!étant!localisé!dans!une!même!région.!Un!module!de!régulation,!variable!entre! les!éléments,!code!des!homologues!de!protéines!clés!impliquées!dans!la!régulation!des!prophages!(arp1,!arp2! et! orfQ)! Le! gène! arp1,! impliqué! dans! la! répression! de! l'excision! d'ICESt1

!. Une and !. , existence!de!2!opérons!distincts!chez!ICESt1!mais!n'a!révélé!qu'une! seule! unité! transcriptionnelle! chez! ICESt3.! Par! ailleurs

!. Résumés, !. Les, and !. , sont! des! îlots! génomiques! qui! codent! leur! excision! du! chromosome,! leur! transfert! par! conjugaison! et! leur! intégration.! Ils! présentent! une! organisation! modulaire,! chaque! module! incluant! tous! les! gènes! nécessaires! pour! conférer!une!fonction!biologique.!Les!ICE!sont!généralement!composés!de!deux!régions!:!i)! une! région! «! core!

!. Ce, !. , !. , !. , !. et al., ICESt1)et!ICESt3,)deux!ICE!de!Streptococcus)thermophilus)présentant!une!région! core!étroitement!apparentée!et!une!région!variable!non!apparentée.!Les!résultats!obtenus! ont! montré! que,! bien! qu'ICESt3) s'excise! et! se! transfère! à! beaucoup! plus! haute! fréquence! qu'ICESt1,!l'excision!des!deux!éléments!est!activée!par!des!stimuli!identiques!(dommages!à! l'ADN,!phase!stationnaire!et/ou!densité!cellulaire)!et!est!dépendante!de!la!souche!hôte.!Les! analyses! bioinformatiques! et! transcriptionnelles! des! modules! de! régulation! d'ICESt1) et! ICESt3)ont!révélé!plusieurs!différences!d'organisation!(opéron,!promoteur,!ORF!spécifiques).! Cependant

!. Selon, !. Ice-!-se, !. , !. , !. et al., ! les! dommages! à! l'ADN! induisent!non!seulement!l'excision!et!le!transfert!d'ICESt3$? $mais!aussi!sa!présence!en!copies! multiples! extrachromosomiques! (8! copies! par! chromosome)

!. La, !. Ice-!-suggère, and !. Qu, une! telle!réplication!pourrait!être!impliquée!dans!le!maintien!de!nombreux!ICE!en!plus!de!leur! intégration.! ! Mots) clés):! Streptococcus) thermophilus,! élément! intégratif! conjugatif,! régulation,! réplication

!. Integrative, !. , !. Conjugative, !. Elements, !. Ices et al., !genes!and!sequences!involved!in!the!same!biological!process!are!grouped!in! the! same! region.! Most! of! the! ICEs! contain! 2! regions:! i)! a! «!core!»! region,! which! encodes! functions! involved! in! the! mobility! and! the! stability! (regulation,! conjugation! and! excision/integration)!;! ii)! a! variable! region!!encoding! functions! that! can! be! useful! for! the! host!cell.! ! This! work! concerns! the! modality! of! transfer! and! maintenance! of! ICESt1! and! ICESt3,! two!ICEs!of!Streptococcus)thermophilus!that!share!closely!related!core!region.!ICESt1!excises! much!less!frequently!than!ICESt3.!Nevertheless,!excision!of!the!two!elements!is!activated!by! the!same!stimuli!(DNA!damage,!stationnary!phase!and/or!cell!density)!and!depends!of!the! host!strain.!Bioinformatical!and!transcriptional!analyses!highlight!several!differences!in!their! organization! (operons,! promoters,! specific! ORFs).! However,! each! of! these! two! ICEs! would! encode! two! different! regulators,! cI! and! ImmR,! suggesting! that! a! complex! and! original! pathway! govern! to! ICESt1'! and! ICESt3'! regulation.! This! regulation! would! be! shared! with! numerous! ICEs! that! we! identified! in! the! genome! of! various! commensal! or! pathogenic! streptococci.! ! According! to! the! original! definition,! ICE's! maintenance! would! be! exclusively! due! to! their! integration! in! the! host! chromosome,! and! ICEs! would! not! be! able! of! extracellular! replication.! However,! in! addition! to! the! induction! of! ICESt3') excision! and! transfer,! DNA! damage! cause! replication! of! its! extrachromosomal! form, !besides!their!integration.! ! ! Key) words! Streptococcus) thermophilus,! Integrative! and! Conjugative! Element,! regulation,! replication.! ! 203! ! 204

!. Les, !. , and !. , sont!des!îlots!génomiques!qui!codent!leur!excision!du! chromosome,! leur! transfert! par! conjugaison! et! leur! intégration.! Ils! présentent! une! organisation! modulaire,! chaque! module! incluant! tous! les! gènes! nécessaires! pour! conférer! une! fonction! biologique.!Les!ICE!sont!généralement!composés!de!deux!régions!:!i)!une!région!«!core!

!. Ce, !. , !. , !. , !. et al., ICESt1) et! ICESt3,) deux! ICE! de! Streptococcus)thermophilus) présentant! une! région! core! étroitement! apparentée! et! une! région! variable! non! apparentée.! Les! résultats! obtenus! ont! montré! que,!bien!qu'ICESt3)s'excise!et!se!transfère!à!beaucoup!plus!haute!fréquence!qu'ICESt1,!l'excision!des! deux!éléments!est!activée!par!des!stimuli!identiques!(dommages!à!l'ADN,!phase!stationnaire!et/ou! densité! cellulaire)! et! est! dépendante! de! la! souche! hôte.! Les! analyses! bioinformatiques! et! transcriptionnelles! des! modules! de! régulation! d'ICESt1) et! ICESt3) ont! révélé! plusieurs! différences! d'organisation! (opéron,! promoteur,! ORF! spécifiques).! Cependant

!. Selon, !. Ice-!-se, !. , !. , !. et al., ! les! dommages! à! l'ADN! induisent! non! seulement! l'excision! et! le! transfert! d'ICESt3$? $ mais! aussi! sa! présence! en! copies! multiples! extrachromosomiques!(8!copies!par!chromosome)

!. Integrative, !. , !. Conjugative, !. Elements, !. Ices et al., !They!harbor!a!modular!organization:!genes! and!sequences!involved!in!the!same!biological!process!are!grouped!in!the!same!region.!Most!of!the! ICEs!contain!2!regions:!i)!a!«!core!»!region,!which!encodes!functions!involved!in!the!mobility!and!the! stability!(regulation,!conjugation!and!excision/integration)!;!ii)!a!variable!region!!encoding!functions! that!can!be!useful!for!the!host!cell.! ! This!work!concerns!the!modality!of!transfer!and!maintenance!of!ICESt1!and!ICESt3,!two!ICEs!of! Streptococcus) thermophilus! that! share! closely! related! core! region.! ICESt1! excises! much! less! frequently!than!ICESt3.!Nevertheless,!excision!of!the!two!elements!is!activated!by!the!same!stimuli! (DNA!damage,!stationary!phase!and/or!cell!density)!and!depends!of!the!host!strain.!Bioinformatical! and!transcriptional!analyses!highlight!several!differences!in!their!organization!(operons,!promoters,! specific!ORFs).!However,!each!of!these!two!ICEs!would!encode!two!different!regulators,!cI!and!ImmR

!. According, !. Definition, and . Ice, s! maintenance! would! be! exclusively! due! to! their! integration!in!the!host!chromosome,!and!ICEs!would!not!be!able!of!extracellular!replication.!However,! in! addition! to! the! induction! of! ICESt3') excision! and! transfer,! DNA! damage! cause! replication! of! its! extrachromosomal! form.! This! unexpected! property! is! encoded! by! the! core! region! and! would! be! implicated!in!the!maintenance!of!the!element.!! Comparision!with!data!recently!published!on!other!ICEs!suggest!that!intracellular!replication!could!be! involved!in!the!maintenance!of!numerous!ICEs