Editorial: The Role of Mobile Genetic Elements in Bacterial Evolution and Their Adaptability

EDITORIAL published: 21 Feb ua y 2022 doi: 10.3389/ micb.2022.849667 F on ie s in Mic obiology | www. on ie sin.o g 1Feb ua y 2022 | Volume 13 | A icle 849667 Edi ed and e iewed by: Ludmila Chis ose do a, Uni e si y o Washing on, Uni ed S a es *Co espondence: Filipa F. Vale [email p o ec ed] Special y sec ion: This a icle was submi ed o E olu iona y and Genomic Mic obiology, a sec ion o he jou nal F on ie s in Mic obiology Recei ed: 06 Janua y 2022 Accep ed: 17 Janua y 2022 Published: 21 Feb ua y 2022 Ci a ion: Vale FF, Lehou s P and Yamaoka Y (2022) Edi o ial: The Role o Mobile Gene ic Elemen s in Bac e ial E olu ion and Thei Adap abili y. F on . Mic obiol. 13:849667. doi: 10.3389/ micb.2022.849667 Edi o ial: The Role o Mobile Gene ic Elemen s in Bac e ial E olu ion and Thei Adap abili y Filipa F. Vale1*, Philippe Lehou s2,3 and Yoshio Yamaoka4 1Pa hogen Genome Bioin o ma ics and Compu a ional Biology, Resea ch Ins i u e o Medicines (iMed-ULisboa), Facul y o Pha macy, Uni e sidade de Lisboa, Lisboa, Po ugal, 2INSERM U1312, Bo deaux Ins i u e o Oncology, BRIC, Bo deaux, F ance, 3Cen e Na ional de Ré é ence des Campylobac e s e des Hélicobac e s, Bo deaux, F ance, 4Depa men o En i onmen al and P e en i e Medicine, Facul y o Medicine, Oi a Uni e si y, Oi a, Japan Keywo ds: mobile elemen s (MEs), e olu ion, adap abili y, bac e iophage, i ulence ac o s, inse ion sequence (Is), es ic ion and modi ica ion Edi o ial on he Resea ch Topic The Role o Mobile Gene ic Elemen s in Bac e ial E olu ion and Thei Adap abili y The bac e ial mobilome, i.e., he g oup o all mobile elemen s p esen in a bac e ial genome, a e impo an playe s in bac e ial e olu ion, shaping he hos genome h ough complex in e ac ions be ween he mobile elemen and hos bac e ia. Mobile elemen is a gene ic e m o a mul i ude o genomic sequences, such as plasmids, p ophages, pa hogenici y islands, es ic ion and modi ica ion sys ems, ansposons, and inse ion sequences, among o he s, ha sha e he abili y o be ansmi ed e ically wi h cell di ision o h ough ho izon al ans e . Thus, hey a e able o mo e wi hin he hos genome as well as jump ac oss genomes, shaping and co-e ol ing wi h ch omosomal genomes. Mobile elemen s can change hei inse ion loca ion, copy numbe , p o ide new gene unc ions, o a ec ch omosomal gene exp ession. Mobile elemen s a e known o po en ia e gene gain and loss, a majo o ce ha can p o oundly change bac e ial i ness. This change can con ibu e o he gene ic adap a ion o new en i onmen s and he eme gence o di e gen bac e ial popula ions ha may p oduce e olu iona y dis inc species. Since hei disco e y, he mechanisms o pe sis ence and in e ac ion o mobile elemen s wi h he bac e ial genome ha e been inc easingly s udied. This special issue, h ough he p esen a ion o pe inen and impo an examples o dis inc mobile elemen s (genomic islands, pa hogenici y islands, inse ion sequences, p ophages, and es ic ion and modi ica ions sys ems), ei he by e iewing, showing new aspec s, o p esen ing new bioin o ma ics ools, shows he impo ance o comp ehending he biology o mobile gene ic elemen s. To s a , he ole o dis inc mobile gene ic elemen s in adap i e e olu ion is add essed. The epigene ic DNA-based me hyla ion plays impo an oles in gene exp ession egula ion. Yano e al. desc ibed a gene exp ession egula ion ne wo k in H. pylo i consis ing o many DNA me hyl ans e ases each equen ly changing i s a ge sequence-speci ici y in sea ch o adap a ion. H. pylo i ca ies a la ge and a iable epe oi e o sequence-speci ic DNA me hyl ans e ases, and mo ili y, oxida i e s ess ole ance, and DNA damage epai a e likewise egula ed by mul iple me hyl ans e ases. The ne wo k p o ides a new pa adigm in unde s anding global gene egula ion and adap i e e olu ion. Mo ing in o ano he mic oo ganism, Esche ichia coli p esen s many accesso y genes acqui ed by ho izon al ans e ha o m syn enic blocks and a e ecognized as genomic islands (GIs). These genomic egions con ibu e o he apid e olu ion, di e si ica ion, and adap a ion o E. coli a ian s. In he pape by Des aux e al. he au ho s e iewed a subg oup o GIs om E. coli e med Vale e al. Edi o ial: The Role o Mobile Gene ic Elemen s in Bac e ial E olu ion and Thei Adap abili y pa hogenici y islands which con ibu e o he eme gence o i ulen bac e ia and o he de elopmen o in es inal and ex ain es inal diseases. Nex , a g oup o manusc ip s highligh s he ole o mobile gene ic elemen s in bac e ia pa hogenici y, o hei use o epidemiologic pu poses. Fische e al. ocused again on he pa hogenic bac e ium H. pylo i, which was acqui ed mul iple ype IV sec e ion sys ems (T4SSs). H. pylo i encodes up o ou T4SSs on i s ch omosome, namely he Cag T4SS p esen in he cag pa hogenici y island (cagPAI), he ComB sys em, as well as he T s3 and T s4 T4SSs, some o which exhibi unique T4SS unc ions. The au ho s nicely highligh ed he cu en knowledge on hese ou T4SSs and he in ol ed mechanisms wi h consequences o H. pylo i adap a ion o he hos ile en i onmen in he human s omach. Inse ions sequences (IS), in pa icula IS900, is exclusi ely p esen in Mycobac e ium a ium subsp. pa a ube culosis (Map), being used as an epidemiological ma ke . Conde e al. de eloped a bioin o ma ics ool, named IS900 RFLP in silico, ha analyses he dis ibu ion and polymo phisms o IS900 by pe o ming an in silico RFLP analysis, o e comple e Map genomes. Thus, he de eloped ool con ibu es o he be e unde s anding o Map e olu ion and o s udying he biological implica ions o IS900 inse ions. Radia ion- esis an bac e ium Deinococcus geo he malis has a o al o 73 IS in genomes, and some o hem a e ac i ely ansposed o o he loci wi h eplica i e mode due o he oxida i e s ess o hyd ogen pe oxide ea men . Lee e al. desc ibed ha LysR amily membe gene dis up ed s ain (1dgeo_2840) e ealed highe esis ance o oxida i e s ess han wild ype s ain a he la e exponen ial g ow h phase. The au ho s concluded ha he e is a LysR amily DNA-binding p o ein dependen ac i e ansposi ion o speci ic ypes o IS and he up- egula ed OxyR has no posi i ely con olled ROS sca enge enzymes in D. geo he malis. Las bu no leas , he mechanism o adap i e immune sys ems agains bac e iophages and he ole o p ophages in bac e ial di e si y a e add essed. Di e se CRISPR-Cas sys ems cons i u e an indispensable pa o he bac e ial adap i e immune sys em agains i al in ec ions. Howe e , o escape om his immune sys em, bac e iophages ha e also e ol ed co esponding an i-de ense measu es. Wang e al. in es iga ed he di e si y o CRISPR-Cas sys ems and he p esence o p ophages in he genomes o 66 Bi idobac e ium pseudoca enula um s ains. Thei esul s indica ed ha he compe i ion be ween B. pseudoca enula um and phages is a majo d i ing ac o o he genomic di e si y o bo h pa ne s. Sequencing echnology is e ol ing apidly, and so-called hi d-gene a ion sequencing echnology (such as PacBio RS II) becomes popula . Using PacBio RS II, Xu e al. ocused on he Bacillus elezensis HAB-2, ha is used as a biological con ol agen in ag icul u al ields. Compa a i e analysis o B. elezensis HAB-2 wi h o he Bacillus spp. s ains e ealed ob ious di e ences in he p ophage egion. The p ophage egions and genes encoding PPTases may p o ide no el insigh o he bac e ios a ic mechanism o Bacillus in he biological con ol o plan diseases. Bac e iophages a e he mos common biological en i y, es ablishing complex phage-bac e ia in e ac ions. Munoz e al. p esen ed an up- o-da e e iew o he bac e iophages ound in he human gu pa hogen H. pylo i. The au ho s discuss he impac o he p ophages in he genomic di e si y, i ulence, and i ness o H. pylo i. Mo eo e , in his s udy i is examined whe he hese i al pa icles can be used as a he apeu ic al e na i e (phage he apy) o add ess bac e ial esis ance and imp o e in ec ion e adica ion a es. Taken oge he , he se o pape s o e ed by his special issue showed ha he bac e ial mobilome is a key elemen o add ess he e olu iona y, ecological, and pa hogenici y success o bac e ia. AUTHOR CONTRIBUTIONS All au ho s lis ed ha e made a subs an ial, di ec , and in ellec ual con ibu ion o he wo k and app o ed i o publica ion. Con lic o In e es : The au ho s decla e ha he esea ch was conduc ed in he absence o any comme cial o inancial ela ionships ha could be cons ued as a po en ial con lic o in e es . Publishe ’s No e: All claims exp essed in his a icle a e solely hose o he au ho s and do no necessa ily ep esen hose o hei a ilia ed o ganiza ions, o hose o he publishe , he edi o s and he e iewe s. Any p oduc ha may be e alua ed in his a icle, o claim ha may be made by i s manu ac u e , is no gua an eed o endo sed by he publishe . Copy igh © 2022 Vale, Lehou s and Yamaoka. This is an open-access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion License (CC BY). The use, dis ibu ion o ep oduc ion in o he o ums is pe mi ed, p o ided he o iginal au ho (s) and he copy igh owne (s) a e c edi ed and ha he o iginal publica ion in his jou nal is ci ed, in acco dance wi h accep ed academic p ac ice. No use, dis ibu ion o ep oduc ion is pe mi ed which does no comply wi h hese e ms. F on ie s in Mic obiology | www. on ie sin.o g 2Feb ua y 2022 | Volume 13 | A icle 849667