Lehours, Philippe

Vale, Filipa F.

Yamaoka, Yoshio

Frontiers in Microbiology

English

PubMed

Universidade de Lisboa: Repositório.UL

EDITORIALpublished: 21 February 2022doi: 10.3389/fmicb.2022.849667Frontiers in Microbiology | www.frontiersin.org 1 February 2022 | Volume 13 | Article 849667Edited and reviewed by:Ludmila Chistoserdova,University of Washington,United States*Correspondence:Filipa F. Valevale.filipa@gmail.comSpecialty section:This article was submitted toEvolutionary and GenomicMicrobiology,a section of the journalFrontiers in MicrobiologyReceived: 06 January 2022Accepted: 17 January 2022Published: 21 February 2022Citation:Vale FF, Lehours P and Yamaoka Y(2022) Editorial: The Role of MobileGenetic Elements in BacterialEvolution and Their Adaptability.Front. Microbiol. 13:849667.doi: 10.3389/fmicb.2022.849667Editorial: The Role of Mobile GeneticElements in Bacterial Evolution andTheir AdaptabilityFilipa F. Vale 1*, Philippe Lehours 2,3 and Yoshio Yamaoka 41 Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty ofPharmacy, Universidade de Lisboa, Lisboa, Portugal, 2 INSERM U1312, Bordeaux Institute of Oncology, BRIC, Bordeaux,France, 3Centre National de Référence des Campylobacters et des Hélicobacters, Bordeaux, France, 4Department ofEnvironmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita, JapanKeywords: mobile elements (MEs), evolution, adaptability, bacteriophage, virulence factors, insertion sequence(Is), restriction and modificationEditorial on the Research TopicThe Role of Mobile Genetic Elements in Bacterial Evolution and Their AdaptabilityThe bacterial mobilome, i.e., the group of all mobile elements present in a bacterial genome, areimportant players in bacterial evolution, shaping the host genome through complex interactionsbetween the mobile element and host bacteria. Mobile element is a generic term for a multitudeof genomic sequences, such as plasmids, prophages, pathogenicity islands, restriction andmodification systems, transposons, and insertion sequences, among others, that share the abilityto be transmitted vertically with cell division or through horizontal transfer. Thus, they areable to move within the host genome as well as jump across genomes, shaping and co-evolvingwith chromosomal genomes. Mobile elements can change their insertion location, copy number,provide new gene functions, or affect chromosomal gene expression. Mobile elements are knownto potentiate gene gain and loss, a major force that can profoundly change bacterial fitness. Thischange can contribute to the genetic adaptation to new environments and the emergence ofdivergent bacterial populations that may produce evolutionary distinct species.Since their discovery, the mechanisms of persistence and interaction of mobile elements withthe bacterial genome have been increasingly studied. This special issue, through the presentationof pertinent and important examples of distinct mobile elements (genomic islands, pathogenicityislands, insertion sequences, prophages, and restriction and modifications systems), either byreviewing, showing new aspects, or presenting new bioinformatics tools, shows the importanceof comprehending the biology of mobile genetic elements.To start, the role of distinct mobile genetic elements in adaptive evolution is addressed.The epigenetic DNA-based methylation plays important roles in gene expression regulation.Yano et al. described a gene expression regulation network in H. pylori consisting of many DNAmethyltransferases each frequently changing its target sequence-specificity in search for adaptation.H. pylori carries a large and variable repertoire of sequence-specific DNA methyltransferases, andmotility, oxidative stress tolerance, and DNA damage repair are likewise regulated by multiplemethyltransferases. The network provides a new paradigm in understanding global gene regulationand adaptive evolution.Moving into another microorganism, Escherichia coli presents many accessory genes acquiredby horizontal transfer that form syntenic blocks and are recognized as genomic islands (GIs).These genomic regions contribute to the rapid evolution, diversification, and adaptation of E. colivariants. In the paper by Desvaux et al. the authors reviewed a subgroup of GIs from E. coli termedVale et al. Editorial: The Role of Mobile Genetic Elements in Bacterial Evolution and Their Adaptabilitypathogenicity islands which contribute to the emergence ofvirulent bacteria and to the development of intestinal andextraintestinal diseases.Next, a group of manuscripts highlights the role of mobilegenetic elements in bacteria pathogenicity, or their use forepidemiologic purposes.Fischer et al. focused again on the pathogenic bacterium H.pylori, which was acquired multiple type IV secretion systems(T4SSs). H. pylori encodes up to four T4SSs on its chromosome,namely the Cag T4SS present in the cag pathogenicity island(cagPAI), the ComB system, as well as the Tfs3 and Tfs4T4SSs, some of which exhibit unique T4SS functions. Theauthors nicely highlighted the current knowledge on thesefour T4SSs and the involved mechanisms with consequencesfor H. pylori adaptation to the hostile environment in thehuman stomach.Insertions sequences (IS), in particular IS900, is exclusivelypresent in Mycobacterium avium subsp. paratuberculosis (Map),being used as an epidemiological marker. Conde et al. developeda bioinformatics tool, named IS900 RFLP in silico, that analysesthe distribution and polymorphisms of IS900 by performingan in silico RFLP analysis, over complete Map genomes. Thus,the developed tool contributes to the better understanding ofMap evolution and to studying the biological implications ofIS900 insertions.Radiation-resistant bacterium Deinococcus geothermalis hasa total of 73 IS in genomes, and some of them are activelytransposed to other loci with replicative mode due to theoxidative stress of hydrogen peroxide treatment. Lee et al.described that LysR family member gene disrupted strain(1dgeo_2840) revealed higher resistance to oxidative stress thanwild type strain at the late exponential growth phase. The authorsconcluded that there is a LysR family DNA-binding proteindependent active transposition of specific types of IS and theup-regulated OxyR has not positively controlled ROS scavengerenzymes in D. geothermalis.Last but not least, the mechanism of adaptive immune systemsagainst bacteriophages and the role of prophages in bacterialdiversity are addressed.Diverse CRISPR-Cas systems constitute an indispensable partof the bacterial adaptive immune system against viral infections.However, to escape from this immune system, bacteriophageshave also evolved corresponding anti-defense measures. Wanget al. investigated the diversity of CRISPR-Cas systems and thepresence of prophages in the genomes of 66 Bifidobacteriumpseudocatenulatum strains. Their results indicated that thecompetition between B. pseudocatenulatum and phages is a majordriving factor for the genomic diversity of both partners.Sequencing technology is evolving rapidly, and so-calledthird-generation sequencing technology (such as PacBio RSII) becomes popular. Using PacBio RS II, Xu et al. focusedon the Bacillus velezensis HAB-2, that is used as a biologicalcontrol agent in agricultural fields. Comparative analysis ofB. velezensis HAB-2 with other Bacillus spp. strains revealedobvious differences in the prophage region. The prophage regionsand genes encoding PPTases may provide novel insight for thebacteriostatic mechanism of Bacillus in the biological control ofplant diseases.Bacteriophages are the most common biological entity,establishing complex phage-bacteria interactions. Munoz et al.presented an up-to-date review of the bacteriophages found inthe human gut pathogen H. pylori. The authors discuss theimpact of the prophages in the genomic diversity, virulence, andfitness ofH. pylori. Moreover, in this study it is examined whetherthese viral particles can be used as a therapeutic alternative (phagetherapy) to address bacterial resistance and improve infectioneradication rates.Taken together, the set of papers offered by this specialissue showed that the bacterial mobilome is a key element toaddress the evolutionary, ecological, and pathogenicity successof bacteria.AUTHOR CONTRIBUTIONSAll authors listed have made a substantial, direct, and intellectualcontribution to the work and approved it for publication.Conflict of Interest: The authors declare that the research was conducted in theabsence of any commercial or financial relationships that could be construed as apotential conflict of interest.Publisher’s Note: All claims expressed in this article are solely those of the authorsand do not necessarily represent those of their affiliated organizations, or those ofthe publisher, the editors and the reviewers. Any product that may be evaluated inthis article, or claim that may be made by its manufacturer, is not guaranteed orendorsed by the publisher.Copyright © 2022 Vale, Lehours and Yamaoka. This is an open-access articledistributed under the terms of the Creative Commons Attribution License (CC BY).The use, distribution or reproduction in other forums is permitted, provided theoriginal author(s) and the copyright owner(s) are credited and that the originalpublication in this journal is cited, in accordance with accepted academic practice.No use, distribution or reproduction is permitted which does not comply with theseterms.Frontiers in Microbiology | www.frontiersin.org 2 February 2022 | Volume 13 | Article 849667

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

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

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