Mobile Genetic Elements in Adaptation of Bacteria to the Changing Environment

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 4343

Special Issue Editors


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Guest Editor
Laboratory of DNA segregation and cell cycle of Proteobacteria. Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
Interests: bacterial DNA segregation; DNA topology; gene expression and bacterial metabolism; biology of broad-host-range plasmids; plasmid maintenance; horizontal transfer; plasmid–host interactions; plasmid adaptation

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Guest Editor
Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
Interests: bacterial genetics; biology of MGEs; impact of MGEs on bacterial metabolism; genome structure and evolution; stable maintenance of bacterial plasmids; transposable elements; integrative and conjugative elements

Special Issue Information

Dear Colleagues,

Mobile genetic elements (including insertion sequences, transposons, integron gene cassettes, plasmids, prophages, casposons, integrative and conjugative elements, and mobile genomic islands) move within and between DNA molecules. Together, they play a central role in facilitating horizontal gene exchange among phylogenetically distant species. Even if these mobile DNA molecules are not crucial for host viability, they promote the acquisition of new phenotypic traits, playing an important role in the adaptation of their host bacterial strains to diverse challenging environments.

Genome-wide analyses have resulted in the identification and characterization of an increasing number of different types of MGEs. Many of these have been extensively studied in recent years; however, there is still a considerable gap in our knowledge concerning the biological and evolutionary role of MGEs – both in environmental and clinical bacterial isolates. One of the most exciting topics is how they survive and evolve and what underlies their persistence in the environment. Their role in enabling the adaptation of their hosts to hostile environments is an enduring question.

We are pleased to invite you to contribute to this Special Issue of Microorganisms concerning MGEs – their impact on bacterial adaptability and evolution. Our aim is to highlight, through original research articles and reviews, the biological roles of MGEs, their importance in the properties they confer to their bacterial hosts, their specific interactions with their host strains, their contribution to diverse phenotypes, and the molecular mechanisms underlying phenotypic traits. An equally important issue is the role of the genetic load of MGEs in adaptation of these elements to new host strains and their survival and persistence in the environment.

We look forward to receiving your contributions.

Prof. Dr. Grazyna Jagura-Burdzy
Prof. Dr. Dariusz Bartosik
Guest Editors

Manuscript Submission Information

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Keywords

  • plasmids
  • transposons
  • integrons
  • integrative conjugative elements
  • mobile genomic islands
  • phages
  • MGE adaptation to the hosts and environment

Published Papers (2 papers)

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Research

20 pages, 2027 KiB  
Article
Beyond the ABCs—Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW)
by Heike M. Freese, Victoria Ringel, Jörg Overmann and Jörn Petersen
Microorganisms 2022, 10(4), 738; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10040738 - 29 Mar 2022
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Abstract
Copiotrophic marine bacteria of the Roseobacter group (Rhodobacterales, Alphaproteobacteria) are characterized by a multipartite genome organization. We sequenced the genomes of Sulfitobacter indolifex DSM 14862T and four related plasmid-rich isolates in order to investigate the composition, distribution, and evolution [...] Read more.
Copiotrophic marine bacteria of the Roseobacter group (Rhodobacterales, Alphaproteobacteria) are characterized by a multipartite genome organization. We sequenced the genomes of Sulfitobacter indolifex DSM 14862T and four related plasmid-rich isolates in order to investigate the composition, distribution, and evolution of their extrachromosomal replicons (ECRs). A combination of long-read PacBio and short-read Illumina sequencing was required to establish complete closed genomes that comprised up to twelve ECRs. The ECRs were differentiated in stably evolving chromids and genuine plasmids. Among the chromids, a diagnostic RepABC-8 replicon was detected in four Sulfitobacter species that likely reflects an evolutionary innovation that originated in their common ancestor. Classification of the ECRs showed that the most abundant plasmid system is RepABC, followed by RepA, DnaA-like, and RepB. However, the strains also contained three novel plasmid types that were designated RepQ, RepY, and RepW. We confirmed the functionality of their replicases, investigated the genetic inventory of the mostly cryptic plasmids, and retraced their evolutionary origin. Remarkably, the RepY plasmid of S. pontiacus DSM 110277 is the first high copy-number plasmid discovered in Rhodobacterales. Full article
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11 pages, 1058 KiB  
Article
A New ICEclc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716
by Jun Hirose, Takahito Watanabe, Taiki Futagami, Hidehiko Fujihara, Nobutada Kimura, Hikaru Suenaga, Masatoshi Goto, Akiko Suyama and Kensuke Furukawa
Microorganisms 2021, 9(12), 2462; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9122462 - 29 Nov 2021
Cited by 8 | Viewed by 1640
Abstract
Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICEclc family [...] Read more.
Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICEclc family carrying biphenyl catabolic bph genes and salicylic acid catabolic sal genes from the PCB-degrading strain Pseudomonas stutzeri KF716. The 117-kb ICEbph-salKF716 contains common core regions exhibiting homology with those of degradative ICEclc from P. knackmussii B13 and ICEXTD from Azoarcus sp. CIB. A comparison of the gene loci collected from the public database revealed that several putative ICEs from P. putida B6-2, P, alcaliphila JAB1, P. stutzeri AN10, and P. stutzeri 2A20 had highly conserved core regions with those of ICEbph-salKF716, along with the variable region that encodes the catabolic genes for biphenyl, naphthalene, toluene, or phenol. These data indicate that this type of ICE subfamily is ubiquitously distributed within aromatic compound-degrading bacteria. ICEbph-salKF716 was transferred from P. stutzeri KF716 to P. aeruginosa PAO1 via a circular extrachromosomal intermediate form. In this study, we describe the structure and genetic features of ICEbph-salKF716 compared to other catabolic ICEs. Full article
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