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New Advances in Bacterial Plasmids
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New Advances in Bacterial Plasmids

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (25 December 2023) | Viewed by 7098

Special Issue Editors

Dr. Mayya Petrova

E-Mail Website
Guest Editor
National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
Interests: horizontal gene transfer; mobile elements; bacteria adaptation
Dr. Mikhail Edelstein

E-Mail Website
Guest Editor
Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
Interests: mechanisms and molecular epidemiology of antimicrobial resistance (AMR); Gram-negative bacteria; mobile genetic elements (MGE)

Special Issue Information

Dear Colleagues,

Bacterial plasmids serve as a platform on which genetic material is constantly exchanged and new combinations of genes necessary for adaptation to environmental conditions are assembled. For this reason, plasmids often bear the genes for resistance to heavy metals, toxins and antibiotics, metabolism of alternative energy substrates and xenobiotics, virulence, and other important traits. Since the discovery of plasmids in the middle of the last century, the interest in their study has constantly increased, and in recent years, it has been further boosted by the development and wide implementation of next-generation sequencing (NGS) technologies. In particular, this has revealed the important role of plasmids in the evolution of antibiotic resistance and the emergence of multidrug-resistant and extensively drug-resistant phenotypes in clinically important bacteria. This Special Issue is aimed at collecting original research and review articles on various aspects of plasmid biology.

Topics include, but are not limited to:

  • Plasmid typing and classification
  • Characterization of new plasmids
  • Plasmid replication and plasmid stability
  • Mobile elements in plasmid diversification
  • Evolutionary and population dynamics of plasmids
  • The role of plasmids in emergence of hypervirulent and/or multidrug-resistant strains

Dr. Mayya Petrova
Dr. Mikhail Edelstein
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • clinically important bacteria

  • environmental bacteria
  • multidrug resistance
  • biodegradation
  • resistance to heavy metals
  • bacterial adaptation, conjugative transfer of plasmids
  • plasmids in biotechnology

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Published Papers (4 papers)

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Research

10 pages, 1857 KiB  
Communication
Distribution Patterns of tfdI and tfdII Gene Clusters and New Insights into the Formation of the Architecture of pJP4, a Canonical 2,4-dichlorophenoxyacetic Acid (2,4-D) Degradation Plasmid
by Timur Iasakov
Int. J. Mol. Sci. 2024, 25(20), 10998; https://doi.org/10.3390/ijms252010998 - 12 Oct 2024
Viewed by 949
Abstract
Currently, pJP4 is one of the best-known plasmids for the biodegradation of xenobiotics that mediate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D), which is associated with serious health and environmental risks. Although the sequencing and proposed theory of pJP4 formation occurred almost 20 years [...] Read more.
Currently, pJP4 is one of the best-known plasmids for the biodegradation of xenobiotics that mediate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D), which is associated with serious health and environmental risks. Although the sequencing and proposed theory of pJP4 formation occurred almost 20 years ago (2004), pJP4 is still the model object of many studies focused on the biodegradation of 2,4-D. The uniqueness of this plasmid is due to the presence of two evolutionarily distinct gene clusters, tfdI and tfdII, controlling the degradation of 2,4-D. Recent advances in plasmid biology, especially those concerning the characterization of new IncP-1 plasmids and the systematization of tfd gene cluster findings, serve as a basis for proposing new insights into the formation of the clusters’ architecture of the canonical plasmid, pJP4, and their distribution among other plasmids. In the present work, a comparative genomic and phylogenetic in silico study of plasmids with tfdI and tfdII clusters was carried out. The possible initial distribution patterns of tfdI clusters among plasmids of different incompatibility groups (non-IncP-1) and tfdII clusters among IncP-1 plasmids using the IS1071-based composite transposon were revealed. A new theory on the formation of the architecture of the tfdI and tfdII clusters of pJP4 through sequential internal rearrangements, recombination, and ISJP4 insertion, is proposed. In addition, small gene clusters resulting from internal rearrangements of pJP4 (tfdIISA and ORF31/32) served as fingerprints for exploring the distribution of tfdI and tfdII clusters. The revealed patterns and formulated theory extend the frontiers of plasmid biology and will be beneficial for understanding the role of plasmids in bacterial adaptation to xenobiotic-contaminated environments. Full article
(This article belongs to the Special Issue New Advances in Bacterial Plasmids)
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16 pages, 4030 KiB  
Article
A Plasmid-Borne Gene Cluster Flanked by Two Restriction-Modification Systems Enables an Arctic Strain of Psychrobacter sp. to Decompose SDS
by Robert Lasek, Ignacy Piszczek, Monika Krolikowski, Adrian Sówka and Dariusz Bartosik
Int. J. Mol. Sci. 2024, 25(1), 551; https://doi.org/10.3390/ijms25010551 - 31 Dec 2023
Cited by 1 | Viewed by 1744
Abstract
The cold-adapted Psychrobacter sp. strain DAB_AL62B, isolated from ornithogenic deposits on the Arctic island of Spitsbergen, harbors a 34.5 kb plasmid, pP62BP1, which carries a genetic SLF module predicted to enable the host bacterium to metabolize alkyl sulfates including sodium dodecyl sulfate (SDS), [...] Read more.
The cold-adapted Psychrobacter sp. strain DAB_AL62B, isolated from ornithogenic deposits on the Arctic island of Spitsbergen, harbors a 34.5 kb plasmid, pP62BP1, which carries a genetic SLF module predicted to enable the host bacterium to metabolize alkyl sulfates including sodium dodecyl sulfate (SDS), a common anionic surfactant. In this work, we experimentally confirmed that the pP62BP1-harboring strain is capable of SDS degradation. The slfCHSL genes were shown to form an operon whose main promoter, PslfC, is negatively regulated by the product of the slfR gene in the absence of potential substrates. We showed that lauryl aldehyde acts as an inducer of the operon. The analysis of the draft genome sequence of the DAB_AL62B strain revealed that the crucial enzyme of the SDS degradation pathway—an alkyl sulfatase—is encoded only within the plasmid. The SLF module is flanked by two restriction–modification systems, which were shown to exhibit the same sequence specificity. We hypothesize that the maintenance of pP62BP1 may be dependent on this unique genetic organization. Full article
(This article belongs to the Special Issue New Advances in Bacterial Plasmids)
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16 pages, 8992 KiB  
Article
Comparative Analysis of Transcriptome and Proteome Revealed the Common Metabolic Pathways Induced by Prevalent ESBL Plasmids in Escherichia coli
by Chuan Huang, Hoa-Quynh Pham, Lina Zhu, Rui Wang, Oi-Kwan Law, Shu-Ling Lin, Qi-Chang Nie, Liang Zhang, Xin Wang and Terrence Chi-Kong Lau
Int. J. Mol. Sci. 2023, 24(18), 14009; https://doi.org/10.3390/ijms241814009 - 12 Sep 2023
Cited by 2 | Viewed by 2207
Abstract
Antibiotic resistance has emerged as one of the most significant threats to global public health. Plasmids, which are highly efficient self-replicating genetic vehicles, play a critical role in the dissemination of drug-resistant genes. Previous studies have mainly focused on drug-resistant genes only, often [...] Read more.
Antibiotic resistance has emerged as one of the most significant threats to global public health. Plasmids, which are highly efficient self-replicating genetic vehicles, play a critical role in the dissemination of drug-resistant genes. Previous studies have mainly focused on drug-resistant genes only, often neglecting the complete functional role of multidrug-resistant (MDR) plasmids in bacteria. In this study, we conducted a comprehensive investigation of the transcriptomes and proteomes of Escherichia coli J53 transconjugants harboring six major MDR plasmids of different incompatibility (Inc) groups, which were clinically isolated from patients. The RNA-seq analysis revealed that MDR plasmids influenced the gene expression in the bacterial host, in particular, the genes related to metabolic pathways. A proteomic analysis demonstrated the plasmid-induced regulation of several metabolic pathways including anaerobic respiration and the utilization of various carbon sources such as serine, threonine, sialic acid, and galactarate. These findings suggested that MDR plasmids confer a growth advantage to bacterial hosts in the gut, leading to the expansion of plasmid-carrying bacteria over competitors without plasmids. Moreover, this study provided insights into the versatility of prevalent MDR plasmids in moderating the cellular gene network of bacteria, which could potentially be utilized in therapeutics development for bacteria carrying MDR plasmids. Full article
(This article belongs to the Special Issue New Advances in Bacterial Plasmids)
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15 pages, 3601 KiB  
Article
Conjugative Plasmid pPPUT-Tik1-1 from a Permafrost Pseudomonas putida Strain and Its Present-Day Counterparts Inhabiting Environments and Clinics
by Olga Maslova, Alexey Beletsky, Sofia Mindlin, Nika Petrova, Andrey Mardanov and Mayya Petrova
Int. J. Mol. Sci. 2023, 24(17), 13518; https://doi.org/10.3390/ijms241713518 - 31 Aug 2023
Viewed by 1447
Abstract
A novel group of conjugative plasmids of Pseudomonas is characterized. The prototype plasmid pPPUT-Tik1-1 (153,663 bp), isolated from a permafrost strain of P. putida Tik1, carries a defective mercury transposon, Tn501, and a streptomycin resistance transposon, Tn5393. Ten plasmids and [...] Read more.
A novel group of conjugative plasmids of Pseudomonas is characterized. The prototype plasmid pPPUT-Tik1-1 (153,663 bp), isolated from a permafrost strain of P. putida Tik1, carries a defective mercury transposon, Tn501, and a streptomycin resistance transposon, Tn5393. Ten plasmids and 34 contigs with backbone regions closely related to pPPUT-Tik1-1 have been found in GenBank. Two of these plasmids from clinical strains of P. putida and P. fulva are almost identical to the ancient plasmid. A characteristic feature of this group of plasmids is the presence of two genes encoding the initiators of replication (repA1 and repA2). None of these genes have high similarity with plasmid replication genes belonging to known incompatibility groups. It has been demonstrated that while pPPUT-Tik1-1-like plasmids have homologous backbone regions, they significantly differ by the molecular structure and the predicted functions of their accessory regions. Some of the pPPUT-Tik1-1-related plasmids carry determinants of antibiotic resistance and/or heavy metal salts. Some plasmids are characterized by the ability to degrade xenobiotics. Plasmids related to pPPUT-Tik1-1 are characterized by a narrow host range and are found in various species of the Pseudomonas genus. Interestingly, we also found shorter plasmid variants containing the same replication module, but lacking conjugation genes and containing other structural changes that strongly distinguish them from plasmids related to pPPUT-Tik1-1, indicating that the structure of the replication module cannot be used as the sole criterion for classifying plasmids. Overall, the results suggest that the plasmids of the novel group can be spread using conjugation in environmental and clinical strains of Pseudomonas and may play diverse adaptive functions due to the presence of various accessory regions. Full article
(This article belongs to the Special Issue New Advances in Bacterial Plasmids)
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