Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2

Mikosa, Malgorzata; Sochacka‐Piętal, Marta; Baj, Jadwiga; Bartosik, Dariusz

doi:10.1099/mic.0.28603-0

Cited by 10 publications

(20 citation statements)

References 36 publications

(32 reference statements)

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“…For this reason, various entrapment vectors have been used for the identification of functional TEs. These are convenient tools, enabling the direct identification of even phenotypically silent elements (4,16,23). In this report, we present the characterization of "atypical" transposable elements "captured" by entrapment vector pMEC1 (4) in a methylotrophic bacterium utilizing dichloromethane, Paracoccus methylutens DM12 (Alphaproteobacteria) (10).…”

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confidence: 99%

Transposable Modules Generated by a Single Copy of Insertion Sequence IS Pme1 and Their Influence on Structure and Evolution of Natural Plasmids of Paracoccus methylutens DM12

et al. 2008

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We demonstrated that a single copy of insertion sequence ISPme1 can mobilize adjacent segments of genomic DNA of Paracoccus methylutens DM12, which leads to the generation of diverse transposable elements of various size and DNA contents. All elements (named transposable modules [TMos]) contain ISPme1 (placed at the 5 ends of the elements) and have variable 3-end regions of between 0.5 and 5 kb. ISPme1 was shown to encode an outwardly oriented promoter, which may activate the transcription of genes transposed within TMos in evolutionarily distinct hosts. TMos may therefore be considered to be natural systems enabling gene capture, expression, and spread. However, unless these elements have been inserted into a highly conserved genetic context to enable a precise definition of their termini, it is extremely difficult or even impossible to identify them in bacterial genomes by in silico sequence analysis. We showed that TMos are present in the chromosome and plasmids of strain DM12. Sequence analysis of plasmid pMTH1 (32 kb) revealed that four TMos, previously identified with a trap vector, pMEC1, comprise 87% of its genome. Repeated TMos within pMTH1 may stimulate other structural rearrangements resulting from homologous recombination between long repeat sequences. This illustrates that TMos may play a significant role in shaping the structure of natural plasmids, which consequently may have a great impact on the evolution of plasmid genomes.Sequencing projects have revealed that bacterial genomes are not static, monolithic structures. They can contain a number of different kinds of integrated mobile genetic elements (e.g., transposable elements, plasmids, bacteriophages, and integrative and conjugative elements) acquired by lateral gene transfer.Insertion sequences (ISs), which are the simplest forms of transposable elements (TEs), are components of nearly all bacterial genomes. To date, more than 1,500 ISs have been identified in over 295 bacterial and archaeal species (21). The transposition of ISs promotes structural changes in DNA that lead to the formation of various mutations (insertions, deletions, inversions, translocations, and replicon fusion). These elements are therefore considered to be the major recombinogenic factors in bacterial genomes. Their activity results in the shuffling of genetic information among various replicons present in a bacterial cell (chromosomes, plasmids, and bacteriophages), which may ultimately enable its spread by lateral gene transfer. These elements thus play the role of a factor that significantly enhances variability and, consequently, the adaptive and evolutionary capacities of their hosts.ISs have a very simple structure, since they carry only the genetic information necessary for their own transposition.

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confidence: 99%

Transposable Modules Generated by a Single Copy of Insertion Sequence IS Pme1 and Their Influence on Structure and Evolution of Natural Plasmids of Paracoccus methylutens DM12

et al. 2008

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“…9,14 Such intracellular transfer of chromosomal housekeeping genes may lead to the generation of chromids -essential replicons sharing features of both plasmids and chromosomes. 28,29 Tn3-family transposons may target all types of mobile genetic element.…”

Section: Mobile Genetic Elementsmentioning

confidence: 99%

“…10 Interestingly, we also identified several TEs of unusual structure, which significantly broaden our knowledge on the diversity and evolution of Tn3 family transposons. These atypical elements are (i) a composite transposon TnPpa1 of Paracoccus pantotrophus DSM 11072 (Alphaproteobacteria) 14 and (ii) a group of non-composite transposons of diverse structure isolated from Pseudomonas spp.…”

Section: Diversity Of Tn3-family Transposonsmentioning

confidence: 99%

“…Genomic rearrangements and the acquisition of additional genetic information, including numerous housekeeping genes, often embedded within other types of TEs, has led to the formation of very large TEs, which may be considered transposable genomic islands (TGEI). 14,18 TIME elements represent the products of evolution of Tn3 family elements in the opposite direction, since they were formed by reduction of the ISs or non-composite transposons. Their mobility is fully dependent on the presence of related autonomous elements in the cell.…”

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“…TnPpa1 (44,286 bp) is composed of 2 divergently oriented copies of cryptic transposon Tn3434 (Tn3 family), which border a large DNA region of chromosomal origin, containing genes encoding enzymes involved in the central intermediary metabolism, plus transporters, transcriptional regulators and conserved proteins of unknown function 9,14 . This element may be considered a composite transposon whose transposition is mediated by 2 copies of the non-composite Tn3434.…”

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Autonomous and non-autonomous Tn3-family transposons and their role in the evolution of mobile genetic elements

Szuplewska

Czarnecki²,

Bartosik³

2014

Mobile Genetic Elements

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Capture of a novel, antibiotic resistance encoding, mobile genetic element from Escherichia coli using a new entrapment vector

Tansirichaiya

Moyo

Al‐Haroni

et al. 2020

J. Appl. Microbiol.

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Aims Antimicrobial resistance genes (ARGs) are often associated with mobile genetic elements (MGEs), which facilitate their movement within and between bacterial populations. Detection of mobility is therefore important to understand the dynamics of MGE dissemination and their associated genes, especially in resistant clinical isolates that often have multiple ARGs associated with MGEs. Therefore, this study aimed to develop an entrapment vector to capture active MGEs and ARGs in clinical isolates of Escherichia coli. Methods and Results We engineered an entrapment vector, called pBACpAK, to capture MGEs in clinical E. coli isolates. It contains a cI‐tetA positive selection cartridge in which the cI gene encodes a repressor that inhibits the expression of tetA. Therefore, any disruption of cI, for example, by insertion of a MGE, will allow tetA to be expressed and result in a selectable tetracycline‐resistant phenotype. The pBACpAK was introduced into clinical E. coli isolates and grown on tetracycline‐containing agar to select for clones with the insertion of MGEs into the entrapment vector. Several insertion sequences were detected within pBACpAK, including IS26, IS903B and ISSbo1. A novel translocatable unit (TU), containing IS26 and dfrA8 was also captured, and dfrA8 was shown to confer trimethoprim resistance when it was cloned into E. coli DH5α. Conclusions The entrapment vector, pBACpAK was developed and shown to be able to capture MGEs and their associated ARGs from clinical E. coli isolates. We have captured, for the first time, a TU encoding antibiotic resistance. Significance and Impact of the Study This is the first time that a TU and associated resistance gene has been captured from clinical E. coli isolates using an entrapment vector. The pBACpAK has the potential to be used not only as a tool to capture MGEs in clinical E. coli isolates, but also to study dynamics, frequency and potentiators of mobility for MGEs.

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Identification of a transposable genomic island of Paracoccus pantotrophus DSM 11072 by its transposition to a novel entrapment vector pMMB2

Cited by 10 publications

References 36 publications

Transposable Modules Generated by a Single Copy of Insertion Sequence IS Pme1 and Their Influence on Structure and Evolution of Natural Plasmids of Paracoccus methylutens DM12

Transposable Modules Generated by a Single Copy of Insertion Sequence IS Pme1 and Their Influence on Structure and Evolution of Natural Plasmids of Paracoccus methylutens DM12

Autonomous and non-autonomous Tn3-family transposons and their role in the evolution of mobile genetic elements

Capture of a novel, antibiotic resistance encoding, mobile genetic element from Escherichia coli using a new entrapment vector

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