A new subgroup of the IS3 family and properties of its representative member ISPpy1

Petrová, Magdalena; Shcherbatova, Natalya; Gorlenko, Zhosephine; Mindlin, S. Z.

doi:10.1099/mic.0.068676-0

Cited by 4 publications

(5 citation statements)

References 33 publications

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“…The accessory region of the pKLH80 plasmid contains five antibiotic resistance genes: previously characterized genes, strA–strB and tetR–tet (H) (Petrova et al , 2009), and an additional gene discovered in this work, bla RTG . Two IS elements, IS Aba14 and IS Psma1 , were also found in this region, in addition to IS Ppy1 identified previously (Petrova et al , 2009, 2013).…”

Section: Resultssupporting

confidence: 72%

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Genetic structure and biological properties of the first ancient multiresistance plasmid pKLH80 isolated from a permafrost bacterium

et al. 2014

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A novel multidrug-resistance plasmid, pKLH80, previously isolated from Psychrobacter maritimus MR29-12 found in ancient permafrost, was completely sequenced and analysed. In our previous studies, we focused on the pKLH80 plasmid region containing streptomycin and tetracycline resistance genes, and their mobilization with an upstream-located ISPpy1 insertion sequence (IS) element. Here, we present the complete sequence of pKLH80 and analysis of its backbone genetic structure, including previously unknown features of the plasmid's accessory region, notably a novel variant of the b-lactamase gene bla . Plasmid pKLH80 was found to be a circular 14 835 bp molecule that has an overall G+C content of 40.3 mol% and encodes 20 putative ORFs. There are two distinctive functional modules within the plasmid backbone sequence: (i) the replication module consisting of repB and the oriV region; and (ii) the mobilization module consisting of mobA, mobC and oriT. All of the aforementioned genes share sequence identities with corresponding genes of different species of Psychrobacter. The plasmid accessory region contains antibiotic resistance genes and IS elements (ISPsma1 of the IS982 family, and ISPpy1 and ISAba14 of the IS3 family) found in environmental and clinical bacterial strains of different taxa. We revealed that the sequences flanking bla RTG-6 and closely related genes from clinical bacteria are nearly identical. This fact suggests that bla RTG-6 from the environmental strain of Psychrobacter is a progenitor of bla RTG genes of clinical bacteria. We also showed that pKLH80 can replicate in different strains of Acinetobacter and Psychrobacter genera. The roles of IS elements in the horizontal transfer of antibiotic resistance genes are examined and discussed.

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Section: Resultssupporting

confidence: 72%

“…It should be noted that in contrast to IS Psma1 , only one copy of each of the two other mobile elements, IS Aba14 () and IS Ppy1 (Petrova et al , 2013), is present in the MR29-12 genome.…”

Section: Resultsmentioning

confidence: 99%

Genetic structure and biological properties of the first ancient multiresistance plasmid pKLH80 isolated from a permafrost bacterium

et al. 2014

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“…Recently, an additional subgroup has been proposed, which includes ISPpy1 (146). However, all members belong to the IS150 subgroup and their Tpases are not separated by our standard multiple alignment and Markov Cluster Analysis (MCL) analysis.…”

Section: (Ii) Organizationmentioning

confidence: 99%

Everyman's Guide to Bacterial Insertion Sequences

et al. 2015

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The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.

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“…1 d). An insertion sequence IS Ppy1 has similar sequence features with IS 1447 in terms of IRs [ 37 ], but its evolutionary relationship is not close to IS 1447 (see below). This indicated that IS 1447 may represent a novel IS 3 -family subgroup that has a diverse phylogenetic relation with known subgroups.…”

Section: Resultsmentioning

confidence: 99%

“…Compared to the Firmicutes branch, the non-Firmicutes branch showed low bootstrap values, indicating low confidence and high variability of the evolutionary relationships [ 38 ] (Additional file 1 : Figure S1). In addition, nucleotide sequence analysis showed that a large proportion (76.5%, 26 of 34 randomly selected sequences) of the insertion sequences from the non-Firmicutes branch exhibited no or − 1 frameshifting for the expression of Tpases, including the IS Ppy1 element from the plasmid pKLH80 of Psychrobacter maritimus MR29-12 (GenBank Accession Number AM992204), which was determined previously to display a subgroup of the IS 3 -family [ 37 ] (Additional file 1 : Figure S1). Thus, IS 1447 -like elements are primarily present in the phylum Firmicutes and not closely related to those from non-Firmicutes species.…”

Section: Resultsmentioning

confidence: 99%

Firmicutes-enriched IS1447 represents a group of IS3-family insertion sequences exhibiting unique + 1 transcriptional slippage

Liu

Zhang

et al. 2018

Biotechnol Biofuels

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BackgroundBacterial insertion sequences (ISs) are ubiquitous mobile genetic elements that play important roles in genome plasticity, cell adaptability, and function evolution. ISs of various families and subgroups contain significantly diverse molecular features and functional mechanisms that are not fully understood.ResultsIS1447 is a member of the widespread IS3 family and was previously detected to have transposing activity in a typical thermophilic and cellulolytic microorganism Clostridium thermocellum. Phylogenetic analysis showed that IS1447-like elements are widely distributed in Firmicutes and possess unique features in the IS3 family. Therefore, IS1447 may represent a novel subgroup of the IS3 family. Unlike other well-known IS3 subgroups performing programmed − 1 translational frameshifting for the expression of the transposase, IS1447 exhibits transcriptional slippage in both the + 1 and − 1 directions, each with a frequency of ~ 16%, and only + 1 slippage results in full-length and functional transposase. The slippage-prone region of IS1447 contains a run of nine A nucleotides following a stem-loop structure in mRNA, but mutagenesis analysis indicated that seven of them are sufficient for the observed slippage. Western blot analysis indicated that IS1447 produces three types of transposases with alternative initiations. Furthermore, the IS1447-subgroup elements are abundant in the genomes of several cellulolytic bacteria.ConclusionOur result indicated that IS1447 represents a new Firmicutes-enriched subgroup of the IS3 family. The characterization of the novel IS3-family member will enrich our understanding of the transposition behavior of IS elements and may provide insight into developing IS-based mutagenesis tools for thermophiles.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1304-8) contains supplementary material, which is available to authorized users.

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A new subgroup of the IS3 family and properties of its representative member ISPpy1

Cited by 4 publications

References 33 publications

Genetic structure and biological properties of the first ancient multiresistance plasmid pKLH80 isolated from a permafrost bacterium

Genetic structure and biological properties of the first ancient multiresistance plasmid pKLH80 isolated from a permafrost bacterium

Everyman's Guide to Bacterial Insertion Sequences

Firmicutes-enriched IS1447 represents a group of IS3-family insertion sequences exhibiting unique + 1 transcriptional slippage

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