Everyman's Guide to Bacterial Insertion Sequences

Abstract

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.

Transposition of Tn 125 Encoding the NDM-1 Carbapenemase in Acinetobacter baumannii

“…This high frequency and high copy number of ISAba125 in Acinetobacter spp. are indicative of frequent transposition events, lateral gene transfer within Acinetobacter spp., a replicative mechanism of transposition (as shown for the IS30 family), and the capacity of ISAba125 to expand within genomes, a general feature of ISs (9). Taken together, these characteristics are suggestive of an evolutionary role of ISAba125 customized for Acinetobacter spp., as proposed for ISAba1 in A. baumannii (32,33).…”

“…1A) (4,7,8). The 1,087-bp ISAba125 element belongs to the IS30 family and encodes a 322-amino-acid-long DDE-type transposase surrounded by imperfect terminal inverted repeat sequences (IRR [inverted repeat right] and IRL [inverted repeat left], sharing 20/26 nucleotide identity) (9,10). The ble MBL gene, which encodes a 121-amino-acid-long protein conferring resistance to bleomycin, a glycopeptide antibiotic used as an antitumor agent, is located downstream of the bla NDM-1 gene (11).…”

Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

“…The typically have imperfect repeats ranging in size from 15 to 39 bp along with 8 bp direct repeats. Additionally, the protein usually includes an α-helical domain (Siguier et al, 2015). In Pseudomonas stutzeri , ISL3 elements' translocation can be induced by zygotic induction after conjugative interaction (Christie-Oleza et al, 2010).…”

Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus

“…Our updated annotation of the IS30-like Tpase indicates that a fusion product of orf1 and orf2 has an N-terminal DNA-binding domain with two putative helix-turn-helix motifs (encoded by orf2) and a C-terminal catalytic domain with the DDE motif (encoded by orf1) (Fig. 2), which is a structural organization common for a Tpase (36). Three poly(A) tracts also occur in orf2 (13) (Fig.…”

“…ICE6013 is now the third family of integrative conjugative elements, after TnGBS and ICEA (15,16), known to use a DDE Tpase as a recombinase and the first example to use the IS30 family of Tpases. While the prototypical IS30 element from E. coli carries a single ORF (36), the IS30-like Tpase from ICE6013 is encoded by two ORFs. A two-ORF structure for an IS30-like element, ISLxc4, has also been reported for the plant-inhabiting bacterium Leifsonia xyli, though it was not linked to an ICE (37).…”