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.

Single strand transposition at the host replication fork

“…IS 911 and IS 3 family members transpose via ‘copy out-paste in’ mechanism where replication is essential for conversion of the first strand transfer product, a single strand bridge between both IS ends, to a ds circular transposition intermediate prior to insertion ( 47 – 49 ).…”

Structural and sequence diversity of eukaryotic transposable elements

“…Their transposase/integrase is distantly related to the transposases of the bacterial IS3 and IS481 families. Most IS3 elements terminate with 5'-TG..CA-3' (Siguier et al, 2015). IS481 is much shorter than the IS3 family members, although their transposases are quite similar.…”

“…DDD/E transposase/integrase is related to RNase H in its protein ternary structure and is classified in RNase H fold. Prokaryotic DNA transposons have more variety than their eukaryotic counterparts, and are classified into many families based on ISfinder (Siguier et al, 2006(Siguier et al, , 2015. IS1, IS3, IS6, IS30, IS21, IS982, IS630, IS4, IS5, IS256, IS481, IS1380, ISL3 and Tn3 (and possibly also IS66) encode a DDD/E transposase, and IS110 encodes a DDED transposase whose structure is more similar to Holliday junction resolvase, RuvC, than to DDD/E transposases.…”

A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes

“…ISs are the smallest and simplest autonomous mobile genetic elements, ranging from 0.7 to 3.5 kbp, and generally include a transposase gene encoding the enzyme that catalyzes IS movement. They are classified into about 28 different families on the basis of the relatedness of transposases and overall genetic organization [13]. The ISfinder database (https://www-is.biotoul.fr/) is the reference center for IS analysis, providing a gold standard method and protocol for IS identification, name attribution, annotation, and classification [25].…”

“…These elements are known to promote genomic expansion and rearrangements, and the emergence of virulence, pathogenicity, and symbiosis. Over the last 15 years, several reviews have focused on the impact of LGT mediated by MGEs [1][2][3][4][5][6][7][8][9][10][11][12][13]. It is now generally recognized that MGEs are central to bacterial and archaeal genome evolution.…”