What is an IS?
The original definition
of an IS (Fig 1.3.1
was: a short, generally phenotypically cryptic, DNA segment encoding only the
enzymes necessary for its transposition and capable of repeated insertion into
many different sites within a genome using mechanisms independent of large
regions of DNA homology between the IS and target (Berg & Howe, 1989, Craig, et al., 2002). Classical IS are between
0.7 and 2.5 kb in length, genetically compact with one or two open reading
which occupy the entire length of the IS and terminate in flanking imperfect terminal repeat sequences
(IR) (Table 1: Characteristics of IS families. The orfs
include the Tpase that catalyzes the DNA cleavages and strand transfers leading
to IS movement and, in some cases, regulatory proteins. Their highly compact
nature is illustrated by the fact that some IS have developed "recoding" strategies such as Programmed Ribosomal
Frameshifting (involving ribosome slippage) and
Programmed Transcriptional Realignment (involving RNA polymerase slippage) (Sharma,
et al., 2011, Siguier, et al.,
2014, Chandler, et al., 2015). These permit assembly of different functional protein
domains effectively encoding two proteins of different function in one DNA
segment. IS also often generates a short flanking directly repeated duplication (DR)
of the target DNA on insertion. These characteristics are not limited to
prokaryotic IS but are also shared with most eukaryotic DNA transposons. Classical
IS generally transpose using a double strand DNA intermediate.
However, for prokaryotic IS, this strict definition has been broadened over the years
with the discovery of an increasing number of non-canonical derivatives and
variants, some of which are described in the following sections. Moreover, as
we learn more about diversity from sequenced genomes, classification is becoming more problematic
because the large degree of MGE diversity is obscuring the borders between
certain types of TE (Fuzzy
Borders (Siguier, et al.,
2014). Despite their abundance and diversity,
the number of different chemical mechanisms used in TE movement is surprisingly
limited and many quite divergent TE share a similar mechanism.
New types of IS
example of this expanding diversity is the identification of another entire
class of IS (Kersulyte, et al., 1998, Kersulyte, et
al., 2002). Members or this class use an entirely different
mechanism of transposition involving single strand circular DNA intermediates
which appear to target stalled replication forks (He, et al., 2015) (Fig 1.3.2). They possess small transposases (~150 aa)
which are completely different to the classical IS in the type of chemistry
they catalyze (Groups with HUH
example are the casposons which are related to CRISPRs but whose transposition
has yet to be fully characterized (Krupovic, et al., 2014)(Hickman &
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