ISfinder and the growing number of IS
IS classification is
needed to cope with the high numbers and diversity of ISs. It also permits
identification of the many IS fragments present in numerous genomes,
contributes to understanding their effects on their host genomes and can
provide insights into their regulation and transposition mechanism. This role
has been assumed by ISfinder (Siguier, et al., 2006) following the
closure of the Stanford repository (Lederberg,
1981). Several criteria are used to classify IS. These include: genetic
organization, similarity of transposase amino acid primary sequence, length and
sequence of terminal inverted repeats, target site preferences, length of
target repeats and the chemistry of transposon DNA strand cleavage and transfer
into the target DNA (Fig
Since 1998, IS have been centralized in the
ISfinder database to provide a basic framework for nomenclature and IS classification into related
groups or families, often divided into subgroups (Fig
1.4.2) (Siguier, et al.,
2006). Initially IS were each assigned a simple number (Campbell, et
al., 1979). However, to provide information about their provenance, IS nomenclature rules were changed
and now resemble those used for restriction enzymes: with the first letter of
the genus followed by the first two letters of the species and a number (Mahillon & Chandler, 2000) (e.g., ISBce1 for Bacillus cereus).
In 1977 only 5 IS (IS1, IS2, IS3,
IS4 and IS5) had been identified (Nevers
& Saedler, 1977). At the time of publication of the first edition of
Mobile DNA I (Berg & Howe, 1989) this
had risen to 50 (Galas & Chandler, 1989);
at the time of the second, Mobile DNA II (Craig, et al., 2002), there were more
than 700 (Chandler & Mahillon, 2002);
and at present (Mobile DNA III) , ISfinder includes more than 4600 examples
distributed into 29
families some of which can be conveniently divided into subgroups (Fig
1; (Siguier, et al.,
2015)). This classification evolves continuously with the accumulation
of additional ISs. The
IS in the ISfinder repository represent only a fraction of IS present in the
public databases. Not only has the number of IS identified increased
dramatically with the advent of high throughput genome sequencing but
examination of the public databases has shown that genes annotated as transposases (Tpases), the
enzymes which catalyse TE movement (or proteins with related functions), are by
far the most abundant functional class (Aziz, et al., 2010).(Fig
RK, Breitbart M & Edwards RA (2010) Transposases are the most abundant,
most ubiquitous genes in nature. Nucleic
Acids Res 38: 4207-4217.
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Ton-Hoang B & Chandler M (2015) Everyman's Guide to Bacterial Insertion
Sequences. Microbiol Spectr 3: MDNA3-0030-2014.