IS Families/ISAs1 family

Original Identification and Distribution

ISAs1 was identified in the fish pathogen Aeromonas salmonicida as insertions into the vapA gene which is responsible for the formation of a virulence factor, the tetragonal paracrystalline surface protein array (A-layer). Southern blot analysis showed it to be restricted to 2 A. salmonicida strains and present in low copy number. The putative ISAs1 transposase was visualized as a 42,000 molecular weight (M(r)) protein .

There are nearly 100 entries for this family in ISfinder from over 50 bacterial species. There are currently no archaeal members. ISAs1 family members are between 1200 and 1326 bp long and generally carry related terminal IRs of between 14 and 22 bp (Fig.ISAs1.1). A single orf of between 294 and 376 amino acids occupies almost the entire length with between 26 and 50% identity. There are several conserved D and E residues but no clear C1 domain. The Tpases of this family include a β-strand insertion domain .

A second, related IS, IS1358, was identified in Vibrio and is linked to surface layer and O-antigen genes . Its putative Tpase of has been visualized using a phage T7 promoter-driven gene and that of ISAs1 has been detected in Escherichia coli minicells .

The family also includes ‘‘H-repeats’’ which form part of several so-called RHS (Rearrangement Hot Spot) elements containing another repeated sequence, the H-rpt element (Hinc-repeat) (see ). Escherichia coli K-12 contains 5 large repetitions of this type (RhsA to RhsE, scattered around the chromosome with lengths of between 3.7 and 9.6 kb). They represent nearly 1 % of the chromosome and provide homology for RecA-dependent rearrangements. These elements are present in many but not all wild-type isolates of E. coli.

The most prominent Rhs component is a giant core orf whose features are suggestive of a cell wall surface ligand-binding protein. Each Rhs element also contains another repeated sequence, the H-rpt element displaying features of typical insertion sequences (called ISSe1), although no transposition activity has yet been detected.

For the sake of clarity, the H-rpt DNA sequences B (RhsB), C1to C3 (RhsC), E (RhsE), and min.5 , as well as H-rptF , have been renamed ISEc1 to ISEc7, respectively (Table 1. Characteristics of insertion sequence families) .

Fig. ISAs1.1. General ISAs1 characteristics, average length, and common ends. Top: Distribution of IS length (base pairs) of ISAs1 family members. The number of examples used in the sample is shown above each column. Bottom: Left (IRL) and right IRR inverted terminal repeats are shown in WebLogo format.

Mechanism

Little is known about the transposition properties of this family of elements. However, recent experiments with the Vibrio cholera element IS1358 and ISPG2 have demonstrated that insertion generates 10-bp or 8-bp DRs.

It is interesting to note that several members of the family (IS1358 , ISAs1 and ISSe1 ) are associated with cell surface component genes in their respective hosts, although this may reflect the interests of the researchers rather than reflecting a specific association.

In Streptococcus agalactiae, IS1548, is also associated with virulence modulation and has been linked to 19 strains associated with neonatal meningitis and endocarditis . It has been reported to impact S. agalactiae in two ways: by inactivating virulence genes such as hylB (hyaluronidase ) or cpsD by insertion and by activating the expression of downstream genes such as lmb (laminin/Zn-binding protein gene) and murB (peptidoglycan biosynthesis) .

Another member, ISPmar4, has been implicated in driving transposition of a mosaic element in Paracoccus .