GENOMES - Cyanobacteria - page 128

10) Insertion sequences : ISs constitute small mobile DNA elements capable of transposition that is
mediated by a self-encoded transposase. These are classifi ed into various families or groups on the
basis of similarity, types of transposases and length of inverted repeats generated by insertion.. Their
number varies from genus to genus. Kaneko et al . (1996) identifi ed 990 ORFs bearing signifi cant
similarities to bacterial transposases spread over the entire genome of Synechocystis sp. strain PCC
6803. Only 26 of these encode functional transposases. The remaining ORFs seem to be disrupted
by mutations such as frame-shift and deletions and also insertion of other ISs suggest that a lot of
genomic rearrangements took place in this organism. In N . punctiforme ATCC 29133 there exist 150
ORFs that regulate the synthesis of transposases. STRR1 and STRR2 also occur frequently in this
organism but STRR3 and LTRR (37-bp repeat) as noted in Anabaena sp. strain PCC 7120 are not found
in N . punctiforme ATCC 29133 (Meeks et al ., 2001). In Anabaena sp. strain PCC 7120 as many as 145
genes encode transposases. The distribution of these genes on the chromosome and plasmids have
been found to be 86 and 59, respectively. The plasmid pCC7120C contains 44 of these genes. The
presence of majority of these genes in regions characteristic of IS-like elements, i.e. inverse repeats
and/or duplications at both termini is signifi cant. In Synechocystis sp. strain PCC 6803, Anabaena sp.
strain PCC 7120, T . elongatus BP-1 and G . violaceus PCC 7421 there are 73 copies (in six families), 65
copies (in seven families), 52 copies (in fi ve families) and 22 copies (in four families), respectively.
A specifi c region designated as 'cold spot' in the genome of T . elongatus BP-1 occupies a 300 kb region
and possesses high numbers of ISs and mobile introns. This region overlaps with a 'hot spot' region
consisting of all the conserved genes among cyanobacterial species. At least 74% of the genes of
T . elongatus BP-1 are common with the genes of Synechocystis sp. strain PCC 6803 and Anabaena sp.
strain PCC 7120 (Nakamura et al ., 2002). In the genome of M . aeruginosa NIES-843 there are a total
of 452 copies of ISs. However, in the genome of M . aeruginosa PCC 7806 there are only four putative
ISs. Put together thus in Microcystis genome there are 456 copies grouped into 37 groups (ISMae 1 to
ISMae37). ISMae1 and ISMae4 are common to both the strains but in M . aeruginosa NIES-843 there are
10 copies of ISMae1 and 33 copies of ISMae4. A second type of insertion sequences, termed as miniature
invert-repeat transposable elements (MITEs) are characteristic in not having an encoded transposase.
As many as 517 copies of MITEs ranging in size from 15 bp to 435 bp are present in the genome of
M . aeruginosa NIES-843 and are classifi ed into eight groups ( MaeMITEa to MaeMITEh ) (Kaneko et al .,
2008). The size of ISs constitute 11.8% of the genome in this organism with ISs (10% of the genome
equal to 583 kb) and MITEs occupying the rest (1.8% of the genome of 105 kb). Importantly, the
presence of ISs and MITEs around the mcy gene cluster signifi es that transposition of this cluster
between the individuals may be more common and thus contributes to a lot of genetic diversity
in the natural populations of this toxic cyanobacterium. Most of the Group II introns are found in
the ISs or intergenic regions. Group II introns are characteristic in coding for self-splicing ribozyme
and with the help of the maturase or reverse transcriptase activity these function as retromobile
genetic elements. In T . elongatus BP-1, 28 copies of Group II introns are present with high sequence
similarity (with 87.2 to 100% for the type TEII3 and 85.3% to 100% for the TEII4) (Nakamura et al .,
2002). In G . violaceus PCC 7421 one copy of Group II intron has been identifi ed at the map position
168,850-171,364 bp (Nakamura et al ., 2003). An eight base palindromic sequence, known as high-
iterated palindrome (HIP1) sequence is present in the genomes of many cyanobacteria. But the
number of copies of this sequence and its distribution varies in different genomes of cyanobacteria.
As for example, the genome of T . elongatus BP-1 possesses as many as 3681 copies and the average
frequency of occurrence is one copy/705 bp which is much higher than that present in Synechocystis
sp. strain PCC 6803 (one copy/1131 bp). In T . elongatus BP-1 the frequency of occurrence of HIP1 is
more in protein-coding regions (one copy/672 bp) than in RNA-encoding regions (one copy/4328