The Insertion Sequences of Anabaena sp. Strain PCC 7120 and Their Effects on Its Open Reading Frames

Anabaena sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs'' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (http://www-is.biotoul.fr/) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others—some encoding proteins of predictable function, including protein kinases, and restriction endonucleases—that were interrupted by ISs. Anabaena sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs.Insertion sequences (ISs) are transposable elements found in prokaryotic and eukaryotic genomes (17). A fully functional bacterial IS comprises one or more transposase genes, ends that are often inverted repeats (IRs), and, between the transposase genes and the ends, sequences termed linkers (32). Diverse bacterial ISs have been classified, and a searchable database of ISs has been constructed (ISfinder http://www-is.biotoul.fr/]) (28). Miniature inverted-repeat transposable elements (MITEs) and even smaller mobile elements lack their own transposases and are also found in Anabaena spp. (11, 12, 33).Anabaena sp. strain PCC 7120 (also known as Nostoc sp. 25], here denoted Anabaena sp.) is widely used to study the patterned differentiation of dinitrogen-fixing cells called heterocysts. Transposition of ISs in Anabaena sp. has been documented (1, 7-9). We earlier reported, with few details, three genes that are intercepted by ISs in Anabaena sp. (23). We here describe the approach more extensively, organize the ISs of Anabaena sp., and present our efforts to identify Anabaena sp. open reading frames (ORFs) interrupted or contributed to by ISs.