Identification and Distribution of New Insertion Sequences in the Genome of Alkaliphilic Bacillus halodurans C-125

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Abstract
Fifteen kinds of new insertion sequences (ISs), IS 641 to IS 643 , IS 650 to IS 658 , IS 660 , IS 662 , and IS 663 , and a group II intron (Bh.Int) were identified in the 4,202,352-bp genome of alkaliphilic Bacillus halodurans C-125. Out of 120 ISs identified in the C-125 genome, 29 were truncated, indicating the occurrence of internal rearrangements of the genome. The ISs other than IS 650 , IS 653 , IS 660 , and IS 663 generated a 2- to 9-bp duplication of the target site sequence, and the ISs other than IS 650 , IS 653 , and IS 657 carry 14- to 64-bp inverted repeats. Sequence analysis revealed that six kinds of ISs (IS 642 , IS 643 , IS 654 , IS 655 , IS 657 , and IS 658 ) belong to a separate IS family (IS 630 , IS 21 , IS 256 , IS 3 , IS 200 /IS 605 , and IS 30 , respectively) as a new member. Also, IS 651 and IS 652 were characterized as new members of the IS L3 family. Significant similarity was found between the transposase (Tpase) sequences between IS 650 and IS 653 (78.2%), IS 651 and IS 652 (56.3%), IS 656 and IS 662 (71.0%), and IS 660 and IS 663 (44.5%), but the others showed no similarity to one another. Tpases in 28 members of IS 651 in the C-125 genome were found to have become diversified. Most of the IS elements widely distributed throughout the genome were inserted in noncoding regions, although some genes, such as those coding for an ATP-binding cassette transporter/permease, a response regulator, and l -indole 2-dehydrogenase, have been mutated through the insertion of IS elements. It is evident, however, that not all IS elements have transposed and caused rearrangements of the genome in the past 17 years during which strain C-125 was subcultured under neutral and alkaline conditions.