HIP1 PROPAGATES IN CYANOBACTERIAL DNA VIA NUCLEOTIDE SUBSTITUTIONS BUT PROMOTES EXCISION AT SIMILAR FREQUENCIES IN ESCHERICHIA-COLI AND SYNECHOCOCCUS PCC-7942

The sequence 5'-GCGATCGC-3', designated HlP1,for highly iterated palin drome, was first identified at the borders of a gene-deletion event an d subsequently shown to constitute up to 2.5% of the DNA in some cyano bacteria. It is now reported that HlP1 is polyphyletic, occurring in s everal distinct cyanobacterial lineages and not defining a clade. HlP1 does not introduce gaps into sequence alignments. It aligns with part ial HlP1 sites in related sequences showing that it propagates by nucl eotide substitutions rather than insertion. Constructs have been creat ed to determine the frequencies at which deletion events occur between palindromes located within the selectable marker neo. Deletion betwee n HlP1 sites was more frequent in Synechococcus PCC 7942 than deletion between control palindromes, 5'-CCGATCGG-3', designated PALO. However , this is not due to a recombinase that recognises HlP1 and is peculia r to cyanobacteria because similar deletion frequencies were detected in Escherichia coli. Furthermore, the frequency of deletion of DNA fla nked asymmetrically by one HlP1 site and one PALO site was less than t he frequency of deletion of DNA flanked symmetrically by identical cop ies of either palindrome. This is consistent with deletion by copy-cho ice.