Novel Miniature Transposable Elements in Thermophilic Synechococcus Strains and Their Impact on an Environmental Population

The genomes of the two closely related freshwater thermophilic cyanobacteria Synechococcus sp. strain JA-3-3Ab and Synechoc-occus sp. strain JA-2-3B=a(2-13) each host several families of insertion sequences (ISSoc families) at various copy numbers, re-sulting in an overall high abundance of insertion sequences in the genomes. In addition to full-length copies, a large number of internal deletion variants have been identified. ISSoc2 has two variants (ISSoc2-1 and ISSoc2-2) that are observed to have multiple near-exact copies. Comparison of environmental metagenomic sequences to the Synechococcus genomes reveals novel placement of copies of ISSoc2, ISSoc2-1, and ISSoc2-2. Thus, ISSoc2-1 and ISSoc2-2 appear to be active nonautonomous mobile elements derived by internal deletion from ISSoc2. Insertion sites interrupting genes that are likely critical for cell viabil-ity were detected; however, most insertions either were intergenic or were within genes of unknown function. Most novel inser-tions detected in the metagenome were rare, suggesting a stringent selective environment. Evidence for mobility of internal dele-tion variants of other insertion sequences in these isolates suggests that this is a general mechanism for the formation of miniature insertion sequences. Transposable elements (TEs), DNA segments that can relocatewithin a genome, are common in eukaryotes, bacteria, and archaea (10). Transposition events can result in deleterious mu-tations within the host cell (21, 24, 29, 40). Indeed, the genomes of most prokaryotes sequenced so far show a low transposon abun