Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population

J Bacteriol. 2012 Jul;194(14):3636-42. doi: 10.1128/JB.00333-12. Epub 2012 May 4.


The genomes of the two closely related freshwater thermophilic cyanobacteria Synechococcus sp. strain JA-3-3Ab and Synechococcus sp. strain JA-2-3B'a(2-13) each host several families of insertion sequences (ISSoc families) at various copy numbers, resulting 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 viability were detected; however, most insertions either were intergenic or were within genes of unknown function. Most novel insertions detected in the metagenome were rare, suggesting a stringent selective environment. Evidence for mobility of internal deletion variants of other insertion sequences in these isolates suggests that this is a general mechanism for the formation of miniature insertion sequences.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • DNA Transposable Elements / genetics*
  • DNA, Bacterial
  • Gene Deletion
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial
  • Molecular Sequence Data
  • Synechococcus / metabolism*


  • DNA Transposable Elements
  • DNA, Bacterial

Associated data

  • GENBANK/CP000239
  • GENBANK/CP000240