Firmicutes-enriched IS represents a group of IS-family insertion sequences exhibiting unique + 1 transcriptional slippage.

Background: Bacterial insertion sequences (ISs) are ubiquitous mobile genetic elements that play important roles in genome plasticity, cell adaptability, and function evolution. ISs of various families and subgroups contain significantly diverse molecular features and functional mechanisms that are not fully understood.

Results: IS is a member of the widespread IS family and was previously detected to have transposing activity in a typical thermophilic and cellulolytic microorganism . Phylogenetic analysis showed that IS-like elements are widely distributed in Firmicutes and possess unique features in the IS family. Therefore, IS may represent a novel subgroup of the IS family. Unlike other well-known IS subgroups performing programmed - 1 translational frameshifting for the expression of the transposase, IS exhibits transcriptional slippage in both the + 1 and - 1 directions, each with a frequency of ~ 16%, and only + 1 slippage results in full-length and functional transposase. The slippage-prone region of IS contains a run of nine A nucleotides following a stem-loop structure in mRNA, but mutagenesis analysis indicated that seven of them are sufficient for the observed slippage. Western blot analysis indicated that IS produces three types of transposases with alternative initiations. Furthermore, the IS-subgroup elements are abundant in the genomes of several cellulolytic bacteria.

Conclusion: Our result indicated that IS represents a new Firmicutes-enriched subgroup of the IS family. The characterization of the novel IS-family member will enrich our understanding of the transposition behavior of IS elements and may provide insight into developing IS-based mutagenesis tools for thermophiles.