Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea

Abstract

Background: Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool.

Results: In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and archaea, predicted based on the previously identified ~1,500 IS elements. Our predicted IS maps are consistent with the NCBI annotations of the IS elements. By linking the predicted IS elements to various characteristics of the organisms under study and the organism's living conditions, we found that (a) the activities of IS elements heavily depend on the environments where the host organisms live; (b) the number of recently active IS elements in a genome tends to increase with the genome size; (c) the flanking regions of the recently active IS elements are significantly enriched with genes encoding DNA binding factors, transporters and enzymes; and (d) IS movements show no tendency to disrupt operonic structures.

Conclusion: This is the first genome-scale maps of IS elements with detailed structural information on the sequence level. These genetic maps of recently active IS elements and the several interesting observations would help to improve our understanding of how IS elements proliferate and how they are involved in the evolution of the host genomes.

Figure 1

Conformation of a typical (a) TIR or (b) non-TIR IS element.

Figure 2

Schematic illustrations of IS group profiles. For each IS group, the ORFs of an IS element in this group are represented as boxes with different colors in the middle, the lengths of left and right linker sequences of the IS elements are illustrated as histograms, and the conservation of their TIR signals, if there are any, are shown by a sequence logo. (a) IS407 group of IS3 family, (b) "-" group of IS66 family, (c) "-" group of IS630 family, (d) "-" group of IS4 family and (e) IS605 group of IS200/IS605 family. Please refer to Supplementary Figure S1 for illustrations of all the profiles.

Figure 3

The bootstrapped neighbor-joining phylogenetic tree of 19 cyanobacteria based on 16S RNA genes. It is rooted by E. coli K12. The number in parentheses after an organism name is the number of annotated raIS elements in that organism. The phylogenetic tree is constructed by MEGA version 3.1 [50].

Figure 4

The bootstrapped neighbor-joining phylogenetic tree of 31 archaea based on 16S RNA genes. It is rooted by E. coli K12. The number in parentheses after an organism name is the number of annotated raIS elements in that organism. The phylogenetic tree is constructed by MEGA version 3.1 [50].

Figure 5

Point plot of genome size and number of raIS elements for each cyanobacteria and archaea.