Positive Selection on Transposase Genes of Insertion Sequences in the Crocosphaera watsonii Genome

Abstract

Insertion sequences (ISs) are mobile elements that are commonly found in bacterial genomes. Here, the structural and functional diversity of these mobile elements in the genome of the cyanobacterium Crocosphaera watsonii WH8501 is analyzed. The number, distribution, and diversity of nucleotide and amino acid stretches with similarity to the transposase gene of this IS family suggested that this genome harbors many functional as well as truncated IS fragments. The selection pressure acting on full-length transposase open reading frames of these ISs suggested (i) the occurrence of positive selection and (ii) the presence of one or more positively selected codons. These results were obtained using three data sets of transposase genes from the same IS family that were collected based on the level of amino acid similarity, the presence of an inverted repeat, and the number of sequences in the data sets. Neither recombination nor ribosomal frameshifting, which may interfere with the selection analyses, appeared to be important forces in the transposase gene family. Some positively selected codons were located in a conserved domain, suggesting that these residues are functionally important. The finding that this type of selection acts on IS-carried genes is intriguing, because although ISs have been associated with the adaptation of the bacterial host to new environments, this has typically been attributed to transposition or transformation, thus involving different genomic locations. Intragenic adaptation of IS-carried genes identified here may constitute a novel mechanism associated with bacterial diversification and adaptation.

Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts

“…The IS density among Ensifer species was highly correlated to the number of items identified in COG class L observed from functional genomics analyzes and explain the variability observed in this particular class (data not shown). These results suggest that in comparison to other species studied here, E. aridi strains possess a lower diversifying agent potential which could limit their adaptation to other ecological niches [61, 62]. However, we found in the genomes of E. aridi that predicted prophage regions were mainly incomplete and intact prophage regions were only identified in the Indian strains suggesting a more recent transfer in Asian isolates.…”

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

“…It has been hypothesized that genetic diversity in C. watsonii may be maintained by genome rearrangement, rather than by gene sequence divergence because the diazotroph has low levels of genome DNA sequence variability between habitats and over time (Zehr et al, 2007a). High transposase activity in C. watsonii is similar to that found in populations of the archaeon Ferroplasma acidarmanus (Allen et al, 2007), and positive selection of transposases has been linked to increased fitness or invasion of new environments (Mes and Doeleman, 2006;Allen et al, 2007;Franguel et al, 2008). The C. watsonii WH8501 genome has a large number of transposases (419 transposases in the B6.3 Mb genome), some of which interrupt reading frames of genes (Zehr et al, 2007a) and may result in phenotypic diversity.…”

Cellular interactions: lessons from the nitrogen‐fixing cyanobacteria

“…). Initial genomic studies found that cultivated and wild Crocosphaera genomes had unusually high numbers of transposases, suggesting a mechanism for adaptation to changing environmental conditions and establishment of the variety of phenotypic differences between strains (Mes and Doeleman , Zehr et al. , Hewson et al.…”