Abstract
This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed 118 genomes representing 26 genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified 24 proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the intein's life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN); smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena), Bacteriodetes (Salinibacter), Betaproteobacteria (Delftia, Acidovorax), Firmicutes (Halanaerobium), Actinobacteria (Longispora), and Deinococcus-Thermus-group.
Highlights
Inteins are self-splicing genetic parasites located in highly conserved sites of slowly evolving genes
HALOBACTERIAL INTEINS The intein content of a collection of halobacterial genomes was analyzed using an intein-allele-specific Position specific scoring matrices (PSSMs)
Seven of these intein alleles were not previously reported in the Halobacteria, and two of the seven have not previously been reported to harbor inteins: a DNA ligase gene involved in double strand break repair, and a deaminase gene involved in nucleotide metabolism (Table 1)
Summary
Inteins are self-splicing genetic parasites located in highly conserved sites of slowly evolving genes. They are found in all three domains of life and in viruses (Perler et al, 1997; Pietrokovski, 2001; Gogarten et al, 2002; Swithers et al, 2009). The association with a HEN domain enables a cyclic invasion pattern, called the homing cycle (Goddard and Burt, 1999; Gogarten and Hilario, 2006). The homing cycle consists of three phases: intein invasion, intein fixation, and eventually loss of the intein enabling invasion to occur again. Inteins with functioning HEN domains were inferred to have persisted in some eukaryotic lineages for several 100 million years (Butler et al, 2006; Gogarten and Hilario, 2006)
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