Distribution and Evolution of the Mobile vma-1b Intein

Abstract

Inteins are self-splicing parasitic genetic elements found in all domains of life. These genetic elements are found in highly conserved positions in conserved proteins. One protein family that has been invaded by inteins is the vacuolar and archaeal catalytic ATPase subunits (vma-1). There are two intein insertion sites in this protein, "a" and "b." The b site was previously thought to be only invaded in archaeal lineages. Here we survey the distribution and evolutionary histories of the b site inteins and show that the intein is present in more lineages than previously annotated, including a bacterial lineage, Mahella australiensis 50-1 BON. We present evidence, through ancestral character state reconstruction and substitution ratios between host genes and inteins, for several transfers of this intein between divergent species, including an interdomain transfer between the archaea and bacteria. Although inteins may persist within a single population or species for long periods of time, transfer of the vma-1b intein between divergent species contributed to the distribution of this intein.

Inteins as indicators of gene flow in the halobacteria

“…They have a naturally wide phylogenetic distribution, enabling detection of HGT between distantly related taxa. This is demonstrated in this work by the intein trees where the Halobacteria were polyphyletic ( pol-II a, polB -a, polB -b, and cdc21 b) indicating intein transfer between the Halobacteria and the taxa that interrupt them, as well as by data from other studies where intein transfer has been detected across phyla and domains (Butler et al, 2006; Swithers et al, 2013). Inteins also have a high substitution rate relative to their extein hosts, and a propensity for accumulating insertions and deletions, which makes detection of transfers between close relatives (generally a difficult task) possible; for example, transfer within the Halorubrum clusters shown in Figure 3.…”

“…The presence of inteins is especially useful in populations where high rates of recombination and widely distributed populations may facilitate the maintenance of intein sequences over long periods of time (Gogarten and Hilario, 2006) and provide a means for distinguishing closely related partners involved in genetic transfers. The phylogenetic distribution of intein alleles, combined with the changing state within intein alleles, and the rapid substitution rate of inteins relative to the extein host sequences (Swithers et al, 2013) will provide a valuable tool to infer gene flow dynamics in and between sampled populations.…”

“…The conservation of the recognition site provides an invasion target even in distantly related strains and species. Also, inteins have a higher substitution rate relative to their extein hosts (Swithers et al, 2013). This substitution rate gives rise to many evolutionarily informative sites when comparing a large collection of homologous inteins.…”

A hydrolase-based reporter system to uncover the protein splicing performance of an archaeal intein

“…The intein sequence consists of 333 amino acid residues and is inserted between Lys 236 and Thr 570 of the AATPase catalytic subunit A. As the related VMA-inteins from several archaeal species and from the bacterium Mahella australiensis, the Pto VMA intein is embedded within the VMA-b insertion site, which has been found to be 20 amino a c i d r e s i d u e s u p s t r e a m o f t h e V M A i n t e i n s i n hemiascomycetous yeast species (Swithers et al 2013). The conserved amino acid residues at the splice junctions are Cys 237 and Asn 569 in the Pto VMA intein (or rather Cys 1 and Asn 333 based on the intein sequence).…”

“…There are two intein insertion sites in homologues of the A-ATPase A subunit. Inteins in hemiascomyceotous yeasts invaded the insertion site Ba,^while divergent archaeal species and a bacterium were shown to exhibit an intein at insertion site Bb^ (Swithers et al 2013).…”