No abstract

Inteins, also called protein introns, are self-splicing mobile elements found in all domains of life. A bioinformatic survey of genomic data highlights a biased distribution of inteins among functional categories of proteins in both bacteria and archaea, with a strong preference for a single network of functions containing replisome proteins. Many nonorthologous, functionally equivalent replicative proteins in bacteria and archaea carry inteins, suggesting a selective retention of inteins in proteins of particular functions across domains of life. Inteins cluster not only in proteins with related roles but also in specific functional units of those proteins, like ATPase domains. This peculiar bias does not fully fit the models describing inteins exclusively as parasitic elements. In such models, evolutionary dynamics of inteins is viewed primarily through their mobility with the intein homing endonuclease (HEN) as the major factor of intein acquisition and loss. Although the HEN is essential for intein invasion and spread in populations, HEN dynamics does not explain the observed biased distribution of inteins among proteins in specific functional categories. We propose that the protein splicing domain of the intein can act as an environmental sensor that adapts to a particular niche and could increase the chance of the intein becoming fixed in a population. We argue that selective retention of some inteins might be beneficial under certain environmental stresses, to act as panic buttons that reversibly inhibit specific networks, consistent with the observed intein distribution.

Post-translational control based on an environmentally sensitive intervening intein sequence is described. Inteins are invasive genetic elements that self-splice at the protein level from the flanking host protein, the exteins. Here we show in Escherichia coli and in vitro that splicing of the RadA intein located in the ATPase domain of the hyperthermophilic archaeon Pyrococcus horikoshii is strongly regulated by the native exteins, which lock the intein in an inactive state. High temperature or solution conditions can unlock the intein for full activity, as can remote extein point mutations. Notably, this splicing trap occurs through interactions between distant residues in the native exteins and the intein, in three-dimensional space. The exteins might thereby serve as an environmental sensor, releasing the intein for full activity only at optimal growth conditions for the native organism, while sparing ATP consumption under conditions of cold-shock. This partnership between the intein and its exteins, which implies coevolution of the parasitic intein and its host protein may provide a novel means of post-translational control.

Inteins are mobile genetic elements capable of self-splicing post-translationally. They exist in all three domains of life including in viruses and bacteriophage, where they have a sporadic distribution even among very closely related species. In this review, we address this anomalous distribution from the point of view of the evolution of the host species as well as the intrinsic features of the inteins that contribute to their genetic mobility. We also discuss the incidence of inteins in functionally important sites of their host proteins. Finally, we describe instances of conditional protein splicing. These latter observations lead us to the hypothesis that some inteins have adapted to become sensors that play regulatory roles within their host protein, to the advantage of the organism in which they reside. Protein SplicingProtein splicing is a naturally occurring biochemical process that mediates the post-translational conversion of a precursor polypeptide into a mature and functional protein through the removal of an internal protein element, called an intein (Fig. 1A). The process is analogous to intron splicing at the RNA level. The protein splicing mechanism involves a series of autocatalytic peptide bond rearrangements, where the intein excises itself from the precursor polypeptide with concurrent ligation of the flanking sequences, called exteins (N-or C-exteins relative to the position of intein) (for review, see Refs. 1-3). As a result of this process, two proteins are produced from a single polypeptide product. The term intein refers to both the genetic element in the DNA or RNA and the protein splicing entity.Most inteins are expressed within a single polypeptide chain (cis-splicing inteins), but some are split into two polypeptides each containing one extein and an intein fragment (trans-splicing inteins) (4, 5). In the case of split inteins, reassociation of the fragments at a zipper-like interface (6) precedes protein splicing (Fig. 1B). Both cis-splicing and trans-splicing inteins are frequently utilized in various biotechnological applications including protein purification, modification, labeling, and posttranslational control of expressed proteins (reviewed in Refs. 7 and 8). The cis-splicing inteins often contain a distinct homing endonuclease (HEN) 2 domain (9). HEN-containing inteins are naturally occurring mobile genetic elements. The presence of a HEN provides inteins the ability to transfer their coding elements into homologous alleles at homing sites that lack the intein sequence (Fig. 1D). This HEN-mediated homing process can result in horizontal gene transfer (HGT) of inteins, by invasion of diverse species, followed by vertical transmission of inteins (10, 11). Moreover, HEN-containing inteins are involved in a so-called "homing cycle" that includes two opposing processes, precise intein loss and reinvasion of a newly formed vacant homing site. It is believed that the homing cycle allows the HEN to avoid fixation and functional decay in one locus (12).