title: Intein Clustering Suggests Functional Importance in Different Domains of Life.
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.
authors.affiliation: Department of Biological Sciences and RNA Institute, University at Albany.
authors.forename: Olga
authors.initials: O
authors.lastname: Novikova
authors.affiliation: Department of Biological Sciences and RNA Institute, University at Albany.
authors.forename: Pradeepa
authors.initials: P
authors.lastname: Jayachandran
authors.affiliation: Department of Biomedical Sciences, School of Public Health, University at Albany.
authors.forename: Danielle S
authors.initials: DS
authors.lastname: Kelley
authors.affiliation: Department of Biological Sciences and RNA Institute, University at Albany.
authors.forename: Zachary
authors.initials: Z
authors.lastname: Morton
authors.affiliation: Department of Biological Sciences, Dartmouth College.
authors.forename: Samantha
authors.initials: S
authors.lastname: Merwin
authors.affiliation: Department of Biological Sciences and RNA Institute, University at Albany.
authors.forename: Natalya I
authors.initials: NI
authors.lastname: Topilina
authors.affiliation: Department of Biological Sciences and RNA Institute, University at Albany Department of Biomedical Sciences, School of Public Health, University at Albany mbelfort@albany.edu.
authors.forename: Marlene
authors.initials: M
authors.lastname: Belfort
mesh_terms: D000818:Animals; D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D016000:Cluster Analysis; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D053488:DnaB Helicases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D056890:Eukaryota / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods; D047668:Inteins / Q000235:genetics*; D064110:Minichromosome Maintenance Proteins / Q000378:metabolism; D008958:Models, Molecular; D010802:Phylogeny; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps
chemical_list: D004259:DNA-Directed DNA Polymerase; D053488:DnaB Helicases; D064110:Minichromosome Maintenance Proteins
keywords: ATPases; Clusters of Orthologous Groups; evolution; replicative helicase; replisome