title: Classification of prokaryotic genetic replicators: between selfishness and altruism.
abstract: Prokaryotes harbor a variety of genetic replicators, including plasmids, viruses, and chromosomes, each having different effects on the phenotype of the hosting cell. Here, we propose a classification for replicators of bacteria and archaea on the basis of their horizontal-transfer potential and the type of relationships (mutualistic, symbiotic, commensal, or parasitic) that they have with the host cell vehicle. Horizontal movement of replicators can be either active or passive, reflecting whether or not the replicator encodes the means to mediate its own transfer from one cell to another. Some replicators also have an infectious extracellular state, thus separating viruses from other mobile elements. From the perspective of the cell vehicle, the different types of replicators form a continuum from genuinely mutualistic to completely parasitic replicators. This classification provides a general framework for dissecting prokaryotic systems into evolutionarily meaningful components.
authors.affiliation: Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
authors.forename: Matti
authors.initials: M
authors.lastname: Jalasvuori
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000821:virology; D023641:Archaeal Viruses / Q000145:classification / Q000235:genetics / Q000502:physiology; D001419:Bacteria / Q000235:genetics* / Q000821:virology; D001435:Bacteriophages / Q000145:classification / Q000235:genetics / Q000502:physiology; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D054884:Host-Pathogen Interactions / Q000235:genetics; D008957:Models, Genetic; D010957:Plasmids / Q000145:classification / Q000235:genetics*; D014779:Virus Replication / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements
keywords: archaea; bacteria; cell vehicles; classification; prokaryotes; replicators