title: The Evolutionary Loss of RNAi Key Determinants in Kinetoplastids as a Multiple Sporadic Phenomenon.
abstract: We screened the genomes of a broad panel of kinetoplastid protists for genes encoding proteins associated with the RNA interference (RNAi) system using probes from the Argonaute (AGO1), Dicer1 (DCL1), and Dicer2 (DCL2) genes of Leishmania brasiliensis and Crithidia fasciculata. We identified homologs for all the three of these genes in the genomes of a subset of these organisms. However, several of these organisms lacked evidence for any of these genes, while others lacked only DCL2. The open reading frames encoding these putative proteins were structurally analyzed in silico. The alignments indicated that the genes are homologous with a high degree of confidence, and three-dimensional structural models strongly supported a functional relationship to previously characterized AGO1, DCL1, and DCL2 proteins. Phylogenetic analysis of these putative proteins showed that these genes, when present, evolved in parallel with other nuclear genes, arguing that the RNAi system genes share a common progenitor, likely across all Kinetoplastea. In addition, the genome segments bearing these genes are highly conserved and syntenic, even among those taxa in which they are absent. However, taxa in which these genes are apparently absent represent several widely divergent branches of kinetoplastids, arguing that these genes were independently lost at least six times in the evolutionary history of these organisms. The mechanisms responsible for the apparent coordinate loss of these RNAi system genes independently in several lineages of kinetoplastids, while being maintained in other related lineages, are currently unknown.
authors.affiliation: Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA. Andrey.Matveyev@VCUhealth.org.
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Matveyev
authors.affiliation: Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.|Department of ParasitologyICB, University of São Paulo, São Paulo, Brazil.
authors.forename: João M P
authors.initials: JM
authors.lastname: Alves
authors.affiliation: Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Myrna G
authors.initials: MG
authors.lastname: Serrano
authors.affiliation: Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Lee
authors.affiliation: Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Ana M
authors.initials: AM
authors.lastname: Lara
authors.affiliation: Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: William A
authors.initials: WA
authors.lastname: Barton
authors.affiliation: Department of ParasitologyICB, University of São Paulo, São Paulo, Brazil.
authors.forename: André G
authors.initials: AG
authors.lastname: Costa-Martins
authors.affiliation: Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Beverley
authors.affiliation: Department of ParasitologyICB, University of São Paulo, São Paulo, Brazil.
authors.forename: Erney P
authors.initials: EP
authors.lastname: Camargo
authors.affiliation: Department of ParasitologyICB, University of São Paulo, São Paulo, Brazil.
authors.forename: Marta M G
authors.initials: MM
authors.lastname: Teixeira
authors.affiliation: Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Buck
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D060565:Argonaute Proteins / Q000235:genetics; D005075:Biological Evolution; D016831:Crithidia fasciculata / Q000235:genetics*; D018105:DNA, Kinetoplast / Q000235:genetics* / Q000378:metabolism; D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome / Q000235:genetics; D007892:Leishmania braziliensis / Q000235:genetics*; D010802:Phylogeny; D034622:RNA Interference / Q000502:physiology; D043244:Ribonuclease III / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D026801:Synteny / Q000235:genetics; D014351:Trypanosomatina / Q000235:genetics*
chemical_list: D060565:Argonaute Proteins; D018105:DNA, Kinetoplast; D043244:Ribonuclease III
keywords: Evolutionary loss of genes; Kinetoplastea; RNAi; Trypanosomatida