The Evolutionary Loss of RNAi Key Determinants in Kinetoplastids as a Multiple Sporadic Phenomenon

Andrey V. Matveyev, João M.P. Alves, Myrna G. Serrano, Vladimir Lee, Ana M. Lara, William A. Barton, André G. Costa-Martins, Stephen M. Beverley, Erney P. Camargo, Marta M.G. Teixeira, Gregory A. Buck

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

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.

Original languageEnglish
Pages (from-to)104-115
Number of pages12
JournalJournal of Molecular Evolution
Volume84
Issue number2-3
DOIs
StatePublished - Mar 1 2017

Keywords

  • Evolutionary loss of genes
  • Kinetoplastea
  • RNAi
  • Trypanosomatida

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