Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes.
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments. Overall, the 15 ncRNAs that were found shared between Encephalitozoon and Nosema spp. may represent the minimal core set required for parasitic life. Interestingly, the systematic presence of a CCC- or GGG-like motif in 5' of all ncRNA and mRNA gene transcripts regardless of the RNA polymerase involved suggests that the RNA polymerase machineries in microsporidia species could use common factors. Our data provide additional insights in accordance with the simplification processes observed in these reduce genomes and underline the usefulness of sequencing closely related species to help identify highly divergent ncRNAs in these parasites.
Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.|CNRS, UMR 6023, LMGE, F-63171 Aubière, France.
Abdel
A
Belkorchia
Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA.
Jean-François
JF
Pombert
Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.|CNRS, UMR 6023, LMGE, F-63171 Aubière, France.
Valérie
V
Polonais
Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
Nicolas
N
Parisot
Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.|CNRS, UMR 6023, LMGE, F-63171 Aubière, France.
Frédéric
F
Delbac
Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
Jean-François
JF
Brugère
Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
Pierre
P
Peyret
MIAT, Université de Toulouse, INRA, Castanet-Tolosan, France.
Christine
C
Gaspin
Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France.
Eric
E
Peyretaillade
D001483:Base Sequence; D003198:Computer Simulation; D016819:Encephalitozoon / Q000235:genetics*; D016681:Genome, Fungal; D023281:Genomics; D016818:Nosema / Q000235:genetics*; D012342:RNA, Small Nuclear / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism*; D014158:Transcription, Genetic
D012342:RNA, Small Nuclear; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated; C405483:U1 small nuclear RNA
Microsporidia; genome evolution; ncRNA prediction; ncRNA structure; transcriptional regulation signals