title: Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation.
abstract: BACKGROUND
  Microsporidia are obligate intracellular eukaryotic parasites with genomes ranging in size from 2.3 Mbp to more than 20 Mbp. The extremely small (2.9 Mbp) and highly compact (approximately 1 gene/kb) genome of the human parasite Encephalitozoon cuniculi has been fully sequenced. The aim of this study was to characterize noncoding motifs that could be involved in regulation of gene expression in E. cuniculi and to show whether these motifs are conserved among the phylum Microsporidia.
  
  
  RESULTS
  To identify such signals, 5' and 3'RACE-PCR experiments were performed on different E. cuniculi mRNAs. This analysis confirmed that transcription overrun occurs in E. cuniculi and may result from stochastic recognition of the AAUAAA polyadenylation signal. Such experiments also showed highly reduced 5'UTR's (<7 nts). Most of the E. cuniculi genes presented a CCC-like motif immediately upstream from the coding start. To characterize other signals involved in differential transcriptional regulation, we then focused our attention on the gene family coding for ribosomal proteins. An AAATTT-like signal was identified upstream from the CCC-like motif. In rare cases the cytosine triplet was shown to be substituted by a GGG-like motif. Comparative genomic studies confirmed that these different signals are also located upstream from genes encoding ribosomal proteins in other microsporidian species including Antonospora locustae, Enterocytozoon bieneusi, Anncaliia algerae (syn. Brachiola algerae) and Nosema ceranae. Based on these results a systematic analysis of the approximately 2000 E. cuniculi coding DNA sequences was then performed and brings to highlight that 364 translation initiation codons (18.29% of total CDSs) had been badly predicted.
  
  
  CONCLUSIONS
  We identified various signals involved in the maturation of E. cuniculi mRNAs. Presence of such signals, in phylogenetically distant microsporidian species, suggests that a common regulatory mechanism exists among the microsporidia. Furthermore, 5'UTRs being strongly reduced, these signals can be used to ensure the accurate prediction of translation initiation codons for microsporidian genes and to improve microsporidian genome annotation.
authors.affiliation: Clermont Université, Université d'Auvergne, Laboratoire: Microorganismes Génome et Environnement, BP 10448, F-63000 CLERMONT-FERRAND. eric.peyretaillade@iut.u-clermont1.fr
authors.forename: Eric
authors.initials: E
authors.lastname: Peyretaillade
authors.forename: Olivier
authors.initials: O
authors.lastname: Gonçalves
authors.forename: Sébastien
authors.initials: S
authors.lastname: Terrat
authors.forename: Eric
authors.initials: E
authors.lastname: Dugat-Bony
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Robert S
authors.initials: RS
authors.lastname: Cornman
authors.forename: Jay D
authors.initials: JD
authors.lastname: Evans
authors.forename: Frédéric
authors.initials: F
authors.lastname: Delbac
authors.forename: Pierre
authors.initials: P
authors.lastname: Peyret
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D009670:Encephalitozoon cuniculi / Q000235:genetics*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006801:Humans; D008969:Molecular Sequence Data; D012331:RNA, Fungal / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger