title: Cross-study analysis of genomic data defines the ciliate multigenic epiplasmin family: strategies for functional analysis in Paramecium tetraurelia.
abstract: BACKGROUND
  The sub-membranous skeleton of the ciliate Paramecium, the epiplasm, is composed of hundreds of epiplasmic scales centered on basal bodies, and presents a complex set of proteins, epiplasmins, which belong to a multigenic family. The repeated duplications observed in the P. tetraurelia genome present an interesting model of the organization and evolution of a multigenic family within a single cell.
  
  
  RESULTS
  To study this multigenic family, we used phylogenetic, structural, and analytical transcriptional approaches. The phylogenetic method defines 5 groups of epiplasmins in the multigenic family. A refined analysis by Hydrophobic Cluster Analysis (HCA) identifies structural characteristics of 51 epiplasmins, defining five separate groups, and three classes. Depending on the sequential arrangement of their structural domains, the epiplasmins are defined as symmetric, asymmetric or atypical. The EST data aid in this classification, in the identification of putative regulating sequences such as TATA or CAAT boxes. When specific RNAi experiments were conducted using sequences from either symmetric or asymmetric classes, phenotypes were drastic. Local effects show either disrupted or ill-shaped epiplasmic scales. In either case, this results in aborted cell division. Using structural features, we show that 4 epiplasmins are also present in another ciliate, Tetrahymena thermophila. Their affiliation with the distinctive structural groups of Paramecium epiplasmins demonstrates an interspecific multigenic family.
  
  
  CONCLUSIONS
  The epiplasmin multigenic family illustrates the history of genomic duplication in Paramecium. This study provides a framework which can guide functional analysis of epiplasmins, the major components of the membrane skeleton in ciliates. We show that this set of proteins handles an important developmental information in Paramecium since maintenance of epiplasm organization is crucial for cell morphogenesis.
authors.affiliation: Laboratoire Microorganismes: Génome et Environnement (ex, LBP) UMR CNRS 6023, Université Blaise Pascal, 63177, Aubière cedex, France. rdamaj82@hotmail.com
authors.forename: Raghida
authors.initials: R
authors.lastname: Damaj
authors.forename: Sébastien
authors.initials: S
authors.lastname: Pomel
authors.forename: Geneviève
authors.initials: G
authors.lastname: Bricheux
authors.forename: Gérard
authors.initials: G
authors.lastname: Coffe
authors.forename: Bernard
authors.initials: B
authors.lastname: Viguès
authors.forename: Viviane
authors.initials: V
authors.lastname: Ravet
authors.forename: Philippe
authors.initials: P
authors.lastname: Bouchard
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D016054:DNA, Protozoan / Q000235:genetics; D019143:Evolution, Molecular; D018503:Genome, Protozoan; D008969:Molecular Sequence Data; D005810:Multigene Family; D016805:Paramecium tetraurelia / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D015800:Protozoan Proteins / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D016808:Tetrahymena thermophila / Q000235:genetics / Q000378:metabolism
chemical_list: D016054:DNA, Protozoan; D015800:Protozoan Proteins