Evolution of Histone H4 and H3 Genes in Different Ciliate Lineages

Abstract

The histones H4 are known as highly conserved proteins. However, in ciliates a high degree of variation was found compared both to other eukaryotes and between the ciliate species. To date, only H4 histones of species belonging to two distantly related classes have been investigated. In order to obtain more detailed information on histone H4 variation in ciliates we undertook a comprehensive sequence analysis of PCR-amplified internal H4 fragments from 12 species belonging to seven out of the nine currently recognized ciliate classes. In addition, we used PCR primers to amplify longer fragments of H3 and H4 genes including the intergenic region. The encoded amino acid sequences reveal a high number of differences when compared with those of other eukaryotes and the ciliate species investigated. Furthermore, in some species H4 gene variants were detected, which result in amino acid differences. The greatest number of substitutions and insertions found was in the amino terminal region of the H4 histones. However, all sequences possess a conserved region corresponding to those of all other eukaryotic H4 histones. The histone gene variations were used to reconstruct phylogenetic relationships. The tree from our data matches perfectly with the ribosomal RNA data: The heterotrichs, which were considered as a late branching lineage, diverge at the base of the ciliate tree and groups formerly thought to represent ancestral lineages now appear as highly derived ciliates.

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

“…In the first molecular study of its histone H4 and H3 genes, Bernhard and Schlegel (1998) showed that Protocruzia had an ambiguous position dependent upon whether nucleotide or protein sequences were used. Subsequent studies using 18S rRNA gene sequences showed the genus to be more closely related to Spirotrichea (in a basal position) than Postciliodesmatophora (Hammerschmidt et al, 1996;Shin et al, 2000).…”

“…Multiple analyses have since been employed using a limited number of genes but the exact phylogenetic position of Protocruzia remains unresolved; it has been considered a karyorelictid, heterotrich and spirotrich (Bernhard and Schlegel, 1998;De Puytorac, 1994;Grolière et al, 1980;Lynn, 1981Lynn, , 1991Lynn, 2008;Shin et al, 2000;Small and Lynn, 1981;Song and Wilbert, 1997). Some investigators have proposed that Protocruzia be given its own lineage status (Li et al, 2010).…”

“…Nevertheless, the monophyly of the class Spirotrichea has been challenged in several studies, notably those that include Protocruzia spp. While Protocruzia has been formally assigned to the Spirotrichea (Lynn, 2008), its phylogenetic position remains as one of the most ambiguous since it is rarely recovered with the Spirotrichea (Bernhard and Schlegel, 1998;Shin et al, 2000;Song and Wilbert, 1997). Some researchers have suggested that Protocruzia be assigned its own independent lineage status (Li et al, 2010).…”

Characterization of the Pneumocystis carinii Histone Acetyltransferase Chaperone Proteins PcAsf1 and PcVps75

“…In addition, we employed chicken embryo H3-H4 tetramers in this study instead of Drosophila melanogaster histone tetramers because of availability and technical difficulties related to purification of adequate quantities of Drosophila histones for these repeated assays. Histones are known to be highly conserved proteins across the eukaryotes (43,44). However, the equilibrium of H3-H4 heterodimers and H3-H4 heterotetramers could differ between chicken embryo and Drosophila histones, particularly under the in vitro conditions used in this study.…”

NSF regulates membrane traffic along multiple pathways inParamecium

“…The occurrence of at least two expressed genes for the same kind of protein is frequent in P. tetraurelia (Hauser et al, 1997;Bernhard and Schlegel, 1998;Kim et al, 1998;Chan et al, 1999).…”