Absence of positive selection on centromeric histones in Tetrahymena suggests unsuppressed centromere: drive in lineages lacking male meiosis

Abstract

Centromere-drive is a process where centromeres compete for transmission through asymmetric "female" meiosis for inclusion into the oocyte. In symmetric "male" meiosis, all meiotic products form viable germ cells. Therefore, the primary incentive for centromere-drive, a potential transmission bias, is believed to be missing from male meiosis. In this article, we consider whether male meiosis also bears the primary cost of centromere-drive. Because different taxa carry out different combinations of meiotic programs (symmetric + asymmetric, symmetric only, asymmetric only), it is possible to consider the evolutionary consequences of centromere-drive in the context of these differing systems. Groups with both types of meiosis have large, rapidly evolving centromeric regions, and their centromeric histones (CenH3s) have been shown to evolve under positive selection, suggesting roles as suppressors of centromere-drive. In contrast, taxa with only symmetric male meiosis have shown no evidence of positive selection in their centromeric histones. In this article, we present the first evolutionary analysis of centromeric histones in ciliated protozoans, a group that only undergoes asymmetric "female" meiosis. We find no evidence of positive selection acting on CNA1, the CenH3 of Tetrahymena species. Cytological observations of a panel of Tetrahymena species are consistent with dynamic karyotype evolution in this lineage. Our findings suggest that defects in male meiosis, and not mitosis or female meiosis, are the primary selective force behind centromere-drive suppression. Our study raises the possibility that taxa like ciliates, with only female meiosis, may therefore undergo unsuppressed centromere drive.

Fig. 1

Taxonomic diversity of meiosis in eukaryotes. Animals and plants undergo two types of meiosis: asymmetric (female) meiosis in which three of four meiotic products are eliminated (shaded), and male meiosis in which all four meiotic products have an equal likelihood of success. In contrast, some lineages (like Fungi) only undergo male meiosis, while other lineages like ciliated protozoans (including Tetrahymena) only undergo female meiosis. Each of these configurations is expected to differ in terms of their susceptibility to "centromere-drive" and its deleterious consequences (Henikoff et al. ; Malik ; Malik and Bayes ; Malik and Henikoff 2009)

Fig. 2

Molecular evolution of CNA1 (a) Amino acid alignment of Cna1p from a panel of Tetrahymena species. Highlighted is the border between the N-terminal tail and histone fold domain, the sequence used as an epitope for antibody production, and the highly variable loop 1 region. Sequences corresponding to primer-binding sites are indicated in lower case. b Maximum likelihood phylogeny of CNA1 nucleic acid sequences. Bootstrap values above 50 are indicated at corresponding branches and the scale of substitutions/site is shown. The arrowhead indicates where the tree would root in the context of more diverse species as shown in c. c A phylogenetic tree of Tetrahymena species based on the histone H3-H4 spacer region (adapted from Brunk et al. 1990). The asterisks (*) denote species that lack a germline micronucleus. ‡The identification of this strain as T. rostrata has been challenged (Segade et al. 2009)

Fig. 3

Evolution of centromeric histones in distinct taxonomic groups. a Cladograms of Tetrahymena, Mammals, Rosids, and Drosophila show rates of synonymous substitution (dS) as a gauge of divergence from T. thermophila, H. sapiens, A. thaliana, and D. melanogaster. b Amino acid positions under positive selection (Bayesian posterior probability >0.9) are shown for Rosids (triangles) and Mammals (circles). Amino acid site numbering is according to CenH3 from A. thaliana and H. sapiens

Fig. 4

CNA1 expression and localization in Tetrahymena species. a Immunoblot analysis of Cna1p expression in a panel of Tetrahymena species and Paramecium tetraurelia. b Fixed cells from Tetrahymena species were labeled with DAPI to stain the larger macronuclei and smaller micronuclei, and anti-Cna1p antibody to visualize centromeres. Background fluorescence was reduced in close-up images of nuclei in top panels by deconvolution. Bar = 5 microns