Evolution of the Arabidopsis telomerase RNA

Abstract

The telomerase reverse transcriptase promotes genome integrity by continually synthesizing a short telomere repeat sequence on chromosome ends. Telomerase is a ribonucleoprotein complex whose integral RNA subunit TER contains a template domain with a sequence complementary to the telomere repeat that is reiteratively copied by the catalytic subunit. Although TER harbors well-conserved secondary structure elements, its nucleotide sequence is highly divergent, even among closely related organisms. Thus, it has been extremely challenging to identify TER orthologs by bioinformatics strategies. Recently, TER was reported in the flowering plant, Arabidopsis thaliana. In contrast to other model organisms, A. thaliana encodes two TER subunits, only one of which is required to maintain telomere tracts in vivo. Here we investigate the evolution of the loci that encode TER in Arabidopsis by comparison to the same locus in its close relatives. We employ a combination of PCR and bioinformatics approaches to identify putative TER loci based on syntenic regions flanking the TER1 and TER2 loci of A. thaliana. Unexpectedly, we discovered that the genomic regions encoding the two A. thaliana TERs occur as a single locus in other Brassicaceae. Moreover, we find striking sequence divergence within the telomere template domain of putative TERs from Brassicaceae, including some orthologous loci that completely lack a template domain. Finally, evolution of the locus is characterized by lineage-specific events rather than changes shared among closely related species. We conclude that the Arabidopsis TER duplication occurred very recently, and further that changes at this locus in other Brassicaceae indicate the process of TER evolution may be different in plants compared with vertebrates and yeast.

Keywords: Brassicaceae; TER; gene duplication; phylogenetics; telomerase.

FIGURE 1

Retention, degradation, and loss of the template domain within putative Brassicaceae TER genes .Partial sequence alignment of TER1, TER2 and the corresponding TAD3–RAD52 intergenic region in Brassicaceae species is shown. Sequence similarity through the start codon of RAD52 (far right) is indicated. The colored nucleotides indicate the template domain in A. thaliana TER1 and TER2, and the putative template or template-like domains in other species. Species are Aara, Aethionema arabicum; At, Arabidopsis thaliana; Aare, A. arenosa; Aneg, A. neglecta; Brap, Brassica rapa; Chis, Camelina hispida; Chir, Cardamine hirsuta; Crho, C. rhomboidea; Crub, Capsella rubella; Clas, Crucihimalaya lasiocarpa; Dwis, Dimorphocarpa wislizenii; Esal, Eutrema salsugineum; Ldra, Lepidium draba; Spar, Schrenkiella parvula.

FIGURE 2

Phylogeny of 330 nt alignment of Arabidopsis TER1 and TER2 with putative TER loci from 14 other Brassicaceae species. Values above nodes are from 100 likelihood bootstrap replicates, only values above 60% are reported. Scale bar is 0.2 substitutions/per site.

FIGURE 3

Phylogeny and organization of the Arabidopsis TER and putative TER loci in Brassicaceae. Left, Brassicaceae tree modified from Beilstein et al. (2010). The most parsimonious reconstruction of the TER locus in Brassicaceae is depicted. Shown are species sampled in this study. Species in lineage III from which TER loci were not obtained are also included for context. Yellow star indicates the duplication event that produced two TER loci in A. thaliana. Right, schematic diagram of the TAD3–RAD52 locus. A. thaliana TER1 and TER2 are encoded on separate chromosomes adjacent to or overlapping these loci. In other Brassicaceae, TAD3 and RAD52 lie on the same chromosome, flanking a single putative TER gene. The region shown is proportional only for the intergenic space. Arrows indicate predicted transcriptional start sites.