The conserved structure of plant telomerase RNA provides the missing link for an evolutionary pathway from ciliates to humans

Jiarui Song; Dhenugen Logeswaran; Claudia Castillo-González; Yang Li; Sreyashree Bose; Behailu Birhanu Aklilu; Zeyang Ma; Alexander Polkhovskiy; Julian J.-L. Chen; Dorothy E. Shippen

doi:10.1073/pnas.1915312116

New Research In

Edited by Thomas R. Cech, University of Colorado Boulder, Boulder, CO, and approved October 24, 2019 (received for review September 4, 2019)

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Significance

While telomerase has been extensively studied, its core RNA component (TR) is extremely divergent in sequence and biogenesis pathways, which has hindered our understanding of the evolutionary pathway from the small ciliate TR to the more complex fungal and vertebrate TRs. Here we report a conserved structure of the authentic TR from Arabidopsis thaliana termed AtTR, which is different from an RNA previously described as the templating telomerase RNA, AtTER1. This breakthrough establishes the correct A. thaliana TR and enables identification of TR homologs across the plant kingdom. Structural and functional analyses of AtTR reveals chimeric structural features similar to those of TRs from ciliates and multicellular eukaryotes, supporting the idea that all TRs are homologous, sharing a common ancestor.

Abstract

Telomerase is essential for maintaining telomere integrity. Although telomerase function is widely conserved, the integral telomerase RNA (TR) that provides a template for telomeric DNA synthesis has diverged dramatically. Nevertheless, TR molecules retain 2 highly conserved structural domains critical for catalysis: a template-proximal pseudoknot (PK) structure and a downstream stem-loop structure. Here we introduce the authentic TR from the plant Arabidopsis thaliana, called AtTR, identified through next-generation sequencing of RNAs copurifying with Arabidopsis TERT. This RNA is distinct from the RNA previously described as the templating telomerase RNA, AtTER1. AtTR is a 268-nt Pol III transcript necessary for telomere maintenance in vivo and sufficient with TERT to reconstitute telomerase activity in vitro. Bioinformatics analysis identified 85 AtTR orthologs from 3 major clades of plants: angiosperms, gymnosperms, and lycophytes. Through phylogenetic comparisons, a secondary structure model conserved among plant TRs was inferred and verified using in vitro and in vivo chemical probing. The conserved plant TR structure contains a template-PK core domain enclosed by a P1 stem and a 3′ long-stem P4/5/6, both of which resemble a corresponding structural element in ciliate and vertebrate TRs. However, the plant TR contains additional stems and linkers within the template-PK core, allowing for expansion of PK structure from the simple PK in the smaller ciliate TR during evolution. Thus, the plant TR provides an evolutionary bridge that unites the disparate structures of previously characterized TRs from ciliates and vertebrates.

Footnotes

↵¹D.L. and C.C.-G. contributed equally to this work.
↵²To whom correspondence may be addressed. Email: jlchen{at}asu.edu or dshippen{at}tamu.edu.

Author contributions: J.S., D.L., C.C.-G., Y.L., J.J.-L.C., and D.E.S. designed research; J.S., D.L., C.C.-G., Y.L., S.B., B.A., and A.P. performed research; J.S., D.L., C.C.-G., Y.L., Z.M., J.J.-L.C., and D.E.S. analyzed data; and J.S., D.L., C.C.-G., Y.L., J.J.-L.C., and D.E.S. wrote the paper.
The authors declare no competing interest.
This article is a PNAS Direct Submission.
Data deposition: Raw data from 2 independent RIP-seq and DMS-MaPseq experiments have been deposited in the Gene Expression Omnibus (GEO) database, https://www.ncbi.nlm.nih.gov/geo (BioProject ID PRJNA588284.). TRs identified in this work have been deposited in GenBank (accession no. TPA: BK011296–BK011375).
This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1915312116/-/DCSupplemental.

Published under the PNAS license.

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