Telomerase RNA gene duplications drive telomeric repeat diversity and evolution in <i>Andrena</i> bees

bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-29

Abstract Most organisms in the animal kingdom require a non-coding telomerease RNA (TR) in conjunction with the telomerase reverse transcriptase (TERT) to add telomere tandem repeats to chromosome ends to genomic instability. Recent studies reported an extensive diversity in the sequence of telomeric repeats in some insect species. Our investigation of TR genes in the Andrena genus provides convincing evidence for the presence of multiple TR gene copies with different template sequences for synthesis of distinct telomeric repeat sequences in several species. In this study we describe the structure, genomic coordinates and abundance of these TR genes, and correlate our findings with the levels of tandem repeats found in DNAseq data. Based on an analysis of the synthenic context of these newly predicted TR genes, we show evidence for the existence of multiple TR paralogs that diverged during the evolution of the genus Andrena . To our knowledge this is the first time such a phenomenon is observed in animals, although recently reported for plants. Interestingly, the comprehensive annotation of all TERT genes found in yet unannotated Andrena species shows no corresponding evolutionary changes in related TERT proteins encoded by a single copy gene. Our study suggests an evolutionary mechanism for diversification of telomeric repeat sequences in certain insect species through telomerase RNA gene duplication.

[Construction and identification of a sizeable naive human Fab phage display antibody library].

PubMed · 2025-02-10

This study successfully constructed two naive human Fab phage display antibody libraries with large capacity and good diversity, which can be used for screening human antibodies for serum epidemiology.

Functional implications of hexameric dynamics in <scp>SARS</scp>‐<scp>CoV</scp>‐2 Nsp15

Protein Science · 2025-05-24 · 1 citations

Abstract SARS‐CoV‐2, the virus responsible for the COVID‐19 pandemic, has undergone continuous evolution, leading to the emergence of variants with altered transmissibility and immune evasion. For the non‐structural proteins (Nsps) of SARS‐CoV‐2, there are limited structural analyses of their naturally occurring mutations. Here, we identified four non‐synonymous single‐nucleotide polymorphisms (nsSNPs) in the Epsilon lineage of SARS‐CoV‐2 within Nsp15, an endoribonuclease critical for immune evasion. Of these Epsilon nsSNPs, E266Q is in the catalytic domain. This study investigates the effects of this on enzymatic activity, structural stability, and oligomeric assembly by serial crystallography. By solving the structure of the Nsp15 hexamer at room temperature of both Nsp15‐E266Q and WT in the P2 1 space group to 3 Å, we observed asymmetric motions within its trimer subunits, a feature not visible in previously reported higher‐symmetry space groups. These asymmetric motions resemble substrate‐induced conformational changes reported in RNA‐bound Nsp15 structures, suggesting functional relevance. Biochemical analyses further reveal that Nsp15‐E266Q exhibited significantly higher enzymatic activity and thermal stability compared to the wild‐type protein. These findings highlight how mutations in Nsp15 contribute to viral replication and immune evasion, offering insights into the molecular mechanisms underlying SARS‐CoV‐2 variant evolution and potential therapeutic strategies.

Monkeyflower (Mimulus) uncovers the evolutionary basis of the eukaryote telomere sequence variation

PLoS Genetics · 2025-06-16 · 2 citations

Telomeres are nucleoprotein complexes with crucial role of protecting chromosome ends. Because of its vital functions, components of the telomere, including its sequence, should be under strong evolutionary constraint. Yet across the tree of life there are numerous examples of telomere sequence variation and the evolutionary mechanism driving this diversification is unclear. Here, we studied the telomeres in Mimulus by investigating the noncoding telomerase RNA (TR), which is a core component of the telomere maintenance complex and determines the telomere sequence in eukaryotes. We conducted de novo transcriptomics and genome analysis of 18 species, and discovered Mimulus has evolved at least three different telomere sequences: (AAACCCT)n, (AAACCCG)n, and (AAACCG)n. We discovered several species with TR duplications, implying functional consequences that could influence telomere evolution. For instance, M. lewisii harbored two sequence-divergent TR paralogs while its sister species the paralog had pseudogenized. Nanopore-sequencing and fluorescence in situ hybridization indicated M. lewisii had a sequence heterogeneous telomere, and Telomeric Repeat Amplification Protocol combined with Terminal Restriction Fragment analysis confirmed the telomerase can use both TR paralogs for telomere synthesis. Interestingly in closely related species M. cardinalis, TR was also duplicated and both paralogs were expressed but its telomere consisted of a single telomere repeat. Evolutionary analysis indicated the TR paralogs arose from an ancient duplication, which also underlies the evolutionary origin of multiple Mimulus species with divergent telomere sequences. We propose sequence variation in eukaryotic telomeres arises from an evolutionary process involving TR duplication, sequence divergence, and loss of TR paralog.

Telomerase RNA Shapes the Evolutionary Diversity of Telomerase Ribonucleoproteins (RNPs)

Cold Spring Harbor Perspectives in Biology · 2025-10-06 · 3 citations

Telomerase emerged in early eukaryotes as a highly specialized reverse transcriptase for maintaining chromosome integrity. The telomerase enzyme contains an integral RNA, providing the template for DNA repeat synthesis. This central telomerase RNA not only provides the template but also contributes to the enzyme's catalytic function and the biogenesis of the ribonucleoprotein. Remarkably, telomerase RNA exhibits significant diversity in sequence, structure, and biogenesis across eukaryotic lineages, a feature that sets it apart from other functional RNAs. In ciliates and plants, telomerase RNA is transcribed by RNA polymerase III, whereas in animals and fungi, it is predominantly transcribed by RNA polymerase II. These differences result in distinct pathways for RNA synthesis, maturation, and trafficking. This work highlights how the diversity in size and structure of telomerase RNAs impacts the complexity and evolution of telomerase ribonucleoproteins, spanning from unicellular eukaryotes to multicellular plants and animals, highlighting telomerase RNA's critical role in telomere biology.

A degenerate telomerase RNA directs telomeric DNA synthesis in lepidopteran insects

Proceedings of the National Academy of Sciences · 2025-02-28 · 4 citations

Telomerase elongates telomeres to maintain chromosome stability in most eukaryotes. Despite extensive studies across eukaryotic kingdoms, the telomerase holoenzyme in arthropods remains poorly understood. In this study, we purify the telomerase ribonucleoprotein complex from the lepidopteran insect Spodoptera frugiperda (fall armyworm) and identify a copurified 135-nucleotide telomerase RNA (TR) component. This miniature S. frugiperda TR (sfTR), the smallest TR known to date, retains a universal pseudoknot structure and a structurally defined template. Despite its small size, sfTR assembles with the recombinant S. frugiperda telomerase reverse transcriptase (sfTERT) protein in vivo to reconstitute telomerase activity for the synthesis of insect telomeric DNA repeats (TTAGG)n. The sfTR gene, like other animal TR genes, features an snRNA-type RNA polymerase II promoter. Uniquely, the sfTR transcript harbors a 5′-7-methylguanosine (M 7 G) cap, as opposed to the more typical snRNA-type 2,2,7-trimethylguanosine (TMG) cap. The difference in 5′-cap is likely because sfTR lacks the H/ACA snoRNA biogenesis domain necessary for cap hypermethylation. Moreover, sfTR also lacks the CR4/5 regulatory domain that is indispensable in vertebrate TRs for telomerase activity. This degenerate sfTR complements an enigmatic sfTERT that is missing certain telomerase-specific elements yet catalytically active in the absence of sfTR. Thus, insects have evolved a simplified telomerase, consisting of a small noncoding RNA that retains only minimal attributes essential for telomerase function. The simplified insect telomerase demonstrates a plausible evolutionary pathway for the emergence of telomerase ribonucleoprotein complex, arising from an ancient reverse transcriptase associated with a simple templating RNA component in early eukaryotes.

Telomerase-Mediated Anti-Ageing Interventions

Sub-cellular biochemistry/Subcellular biochemistry · 2024-01-01 · 1 citations

Identification and characterization of E266Q mutation in Nsp15 endoribonuclease from SARS-CoV-2 Epsilon variant

Biophysical Journal · 2023-02-01

Transposition, duplication, and divergence of the telomerase RNA underlies the evolution of <i>Mimulus</i> telomeres

bioRxiv (Cold Spring Harbor Laboratory) · 2023-12-07

Abstract Telomeres are nucleoprotein complexes with a crucial role of protecting chromosome ends. It consists of simple repeat sequences and dedicated telomere-binding proteins. Because of its vital functions, components of the telomere, for example its sequence, should be under strong evolutionary constraint. But across all plants, telomere sequences display a range of variation and the evolutionary mechanism driving this diversification is largely unknown. Here, we discovered in Monkeyflower ( Mimulus ) the telomere sequence is even variable between species. We investigated the basis of Mimulus telomere sequence evolution by studying the long noncoding telomerase RNA (TR), which is a core component of the telomere maintenance complex and determines the telomere sequence. We conducted total RNA-based de novo transcriptomics from 16 Mimulus species and analyzed reference genomes from 6 species, and discovered Mimulus species have evolved at least three different telomere sequences: (AAACCCT) n , (AAACCCG) n , and (AAACCG) n . Unexpectedly, we discovered several species with TR duplications and the paralogs had functional consequences that could influence telomere evolution. For instance, M. lewisii had two sequence-divergent TR paralogs and synthesized a telomere with sequence heterogeneity, consisting of AAACCG and AAACCCG repeats. Evolutionary analysis of the M. lewisii TR paralogs indicated it had arisen from a transposition-mediate duplication process. Further analysis of the TR from multiple Mimulus species showed the gene had frequently transposed and inserted into new chromosomal positions during Mimulus evolution. From our results, we propose the TR transposition, duplication, and divergence model to explain the evolutionary sequence turnovers in Mimulus and potentially all plant telomeres.

Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser

Structure · 2023 · 16 citations

• Chemistry
• Crystallography
• Biophysics