Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae

AbstractTelomerase RNA (TR) carries the template for synthesis of telomere DNA and provides a scaffold for telomerase assembly. Fungal TRs are long and have been compared to higher eukaryotes, where they show considerable diversity within phylogenetically close groups. TRs of several Saccharomycetaceae were recently identified, however, many of these remained uncharacterised in the template region. Here we show that this is mainly due to high variability in telomere sequence. We predicted the telomere sequences using Tandem Repeats Finder and then we identified corresponding putative template regions in TR candidates. Remarkably long telomere units and the corresponding putative TRs were found in Tetrapisispora species. Notably, variable lengths of the annealing sequence of the template region (1–10 nt) were found. Consequently, species with the same telomere sequence may not harbour identical TR templates. Thus, TR sequence alone can be used to predict a template region and telomere sequence, but not to determine these exactly. A conserved feature of telomere sequences, tracts of adjacent Gs, led us to test the propensity of individual telomere sequences to form G4. The results show highly diverse values of G4-propensity, indicating the lack of ubiquitous conservation of this feature across Saccharomycetaceae.

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UPF1-Mediated RNA Decay—Danse Macabre in a Cloud

Biomolecules ◽

10.3390/biom10070999 ◽

2020 ◽

Vol 10 (7) ◽

pp. 999 ◽

Cited By ~ 2

Author(s):

Daria Lavysh ◽

Gabriele Neu-Yilik

Keyword(s):

High Variability ◽

Effector Proteins ◽

Degradation Efficiency ◽

Rna Decay ◽

User Needs ◽

Effector Protein ◽

Higher Eukaryotes ◽

Flexible Infrastructure ◽

Nonsense Mediated Rna Decay ◽

Central Effector

Nonsense-mediated RNA decay (NMD) is the prototype example of a whole family of RNA decay pathways that unfold around a common central effector protein called UPF1. While NMD in yeast appears to be a linear pathway, NMD in higher eukaryotes is a multifaceted phenomenon with high variability with respect to substrate RNAs, degradation efficiency, effector proteins and decay-triggering RNA features. Despite increasing knowledge of the mechanistic details, it seems ever more difficult to define NMD and to clearly distinguish it from a growing list of other UPF1-mediated RNA decay pathways (UMDs). With a focus on mammalian NMD, we here critically examine the prevailing NMD models and the gaps and inconsistencies in these models. By exploring the minimal requirements for NMD and other UMDs, we try to elucidate whether they are separate and definable pathways, or rather variations of the same phenomenon. Finally, we suggest that the operating principle of the UPF1-mediated decay family could be considered similar to that of a computing cloud providing a flexible infrastructure with rapid elasticity and dynamic access according to specific user needs.

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Structural features of mouse telomerase RNA are responsible for the lower activity of mouse telomerase versus human telomerase

Biochemical Journal ◽

10.1042/bj20060456 ◽

2006 ◽

Vol 397 (3) ◽

pp. 399-406 ◽

Cited By ~ 9

Author(s):

Scott J. Garforth ◽

Yan Yun Wu ◽

Vinayaka R. Prasad

Keyword(s):

Telomerase Activity ◽

Structural Features ◽

In Vitro Translation ◽

Telomerase Rna ◽

Level Of Activity ◽

Human Telomerase ◽

High Degree ◽

Made In ◽

Template Region

Human and mouse telomerases show a high degree of similarity in both the protein and RNA components. Human telomerase is more active and more processive than the mouse telomerase. There are two key differences between hTR [human TR (telomerase RNA)] and mTR (mouse TR) structures. First, the mouse telomerase contains only 2 nt upstream of its template region, whereas the human telomerase contains 45 nt. Secondly, the template region of human telomerase contains a 5-nt alignment domain, whereas that of mouse has only 2 nt. We hypothesize that these differences are responsible for the differential telomerase activities. Mutations were made in both the hTR and mTR, changing the template length and the length of the RNA upstream of the template, and telomerase was reconstituted in vitro using mouse telomerase reverse transcriptase generated by in vitro translation. We show that the sequences upstream of the template region, with a potential to form a double-stranded helix (the P1 helix) as in hTR, increase telomerase activity. The longer alignment domain increases telomerase activity only in the context of the P1 helix. Thus the TR contributes to regulating the level of activity of mammalian telomerases.

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Divalent hammerhead ribozyme targeting template region of human telomerase RNA has potent cleavage activity, but less inhibitory activity on telomerase

Archives of Biochemistry and Biophysics ◽

10.1016/s0003-9861(02)00284-9 ◽

2002 ◽

Vol 405 (1) ◽

pp. 32-37 ◽

Cited By ~ 4

Author(s):

Yasuhiro Yokoyama ◽

Xiaoyun Wan ◽

Yuichiro Takahashi ◽

Ariyoshi Shinohara ◽

Tang Liulin ◽

...

Keyword(s):

Inhibitory Activity ◽

Hammerhead Ribozyme ◽

Telomerase Rna ◽

Cleavage Activity ◽

Human Telomerase ◽

Template Region

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Evidence for an Additional Base-Pairing Element between the Telomeric Repeat and the Telomerase RNA Template in Kluyveromyces lactis and Other Yeasts

Molecular and Cellular Biology ◽

10.1128/mcb.00528-09 ◽

2009 ◽

Vol 29 (20) ◽

pp. 5389-5398 ◽

Cited By ~ 7

Author(s):

Zhi-Ru Wang ◽

Leilei Guo ◽

Lizhen Chen ◽

Michael J. McEachern

Keyword(s):

Yeast Species ◽

Kluyveromyces Lactis ◽

Telomeric Repeat ◽

Telomerase Rna ◽

Base Pairing ◽

Telomeric Dna ◽

Dna Mutation ◽

Additional Base ◽

Pairing Potential ◽

Template Region

ABSTRACT In all telomerases, the template region of the RNA subunit contains a region of telomere homology that is longer than the unit telomeric repeat. This allows a newly synthesized telomeric repeat to translocate back to the 3′ end of the template prior to a second round of telomeric repeat synthesis. In the yeast Kluyveromyces lactis, the telomerase RNA (Ter1) template has 30 nucleotides of perfect homology to the 25-bp telomeric repeat. Here we provide strong evidence that three additional nucleotides at positions −2 through −4 present on the 3′ side of the template form base-pairing interactions with telomeric DNA. Mutation of these bases can lead to opposite effects on telomere length depending on the sequence permutation of the template in a manner consistent with whether the mutation increases or decreases the base-pairing potential with the telomere. Additionally, mutations in the −2 and −3 positions that restore base-pairing potential can suppress corresponding sequence changes in the telomeric repeat. Finally, multiple other yeast species were found to also have telomerase RNAs that encode relatively long 7- to 10-nucleotide domains predicted to base pair, often with imperfect pairing, with telomeric DNA. We further demonstrate that K. lactis telomeric fragments produce banded patterns with a 25-bp periodicity. This indicates that K. lactis telomeres have preferred termination points within the 25-bp telomeric repeat.

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Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1503157112 ◽

2015 ◽

Vol 112 (36) ◽

pp. 11312-11317 ◽

Cited By ~ 13

Author(s):

Christopher J. Webb ◽

Virginia A. Zakian

Keyword(s):

Schizosaccharomyces Pombe ◽

Boundary Element ◽

Telomerase Activity ◽

Telomere Maintenance ◽

Telomerase Rna ◽

Loss Of Function ◽

Telomere Sequence ◽

Human Telomerase ◽

Element Function

The stem terminus element (STE), which was discovered 13 y ago in human telomerase RNA, is required for telomerase activity, yet its mode of action is unknown. We report that the Schizosaccharomyces pombe telomerase RNA, TER1 (telomerase RNA 1), also contains a STE, which is essential for telomere maintenance. Cells expressing a partial loss-of-function TER1 STE allele maintained short stable telomeres by a recombination-independent mechanism. Remarkably, the mutant telomere sequence was different from that of wild-type cells. Generation of the altered sequence is explained by reverse transcription into the template boundary element, demonstrating that the STE helps maintain template boundary element function. The altered telomeres bound less Pot1 (protection of telomeres 1) and Taz1 (telomere-associated in Schizosaccharomyces pombe 1) in vivo. Thus, the S. pombe STE, although distant from the template, ensures proper telomere sequence, which in turn promotes proper assembly of the shelterin complex.

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Non-enzymatic in vitro production of circular hammerhead ribozyme targeting the template region of human telomerase RNA

Nucleic Acids Symposium Series ◽

10.1093/nass/nrp138 ◽

2009 ◽

Vol 53 (1) ◽

pp. 275-276 ◽

Cited By ~ 3

Author(s):

A. Ochi ◽

S. Umekage ◽

Y. Kikuchi

Keyword(s):

Hammerhead Ribozyme ◽

Telomerase Rna ◽

In Vitro Production ◽

Human Telomerase ◽

Vitro Production ◽

Template Region

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Stem-Loop IV of Tetrahymena Telomerase RNA Stimulates Processivity in trans

Molecular and Cellular Biology ◽

10.1128/mcb.23.16.5606-5613.2003 ◽

2003 ◽

Vol 23 (16) ◽

pp. 5606-5613 ◽

Cited By ~ 43

Author(s):

Douglas X. Mason ◽

Elizabeth Goneska ◽

Carol W. Greider

Keyword(s):

Telomerase Activity ◽

Telomerase Rna ◽

In Vitro Activity ◽

Wild Type ◽

Protein Subunit ◽

Stem Loop ◽

Cell Growth Arrest ◽

In Trans ◽

Template Region

ABSTRACT Telomerase is a ribonucleoprotein enzyme responsible for the addition of telomeres onto the ends of chromosomes. Short or dysfunctional telomeres can lead to cell growth arrest, apoptosis, and genomic instability. Telomerase uses its RNA subunit to copy a short template region for telomere synthesis. To probe for regions of Tetrahymena telomerase RNA essential for function, we assayed 27 circularly permuted RNA deletions for telomerase in vitro activity and binding to the telomerase reverse transcriptase catalytic protein subunit. We found that stem-loop IV is required for wild-type telomerase activity in vitro and will stimulate processivity when added in trans.

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Nutrient-regulated gene expression in eukaryotes

Biochemical Society Symposium ◽

10.1042/bss0730085 ◽

2006 ◽

Vol 73 ◽

pp. 85-96 ◽

Cited By ~ 8

Author(s):

Richard J. Reece ◽

Laila Beynon ◽

Stacey Holden ◽

Amanda D. Hughes ◽

Karine Rébora ◽

...

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcriptional Control ◽

Direct Interaction ◽

Signalling Pathways ◽

A Cell ◽

One Step ◽

Higher Eukaryotes ◽

Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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