1
|
Bansal A, Phogat P, Kukreti S. A novel G·G·T non-conventional intramolecular triplex formed by the double repeat sequence of Chlamydomonas telomeric DNA. RSC Adv 2022; 12:15918-15924. [PMID: 35733691 PMCID: PMC9134377 DOI: 10.1039/d2ra00861k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022] Open
Abstract
The competition among the DNA non-canonical structures has been widely studied in repetitive DNA sequences. The Chlamydomonas reinhardtii telomere (TTTTAGGG)n is found an exception to the general idea of forming folded G-quadruplex by few repeats of any telomeric sequence.
Collapse
Affiliation(s)
- Aparna Bansal
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
- Department of Chemistry, Hansraj College, University of Delhi, (North Campus), Delhi, 110007, India
| | - Priyanka Phogat
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
| | - Shrikant Kukreti
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
| |
Collapse
|
2
|
Eberhard S, Valuchova S, Ravat J, Fulneček J, Jolivet P, Bujaldon S, Lemaire SD, Wollman FA, Teixeira MT, Riha K, Xu Z. Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants. Life Sci Alliance 2019; 2:2/3/e201900315. [PMID: 31160377 PMCID: PMC6549138 DOI: 10.26508/lsa.201900315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
This study characterizes the sequence, end structure, and length distribution of Chlamydomonas reinhardtii telomeres and shows that telomerase mutants are defective in telomere maintenance. Telomeres are repeated sequences found at the end of the linear chromosomes of most eukaryotes and are required for chromosome integrity. Expression of the reverse-transcriptase telomerase allows for extension of telomeric repeats to counteract natural telomere shortening. Although Chlamydomonas reinhardtii, a photosynthetic unicellular green alga, is widely used as a model organism in photosynthesis and flagella research, and for biotechnological applications, the biology of its telomeres has not been investigated in depth. Here, we show that the C. reinhardtii (TTTTAGGG)n telomeric repeats are mostly nondegenerate and that the telomeres form a protective structure, with a subset ending with a 3′ overhang and another subset presenting a blunt end. Although telomere size and length distributions are stable under various standard growth conditions, they vary substantially between 12 genetically close reference strains. Finally, we identify CrTERT, the gene encoding the catalytic subunit of telomerase and show that telomeres shorten progressively in mutants of this gene. Telomerase mutants eventually enter replicative senescence, demonstrating that telomerase is required for long-term maintenance of telomeres in C. reinhardtii.
Collapse
Affiliation(s)
- Stephan Eberhard
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Sona Valuchova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Julie Ravat
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Jaroslav Fulneček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pascale Jolivet
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Sandrine Bujaldon
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Stéphane D Lemaire
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Francis-André Wollman
- Sorbonne Université, CNRS, UMR 7141, Institut de Biologie Physico-Chimique, Biologie du Chloroplaste et Perception de la Lumière chez les Micro-algues, Paris, France
| | - Maria Teresa Teixeira
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zhou Xu
- Sorbonne Université, PSL Research University, CNRS, UMR 8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Paris, France .,Sorbonne Université, CNRS, UMR 7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France
| |
Collapse
|
3
|
Damodaran SP, Eberhard S, Boitard L, Rodriguez JG, Wang Y, Bremond N, Baudry J, Bibette J, Wollman FA. A millifluidic study of cell-to-cell heterogeneity in growth-rate and cell-division capability in populations of isogenic cells of Chlamydomonas reinhardtii. PLoS One 2015; 10:e0118987. [PMID: 25760649 PMCID: PMC4356620 DOI: 10.1371/journal.pone.0118987] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/08/2015] [Indexed: 12/31/2022] Open
Abstract
To address possible cell-to-cell heterogeneity in growth dynamics of isogenic cell populations of Chlamydomonas reinhardtii, we developed a millifluidic drop-based device that not only allows the analysis of populations grown from single cells over periods of a week, but is also able to sort and collect drops of interest, containing viable and healthy cells, which can be used for further experimentation. In this study, we used isogenic algal cells that were first synchronized in mixotrophic growth conditions. We show that these synchronized cells, when placed in droplets and kept in mixotrophic growth conditions, exhibit mostly homogeneous growth statistics, but with two distinct subpopulations: a major population with a short doubling-time (fast-growers) and a significant subpopulation of slowly dividing cells (slow-growers). These observations suggest that algal cells from an isogenic population may be present in either of two states, a state of restricted division and a state of active division. When isogenic cells were allowed to propagate for about 1000 generations on solid agar plates, they displayed an increased heterogeneity in their growth dynamics. Although we could still identify the original populations of slow- and fast-growers, drops inoculated with a single progenitor cell now displayed a wider diversity of doubling-times. Moreover, populations dividing with the same growth-rate often reached different cell numbers in stationary phase, suggesting that the progenitor cells differed in the number of cell divisions they could undertake. We discuss possible explanations for these cell-to-cell heterogeneities in growth dynamics, such as mutations, differential aging or stochastic variations in metabolites and macromolecules yielding molecular switches, in the light of single-cell heterogeneities that have been reported among isogenic populations of other eu- and prokaryotes.
Collapse
Affiliation(s)
- Shima P. Damodaran
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Stephan Eberhard
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC 7141, Paris, France
| | - Laurent Boitard
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jairo Garnica Rodriguez
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Yuxing Wang
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
- Optical Science & Engineering Research Center, Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - Nicolas Bremond
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jean Baudry
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
| | - Jérôme Bibette
- Laboratoire de Colloïdes et Matériaux Divisés, Institute of Chemistry, Biology and Innovation ESPCI ParisTech/CNRS UMR 8231/PSL* Research University, Paris, France
- * E-mail: (JB); (FAW)
| | - Francis-André Wollman
- Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, UMR CNRS/UPMC 7141, Paris, France
- * E-mail: (JB); (FAW)
| |
Collapse
|
4
|
Abstract
In most eukaryotes, telomeric DNA consists of repeats of a short motif that includes consecutive guanines and may hence fold into G-quadruplexes. Budding yeasts have telomeres composed of longer repeats and show variation in the degree of repeat homogeneity. Although telomeric sequences from several organisms have been shown to fold into G-quadruplexes in vitro, surprisingly, no study has been dedicated to the comparison of G-quadruplex folding and stability of known telomeric sequences. Furthermore, to our knowledge, folding of yeast telomeric sequences into intramolecular G-quadruplexes has never been investigated. Using biophysical and biochemical methods, we studied sequences mimicking about four repetitions of telomeric motifs from a variety of organisms, including yeasts, with the aim of comparing the G-quadruplex folding potential of telomeric sequences among eukaryotes. G-quadruplex folding did not appear to be a conserved feature among yeast telomeric sequences. By contrast, all known telomeric sequences from eukaryotes other than yeasts folded into G-quadruplexes. Nevertheless, while G(3)T(1-4)A repeats (found in a variety of organisms) and G(4)T(2,4) repeats (found in ciliates) folded into stable G-quadruplexes, G-quadruplexes formed by repetitions of G(2)T(2)A and G(2)CT(2)A motifs (found in many insects and in nematodes, respectively) appeared to be in equilibrium with non-G-quadruplex structures (likely hairpin-duplexes).
Collapse
Affiliation(s)
- Phong Lan Thao Tran
- INSERM, U565, Acides Nucléiques: Dynamique, Ciblage et Fonctions Biologiques, Muséum National d'Histoire Naturelle, CNRS, UMR7196, Département de Régulations, Développement et Diversité Moléculaire, 43 rue Cuvier, CP26, Paris Cedex 5 -75231, France
| | | | | |
Collapse
|
5
|
Johnston SD, Lew JE, Berman J. Gbp1p, a protein with RNA recognition motifs, binds single-stranded telomeric DNA and changes its binding specificity upon dimerization. Mol Cell Biol 1999; 19:923-33. [PMID: 9858616 PMCID: PMC83950 DOI: 10.1128/mcb.19.1.923] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/1998] [Accepted: 10/20/1998] [Indexed: 01/09/2023] Open
Abstract
Gbp1p is a putative telomere-binding protein from Chlamydomonas reinhardtii that contains two RNA recognition motifs (RRMs) which are commonly found in heterogeneous nuclear ribonucleoproteins (hnRNPs). Previously we demonstrated that Gbp1p binds single-stranded DNA (ssDNA) containing the Chlamydomonas telomeric sequence but not the RNA containing the cognate sequence. Here we show that at lower protein concentrations Gbp1 can also bind an RNA containing the cognate sequence. We found that mutation of the two RRM motifs of Gbp1p to match the highly conserved region of hnRNP RRMs did not alter the affinity of Gbp1p for either RNA or DNA. The ability of Gbp1p to associate with either of these two nucleic acids is governed by the dimerization state of the protein. Monomeric Gbp1p associates with either ssDNA or RNA, showing a small binding preference for RNA. Dimeric Gbp1p has a strong preference for binding ssDNA and shows little affinity for RNA. To the best of our knowledge, this is the first example of a protein that qualitatively shifts its nucleic acid binding preference upon dimerization. The biological implications of a telomere-binding protein that is regulated by dimerization are discussed.
Collapse
Affiliation(s)
- S D Johnston
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
| | | | | |
Collapse
|
6
|
Hails T, Huttner O, Day A. Isolation of a Chlamydomonas reinhardtii telomere by functional complementation in yeast. Curr Genet 1995; 28:437-40. [PMID: 8575016 DOI: 10.1007/bf00310812] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We attempted to determine whether Chlamydomonas reinhardtii telomeres, which do not form G-quartet structures readily in vitro, are able to nucleate telomere addition in Saccharomyces cerevisiae. Restricted C. reinhardtii genomic DNA was ligated to a linear S. cerevisiae vector lacking a telomere. A C. reinhardtii telomere ligated to this unprotected end allowed vector replication as a linear DNA molecule in S. cerevisiae. DNA sequencing revealed common [T4AG3]n and variant T6AG3 and T5AG3 C. reinhardtii telomere repeats capped by S. cerevisiae telomere repeat units. The recognition of a C. reinhardtii telomere by the telomere maintenance machinery of S. cerevisiae is consistent with a common theme for telomere structure in organisms with divergent telomere repeats.
Collapse
Affiliation(s)
- T Hails
- Biochemistry Department, Oxford University, UK
| | | | | |
Collapse
|
7
|
Konkel LM, Enomoto S, Chamberlain EM, McCune-Zierath P, Iyadurai SJ, Berman J. A class of single-stranded telomeric DNA-binding proteins required for Rap1p localization in yeast nuclei. Proc Natl Acad Sci U S A 1995; 92:5558-62. [PMID: 7777547 PMCID: PMC41735 DOI: 10.1073/pnas.92.12.5558] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We have identified a class of proteins that bind single-stranded telomeric DNA and are required for the nuclear organization of telomeres and/or telomere-associated proteins. Rlf6p was identified by its sequence similarity to Gbp1p, a single-stranded telomeric DNA-binding protein from Chlamydomonas reinhardtii. Rlf6p and Gbp1p bind yeast single-stranded G-strand telomeric DNA. Both proteins include at least two RNA recognition motifs, which are found in many proteins that interact with single-stranded nucleic acids. Disruption of RLF6 alters the distribution of repressor/activator protein 1 (Rap1p), a telomere-associated protein. In wild-type yeast cells, Rap1p localizes to a small number of perinuclear spots, while in rlf6 cells Rap1p appears diffuse and nuclear. Interestingly, telomere position effect and telomere length control, which require RAP1, are unaffected by rlf6 mutations, demonstrating that Rap1p localization can be uncoupled from other Rap1p-dependent telomere functions. In addition, expression of Chlamydomonas GBP1 restores perinuclear, punctate Rap1p localization in rlf6 mutant cells. The functional complementation of a fungal gene by an algal gene suggests that Rlf6p and Gbp1p are members of a conserved class of single-stranded telomeric DNA-binding proteins that influence nuclear organization. Furthermore, it demonstrates that, despite their unusual codon bias, C. reinhardtii genes can be efficiently translated in Saccharomyces cerevisiae cells.
Collapse
Affiliation(s)
- L M Konkel
- Department of Plant Biology, University of Minnesota, St. Paul 55108, USA
| | | | | | | | | | | |
Collapse
|
8
|
Abstract
Centromeres and telomeres are both composed of specific DNA sequences and unique chromosomal proteins. Isolation and characterization of some of these sequences and proteins has greatly increased our knowledge of centromere and telomere structure. This information is allowing us to determine how centromeres and telomeres perform their various roles in a cell.
Collapse
Affiliation(s)
- C M Price
- Department of Chemistry, University of Nebraska, Lincoln 68588
| |
Collapse
|