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Troisi R, Sica F. Structural overview of DNA and RNA G-quadruplexes in their interaction with proteins. Curr Opin Struct Biol 2024; 87:102846. [PMID: 38848656 DOI: 10.1016/j.sbi.2024.102846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 06/09/2024]
Abstract
Since the discovery of G-quadruplex (G4) participation in vital cellular processes, the regulation of the interaction of naturally occurring G4s with the relative target proteins has emerged as a promising approach for therapeutic development. Additionally, a synthetic strategy has produced several oligonucleotide aptamers, embodying a G4 module, which exhibit relevant biological activity by binding selectively to a target protein. In this context, the G4-protein structures available in the Protein Data Bank represent a valuable molecular view of the different G4 topologies involved in protein interaction. Interestingly, recent results have shown the co-existence of G4s with other structural domains such as duplexes. Overall, these findings allow a better understanding of the mechanisms that regulate intricate biological functions and suggest new design for innovative medical treatments.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, 80126 Naples, Italy; Institute of Biostructures and Bioimaging, CNR, via Pietro Castellino 111, 80131 Naples, Italy. https://twitter.com/TroRom
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, 80126 Naples, Italy.
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2
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Padmanaban S, Lambacher NJ, Tesmer VM, Zhang J, Shibuya H, Nandakumar J. Caenorhabditis elegans telomere-binding proteins TEBP-1 and TEBP-2 adapt the Myb module to dimerize and bind telomeric DNA. Proc Natl Acad Sci U S A 2024; 121:e2316651121. [PMID: 38588418 PMCID: PMC11032478 DOI: 10.1073/pnas.2316651121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/17/2024] [Indexed: 04/10/2024] Open
Abstract
Protecting chromosome ends from misrecognition as double-stranded (ds) DNA breaks is fundamental to eukaryotic viability. The protein complex shelterin prevents a DNA damage response at mammalian telomeres. Mammalian shelterin proteins TRF1 and TRF2 and their homologs in yeast and protozoa protect telomeric dsDNA. N-terminal homodimerization and C-terminal Myb-domain-mediated dsDNA binding are two structural hallmarks of end protection by TRF homologs. Yet our understanding of how Caenorhabditis elegans protects its telomeric dsDNA is limited. Recently identified C. elegans proteins TEBP-1 (also called DTN-1) and TEBP-2 (also called DTN-2) are functional homologs of TRF proteins, but how they bind DNA and whether or how they dimerize is not known. TEBP-1 and TEBP-2 harbor three Myb-containing domains (MCDs) and no obvious dimerization domain. We demonstrate biochemically that only the third MCD binds DNA. We solve the X-ray crystal structure of TEBP-2 MCD3 with telomeric dsDNA to reveal the structural mechanism of telomeric dsDNA protection in C. elegans. Mutagenesis of the DNA-binding site of TEBP-1 and TEBP-2 compromises DNA binding in vitro, and increases DNA damage signaling, lengthens telomeres, and decreases brood size in vivo. Via an X-ray crystal structure, biochemical validation of the dimerization interface, and SEC-MALS analysis, we demonstrate that MCD1 and MCD2 form a composite dimerization module that facilitates not only TEBP-1 and TEBP-2 homodimerization but also heterodimerization. These findings provide fundamental insights into C. elegans telomeric dsDNA protection and highlight how different eukaryotes have evolved distinct strategies to solve the chromosome end protection problem.
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Affiliation(s)
- Shilpa Padmanaban
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Nils J. Lambacher
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden41390
| | - Valerie M. Tesmer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
| | - Jingjing Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden41390
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden41390
- Laboratory for Gametogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe650-0047, Japan
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI48109
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3
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Gresh N, El Hage K, Lagardère L, Brégier F, Godard J, Piquemal JP, Perrée-Fauvet M, Sol V. Enforcing Local DNA Kinks by Sequence-Selective Trisintercalating Oligopeptides of a Tricationic Porphyrin: A Polarizable Molecular Dynamics Study. Chemphyschem 2024; 25:e202300776. [PMID: 38088522 DOI: 10.1002/cphc.202300776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/24/2023] [Indexed: 02/03/2024]
Abstract
Bisacridinyl-bisarginyl porphyrin (BABAP) is a trisintercalating derivative of a tricationic porphyrin, formerly designed and synthesized in order to selectively target and photosensitize the ten-base pair palindromic sequence d(CGGGCGCCCG)2 . We resorted to the previously derived (Far et al., 2004) lowest energy-minimized (EM) structure of the BABAP complex with this sequence as a starting point. We performed polarizable molecular dynamics (MD) on this complex. It showed, over a 150 ns duration, the persistent binding of the Arg side-chain on each BABAP arm to the two G bases upstream from the central porphyrin intercalation site. We subsequently performed progressive shortenings of the connector chain linking the Arg-Gly backbone to the acridine, from n=6 methylenes to 4, followed by removal of the Gly backbone and further connector shortenings, from n=4 to n=1. These resulted into progressive deformations ('kinks') of the DNA backbone. In its most accented kinked structure, the DNA backbone was found to have a close overlap with that of DNA bound to Cre recombinase, with, at the level of one acridine intercalation site, negative roll and positive tilt values consistent with those experimentally found for this DNA at its own kinked dinucleotide sequence. Thus, in addition to their photosensitizing properties, some BABAP derivatives could induce sequence-selective, controlled DNA deformations, which are targets for cleavage by endonucleases or for repair enzymes.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique UMR 7616, Sorbonne Université, 75005, Paris, France
| | - Krystel El Hage
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint-Jacques, 75014, Paris, France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique UMR 7616, Sorbonne Université, 75005, Paris, France
| | | | - Jérémy Godard
- LABCiS UR22722, Univ. Limoges, F-87000, Limoges, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique UMR 7616, Sorbonne Université, 75005, Paris, France
| | | | - Vincent Sol
- LABCiS UR22722, Univ. Limoges, F-87000, Limoges, France
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4
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Li B. Unwrap RAP1's Mystery at Kinetoplastid Telomeres. Biomolecules 2024; 14:67. [PMID: 38254667 PMCID: PMC10813129 DOI: 10.3390/biom14010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Although located at the chromosome end, telomeres are an essential chromosome component that helps maintain genome integrity and chromosome stability from protozoa to mammals. The role of telomere proteins in chromosome end protection is conserved, where they suppress various DNA damage response machineries and block nucleolytic degradation of the natural chromosome ends, although the detailed underlying mechanisms are not identical. In addition, the specialized telomere structure exerts a repressive epigenetic effect on expression of genes located at subtelomeres in a number of eukaryotic organisms. This so-called telomeric silencing also affects virulence of a number of microbial pathogens that undergo antigenic variation/phenotypic switching. Telomere proteins, particularly the RAP1 homologs, have been shown to be a key player for telomeric silencing. RAP1 homologs also suppress the expression of Telomere Repeat-containing RNA (TERRA), which is linked to their roles in telomere stability maintenance. The functions of RAP1s in suppressing telomere recombination are largely conserved from kinetoplastids to mammals. However, the underlying mechanisms of RAP1-mediated telomeric silencing have many species-specific features. In this review, I will focus on Trypanosoma brucei RAP1's functions in suppressing telomeric/subtelomeric DNA recombination and in the regulation of monoallelic expression of subtelomere-located major surface antigen genes. Common and unique mechanisms will be compared among RAP1 homologs, and their implications will be discussed.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA;
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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5
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Pan Y, Hu C, Hou LJ, Chen YL, Shi J, Liu JC, Zhou JQ. Swc4 protects nucleosome-free rDNA, tDNA and telomere loci to inhibit genome instability. DNA Repair (Amst) 2023; 127:103512. [PMID: 37230009 DOI: 10.1016/j.dnarep.2023.103512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/17/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
In the baker's yeast Saccharomyces cerevisiae, NuA4 and SWR1-C, two multisubunit complexes, are involved in histone acetylation and chromatin remodeling, respectively. Eaf1 is the assembly platform subunit of NuA4, Swr1 is the assembly platform and catalytic subunit of SWR1-C, while Swc4, Yaf9, Arp4 and Act1 form a functional module, and is present in both NuA4 and SWR1 complexes. ACT1 and ARP4 are essential for cell survival. Deletion of SWC4, but not YAF9, EAF1 or SWR1 results in a severe growth defect, but the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display defects in DNA ploidy and chromosome segregation, suggesting that the defects observed in swc4Δ cells are independent of NuA4 or SWR1-C integrity. Swc4 is enriched in the nucleosome-free regions (NFRs) of the genome, including characteristic regions of RDN5s, tDNAs and telomeres, independently of Yaf9, Eaf1 or Swr1. In particular, rDNA, tDNA and telomere loci are more unstable and prone to recombination in the swc4Δ cells than in wild-type cells. Taken together, we conclude that the chromatin associated Swc4 protects nucleosome-free chromatin of rDNA, tDNA and telomere loci to ensure genome integrity.
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Affiliation(s)
- Yue Pan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin-Jun Hou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Long Chen
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiantao Shi
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jin-Qiu Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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6
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Wilkinson ME, Frangieh CJ, Macrae RK, Zhang F. Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription. Science 2023; 380:301-308. [PMID: 37023171 PMCID: PMC10499050 DOI: 10.1126/science.adg7883] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023]
Abstract
Non-long terminal repeat (non-LTR) retrotransposons, or long interspersed nuclear elements (LINEs), are an abundant class of eukaryotic transposons that insert into genomes by target-primed reverse transcription (TPRT). During TPRT, a target DNA sequence is nicked and primes reverse transcription of the retrotransposon RNA. Here, we report the cryo-electron microscopy structure of the Bombyx mori R2 non-LTR retrotransposon initiating TPRT at its ribosomal DNA target. The target DNA sequence is unwound at the insertion site and recognized by an upstream motif. An extension of the reverse transcriptase (RT) domain recognizes the retrotransposon RNA and guides the 3' end into the RT active site to template reverse transcription. We used Cas9 to retarget R2 in vitro to non-native sequences, suggesting future use as a reprogrammable RNA-based gene-insertion tool.
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Affiliation(s)
- Max E. Wilkinson
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Chris J. Frangieh
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
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7
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Wang WH, Lai TX, Wu YC, Chen ZT, Tseng KY, Lan CY. Associations of Rap1 with Cell Wall Integrity, Biofilm Formation, and Virulence in Candida albicans. Microbiol Spectr 2022; 10:e0328522. [PMID: 36416583 PMCID: PMC9769648 DOI: 10.1128/spectrum.03285-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022] Open
Abstract
Rap1 (repressor activator protein 1) is a multifunctional protein, playing important roles in telomeric and nontelomeric functions in many eukaryotes. Candida albicans Rap1 has been previously shown to be involved in telomeric regulation, but its other functions are still mostly unknown. In this study, we found that the deletion of the RAP1 gene altered cell wall properties, composition, and gene expression. In addition, deletion of RAP1 affected C. albicans biofilm formation and modulated phagocytosis and cytokine release by host immune cells. Finally, the RAP1 gene deletion mutant showed attenuation of C. albicans virulence in a Galleria mellonella infection model. Therefore, these findings provide new insights into Rap1 functions that are particularly relevant to pathogenesis and virulence of C. albicans. IMPORTANCE C. albicans is an important fungal pathogen of humans. The cell wall is the outermost layer of C. albicans and is important for commensalism and infection by this pathogen. Moreover, the cell wall is also an important target for antifungals. Studies of how C. albicans maintains its cell wall integrity are critical for a better understanding of fungal pathogenesis and virulence. This work focuses on exploring unknown functions of C. albicans Rap1 and reveals its contribution to cell wall integrity, biofilm formation, and virulence. Notably, these findings will also improve our general understanding of complex machinery to control pathogenesis and virulence of fungal pathogens.
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Affiliation(s)
- Wen-Han Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ting-Xiu Lai
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Chia Wu
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Zzu-Ting Chen
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Kuo-Yun Tseng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Taiwan Mycology Reference Center, National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan
| | - Chung-Yu Lan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan
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8
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Casari E, Gnugnoli M, Rinaldi C, Pizzul P, Colombo CV, Bonetti D, Longhese MP. To Fix or Not to Fix: Maintenance of Chromosome Ends Versus Repair of DNA Double-Strand Breaks. Cells 2022; 11:cells11203224. [PMID: 36291091 PMCID: PMC9601279 DOI: 10.3390/cells11203224] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 02/08/2023] Open
Abstract
Early work by Muller and McClintock discovered that the physical ends of linear chromosomes, named telomeres, possess an inherent ability to escape unwarranted fusions. Since then, extensive research has shown that this special feature relies on specialized proteins and structural properties that confer identity to the chromosome ends, thus allowing cells to distinguish them from intrachromosomal DNA double-strand breaks. Due to the inability of conventional DNA replication to fully replicate the chromosome ends and the downregulation of telomerase in most somatic human tissues, telomeres shorten as cells divide and lose this protective capacity. Telomere attrition causes the activation of the DNA damage checkpoint that leads to a cell-cycle arrest and the entering of cells into a nondividing state, called replicative senescence, that acts as a barrier against tumorigenesis. However, downregulation of the checkpoint overcomes this barrier and leads to further genomic instability that, if coupled with re-stabilization of telomeres, can drive tumorigenesis. This review focuses on the key experiments that have been performed in the model organism Saccharomyces cerevisiae to uncover the mechanisms that protect the chromosome ends from eliciting a DNA damage response, the conservation of these pathways in mammals, as well as the consequences of their loss in human cancer.
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9
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Overexpression of a Malus baccata MYB Transcription Factor Gene MbMYB4 Increases Cold and Drought Tolerance in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23031794. [PMID: 35163716 PMCID: PMC8836155 DOI: 10.3390/ijms23031794] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022] Open
Abstract
In the natural environment, plants often face unfavorable factors such as drought, cold, and freezing, which affect their growth and yield. The MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factor family is widely involved in plant responses to biotic and abiotic stresses. In this study, Malus baccata (L.) Borkh was used as the research material, and a gene MbMYB4 of the MYB family was cloned from it. The open reading frame (ORF) of MbMYB4 was found to be 762 bp, encoding 253 amino acids; sequence alignment results and predictions of the protein structure indicated that the MbMYB4 protein contained the conserved MYB domain. Subcellular localization showed that MbMYB4 was localized in the nucleus. In addition, the use of quantitative real-time PCR (qPCR) technology found that the expression of MbMYB4 was enriched in the young leaf and root, and it was highly affected by cold and drought treatments in M. baccata seedlings. When MbMYB4 was introduced into Arabidopsis thaliana, it greatly increased the cold and drought tolerance in the transgenic plant. Under cold and drought stresses, the proline and chlorophyll content, and peroxidase (POD) and catalase (CAT) activities of transgenic A. thaliana increased significantly, and the content of malondialdehyde (MDA) and the relative conductivity decreased significantly, indicating that the plasma membrane damage of transgenic A. thaliana was lesser. Therefore, the overexpression of the MbMYB4 gene in A. thaliana can enhance the tolerance of transgenic plants to cold and drought stresses.
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10
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Zhang K, Tarczykowska A, Gupta DK, Pendlebury DF, Zuckerman C, Nandakumar J, Shibuya H. The TERB1 MYB domain suppresses telomere erosion in meiotic prophase I. Cell Rep 2022; 38:110289. [PMID: 35081355 PMCID: PMC8867601 DOI: 10.1016/j.celrep.2021.110289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/08/2021] [Accepted: 12/29/2021] [Indexed: 11/24/2022] Open
Abstract
The meiosis-specific telomere-binding protein TERB1 anchors telomeres to the nuclear envelope and drives chromosome movements for the pairing of homologous chromosomes. TERB1 has an MYB-like DNA-binding (MYB) domain, which is a hallmark of telomeric DNA-binding proteins. Here, we demonstrate that the TERB1 MYB domain has lost its canonical DNA-binding activity. The analysis of Terb1 point mutant mice expressing TERB1 lacking its MYB domain showed that the MYB domain is dispensable for telomere localization of TERB1 and the downstream TERB2-MAJIN complex, the promotion of homologous pairing, and even fertility. Instead, the TERB1 MYB domain regulates the enrichment of cohesin and promotes the remodeling of axial elements in the early-to-late pachytene transition, which suppresses telomere erosion. Considering its conservation across metazoan phyla, the TERB1 MYB domain is likely to be important for the maintenance of telomeric DNA and thus for genomic integrity by suppressing meiotic telomere erosion over long evolutionary timescales.
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Affiliation(s)
- Kexin Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-41390, Sweden
| | - Agata Tarczykowska
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-41390, Sweden
| | - Deepesh Kumar Gupta
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-41390, Sweden
| | - Devon F Pendlebury
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cassandra Zuckerman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-41390, Sweden.
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11
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Itriago H, Jaiswal RK, Philipp S, Cohn M. The telomeric 5' end nucleotide is regulated in the budding yeast Naumovozyma castellii. Nucleic Acids Res 2021; 50:281-292. [PMID: 34908133 PMCID: PMC8754665 DOI: 10.1093/nar/gkab1229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 11/14/2022] Open
Abstract
The junction between the double-stranded and single-stranded telomeric DNA (ds-ss junction) is fundamental in the maintenance of the telomeric chromatin, as it directs the assembly of the telomere binding proteins. In budding yeast, multiple Rap1 proteins bind the telomeric dsDNA, while ssDNA repeats are bound by the Cdc13 protein. Here, we aimed to determine, for the first time, the telomeric 5' end nucleotide in a budding yeast. To this end, we developed a permutation-specific PCR-based method directed towards the regular 8-mer telomeric repeats in Naumovozyma castellii. We find that, in logarithmically growing cells, the 320 ± 30 bp long telomeres mainly terminate in either of two specific 5' end permutations of the repeat, both corresponding to a terminal adenine nucleotide. Strikingly, two permutations are completely absent at the 5' end, indicating that not all ds-ss junction structures would allow the establishment of the protective telomere chromatin cap structure. Using in vitro DNA end protection assays, we determined that binding of Rap1 and Cdc13 around the most abundant ds-ss junction ensures the protection of both 5' ends and 3' overhangs from exonucleolytic degradation. Our results provide mechanistic insights into telomere protection, and reveal that Rap1 and Cdc13 have complementary roles.
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Affiliation(s)
- Humberto Itriago
- Department of Biology, Genetics group, Lund University, SE-223 62 Lund, Sweden
| | - Rishi K Jaiswal
- Department of Biology, Genetics group, Lund University, SE-223 62 Lund, Sweden
| | - Susanne Philipp
- Department of Biology, Genetics group, Lund University, SE-223 62 Lund, Sweden
| | - Marita Cohn
- Department of Biology, Genetics group, Lund University, SE-223 62 Lund, Sweden
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12
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Islam K, Rawoof A, Ahmad I, Dubey M, Momo J, Ramchiary N. Capsicum chinense MYB Transcription Factor Genes: Identification, Expression Analysis, and Their Conservation and Diversification With Other Solanaceae Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:721265. [PMID: 34721453 PMCID: PMC8548648 DOI: 10.3389/fpls.2021.721265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/08/2021] [Indexed: 05/27/2023]
Abstract
Myeloblastosis (MYB) genes are important transcriptional regulators of plant growth, development, and secondary metabolic biosynthesis pathways, such as capsaicinoid biosynthesis in Capsicum. Although MYB genes have been identified in Capsicum annuum, no comprehensive study has been conducted on other Capsicum species. We identified a total of 251 and 240 MYB encoding genes in Capsicum chinense MYBs (CcMYBs) and Capsicum baccatum MYBs (CbMYBs). The observation of twenty tandem and 41 segmental duplication events indicated expansion of the MYB gene family in the C. chinense genome. Five CcMYB genes, i.e., CcMYB101, CcMYB46, CcMYB6, CcPHR8, and CcRVE5, and two CaMYBs, i.e., CaMYB3 and CaHHO1, were found within the previously reported capsaicinoid biosynthesis quantitative trait loci. Based on phylogenetic analysis with tomato MYB proteins, the Capsicum MYBs were classified into 24 subgroups supported by conserved amino acid motifs and gene structures. Also, a total of 241 CcMYBs were homologous with 225 C. annuum, 213 C. baccatum, 125 potato, 79 tomato, and 23 Arabidopsis MYBs. Synteny analysis showed that all 251 CcMYBs were collinear with C. annuum, C. baccatum, tomato, potato, and Arabidopsis MYBs spanning over 717 conserved syntenic segments. Using transcriptome data from three fruit developmental stages, a total of 54 CcMYBs and 81 CaMYBs showed significant differential expression patterns. Furthermore, the expression of 24 CcMYBs from the transcriptome data was validated by quantitative real-time (qRT) PCR analysis. Eight out of the 24 CcMYBs validated by the qRT-PCR were highly expressed in fiery hot C. chinense than in the lowly pungent C. annuum. Furthermore, the co-expression analysis revealed several MYB genes clustered with genes from the capsaicinoid, anthocyanin, phenylpropanoid, carotenoid, and flavonoids biosynthesis pathways, and related to determining fruit shape and size. The homology modeling of 126 R2R3 CcMYBs showed high similarity with that of the Arabidopsis R2R3 MYB domain template, suggesting their potential functional similarity at the proteome level. Furthermore, we have identified simple sequence repeat (SSR) motifs in the CcMYB genes, which could be used in Capsicum breeding programs. The functional roles of the identified CcMYBs could be studied further so that they can be manipulated for Capsicum trait improvement.
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Affiliation(s)
- Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Meenakshi Dubey
- Department of Biotechnology, Delhi Technological University, New Delhi, India
| | - John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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13
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Duveau F, Vande Zande P, Metzger BP, Diaz CJ, Walker EA, Tryban S, Siddiq MA, Yang B, Wittkopp PJ. Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae. eLife 2021; 10:67806. [PMID: 34463616 PMCID: PMC8456550 DOI: 10.7554/elife.67806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
Heritable variation in a gene’s expression arises from mutations impacting cis- and trans-acting components of its regulatory network. Here, we investigate how trans-regulatory mutations are distributed within the genome and within a gene regulatory network by identifying and characterizing 69 mutations with trans-regulatory effects on expression of the same focal gene in Saccharomyces cerevisiae. Relative to 1766 mutations without effects on expression of this focal gene, we found that these trans-regulatory mutations were enriched in coding sequences of transcription factors previously predicted to regulate expression of the focal gene. However, over 90% of the trans-regulatory mutations identified mapped to other types of genes involved in diverse biological processes including chromatin state, metabolism, and signal transduction. These data show how genetic changes in diverse types of genes can impact a gene’s expression in trans, revealing properties of trans-regulatory mutations that provide the raw material for trans-regulatory variation segregating within natural populations.
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Affiliation(s)
- Fabien Duveau
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States.,Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon, Université de Lyon, Lyon, France
| | - Petra Vande Zande
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Brian Ph Metzger
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Crisandra J Diaz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Elizabeth A Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Stephen Tryban
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Mohammad A Siddiq
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States
| | - Bing Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, United States.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
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14
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Li B, Zhao Y. Regulation of Antigenic Variation by Trypanosoma brucei Telomere Proteins Depends on Their Unique DNA Binding Activities. Pathogens 2021; 10:pathogens10080967. [PMID: 34451431 PMCID: PMC8402208 DOI: 10.3390/pathogens10080967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 01/17/2023] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, Variant Surface Glycoprotein (VSG), to evade the host immune response. Such antigenic variation is a key pathogenesis mechanism that enables T. brucei to establish long-term infections. VSG is expressed exclusively from subtelomere loci in a strictly monoallelic manner, and DNA recombination is an important VSG switching pathway. The integrity of telomere and subtelomere structure, maintained by multiple telomere proteins, is essential for T. brucei viability and for regulating the monoallelic VSG expression and VSG switching. Here we will focus on T. brucei TRF and RAP1, two telomere proteins with unique nucleic acid binding activities, and summarize their functions in telomere integrity and stability, VSG switching, and monoallelic VSG expression. Targeting the unique features of TbTRF and TbRAP1′s nucleic acid binding activities to perturb the integrity of telomere structure and disrupt VSG monoallelic expression may serve as potential therapeutic strategy against T. brucei.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
- Center for RNA Science and Therapeutics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence: (B.L.); (Y.Z.)
| | - Yanxiang Zhao
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen, China
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
- Correspondence: (B.L.); (Y.Z.)
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15
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Li B. Keeping Balance Between Genetic Stability and Plasticity at the Telomere and Subtelomere of Trypanosoma brucei. Front Cell Dev Biol 2021; 9:699639. [PMID: 34291053 PMCID: PMC8287324 DOI: 10.3389/fcell.2021.699639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Telomeres, the nucleoprotein complexes at chromosome ends, are well-known for their essential roles in genome integrity and chromosome stability. Yet, telomeres and subtelomeres are frequently less stable than chromosome internal regions. Many subtelomeric genes are important for responding to environmental cues, and subtelomeric instability can facilitate organismal adaptation to extracellular changes, which is a common theme in a number of microbial pathogens. In this review, I will focus on the delicate and important balance between stability and plasticity at telomeres and subtelomeres of a kinetoplastid parasite, Trypanosoma brucei, which causes human African trypanosomiasis and undergoes antigenic variation to evade the host immune response. I will summarize the current understanding about T. brucei telomere protein complex, the telomeric transcript, and telomeric R-loops, focusing on their roles in maintaining telomere and subtelomere stability and integrity. The similarities and differences in functions and underlying mechanisms of T. brucei telomere factors will be compared with those in human and yeast cells.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, Cleveland, OH, United States.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States.,Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, United States
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16
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Kumar A, Chan J, Taguchi M, Kono H. Interplay among transacting factors around promoter in the initial phases of transcription. Curr Opin Struct Biol 2021; 71:7-15. [PMID: 34111671 DOI: 10.1016/j.sbi.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
The initiation signals are raised around the promoter by one of the general transcription factors, triggering a sequence of events that lead to mRNA transcript formation from target genes. Both specific noncoding DNA regions and transacting, macromolecular assemblies are intricately involved and indispensable. The transition between the subsequent transcriptional stages is accompanied by stage-specific signals and structural changes in the macromolecular assemblies and facilitated by the recruitment/removal of other chromatin and transcription-associated elements. Here, we discuss the choreography of transacting factors around promoter in the establishment and effectuation of the initial phases of transcription such as NDR formation, +1 nucleosome positioning, promoter DNA opening, and RNAPII promoter escape from a structural viewpoint.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Justin Chan
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Masahiko Taguchi
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.
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17
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Douglas ME, Diffley JFX. Budding yeast Rap1, but not telomeric DNA, is inhibitory for multiple stages of DNA replication in vitro. Nucleic Acids Res 2021; 49:5671-5683. [PMID: 34048583 PMCID: PMC8191780 DOI: 10.1093/nar/gkab416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/27/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022] Open
Abstract
Telomeres are copied and reassembled each cell division cycle through a multistep process called telomere replication. Most telomeric DNA is duplicated semiconservatively during this process, but replication forks frequently pause or stall at telomeres in yeast, mouse and human cells, potentially causing chronic telomere shortening or loss in a single cell cycle. We have investigated the cause of this effect by examining the replication of telomeric templates in vitro. Using a reconstituted assay for eukaryotic DNA replication in which a complete eukaryotic replisome is assembled and activated with purified proteins, we show that budding yeast telomeric DNA is efficiently duplicated in vitro unless the telomere binding protein Rap1 is present. Rap1 acts as a roadblock that prevents replisome progression and leading strand synthesis, but also potently inhibits lagging strand telomere replication behind the fork. Both defects can be mitigated by the Pif1 helicase. Our results suggest that GC-rich sequences do not inhibit DNA replication per se, and that in the absence of accessory factors, telomere binding proteins can inhibit multiple, distinct steps in the replication process.
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Affiliation(s)
- Max E Douglas
- Telomere Biology Laboratory, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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18
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The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1. Nat Commun 2021; 12:2668. [PMID: 33976151 PMCID: PMC8113555 DOI: 10.1038/s41467-021-22861-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
Telomeres are bound by dedicated proteins, which protect them from DNA damage and regulate telomere length homeostasis. In the nematode Caenorhabditis elegans, a comprehensive understanding of the proteins interacting with the telomere sequence is lacking. Here, we harnessed a quantitative proteomics approach to identify TEBP-1 and TEBP-2, two paralogs expressed in the germline and embryogenesis that associate to telomeres in vitro and in vivo. tebp-1 and tebp-2 mutants display strikingly distinct phenotypes: tebp-1 mutants have longer telomeres than wild-type animals, while tebp-2 mutants display shorter telomeres and a Mortal Germline. Notably, tebp-1;tebp-2 double mutant animals have synthetic sterility, with germlines showing signs of severe mitotic and meiotic arrest. Furthermore, we show that POT-1 forms a telomeric complex with TEBP-1 and TEBP-2, which bridges TEBP-1/-2 with POT-2/MRT-1. These results provide insights into the composition and organization of a telomeric protein complex in C. elegans.
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19
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Galli M, Frigerio C, Longhese MP, Clerici M. The regulation of the DNA damage response at telomeres: focus on kinases. Biochem Soc Trans 2021; 49:933-943. [PMID: 33769480 DOI: 10.1042/bst20200856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/17/2022]
Abstract
The natural ends of linear chromosomes resemble those of accidental double-strand breaks (DSBs). DSBs induce a multifaceted cellular response that promotes the repair of lesions and slows down cell cycle progression. This response is not elicited at chromosome ends, which are organized in nucleoprotein structures called telomeres. Besides counteracting DSB response through specialized telomere-binding proteins, telomeres also prevent chromosome shortening. Despite of the different fate of telomeres and DSBs, many proteins involved in the DSB response also localize at telomeres and participate in telomere homeostasis. In particular, the DSB master regulators Tel1/ATM and Mec1/ATR contribute to telomere length maintenance and arrest cell cycle progression when chromosome ends shorten, thus promoting a tumor-suppressive process known as replicative senescence. During senescence, the actions of both these apical kinases and telomere-binding proteins allow checkpoint activation while bulk DNA repair activities at telomeres are still inhibited. Checkpoint-mediated cell cycle arrest also prevents further telomere erosion and deprotection that would favor chromosome rearrangements, which are known to increase cancer-associated genome instability. This review summarizes recent insights into functions and regulation of Tel1/ATM and Mec1/ATR at telomeres both in the presence and in the absence of telomerase, focusing mainly on discoveries in budding yeast.
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Affiliation(s)
- Michela Galli
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Chiara Frigerio
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
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20
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Yamamoto I, Zhang K, Zhang J, Vorontsov E, Shibuya H. Telomeric double-strand DNA-binding proteins DTN-1 and DTN-2 ensure germline immortality in Caenorhabditis elegans. eLife 2021; 10:64104. [PMID: 33476260 PMCID: PMC7819708 DOI: 10.7554/elife.64104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
Telomeres are nucleoprotein complexes at the ends of chromosomes and are indispensable for the protection and lengthening of terminal DNA. Despite the evolutionarily conserved roles of telomeres, the telomeric double-strand DNA (dsDNA)-binding proteins have evolved rapidly. Here, we identified double-strand telomeric DNA-binding proteins (DTN-1 and DTN-2) in Caenorhabditis elegans as non-canonical telomeric dsDNA-binding proteins. DTN-1 and DTN-2 are paralogous proteins that have three putative MYB-like DNA-binding domains and bind to telomeric dsDNA in a sequence-specific manner. DTN-1 and DTN-2 form complexes with the single-strand telomeric DNA-binding proteins POT-1 and POT-2 and constitutively localize to telomeres. The dtn-1 and dtn-2 genes function redundantly, and their simultaneous deletion results in progressive germline mortality, which accompanies telomere hyper-elongation and chromosomal bridges. Our study suggests that DTN-1 and DTN-2 are core shelterin components in C. elegans telomeres that act as negative regulators of telomere length and are essential for germline immortality.
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Affiliation(s)
- Io Yamamoto
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Kexin Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jingjing Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Egor Vorontsov
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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21
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Červenák F, Sepšiová R, Nosek J, Tomáška Ľ. Step-by-Step Evolution of Telomeres: Lessons from Yeasts. Genome Biol Evol 2020; 13:6127219. [PMID: 33537752 PMCID: PMC7857110 DOI: 10.1093/gbe/evaa268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2020] [Indexed: 12/23/2022] Open
Abstract
In virtually every eukaryotic species, the ends of nuclear chromosomes are protected by telomeres, nucleoprotein structures counteracting the end-replication problem and suppressing recombination and undue DNA repair. Although in most cases, the primary structure of telomeric DNA is conserved, there are several exceptions to this rule. One is represented by the telomeric repeats of ascomycetous yeasts, which encompass a great variety of sequences, whose evolutionary origin has been puzzling for several decades. At present, the key questions concerning the driving force behind their rapid evolution and the means of co-evolution of telomeric repeats and telomere-binding proteins remain largely unanswered. Previously published studies addressed mostly the general concepts of the evolutionary origin of telomeres, key properties of telomeric proteins as well as the molecular mechanisms of telomere maintenance; however, the evolutionary process itself has not been analyzed thoroughly. Here, we aimed to inspect the evolution of telomeres in ascomycetous yeasts from the subphyla Saccharomycotina and Taphrinomycotina, with special focus on the evolutionary origin of species-specific telomeric repeats. We analyzed the sequences of telomeric repeats from 204 yeast species classified into 20 families and as a result, we propose a step-by-step model, which integrates the diversity of telomeric repeats, telomerase RNAs, telomere-binding protein complexes and explains a propensity of certain species to generate the repeat heterogeneity within a single telomeric array.
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Affiliation(s)
- Filip Červenák
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Regina Sepšiová
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
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22
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Sparks MA, Burgers PM, Galletto R. Pif1, RPA, and FEN1 modulate the ability of DNA polymerase δ to overcome protein barriers during DNA synthesis. J Biol Chem 2020; 295:15883-15891. [PMID: 32913126 DOI: 10.1074/jbc.ra120.015699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/09/2020] [Indexed: 01/20/2023] Open
Abstract
Successful DNA replication requires carefully regulated mechanisms to overcome numerous obstacles that naturally occur throughout chromosomal DNA. Scattered across the genome are tightly bound proteins, such as transcription factors and nucleosomes, that are necessary for cell function, but that also have the potential to impede timely DNA replication. Using biochemically reconstituted systems, we show that two transcription factors, yeast Reb1 and Tbf1, and a tightly positioned nucleosome, are strong blocks to the strand displacement DNA synthesis activity of DNA polymerase δ. Although the block imparted by Tbf1 can be overcome by the DNA-binding activity of the single-stranded DNA-binding protein RPA, efficient DNA replication through either a Reb1 or a nucleosome block occurs only in the presence of the 5'-3' DNA helicase Pif1. The Pif1-dependent stimulation of DNA synthesis across strong protein barriers may be beneficial during break-induced replication where barriers are expected to pose a problem to efficient DNA bubble migration. However, in the context of lagging strand DNA synthesis, the efficient disruption of a nucleosome barrier by Pif1 could lead to the futile re-replication of newly synthetized DNA. In the presence of FEN1 endonuclease, the major driver of nick translation during lagging strand replication, Pif1-dependent stimulation of DNA synthesis through a nucleosome or Reb1 barrier is prevented. By cleaving the short 5' tails generated during strand displacement, FEN1 eliminates the entry point for Pif1. We propose that this activity would protect the cell from potential DNA re-replication caused by unwarranted Pif1 interference during lagging strand replication.
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Affiliation(s)
- Melanie A Sparks
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri USA.
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri USA.
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23
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Afrin M, Gaurav AK, Yang X, Pan X, Zhao Y, Li B. TbRAP1 has an unusual duplex DNA binding activity required for its telomere localization and VSG silencing. SCIENCE ADVANCES 2020; 6:6/38/eabc4065. [PMID: 32948591 PMCID: PMC7500927 DOI: 10.1126/sciadv.abc4065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/31/2020] [Indexed: 05/10/2023]
Abstract
Localization of Repressor Activator Protein 1 (RAP1) to the telomere is essential for its telomeric functions. RAP1 homologs either directly bind the duplex telomere DNA or interact with telomere-binding proteins. We find that Trypanosoma brucei RAP1 relies on a unique double-stranded DNA (dsDNA) binding activity to achieve this goal. T. brucei causes human sleeping sickness and regularly switches its major surface antigen, variant surface glycoprotein (VSG), to evade the host immune response. VSGs are monoallelically expressed from subtelomeres, and TbRAP1 is essential for VSG regulation. We identify dsDNA and single-stranded DNA binding activities in TbRAP1, which require positively charged 737RKRRR741 residues that overlap with TbRAP1's nuclear localization signal in the MybLike domain. Both DNA binding activities are electrostatics-based and sequence nonspecific. The dsDNA binding activity can be substantially diminished by phosphorylation of two 737RKRRR741-adjacent S residues and is essential for TbRAP1's telomere localization, VSG silencing, telomere integrity, and cell proliferation.
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Affiliation(s)
- Marjia Afrin
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
| | - Amit Kumar Gaurav
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA
| | - Xian Yang
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China
| | - Xuehua Pan
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China
| | - Yanxiang Zhao
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, People's Republic of China.
| | - Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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24
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Traczyk A, Liew CW, Gill DJ, Rhodes D. Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1. Nucleic Acids Res 2020; 48:4562-4571. [PMID: 32187364 PMCID: PMC7192608 DOI: 10.1093/nar/gkaa171] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/04/2020] [Accepted: 03/15/2020] [Indexed: 12/14/2022] Open
Abstract
G-quadruplexes are four-stranded nucleic acid structures involved in multiple cellular pathways including DNA replication and telomere maintenance. Such structures are formed by G-rich DNA sequences typified by telomeric DNA repeats. Whilst there is evidence for proteins that bind and regulate G-quadruplex formation, the molecular basis for this remains poorly understood. The budding yeast telomeric protein Rap1, originally identified as a transcriptional regulator functioning by recognizing double-stranded DNA binding sites, was one of the first proteins to be discovered to also bind and promote G-quadruplex formation in vitro. Here, we present the 2.4 Å resolution crystal structure of the Rap1 DNA-binding domain in complex with a G-quadruplex. Our structure not only provides a detailed insight into the structural basis for G-quadruplex recognition by a protein, but also gives a mechanistic understanding of how the same DNA-binding domain adapts to specifically recognize different DNA structures. The key observation is the DNA-recognition helix functions in a bimodal manner: In double-stranded DNA recognition one helix face makes electrostatic interactions with the major groove of DNA, whereas in G-quadruplex recognition a different helix face is used to make primarily hydrophobic interactions with the planar face of a G-tetrad.
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Affiliation(s)
- Anna Traczyk
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore 636921, Singapore
| | - David James Gill
- NTU Institute of Structural Biology, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore 636921, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Daniela Rhodes
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University Singapore, 59 Nanyang Drive, Singapore 636921, Singapore.,School of Chemical and Biomedical Engineering, Nanyang Technological University Singapore, 62 Nanyang Drive, Singapore 637459, Singapore
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Bonetti D, Rinaldi C, Vertemara J, Notaro M, Pizzul P, Tisi R, Zampella G, Longhese MP. DNA binding modes influence Rap1 activity in the regulation of telomere length and MRX functions at DNA ends. Nucleic Acids Res 2020; 48:2424-2441. [PMID: 31879780 PMCID: PMC7049697 DOI: 10.1093/nar/gkz1203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 12/09/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
The cellular response to DNA double-strand breaks (DSBs) is initiated by the Mre11–Rad50–Xrs2 (MRX) complex that has structural and catalytic functions. MRX association at DSBs is counteracted by Rif2, which is known to interact with Rap1 that binds telomeric DNA through two tandem Myb-like domains. Whether and how Rap1 acts at DSBs is unknown. Here we show that Rif2 inhibits MRX association to DSBs in a manner dependent on Rap1, which binds to DSBs and promotes Rif2 association to them. Rap1 in turn can negatively regulate MRX function at DNA ends also independently of Rif2. In fact, a characterization of Rap1 mutant variants shows that Rap1 binding to DNA through both Myb-like domains results in formation of Rap1-DNA complexes that control MRX functions at both DSBs and telomeres primarily through Rif2. By contrast, Rap1 binding to DNA through a single Myb-like domain results in formation of high stoichiometry complexes that act at DNA ends mostly in a Rif2-independent manner. Altogether these findings indicate that the DNA binding modes of Rap1 influence its functional properties, thus highlighting the structural plasticity of this protein.
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Affiliation(s)
- Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Marco Notaro
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Giuseppe Zampella
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
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Després PC, Dubé AK, Seki M, Yachie N, Landry CR. Perturbing proteomes at single residue resolution using base editing. Nat Commun 2020; 11:1871. [PMID: 32313011 PMCID: PMC7170841 DOI: 10.1038/s41467-020-15796-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 03/27/2020] [Indexed: 01/18/2023] Open
Abstract
Base editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of the Target-AID base editor to systematically modify genes genome-wide by targeting yeast essential genes. We mutate around 17,000 individual sites in parallel across more than 1500 genes. We identify over 700 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we find that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious based on residue conservation and predicted protein destabilization. We identify key features influencing effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.
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Affiliation(s)
- Philippe C Després
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Alexandre K Dubé
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Motoaki Seki
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Japan
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, Synthetic Biology Division, University of Tokyo, Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
| | - Christian R Landry
- Département de Biochimie, Microbiologie et Bio-informatique, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada.
- PROTEO, le regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada.
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, G1V 0A6, Canada.
- Département de Biologie, Faculté de Sciences et Génie, Université Laval, Québec, QC, G1V 0A6, Canada.
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Trypanosoma brucei RAP1 Has Essential Functional Domains That Are Required for Different Protein Interactions. mSphere 2020; 5:5/1/e00027-20. [PMID: 32102938 PMCID: PMC7045384 DOI: 10.1128/msphere.00027-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, to evade the host immune response. VSGs are expressed from subtelomeres in a monoallelic fashion. TbRAP1, a telomere protein, is essential for cell viability and VSG monoallelic expression and suppresses VSG switching. Although TbRAP1 has conserved functional domains in common with its orthologs from yeasts to mammals, the domain functions are unknown. RAP1 orthologs have pleiotropic functions, and interaction with different partners is an important means by which RAP1 executes its different roles. We have established a Cre-loxP-mediated conditional knockout system for TbRAP1 and examined the roles of various functional domains in protein expression, nuclear localization, and protein-protein interactions. This system enables further studies of TbRAP1 point mutation phenotypes. We have also determined functional domains of TbRAP1 that are required for several different protein interactions, shedding light on the underlying mechanisms of TbRAP1-mediated VSG silencing. RAP1 is a telomere protein that is well conserved from protozoa to mammals. It plays important roles in chromosome end protection, telomere length control, and gene expression/silencing at both telomeric and nontelomeric loci. Interaction with different partners is an important mechanism by which RAP1 executes its different functions in yeast. The RAP1 ortholog in Trypanosoma brucei is essential for variant surface glycoprotein (VSG) monoallelic expression, an important aspect of antigenic variation, where T. brucei regularly switches its major surface antigen, VSG, to evade the host immune response. Like other RAP1 orthologs, T. brucei RAP1 (TbRAP1) has conserved functional domains, including BRCA1 C terminus (BRCT), Myb, MybLike, and RAP1 C terminus (RCT). To study functions of various TbRAP1 domains, we established a strain in which one endogenous allele of TbRAP1 is flanked by loxP repeats, enabling its conditional deletion by Cre-mediated recombination. We replaced the other TbRAP1 allele with various mutant alleles lacking individual functional domains and examined their nuclear localization and protein interaction abilities. The N terminus, BRCT, and RCT of TbRAP1 are required for normal protein levels, while the Myb and MybLike domains are essential for normal cell growth. Additionally, the Myb domain of TbRAP1 is required for its interaction with T. brucei TTAGGG repeat-binding factor (TbTRF), while the BRCT domain is required for its self-interaction. Furthermore, the TbRAP1 MybLike domain contains a bipartite nuclear localization signal that is required for its interaction with importin α and its nuclear localization. Interestingly, RAP1’s self-interaction and the interaction between RAP1 and TRF are conserved from kinetoplastids to mammals. However, details of the interaction interfaces have changed throughout evolution. IMPORTANCETrypanosoma brucei causes human African trypanosomiasis and regularly switches its major surface antigen, VSG, to evade the host immune response. VSGs are expressed from subtelomeres in a monoallelic fashion. TbRAP1, a telomere protein, is essential for cell viability and VSG monoallelic expression and suppresses VSG switching. Although TbRAP1 has conserved functional domains in common with its orthologs from yeasts to mammals, the domain functions are unknown. RAP1 orthologs have pleiotropic functions, and interaction with different partners is an important means by which RAP1 executes its different roles. We have established a Cre-loxP-mediated conditional knockout system for TbRAP1 and examined the roles of various functional domains in protein expression, nuclear localization, and protein-protein interactions. This system enables further studies of TbRAP1 point mutation phenotypes. We have also determined functional domains of TbRAP1 that are required for several different protein interactions, shedding light on the underlying mechanisms of TbRAP1-mediated VSG silencing.
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Song S, Perez JV, Svitko W, Ricketts MD, Dean E, Schultz D, Marmorstein R, Johnson FB. Rap1-mediated nucleosome displacement can regulate gene expression in senescent cells without impacting the pace of senescence. Aging Cell 2020; 19:e13061. [PMID: 31742863 PMCID: PMC6974733 DOI: 10.1111/acel.13061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/19/2019] [Accepted: 10/13/2019] [Indexed: 01/18/2023] Open
Abstract
Cell senescence is accompanied, and in part mediated, by changes in chromatin, including histone losses, but underlying mechanisms are not well understood. We reported previously that during yeast cell senescence driven by telomere shortening, the telomeric protein Rap1 plays a major role in reprogramming gene expression by relocalizing hundreds of new target genes (called NRTS, for new Rap1 targets at senescence) to the promoters. This leads to two types of histone loss: Rap1 lowers histone level globally by repressing histone gene expression, and it also causes local nucleosome displacement at the promoters of upregulated NRTS. Here, we present evidence of direct binding between Rap1 and histone H3/H4 heterotetramers, and map amino acids involved in the interaction within the Rap1 SANT domain to amino acids 392-394 (SHY). Introduction of a point mutation within the native RAP1 locus that converts these residues to alanines (RAP1SHY ), and thus disrupts Rap1-H3/H4 interaction, does not interfere with Rap1 relocalization to NRTS at senescence, but prevents full nucleosome displacement and gene upregulation, indicating direct Rap1-H3/H4 contacts are involved in nucleosome displacement. Consistent with this, the histone H3/H4 chaperone Asf1 is similarly unnecessary for Rap1 localization to NRTS but is required for full Rap1-mediated nucleosome displacement and gene activation. Remarkably, RAP1SHY does not affect the pace of senescence-related cell cycle arrest, indicating that some changes in gene expression at senescence are not coupled to this arrest.
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Affiliation(s)
- Shufei Song
- Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Graduate Group in Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia PA USA
| | - Javier V. Perez
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia PA USA
| | - William Svitko
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia PA USA
| | - M. Daniel Ricketts
- Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Abramson Family Cancer Research Institute University of Pennsylvania Philadelphia PA USA
| | - Elliot Dean
- High‐Throughput Screening Core University of Pennsylvania Philadelphia PA USA
| | - David Schultz
- High‐Throughput Screening Core University of Pennsylvania Philadelphia PA USA
| | - Ronen Marmorstein
- Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Abramson Family Cancer Research Institute University of Pennsylvania Philadelphia PA USA
| | - F. Brad Johnson
- Department of Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA USA
- Department of Pathology and Laboratory Medicine University of Pennsylvania Philadelphia PA USA
- Institute on Aging University of Pennsylvania Philadelphia PA USA
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Millard PS, Kragelund BB, Burow M. R2R3 MYB Transcription Factors - Functions outside the DNA-Binding Domain. TRENDS IN PLANT SCIENCE 2019; 24:934-946. [PMID: 31358471 DOI: 10.1016/j.tplants.2019.07.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 05/20/2023]
Abstract
Several transcription factor (TF) families, including the MYB family, regulate a wide array of biological processes. TFs contain DNA-binding domains (DBDs) and regulatory regions; although information on protein structure is scarce for plant MYB TFs, various in silico methods suggest that the non-MYB regions contain extensive intrinsically disordered regions (IDRs). Although IDRs do not fold into stable globular structures, they comprise functional regions including interaction motifs, and recent research has shown that IDRs perform crucial biological roles. We map here domain organization, disorder predictions, and functional regions across the entire Arabidopsis thaliana R2R3 MYB TF family, and highlight where an increased research focus will be necessary to shape a new understanding of structure-function relationships in plant TFs.
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Affiliation(s)
- Peter S Millard
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark; Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark; Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
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30
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Červenák F, Juríková K, Devillers H, Kaffe B, Khatib A, Bonnell E, Sopkovičová M, Wellinger RJ, Nosek J, Tzfati Y, Neuvéglise C, Tomáška Ľ. Identification of telomerase RNAs in species of the Yarrowia clade provides insights into the co-evolution of telomerase, telomeric repeats and telomere-binding proteins. Sci Rep 2019; 9:13365. [PMID: 31527614 PMCID: PMC6746865 DOI: 10.1038/s41598-019-49628-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/29/2019] [Indexed: 12/17/2022] Open
Abstract
Telomeric repeats in fungi of the subphylum Saccharomycotina exhibit great inter- and intra-species variability in length and sequence. Such variations challenged telomeric DNA-binding proteins that co-evolved to maintain their functions at telomeres. Here, we compare the extent of co-variations in telomeric repeats, encoded in the telomerase RNAs (TERs), and the repeat-binding proteins from 13 species belonging to the Yarrowia clade. We identified putative TER loci, analyzed their sequence and secondary structure conservation, and predicted functional elements. Moreover, in vivo complementation assays with mutant TERs showed the functional importance of four novel TER substructures. The TER-derived telomeric repeat unit of all species, except for one, is 10 bp long and can be represented as 5′-TTNNNNAGGG-3′, with repeat sequence variations occuring primarily outside the vertebrate telomeric motif 5′-TTAGGG-3′. All species possess a homologue of the Yarrowia lipolytica Tay1 protein, YlTay1p. In vitro, YlTay1p displays comparable DNA-binding affinity to all repeat variants, suggesting a conserved role among these species. Taken together, these results add significant insights into the co-evolution of TERs, telomeric repeats and telomere-binding proteins in yeasts.
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Affiliation(s)
- Filip Červenák
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia
| | - Katarína Juríková
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Binyamin Kaffe
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem, 91904, Israel
| | - Areej Khatib
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem, 91904, Israel
| | - Erin Bonnell
- Department of Microbiology and Infectiology, RNA Group, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Martina Sopkovičová
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia
| | - Raymund J Wellinger
- Department of Microbiology and Infectiology, RNA Group, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Jozef Nosek
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem, 91904, Israel.
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Ľubomír Tomáška
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia.
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Abstract
The telomere regulator and transcription factor Rap1 is the only telomere protein conserved in yeasts and mammals. Its functional repertoire in budding yeasts is a particularly interesting field for investigation, given the high evolutionary diversity of this group of unicellular organisms. In the methylotrophic thermotolerant species Hansenula polymorpha DL-1 the RAP1 gene is duplicated (HpRAP1A and HpRAP1B). Here, we report the functional characterization of the two paralogues from H. polymorpha DL-1. We uncover distinct (but overlapping) DNA binding preferences of HpRap1A and HpRap1B proteins. We show that only HpRap1B is able to recognize telomeric DNA directly and to protect it from excessive recombination, whereas HpRap1A is associated with subtelomere regions. Furthermore, we identify specific binding sites for both HpRap1A and HpRap1B within promoters of a large number of ribosomal protein genes (RPGs), implicating Rap1 in the control of the RP regulon in H. polymorpha. Our bioinformatic analysis suggests that RAP1 was duplicated early in the evolution of the “methylotrophs” clade, and the two genes evolved independently. Therefore, our characterization of Rap1 paralogues in H. polymorpha may be relevant to other “methylotrophs”, yielding valuable insights into the evolution of budding yeasts.
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Aksenova AY, Mirkin SM. At the Beginning of the End and in the Middle of the Beginning: Structure and Maintenance of Telomeric DNA Repeats and Interstitial Telomeric Sequences. Genes (Basel) 2019; 10:genes10020118. [PMID: 30764567 PMCID: PMC6410037 DOI: 10.3390/genes10020118] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Tandem DNA repeats derived from the ancestral (TTAGGG)n run were first detected at chromosome ends of the majority of living organisms, hence the name telomeric DNA repeats. Subsequently, it has become clear that telomeric motifs are also present within chromosomes, and they were suitably called interstitial telomeric sequences (ITSs). It is well known that telomeric DNA repeats play a key role in chromosome stability, preventing end-to-end fusions and precluding the recurrent DNA loss during replication. Recent data suggest that ITSs are also important genomic elements as they confer its karyotype plasticity. In fact, ITSs appeared to be among the most unstable microsatellite sequences as they are highly length polymorphic and can trigger chromosomal fragility and gross chromosomal rearrangements. Importantly, mechanisms responsible for their instability appear to be similar to the mechanisms that maintain the length of genuine telomeres. This review compares the mechanisms of maintenance and dynamic properties of telomeric repeats and ITSs and discusses the implications of these dynamics on genome stability.
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Affiliation(s)
- Anna Y Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
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Abstract
For more than a decade, it has been known that mammalian cells use shelterin to protect chromosome ends. Much progress has been made on the mechanism by which shelterin prevents telomeres from inadvertently activating DNA damage signaling and double-strand break (DSB) repair pathways. Shelterin averts activation of three DNA damage response enzymes [the ataxia-telangiectasia-mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) kinases and poly(ADP-ribose) polymerase 1 (PARP1)], blocks three DSB repair pathways [classical nonhomologous end joining (c-NHEJ), alternative (alt)-NHEJ, and homology-directed repair (HDR)], and prevents hyper-resection at telomeres. For several of these functions, mechanistic insights have emerged. In addition, much has been learned about how shelterin maintains the telomeric 3' overhang, forms and protects the t-loop structure, and promotes replication through telomeres. These studies revealed that shelterin is compartmentalized, with individual subunits dedicated to distinct aspects of the end-protection problem. This review focuses on the current knowledge of shelterin-mediated telomere protection, highlights differences between human and mouse shelterin, and discusses some of the questions that remain.
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Affiliation(s)
- Titia de Lange
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY 10065, USA;
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34
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Fontana GA, Reinert JK, Thomä NH, Rass U. Shepherding DNA ends: Rif1 protects telomeres and chromosome breaks. MICROBIAL CELL 2018; 5:327-343. [PMID: 29992129 PMCID: PMC6035837 DOI: 10.15698/mic2018.07.639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells have evolved conserved mechanisms to protect DNA ends, such as those at the termini of linear chromosomes, or those at DNA double-strand breaks (DSBs). In eukaryotes, DNA ends at chromosomal termini are packaged into proteinaceous structures called telomeres. Telomeres protect chromosome ends from erosion, inadvertent activation of the cellular DNA damage response (DDR), and telomere fusion. In contrast, cells must respond to damage-induced DNA ends at DSBs by harnessing the DDR to restore chromosome integrity, avoiding genome instability and disease. Intriguingly, Rif1 (Rap1-interacting factor 1) has been implicated in telomere homeostasis as well as DSB repair. The protein was first identified in Saccharomyces cerevisiae as being part of the proteinaceous telosome. In mammals, RIF1 is not associated with intact telomeres, but was found at chromosome breaks, where RIF1 has emerged as a key mediator of pathway choice between the two evolutionary conserved DSB repair pathways of non-homologous end-joining (NHEJ) and homologous recombination (HR). While this functional dichotomy has long been a puzzle, recent findings link yeast Rif1 not only to telomeres, but also to DSB repair, and mechanistic parallels likely exist. In this review, we will provide an overview of the actions of Rif1 at DNA ends and explore how exclusion of end-processing factors might be the underlying principle allowing Rif1 to fulfill diverse biological roles at telomeres and chromosome breaks.
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Affiliation(s)
- Gabriele A Fontana
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Julia K Reinert
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.,University of Basel, Petersplatz 10, CH-4003 Basel, Switzerland
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Ulrich Rass
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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35
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Structure of the fission yeast S. pombe telomeric Tpz1-Poz1-Rap1 complex. Cell Res 2017; 27:1503-1520. [PMID: 29160296 DOI: 10.1038/cr.2017.145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/29/2017] [Accepted: 10/19/2017] [Indexed: 01/01/2023] Open
Abstract
Telomeric shelterin complex caps chromosome ends and plays a crucial role in telomere maintenance and protection. In the fission yeast Schizosaccharomyces pombe, shelterin is composed of telomeric single- and double-stranded DNA-binding protein subcomplexes Pot1-Tpz1 and Taz1-Rap1, which are bridged by their interacting protein Poz1. However, the structure of Poz1 and how Poz1 functions as an interaction hub in the shelterin complex remain unclear. Here we report the crystal structure of Poz1 in complex with Poz1-binding motifs of Tpz1 and Rap1. The crystal structure shows that Poz1 employs two different binding surfaces to interact with Tpz1 and Rap1. Unexpectedly, the structure also reveals that Poz1 adopts a dimeric conformation. Mutational analyses suggest that proper interactions between Tpz1, Poz1, and Rap1 in the shelterin core complex are required for telomere length homeostasis and heterochromatin structure maintenance at telomeres. Structural resemblance between Poz1 and the TRFH domains of other shelterin proteins in fission yeast and humans suggests a model for the evolution of shelterin proteins.
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36
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Baek IJ, Moss DS, Lustig AJ. The mre11 A470 alleles influence the hereditability and the segregation of telosomes in Saccharomyces cerevisiae. PLoS One 2017; 12:e0183549. [PMID: 28886051 PMCID: PMC5590830 DOI: 10.1371/journal.pone.0183549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 08/07/2017] [Indexed: 11/18/2022] Open
Abstract
Telomeres, the nucleoprotein complexes at the termini of linear chromosomes, are essential for the processes of end replication, end protection, and chromatin segregation. The Mre11 complex is involved in multiple cellular roles in DNA repair and structure in the regulation and function of telomere size homeostasis. In this study, we characterize yeast telomere chromatin structure, phenotypic heritability, and chromatin segregation in both wild-type [MRE11] and A470 motif alleles. MRE11 strains confer a telomere size of 300 base pairs of G+T irregular simple sequence repeats. This DNA and a portion of subtelomeric DNA is embedded in a telosome: a MNase-resistant non-nucleosomal particle. Chromatin immunoprecipitation shows a three to four-fold lower occupancy of Mre11A470T proteins than wild-type proteins in telosomes. Telosomes containing the Mre11A470T protein confer a greater resistance to MNase digestion than wild-type telosomes. The integration of a wild-type MRE11 allele into an ectopic locus in the genome of an mre11A470T mutant and the introduction of an mre11A470T allele at an ectopic site in a wild-type strain lead to unexpectedly differing results. In each case, the replicated sister chromatids inherit telosomes containing only the protein encoded by the genomic mre11 locus, even in the presence of protein encoded by the opposing ectopic allele. We hypothesize that the telosome segregates by a conservative mechanism. These data support a mechanism for the linkage between sister chromatid replication and maintenance of either identical mutant or identical wild-type telosomes after replication of sister chromatids. These data suggest the presence of an active mechanism for chromatin segregation in yeast.
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Affiliation(s)
- In-Joon Baek
- Department of Biochemistry and Molecular Biology, Tulane University Medical Center, New Orleans, Louisiana, United States of America
| | - Daniel S. Moss
- Department of Biochemistry and Molecular Biology, Tulane University Medical Center, New Orleans, Louisiana, United States of America
| | - Arthur J. Lustig
- Department of Biochemistry and Molecular Biology, Tulane University Medical Center, New Orleans, Louisiana, United States of America
- * E-mail:
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Cai Y, Kandula V, Kosuru R, Ye X, Irwin MG, Xia Z. Decoding telomere protein Rap1: Its telomeric and nontelomeric functions and potential implications in diabetic cardiomyopathy. Cell Cycle 2017; 16:1765-1773. [PMID: 28853973 PMCID: PMC5628636 DOI: 10.1080/15384101.2017.1371886] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mammalian Rap1, the most conserved telomere-interacting protein, beyond its role within nucleus for the maintenance of telomeric functions, is also well known for its pleiotropic functions in various physiological and pathological conditions associated with metabolism, inflammation and oxidative stress. For all these, nowadays Rap1 is the subject of critical investigations aimed to unveil its molecular signaling pathways and to scrutinize the applicability of its modulation as a promising therapeutic strategy with clinical relevance. However, the underlying intimate mechanisms of Rap1 are not extensively studied, but any modulation of this protein level has been associated with pathologies like inflammation, oxidative stress and deregulated metabolism. This is considerably important in light of the recent discovery of Rap1 modulation in diseases like cancer and cardiac metabolic disorders. In this review, we focus on both the telomeric and nontelomeric functions of Rap1 and its modulation in various health risks, especially on the heart.
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Affiliation(s)
- Yin Cai
- a Department of Anaesthesiology , The University of Hong Kong , Hong Kong SAR , China
| | - Vidya Kandula
- a Department of Anaesthesiology , The University of Hong Kong , Hong Kong SAR , China
| | - Ramoji Kosuru
- a Department of Anaesthesiology , The University of Hong Kong , Hong Kong SAR , China
| | - Xiaodong Ye
- a Department of Anaesthesiology , The University of Hong Kong , Hong Kong SAR , China
| | - Michael G Irwin
- a Department of Anaesthesiology , The University of Hong Kong , Hong Kong SAR , China
| | - Zhengyuan Xia
- a Department of Anaesthesiology , The University of Hong Kong , Hong Kong SAR , China
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38
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Zhang J, Liu B. PSFM-DBT: Identifying DNA-Binding Proteins by Combing Position Specific Frequency Matrix and Distance-Bigram Transformation. Int J Mol Sci 2017; 18:ijms18091856. [PMID: 28841194 PMCID: PMC5618505 DOI: 10.3390/ijms18091856] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/19/2017] [Accepted: 08/22/2017] [Indexed: 12/30/2022] Open
Abstract
DNA-binding proteins play crucial roles in various biological processes, such as DNA replication and repair, transcriptional regulation and many other biological activities associated with DNA. Experimental recognition techniques for DNA-binding proteins identification are both time consuming and expensive. Effective methods for identifying these proteins only based on protein sequences are highly required. The key for sequence-based methods is to effectively represent protein sequences. It has been reported by various previous studies that evolutionary information is crucial for DNA-binding protein identification. In this study, we employed four methods to extract the evolutionary information from Position Specific Frequency Matrix (PSFM), including Residue Probing Transformation (RPT), Evolutionary Difference Transformation (EDT), Distance-Bigram Transformation (DBT), and Trigram Transformation (TT). The PSFMs were converted into fixed length feature vectors by these four methods, and then respectively combined with Support Vector Machines (SVMs); four predictors for identifying these proteins were constructed, including PSFM-RPT, PSFM-EDT, PSFM-DBT, and PSFM-TT. Experimental results on a widely used benchmark dataset PDB1075 and an independent dataset PDB186 showed that these four methods achieved state-of-the-art-performance, and PSFM-DBT outperformed other existing methods in this field. For practical applications, a user-friendly webserver of PSFM-DBT was established, which is available at http://bioinformatics.hitsz.edu.cn/PSFM-DBT/.
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Affiliation(s)
- Jun Zhang
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China.
| | - Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China.
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39
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Rap1 and Cdc13 have complementary roles in preventing exonucleolytic degradation of telomere 5' ends. Sci Rep 2017; 7:8729. [PMID: 28821750 PMCID: PMC5562816 DOI: 10.1038/s41598-017-08663-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/11/2017] [Indexed: 11/23/2022] Open
Abstract
Telomere DNA ends with a single-stranded 3′ overhang. Long 3′ overhangs may cause aberrant DNA damage responses and accelerate telomere attrition, which is associated with cancer and aging, respectively. Genetic studies have indicated several important players in preventing 5′ end hyper-resection, yet detailed knowledge about the molecular mechanism in which they act is still lacking. Here, we use an in vitro DNA 5′ end protection assay, to study how N. castellii Cdc13 and Rap1 protect against 5′ exonucleolytic degradation by λ-exonuclease. The homogeneous telomeric repeat sequence of N. castellii allows us to study their protection ability at exact binding sites relative to the 5′ end. We find efficient protection by both Cdc13 and Rap1 when bound close to the 5′ end. Notably, Rap1 provides protection when binding dsDNA at a distance from the 5′ end. The DNA binding domain of Rap1 is sufficient for 5′ end protection, and its wrapping loop region is essential. Intriguingly, Rap1 facilitates protection also when its binding site contains 2 nt of ssDNA, thus spanning across the ds-ss junction. These results highlight a role of Rap1 in 5′ end protection and indicate that Cdc13 and Rap1 have complementary roles in maintaining proper 3′ overhang length.
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40
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Červenák F, Juríková K, Sepšiová R, Neboháčová M, Nosek J, Tomáška L. Double-stranded telomeric DNA binding proteins: Diversity matters. Cell Cycle 2017; 16:1568-1577. [PMID: 28749196 DOI: 10.1080/15384101.2017.1356511] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Telomeric sequences constitute only a small fraction of the whole genome yet they are crucial for ensuring genomic stability. This function is in large part mediated by protein complexes recruited to telomeric sequences by specific telomere-binding proteins (TBPs). Although the principal tasks of nuclear telomeres are the same in all eukaryotes, TBPs in various taxa exhibit a surprising diversity indicating their distinct evolutionary origin. This diversity is especially pronounced in ascomycetous yeasts where they must have co-evolved with rapidly diversifying sequences of telomeric repeats. In this article we (i) provide a historical overview of the discoveries leading to the current list of TBPs binding to double-stranded (ds) regions of telomeres, (ii) describe examples of dsTBPs highlighting their diversity in even closely related species, and (iii) speculate about possible evolutionary trajectories leading to a long list of various dsTBPs fulfilling the same general role(s) in their own unique ways.
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Affiliation(s)
- Filip Červenák
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Katarína Juríková
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Regina Sepšiová
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Martina Neboháčová
- b Department of Biochemistry , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Jozef Nosek
- b Department of Biochemistry , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - L'ubomír Tomáška
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
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41
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Mattarocci S, Reinert JK, Bunker RD, Fontana GA, Shi T, Klein D, Cavadini S, Faty M, Shyian M, Hafner L, Shore D, Thomä NH, Rass U. Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends. Nat Struct Mol Biol 2017; 24:588-595. [PMID: 28604726 DOI: 10.1038/nsmb.3420] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/09/2017] [Indexed: 12/29/2022]
Abstract
In yeast, Rif1 is part of the telosome, where it inhibits telomerase and checkpoint signaling at chromosome ends. In mammalian cells, Rif1 is not telomeric, but it suppresses DNA end resection at chromosomal breaks, promoting repair by nonhomologous end joining (NHEJ). Here, we describe crystal structures for the uncharacterized and conserved ∼125-kDa N-terminal domain of Rif1 from Saccharomyces cerevisiae (Rif1-NTD), revealing an α-helical fold shaped like a shepherd's crook. We identify a high-affinity DNA-binding site in the Rif1-NTD that fully encases DNA as a head-to-tail dimer. Engagement of the Rif1-NTD with telomeres proved essential for checkpoint control and telomere length regulation. Unexpectedly, Rif1-NTD also promoted NHEJ at DNA breaks in yeast, revealing a conserved role of Rif1 in DNA repair. We propose that tight associations between the Rif1-NTD and DNA gate access of processing factors to DNA ends, enabling Rif1 to mediate diverse telomere maintenance and DNA repair functions.
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Affiliation(s)
- Stefano Mattarocci
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Julia K Reinert
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Gabriele A Fontana
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Tianlai Shi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Dominique Klein
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mahamadou Faty
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Maksym Shyian
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Lukas Hafner
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ulrich Rass
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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42
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Johnson AN, Weil PA. Identification of a transcriptional activation domain in yeast repressor activator protein 1 (Rap1) using an altered DNA-binding specificity variant. J Biol Chem 2017; 292:5705-5723. [PMID: 28196871 PMCID: PMC5392566 DOI: 10.1074/jbc.m117.779181] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/13/2017] [Indexed: 01/06/2023] Open
Abstract
Repressor activator protein 1 (Rap1) performs multiple vital cellular functions in the budding yeast Saccharomyces cerevisiae These include regulation of telomere length, transcriptional repression of both telomere-proximal genes and the silent mating type loci, and transcriptional activation of hundreds of mRNA-encoding genes, including the highly transcribed ribosomal protein- and glycolytic enzyme-encoding genes. Studies of the contributions of Rap1 to telomere length regulation and transcriptional repression have yielded significant mechanistic insights. However, the mechanism of Rap1 transcriptional activation remains poorly understood because Rap1 is encoded by a single copy essential gene and is involved in many disparate and essential cellular functions, preventing easy interpretation of attempts to directly dissect Rap1 structure-function relationships. Moreover, conflicting reports on the ability of Rap1-heterologous DNA-binding domain fusion proteins to serve as chimeric transcriptional activators challenge use of this approach to study Rap1. Described here is the development of an altered DNA-binding specificity variant of Rap1 (Rap1AS). We used Rap1AS to map and characterize a 41-amino acid activation domain (AD) within the Rap1 C terminus. We found that this AD is required for transcription of both chimeric reporter genes and authentic chromosomal Rap1 enhancer-containing target genes. Finally, as predicted for a bona fide AD, mutation of this newly identified AD reduced the efficiency of Rap1 binding to a known transcriptional coactivator TFIID-binding target, Taf5. In summary, we show here that Rap1 contains an AD required for Rap1-dependent gene transcription. The Rap1AS variant will likely also be useful for studies of the functions of Rap1 in other biological pathways.
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Affiliation(s)
- Amanda N Johnson
- From the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - P Anthony Weil
- From the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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43
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Duan YM, Zhou BO, Peng J, Tong XJ, Zhang QD, Zhou JQ. Molecular dynamics of de novo telomere heterochromatin formation in budding yeast. J Genet Genomics 2016; 43:451-65. [DOI: 10.1016/j.jgg.2016.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/09/2016] [Accepted: 03/17/2016] [Indexed: 11/26/2022]
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44
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Abstract
Abstract The i-motif is an intercalated structure formed by association in a head to tail orientation of two parallel duplexes whose strands are held together by hemiprotonated C·C(+) pairs. The i-motif may be formed by a single strand containing four cytidine repeats, by association of two strands containing two cytidine repeats or by four strands containing a single cytidine stretch. The repeated C-rich sequences of centromeric and telomeric regions can potentially fold into an intramolecular i-motif. We have investigated by NMR spectroscopy the structure of d(CCCTA(2)CCCTA(2)CCCTA(2)CCCT), a fragment of the vertebrate telomere. It includes an i-motif core of six intercalated C·C(+) pairs. At one end (the "top"), the central TA(2) linker loops across one of the narrow grooves, and the core is extended by base stacking in the loop. At the bottom, where the two other TA(2) linkers loop across the wide grooves, the NMR spectra reveal motions in the microsecond to millisecond scale. The pseudo-symmetry of the structure, which results in degenerate spectra and poor resolution, was broken by appropriate substitution of T by U and of C by 5-methylcytidine (5mC). This allowed us to solve the structure of d(CCCTA(2)5mCCCTA(2)CCCUA(2)CCCT). The motion is restricted to a flip of A18 around the glycosidic bond. Returning to the pseudo-symmetrical sequence, we find that each of the bottom loops switches between the structures of the first and third loops of the non-symmetrical sequence. We also analyzed the effects of the loop sequence and of the length of the C-stretches on the topology and stability of the intramolecular i-motif structure.
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Affiliation(s)
- A T Phan
- a Groupe de Biophysique de l'Ecole Polytechnique et de l'UMR 7643 du CNRS , 91128 , Palaiseau , France
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45
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Karamychev VN, Panyutin IG, Neumann RD, Zhurkin VB. DNA and RNA folds in transcription complex as evidenced by iodine-125 radioprobing. J Biomol Struct Dyn 2016; 17 Suppl 1:155-67. [PMID: 22607419 DOI: 10.1080/07391102.2000.10506616] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Folding of the DNA and RNA strands in an arrested T7 RNA polymerase (RNAP) transcription complex was studied by radioprobing, a novel method based on an analysis of the strand breaks produced by decay of the iodine-125 incorporated at the C5 position of cytosine. (125)I-labeled cytosines were incorporated into transcripts at different positions relative to the site of the arrest. The intensities of the DNA breaks inversely correlate with the distances from the (125)I decay site, so the radioprobing data provide information about the spatial RNA/DNA folding during transcription. We found that the yield of DNA strand breaks is significantly higher in the template than the non-template strand. This is consistent with local opening of the DNA duplex and formation of a hybrid between RNA and the template DNA strand. Our data demonstrate that the RNA-DNA hybrid has a nonuni form A-like structure. When the (125)I is incorporatedseven nucleotides from the active center of RNAP, the yield of strand breaks is substantially lower than if (125)I is positioned at the ends of the hybrid. Consequently, the DNA and RNA strands are located closer to each other at the ends of the hybrid and somehow separated in the middle. Surprisingly, the (125)I-induced breaks were detected in both DNA strands upstream from the transcription "bubble" indicating that DNA and RNA are closely associated outside the RNAP cleft. Thus, radioprobing data imply that the RNA/DNA fold in the complex with T7 RNAP is more complicated than had been anticipated by the existing models. Based on the present data, we suggest a sterically feasible model explaining how formation of the long RNA-DNA hybrid can result in the initiation-to-elongation switch in the T7 transcription complex. According to this model, the topological linkage between the DNA and RNA strands provides the necessary stability for the elongation complex, while permitting movement of the polymerase along the DNA duplex.
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Affiliation(s)
- V N Karamychev
- a Department of Nuclear Medicine, Warren G. Magnuson Clinical Center
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46
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Koc KN, Singh SP, Stodola JL, Burgers PM, Galletto R. Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase δ. Nucleic Acids Res 2016; 44:3811-9. [PMID: 27001517 PMCID: PMC4856994 DOI: 10.1093/nar/gkw181] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/08/2016] [Indexed: 11/13/2022] Open
Abstract
Using an in vitro reconstituted system in this work we provide direct evidence that the yeast repressor/activator protein 1 (Rap1), tightly bound to its consensus site, forms a strong non-polar barrier for the strand displacement activity of DNA polymerase δ. We propose that relief of inhibition may be mediated by the activity of an accessory helicase. To this end, we show that Pif1, a 5'-3' helicase, not only stimulates the strand displacement activity of Pol δ but it also allows efficient replication through the block, by removing bound Rap1 in front of the polymerase. This stimulatory activity of Pif1 is not limited to the displacement of a single Rap1 molecule; Pif1 also allows Pol δ to carry out DNA synthesis across an array of bound Rap1 molecules that mimics a telomeric DNA-protein assembly. This activity of Pif1 represents a novel function of this helicase during DNA replication.
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Affiliation(s)
- Katrina N Koc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph L Stodola
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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47
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TRF2-RAP1 is required to protect telomeres from engaging in homologous recombination-mediated deletions and fusions. Nat Commun 2016; 7:10881. [PMID: 26941064 PMCID: PMC4785230 DOI: 10.1038/ncomms10881] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/29/2016] [Indexed: 12/27/2022] Open
Abstract
Repressor/activator protein 1 (RAP1) is a highly conserved telomere-interacting protein. Yeast Rap1 protects telomeres from non-homologous end joining (NHEJ), plays important roles in telomere length control and is involved in transcriptional gene regulation. However, a role for mammalian RAP1 in telomere end protection remains controversial. Here we present evidence that mammalian RAP1 is essential to protect telomere from homology directed repair (HDR) of telomeres. RAP1 cooperates with the basic domain of TRF2 (TRF2B) to repress PARP1 and SLX4 localization to telomeres. Without RAP1 and TRF2B, PARP1 and SLX4 HR factors promote rapid telomere resection, resulting in catastrophic telomere loss and the generation of telomere-free chromosome fusions in both mouse and human cells. The RAP1 Myb domain is required to repress both telomere loss and formation of telomere-free fusions. Our results highlight the importance of the RAP1-TRF2 heterodimer in protecting telomeres from inappropriate processing by the HDR pathway. While yeast Rap1 regulates telomere length and protects telomeres from non-homologous end joining, its role in higher eukaryotes is controversial. Here the authors present evidence that in mammals, RAP1 cooperates with TRF2 to prevent homologous recombination-mediated repair of telomeres.
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48
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Ellahi A, Rine J. Evolution and Functional Trajectory of Sir1 in Gene Silencing. Mol Cell Biol 2016; 36:1164-79. [PMID: 26811328 PMCID: PMC4800792 DOI: 10.1128/mcb.01013-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/08/2015] [Accepted: 01/21/2016] [Indexed: 01/28/2023] Open
Abstract
We used the budding yeasts Saccharomyces cerevisiae and Torulaspora delbrueckii to examine the evolution of Sir-based silencing, focusing on Sir1, silencers, the molecular topography of silenced chromatin, and the roles of SIR and RNA interference (RNAi) genes in T. delbrueckii. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) analysis of Sir proteins in T. delbrueckii revealed a different topography of chromatin at the HML and HMR loci than was observed in S. cerevisiae. S. cerevisiae Sir1, enriched at the silencers of HMLα and HMR A: , was absent from telomeres and did not repress subtelomeric genes. In contrast to S. cerevisiae SIR1's partially dispensable role in silencing, the T. delbrueckii SIR1 paralog KOS3 was essential for silencing. KOS3 was also found at telomeres with T. delbrueckii Sir2 (Td-Sir2) and Td-Sir4 and repressed subtelomeric genes. Silencer mapping in T. delbrueckii revealed single silencers at HML and HMR, bound by Td-Kos3, Td-Sir2, and Td-Sir4. The KOS3 gene mapped near HMR, and its expression was regulated by Sir-based silencing, providing feedback regulation of a silencing protein by silencing. In contrast to the prominent role of Sir proteins in silencing, T. delbrueckii RNAi genes AGO1 and DCR1 did not function in heterochromatin formation. These results highlighted the shifting role of silencing genes and the diverse chromatin architectures underlying heterochromatin.
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Affiliation(s)
- Aisha Ellahi
- Department of Molecular and Cell Biology and California Institute of Quantitative Biology, University of California Berkeley, Berkeley, California, USA
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute of Quantitative Biology, University of California Berkeley, Berkeley, California, USA
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49
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Goto GH, Zencir S, Hirano Y, Ogi H, Ivessa A, Sugimoto K. Binding of Multiple Rap1 Proteins Stimulates Chromosome Breakage Induction during DNA Replication. PLoS Genet 2015; 11:e1005283. [PMID: 26263073 PMCID: PMC4532487 DOI: 10.1371/journal.pgen.1005283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 05/14/2015] [Indexed: 02/07/2023] Open
Abstract
Telomeres, the ends of linear eukaryotic chromosomes, have a specialized chromatin structure that provides a stable chromosomal terminus. In budding yeast Rap1 protein binds to telomeric TG repeat and negatively regulates telomere length. Here we show that binding of multiple Rap1 proteins stimulates DNA double-stranded break (DSB) induction at both telomeric and non-telomeric regions. Consistent with the role of DSB induction, Rap1 stimulates nearby recombination events in a dosage-dependent manner. Rap1 recruits Rif1 and Rif2 to telomeres, but neither Rif1 nor Rif2 is required for DSB induction. Rap1-mediated DSB induction involves replication fork progression but inactivation of checkpoint kinase Mec1 does not affect DSB induction. Rap1 tethering shortens artificially elongated telomeres in parallel with telomerase inhibition, and this telomere shortening does not require homologous recombination. These results suggest that Rap1 contributes to telomere homeostasis by promoting chromosome breakage. Telomere length is maintained primarily through equilibrium between telomerase-mediated lengthening and the loss of telomeric sequence through the end-replication problem. In budding yeast Rap1 protein binds to telomeric TG repeat and negatively regulates telomerase recruitment in a dosage-dependent manner. In this paper we provide evidence suggesting an alternative Rap1-dependent telomere shortening mechanism in which binding of multiple Rap1 proteins mediates DNA break induction during DNA replication. This process does not involve recombination events; therefore, it is distinct from loop-mediated telomere trimming.
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Affiliation(s)
- Greicy H. Goto
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Sevil Zencir
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Yukinori Hirano
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Hiroo Ogi
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Andreas Ivessa
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
- * E-mail:
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Steinberg-Neifach O, Lue NF. Telomere DNA recognition in Saccharomycotina yeast: potential lessons for the co-evolution of ssDNA and dsDNA-binding proteins and their target sites. Front Genet 2015; 6:162. [PMID: 25983743 PMCID: PMC4416457 DOI: 10.3389/fgene.2015.00162] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/10/2015] [Indexed: 01/22/2023] Open
Abstract
In principle, alterations in the telomere repeat sequence would be expected to disrupt the protective nucleoprotein complexes that confer stability to chromosome ends, and hence relatively rare events in evolution. Indeed, numerous organisms in diverse phyla share a canonical 6 bp telomere repeat unit (5'-TTAGGG-3'/5'-CCCTAA-3'), suggesting common descent from an ancestor that carries this particular repeat. All the more remarkable, then, are the extraordinarily divergent telomere sequences that populate the Saccharomycotina subphylum of budding yeast. These sequences are distinguished from the canonical telomere repeat in being long, occasionally degenerate, and frequently non-G/C-rich. Despite the divergent telomere repeat sequences, studies to date indicate that the same families of single-strand and double-strand telomere binding proteins (i.e., the Cdc13 and Rap1 families) are responsible for telomere protection in Saccharomycotina yeast. The recognition mechanisms of the protein family members therefore offer an informative paradigm for understanding the co-evolution of DNA-binding proteins and the cognate target sequences. Existing data suggest three potential, inter-related solutions to the DNA recognition problem: (i) duplication of the recognition protein and functional modification; (ii) combinatorial recognition of target site; and (iii) flexibility of the recognition surfaces of the DNA-binding proteins to adopt alternative conformations. Evidence in support of these solutions and the relevance of these solutions to other DNA-protein regulatory systems are discussed.
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Affiliation(s)
- Olga Steinberg-Neifach
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Medical College, Cornell University , New York, NY, USA ; Hostos Community College, City University of New York , Bronx, NY, USA
| | - Neal F Lue
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Medical College, Cornell University , New York, NY, USA
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