1
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Joo SY, Sung K, Lee H. Balancing act: BRCA2's elaborate management of telomere replication through control of G-quadruplex dynamicity. Bioessays 2024; 46:e2300229. [PMID: 38922965 DOI: 10.1002/bies.202300229] [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: 11/29/2023] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
In billion years of evolution, eukaryotes preserved the chromosome ends with arrays of guanine repeats surrounded by thymines and adenines, which can form stacks of four-stranded planar structure known as G-quadruplex (G4). The rationale behind the evolutionary conservation of the G4 structure at the telomere remained elusive. Our recent study has shed light on this matter by revealing that telomere G4 undergoes oscillation between at least two distinct folded conformations. Additionally, tumor suppressor BRCA2 exhibits a unique mode of interaction with telomere G4. To elaborate, BRCA2 directly interacts with G-triplex (G3)-derived intermediates that form during the interconversion of the two different G4 states. In doing so, BRCA2 remodels the G4, facilitating the restart of stalled replication forks. In this review, we succinctly summarize the findings regarding the dynamicity of telomeric G4, emphasize its importance in maintaining telomere replication homeostasis, and the physiological consequences of losing G4 dynamicity at the telomere.
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Affiliation(s)
- So Young Joo
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
| | - Keewon Sung
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, South Korea
| | - Hyunsook Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
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2
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JCA. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. Nucleic Acids Res 2024; 52:4702-4722. [PMID: 38572746 PMCID: PMC11077067 DOI: 10.1093/nar/gkae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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3
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JC. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558871. [PMID: 37790366 PMCID: PMC10542165 DOI: 10.1101/2023.09.21.558871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R. Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L. Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J. Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C.A. Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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4
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Olson CL, Wuttke DS. Guardians of the Genome: How the Single-Stranded DNA-Binding Proteins RPA and CST Facilitate Telomere Replication. Biomolecules 2024; 14:263. [PMID: 38540683 PMCID: PMC10968030 DOI: 10.3390/biom14030263] [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: 12/21/2023] [Revised: 02/02/2024] [Accepted: 02/20/2024] [Indexed: 04/26/2024] Open
Abstract
Telomeres act as the protective caps of eukaryotic linear chromosomes; thus, proper telomere maintenance is crucial for genome stability. Successful telomere replication is a cornerstone of telomere length regulation, but this process can be fraught due to the many intrinsic challenges telomeres pose to the replication machinery. In addition to the famous "end replication" problem due to the discontinuous nature of lagging strand synthesis, telomeres require various telomere-specific steps for maintaining the proper 3' overhang length. Bulk telomere replication also encounters its own difficulties as telomeres are prone to various forms of replication roadblocks. These roadblocks can result in an increase in replication stress that can cause replication forks to slow, stall, or become reversed. Ultimately, this leads to excess single-stranded DNA (ssDNA) that needs to be managed and protected for replication to continue and to prevent DNA damage and genome instability. RPA and CST are single-stranded DNA-binding protein complexes that play key roles in performing this task and help stabilize stalled forks for continued replication. The interplay between RPA and CST, their functions at telomeres during replication, and their specialized features for helping overcome replication stress at telomeres are the focus of this review.
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Affiliation(s)
- Conner L. Olson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
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5
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Ling X, Yao Y, Ding L, Ma J. The mechanism of UP1 binding and unfolding of human telomeric DNA G-quadruplex. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194985. [PMID: 37717939 DOI: 10.1016/j.bbagrm.2023.194985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
The human telomere contains multiple copies of the DNA sequence d(TTAGGG) which can fold into higher order intramolecular G-quadruplexes and regulate the maintenance of telomere length and chromosomal integrity. The nucleic acid binding protein heteronuclear ribonucleoprotein A1 (hnRNP A1) and its N-terminus proteolytic product UP1 have been shown to efficiently bind and unfold telomeric DNA G-quadruplex. However, the understanding of the molecular mechanism of the UP1 binding and unfolding telomeric G-quadruplexes is still limited. Here, we performed biochemical and biophysical characterizations of UP1 binding and unfolding of human telomeric DNA G-quadruplex d[AGGG(TTAGGG)3], and in combination of systematic site-direct mutagenesis of two tandem RNA recognition motifs (RRMs) in UP1, revealed that RRM1 is responsible for initial binding and unfolding, whereas RRM2 assists RRM1 to complete the unfolding of G-quadruplex. Isothermal titration calorimetry (ITC) and circular dichroism (CD) studies of the interactions between UP1 and DNA G-quadruplex variants indicate that the "TAG" binding motif in Loop2 of telomeric G-quadruplex is critical for UP1 recognition and G-quadruplex unfolding initiation. Together we depict a model for molecular mechanism of hnRNP A1 (UP1) binding and unfolding of the human telomeric DNA G-quadruplex.
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Affiliation(s)
- Xiaobin Ling
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuqi Yao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lei Ding
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States of America
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.
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6
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Sato K, Knipscheer P. G-quadruplex resolution: From molecular mechanisms to physiological relevance. DNA Repair (Amst) 2023; 130:103552. [PMID: 37572578 DOI: 10.1016/j.dnarep.2023.103552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Guanine-rich DNA sequences can fold into stable four-stranded structures called G-quadruplexes or G4s. Research in the past decade demonstrated that G4 structures are widespread in the genome and prevalent in regulatory regions of actively transcribed genes. The formation of G4s has been tightly linked to important biological processes including regulation of gene expression and genome maintenance. However, they can also pose a serious threat to genome integrity especially by impeding DNA replication, and G4-associated somatic mutations have been found accumulated in the cancer genomes. Specialised DNA helicases and single stranded DNA binding proteins that can resolve G4 structures play a crucial role in preventing genome instability. The large variety of G4 unfolding proteins suggest the presence of multiple G4 resolution mechanisms in cells. Recently, there has been considerable progress in our detailed understanding of how G4s are resolved, especially during DNA replication. In this review, we first discuss the current knowledge of the genomic G4 landscapes and the impact of G4 structures on DNA replication and genome integrity. We then describe the recent progress on the mechanisms that resolve G4 structures and their physiological relevance. Finally, we discuss therapeutic opportunities to target G4 structures.
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Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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7
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Olson CL, Barbour AT, Wieser TA, Wuttke DS. RPA engages telomeric G-quadruplexes more effectively than CST. Nucleic Acids Res 2023; 51:5073-5086. [PMID: 37140062 PMCID: PMC10250233 DOI: 10.1093/nar/gkad315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/11/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
G-quadruplexes (G4s) are a set of stable secondary structures that form within guanine-rich regions of single-stranded nucleic acids that pose challenges for DNA maintenance. The G-rich DNA sequence at telomeres has a propensity to form G4s of various topologies. The human protein complexes Replication Protein A (RPA) and CTC1-STN1-TEN1 (CST) are implicated in managing G4s at telomeres, leading to DNA unfolding and allowing telomere replication to proceed. Here, we use fluorescence anisotropy equilibrium binding measurements to determine the ability of these proteins to bind various telomeric G4s. We find that the ability of CST to specifically bind G-rich ssDNA is substantially inhibited by the presence of G4s. In contrast, RPA tightly binds telomeric G4s, showing negligible changes in affinity for G4 structure compared to linear ssDNAs. Using a mutagenesis strategy, we found that RPA DNA-binding domains work together for G4 binding, and simultaneous disruption of these domains reduces the affinity of RPA for G4 ssDNA. The relative inability of CST to disrupt G4s, combined with the greater cellular abundance of RPA, suggests that RPA could act as a primary protein complex responsible for resolving G4s at telomeres.
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Affiliation(s)
- Conner L Olson
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Alexandra T Barbour
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Thomas A Wieser
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
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8
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Zade NH, Khattar E. POT1 mutations cause differential effects on telomere length leading to opposing disease phenotypes. J Cell Physiol 2023; 238:1237-1255. [PMID: 37183325 DOI: 10.1002/jcp.31034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
The protection of telomere protein (POT1) is a telomere-binding protein and is an essential component of the six-membered shelterin complex, which is associated with the telomeres. POT1 directly binds to the 3' single-stranded telomeric overhang and prevents the activation of DNA damage response at telomeres thus preventing the telomere-telomere fusions and genomic instability. POT1 also plays a pivotal role in maintaining telomere length by regulating telomerase-mediated telomere elongation. Mutations in POT1 proteins result in three different telomere phenotypes, which include long, short, or aberrant telomere length. Long telomeres predispose individuals to cancer, while short or aberrant telomere phenotypes result in pro-aging diseases referred to as telomeropathies. Here, we review the function of POT1 proteins in telomere length hemostasis and how the spectrum of mutations reported in POT1 can be segregated toward developing very distinct disease phenotypes of cancer and telomeropathies.
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Affiliation(s)
- Nikita Harish Zade
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
| | - Ekta Khattar
- Sunandan Divatia School of Science, SVKM's NMIMS (Deemed to be) University, Mumbai, India
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9
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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10
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Shiekh S, Jack A, Saurabh A, Mustafa G, Kodikara S, Gyawali P, Hoque M, Pressé S, Yildiz A, Balci H. Shelterin reduces the accessibility of telomeric overhangs. Nucleic Acids Res 2022; 50:12885-12895. [PMID: 36511858 PMCID: PMC9825182 DOI: 10.1093/nar/gkac1176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/25/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
Telomeres terminate with a 50-300 bases long single-stranded G-rich overhang, which can be misrecognized as a DNA damage repair site. Shelterin plays critical roles in maintaining and protecting telomere ends by regulating access of various physiological agents to telomeric DNA, but the underlying mechanism is not well understood. Here, we measure how shelterin affects the accessibility of long telomeric overhangs by monitoring transient binding events of a short complementary peptide nucleic acid (PNA) probe using FRET-PAINT in vitro. We observed that the POT1 subunit of shelterin reduces the accessibility of the PNA probe by ∼2.5-fold, indicating that POT1 effectively binds to and protects otherwise exposed telomeric sequences. In comparison, a four-component shelterin stabilizes POT1 binding to the overhang by tethering POT1 to the double-stranded telomeric DNA and reduces the accessibility of telomeric overhangs by ∼5-fold. This enhanced protection suggests shelterin restructures the junction between single and double-stranded telomere, which is otherwise the most accessible part of the telomeric overhang.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Amanda Jack
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Ayush Saurabh
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Mohammed Enamul Hoque
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Science, Arizona State University, Tempe, AZ 85287, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Physics Department, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
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11
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Gao J, Pickett HA. Targeting telomeres: advances in telomere maintenance mechanism-specific cancer therapies. Nat Rev Cancer 2022; 22:515-532. [PMID: 35790854 DOI: 10.1038/s41568-022-00490-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/31/2022]
Abstract
Cancer cells establish replicative immortality by activating a telomere-maintenance mechanism (TMM), be it telomerase or the alternative lengthening of telomeres (ALT) pathway. Targeting telomere maintenance represents an intriguing opportunity to treat the vast majority of all cancer types. Whilst telomerase inhibitors have historically been heralded as promising anticancer agents, the reality has been more challenging, and there are currently no therapeutic options for cancer types that use ALT despite their aggressive nature and poor prognosis. In this Review, we discuss the mechanistic differences between telomere maintenance by telomerase and ALT, the current methods used to detect each mechanism, the utility of these tests for clinical diagnosis, and recent developments in the therapeutic strategies being employed to target both telomerase and ALT. We present notable developments in repurposing established therapeutic agents and new avenues that are emerging to target cancer types according to which TMM they employ. These opportunities extend beyond inhibition of telomere maintenance, by finding and exploiting inherent weaknesses in the telomeres themselves to trigger rapid cellular effects that lead to cell death.
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Affiliation(s)
- Jixuan Gao
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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12
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Kelich J, Aramburu T, van der Vis JJ, Showe L, Kossenkov A, van der Smagt J, Massink M, Schoemaker A, Hennekam E, Veltkamp M, van Moorsel CH, Skordalakes E. Telomere dysfunction implicates POT1 in patients with idiopathic pulmonary fibrosis. J Exp Med 2022; 219:e20211681. [PMID: 35420632 PMCID: PMC9014792 DOI: 10.1084/jem.20211681] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/28/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
Exonic sequencing identified a family with idiopathic pulmonary fibrosis (IPF) containing a previously unreported heterozygous mutation in POT1 p.(L259S). The family displays short telomeres and genetic anticipation. We found that POT1(L259S) is defective in binding the telomeric overhang, nuclear accumulation, negative regulation of telomerase, and lagging strand maintenance. Patient cells containing the mutation display telomere loss, lagging strand defects, telomere-induced DNA damage, and premature senescence with G1 arrest. Our data suggest POT1(L259S) is a pathogenic driver of IPF and provide insights into gene therapy options.
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Affiliation(s)
| | | | - Joanne J. van der Vis
- Department of Pulmonology, Interstitial Lung Disease Center of Excellence, St Antonius Hospital, Nieuwegein, Netherlands
| | | | | | - Jasper van der Smagt
- Department of Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Maarten Massink
- Department of Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Angela Schoemaker
- Department of Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Eric Hennekam
- Department of Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marcel Veltkamp
- Department of Pulmonology, Interstitial Lung Disease Center of Excellence, St Antonius Hospital, Nieuwegein, Netherlands
| | - Coline H.M. van Moorsel
- Department of Pulmonology, Interstitial Lung Disease Center of Excellence, St Antonius Hospital, Nieuwegein, Netherlands
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13
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Shu H, Zhang R, Xiao K, Yang J, Sun X. G-Quadruplex-Binding Proteins: Promising Targets for Drug Design. Biomolecules 2022; 12:biom12050648. [PMID: 35625576 PMCID: PMC9138358 DOI: 10.3390/biom12050648] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical secondary nucleic acid structures. Sequences with the potential to form G4s are abundant in regulatory regions of the genome including telomeres, promoters and 5′ non-coding regions, indicating they fulfill important genome regulatory functions. Generally, G4s perform various biological functions by interacting with proteins. In recent years, an increasing number of G-quadruplex-binding proteins have been identified with biochemical experiments. G4-binding proteins are involved in vital cellular processes such as telomere maintenance, DNA replication, gene transcription, mRNA processing. Therefore, G4-binding proteins are also associated with various human diseases. An intensive study of G4-protein interactions provides an attractive approach for potential therapeutics and these proteins can be considered as drug targets for novel medical treatment. In this review, we present biological functions and structural properties of G4-binding proteins, and discuss how to exploit G4-protein interactions to develop new therapeutic targets.
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Vertecchi E, Rizzo A, Salvati E. Telomere Targeting Approaches in Cancer: Beyond Length Maintenance. Int J Mol Sci 2022; 23:ijms23073784. [PMID: 35409143 PMCID: PMC8998427 DOI: 10.3390/ijms23073784] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/19/2022] Open
Abstract
Telomeres are crucial structures that preserve genome stability. Their progressive erosion over numerous DNA duplications determines the senescence of cells and organisms. As telomere length homeostasis is critical for cancer development, nowadays, telomere maintenance mechanisms are established targets in cancer treatment. Besides telomere elongation, telomere dysfunction impinges on intracellular signaling pathways, in particular DNA damage signaling and repair, affecting cancer cell survival and proliferation. This review summarizes and discusses recent findings in anticancer drug development targeting different “telosome” components.
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Affiliation(s)
- Eleonora Vertecchi
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy, c/o Department of Biology and Biotechnology, Sapienza University of Rome, Via degli Apuli 4, 00185 Rome, Italy;
| | - Angela Rizzo
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy;
| | - Erica Salvati
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy, c/o Department of Biology and Biotechnology, Sapienza University of Rome, Via degli Apuli 4, 00185 Rome, Italy;
- Correspondence:
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15
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Smith EW, Lattmann S, Liu ZB, Ahsan B, Rhodes D. Insights into POT1 structural dynamics revealed by cryo-EM. PLoS One 2022; 17:e0264073. [PMID: 35176105 PMCID: PMC8853558 DOI: 10.1371/journal.pone.0264073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Telomeres are protein-DNA complexes that protect the ends of linear eukaryotic chromosomes. Mammalian telomeric DNA consists of 5′-(TTAGGG)n-3′ double-stranded repeats, followed by up to several hundred bases of a 3′ single-stranded G-rich overhang. The G-rich overhang is bound by the shelterin component POT1 which interacts with TPP1, the component involved in telomerase recruitment. A previously published crystal structure of the POT1 N-terminal half bound to the high affinity telomeric ligand 5′-TTAGGGTTAG-3′ showed that the first six nucleotides, TTAGGG, are bound by the OB1 fold, while the adjacent OB2 binds the last four, TTAG. Here, we report two cryo-EM structures of full-length POT1 bound by the POT1-binding domain of TPP1. The structures differ in the relative orientation of the POT1 OB1 and OB2, suggesting that these two DNA-binding OB folds take up alternative conformations. Supporting DNA binding studies using telomeric ligands in which the OB1 and OB2 binding sites were spaced apart, show that POT1 binds with similar affinities to spaced or contiguous binding sites, suggesting plasticity in DNA binding and a role for the alternative conformations observed. A likely explanation is that the structural flexibility of POT1 enhances binding to the tandemly arranged telomeric repeats and hence increases telomere protection.
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Affiliation(s)
- Emmanuel W. Smith
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Simon Lattmann
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Zhehui Barry Liu
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Bilal Ahsan
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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16
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Liu Y, Zhu X, Wang K, Zhang B, Qiu S. The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans. Front Mol Biosci 2021; 8:783889. [PMID: 34912850 PMCID: PMC8667583 DOI: 10.3389/fmolb.2021.783889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/19/2023] Open
Abstract
G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.
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Affiliation(s)
- Yang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Xinting Zhu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
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17
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Chatain J, Hatem G, Delagoutte E, Riou JF, Alberti P, Saintomé C. Multiple hPOT1-TPP1 cooperatively unfold contiguous telomeric G-quadruplexes proceeding from 3' toward 5', a feature due to a 3'-end binding preference and to structuring of telomeric DNA. Nucleic Acids Res 2021; 49:10735-10746. [PMID: 34534331 PMCID: PMC8501996 DOI: 10.1093/nar/gkab768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 08/04/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Telomeres are DNA repeated sequences that associate with shelterin proteins and protect the ends of eukaryotic chromosomes. Human telomeres are composed of 5'TTAGGG repeats and ends with a 3' single-stranded tail, called G-overhang, that can be specifically bound by the shelterin protein hPOT1 (human Protection of Telomeres 1). In vitro studies have shown that the telomeric G-strand can fold into stable contiguous G-quadruplexes (G4). In the present study we investigated how hPOT1, in complex with its shelterin partner TPP1, binds to telomeric sequences structured into contiguous G4 in potassium solutions. We observed that binding of multiple hPOT1-TPP1 preferentially proceeds from 3' toward 5'. We explain this directionality in terms of two factors: (i) the preference of hPOT1-TPP1 for the binding site situated at the 3' end of a telomeric sequence and (ii) the cooperative binding displayed by hPOT1-TPP1 in potassium. By comparing binding in K+ and in Li+, we demonstrate that this cooperative behaviour does not stem from protein-protein interactions, but from structuring of the telomeric DNA substrate into contiguous G4 in potassium. Our study suggests that POT1-TPP1, in physiological conditions, might preferentially cover the telomeric G-overhang starting from the 3'-end and proceeding toward 5'.
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Affiliation(s)
- Jean Chatain
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Georges Hatem
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Emmanuelle Delagoutte
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Jean-François Riou
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France
| | - Carole Saintomé
- Structure et Instabilité des Génomes, Muséum national d'Histoire naturelle, CNRS, INSERM, 43 rue Cuvier, F-75005 Paris, France.,Sorbonne Université, UFR927, F-75005 Paris, France
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18
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Teng FY, Jiang ZZ, Guo M, Tan XZ, Chen F, Xi XG, Xu Y. G-quadruplex DNA: a novel target for drug design. Cell Mol Life Sci 2021; 78:6557-6583. [PMID: 34459951 PMCID: PMC11072987 DOI: 10.1007/s00018-021-03921-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
G-quadruplex (G4) DNA is a type of quadruple helix structure formed by a continuous guanine-rich DNA sequence. Emerging evidence in recent years authenticated that G4 DNA structures exist both in cell-free and cellular systems, and function in different diseases, especially in various cancers, aging, neurological diseases, and have been considered novel promising targets for drug design. In this review, we summarize the detection method and the structure of G4, highlighting some non-canonical G4 DNA structures, such as G4 with a bulge, a vacancy, or a hairpin. Subsequently, the functions of G4 DNA in physiological processes are discussed, especially their regulation of DNA replication, transcription of disease-related genes (c-MYC, BCL-2, KRAS, c-KIT et al.), telomere maintenance, and epigenetic regulation. Typical G4 ligands that target promoters and telomeres for drug design are also reviewed, including ellipticine derivatives, quinoxaline analogs, telomestatin analogs, berberine derivatives, and CX-5461, which is currently in advanced phase I/II clinical trials for patients with hematologic cancer and BRCA1/2-deficient tumors. Furthermore, since the long-term stable existence of G4 DNA structures could result in genomic instability, we summarized the G4 unfolding mechanisms emerged recently by multiple G4-specific DNA helicases, such as Pif1, RecQ family helicases, FANCJ, and DHX36. This review aims to present a general overview of the field of G-quadruplex DNA that has progressed in recent years and provides potential strategies for drug design and disease treatment.
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Affiliation(s)
- Fang-Yuan Teng
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zong-Zhe Jiang
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiao-Zhen Tan
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Feng Chen
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61, Avenue du Président Wilson, 94235, Cachan, France.
| | - Yong Xu
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
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19
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Glousker G, Lingner J. Challenging endings: How telomeres prevent fragility. Bioessays 2021; 43:e2100157. [PMID: 34436787 DOI: 10.1002/bies.202100157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022]
Abstract
It has become apparent that difficulties to replicate telomeres concern not only the very ends of eukaryotic chromosomes. The challenges already start when the replication fork enters the telomeric repeats. The obstacles encountered consist mainly of noncanonical nucleic acid structures that interfere with replication if not resolved. Replication stress at telomeres promotes the formation of so-called fragile telomeres displaying an abnormal appearance in metaphase chromosomes though their exact molecular nature remains to be elucidated. A substantial number of factors is required to counteract fragility. In this review we promote the hypothesis that telomere fragility is not caused directly by an initial insult during replication but it results as a secondary consequence of DNA repair of damaged replication forks by the homologous DNA recombination machinery. Incomplete DNA synthesis at repair sites or partial chromatin condensation may become apparent as telomere fragility. Fragility and DNA repair during telomere replication emerges as a common phenomenon which exacerbates in multiple disease conditions.
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Affiliation(s)
- Galina Glousker
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Joachim Lingner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
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20
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Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13153755. [PMID: 34359660 PMCID: PMC8345052 DOI: 10.3390/cancers13153755] [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: 05/12/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Multiple myeloma is a hematologic cancer characterized by the accumulation of malignant plasma cells in the bone marrow. It remains a mostly incurable disease due to the inability to overcome refractory disease and drug-resistant relapse. Oncogenic transformation of PC in multiple myeloma is thought to occur within the secondary lymphoid organs. However, the precise molecular events leading to myelomagenesis remain obscure. Here, we identified genes involved in the prevention and the resolution of conflicts between the replication and transcription significantly overexpressed during the plasma cell differentiation process and in multiple myeloma cells. We discussed the potential role of these factors in myelomagenesis and myeloma biology. The specific targeting of these factors might constitute a new therapeutic strategy in multiple myeloma. Abstract Plasma cells (PCs) have an essential role in humoral immune response by secretion of antibodies, and represent the final stage of B lymphocytes differentiation. During this differentiation, the pre-plasmablastic stage is characterized by highly proliferative cells that start to secrete immunoglobulins (Igs). Thus, replication and transcription must be tightly regulated in these cells to avoid transcription/replication conflicts (TRCs), which could increase replication stress and lead to genomic instability. In this review, we analyzed expression of genes involved in TRCs resolution during B to PC differentiation and identified 41 genes significantly overexpressed in the pre-plasmablastic stage. This illustrates the importance of mechanisms required for adequate processing of TRCs during PCs differentiation. Furthermore, we identified that several of these factors were also found overexpressed in purified PCs from patients with multiple myeloma (MM) compared to normal PCs. Malignant PCs produce high levels of Igs concomitantly with cell cycle deregulation. Therefore, increasing the TRCs occurring in MM cells could represent a potent therapeutic strategy for MM patients. Here, we describe the potential roles of TRCs resolution factors in myelomagenesis and discuss the therapeutic interest of targeting the TRCs resolution machinery in MM.
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21
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POT1 stability and binding measured by fluorescence thermal shift assays. PLoS One 2021; 16:e0245675. [PMID: 33784306 PMCID: PMC8009405 DOI: 10.1371/journal.pone.0245675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 11/19/2022] Open
Abstract
The protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 -DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding.
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22
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Monsen RC, Chakravarthy S, Dean WL, Chaires JB, Trent JO. The solution structures of higher-order human telomere G-quadruplex multimers. Nucleic Acids Res 2021; 49:1749-1768. [PMID: 33469644 PMCID: PMC7897503 DOI: 10.1093/nar/gkaa1285] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/21/2020] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Human telomeres contain the repeat DNA sequence 5′-d(TTAGGG), with duplex regions that are several kilobases long terminating in a 3′ single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate models proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5′-d(TTAGGG)n, with n = 8, 12 and 16, fold into multimeric structures containing the maximal number (2, 3 and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of ∼34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.
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Affiliation(s)
- Robert C Monsen
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Jonathan B Chaires
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
| | - John O Trent
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
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23
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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24
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Wu Y, Poulos RC, Reddel RR. Role of POT1 in Human Cancer. Cancers (Basel) 2020; 12:cancers12102739. [PMID: 32987645 PMCID: PMC7598640 DOI: 10.3390/cancers12102739] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/20/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary The segmentation of eukaryotic genomes into discrete linear chromosomes requires processes to solve several major biological problems, including prevention of the chromosome ends being recognized as DNA breaks and compensation for the shortening that occurs when linear DNA is replicated. A specialized set of six proteins, collectively referred to as shelterin, is involved in both of these processes, and mutations in several of these are now known to be involved in cancer. Here, we focus on Protection of Telomeres 1 (POT1), the shelterin protein that appears to be most commonly involved in cancer, and consider the clinical significance of findings about its biological functions and the prevalence of inherited and acquired mutations in the POT1 gene. Abstract Telomere abnormalities facilitate cancer development by contributing to genomic instability and cellular immortalization. The Protection of Telomeres 1 (POT1) protein is an essential subunit of the shelterin telomere binding complex. It directly binds to single-stranded telomeric DNA, protecting chromosomal ends from an inappropriate DNA damage response, and plays a role in telomere length regulation. Alterations of POT1 have been detected in a range of cancers. Here, we review the biological functions of POT1, the prevalence of POT1 germline and somatic mutations across cancer predisposition syndromes and tumor types, and the dysregulation of POT1 expression in cancers. We propose a framework for understanding how POT1 abnormalities may contribute to oncogenesis in different cell types. Finally, we summarize the clinical implications of POT1 alterations in the germline and in cancer, and possible approaches for the development of targeted cancer therapies.
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Affiliation(s)
- Yangxiu Wu
- Cancer Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead NSW 2145, Australia;
- ProCan® Cancer Data Science Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead NSW 2145, Australia;
| | - Rebecca C. Poulos
- ProCan® Cancer Data Science Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead NSW 2145, Australia;
| | - Roger R. Reddel
- Cancer Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead NSW 2145, Australia;
- Correspondence: ; Tel.: +61-2-8865-2901
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25
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Antisense Oligonucleotides Used to Identify Telomeric G-Quadruplexes in Metaphase Chromosomes and Fixed Cells by Fluorescence Lifetime Imaging Microscopy of o-BMVC Foci. Molecules 2020; 25:molecules25184083. [PMID: 32906697 PMCID: PMC7570708 DOI: 10.3390/molecules25184083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 01/01/2023] Open
Abstract
Identification of the existence of G-quadruplex (G4) structure, from a specific G-rich sequence in cells, is critical to the studies of structural biology and drug development. Accumulating evidence supports the existence of G4 structure in vivo. Particularly, time-gated fluorescence lifetime imaging microscopy (FLIM) of a G4 fluorescent probe, 3,6-bis(1-methyl-2-vinylpyridinium) carbazole diiodide (o-BMVC), was used to quantitatively measure the number of G4 foci, not only in different cell lines, but also in tissue biopsy. Here, circular dichroism spectra and polyacrylamide gel electrophoresis assays show that the use of antisense oligonucleotides unfolds their G4 structures in different percentages. Using antisense oligonucleotides, quantitative measurement of the number of o-BMVC foci in time-gated FLIM images provides a method for identifying which G4 motifs form G4 structures in fixed cells. Here, the decrease of the o-BMVC foci number, upon the pretreatment of antisense sequences, (CCCTAA)3CCCTA, in fixed cells and at the end of metaphase chromosomes, allows us to identify the formation of telomeric G4 structures from TTAGGG repeats in fixed cells.
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26
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Bryan TM. G-Quadruplexes at Telomeres: Friend or Foe? Molecules 2020; 25:molecules25163686. [PMID: 32823549 PMCID: PMC7464828 DOI: 10.3390/molecules25163686] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Telomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by either the enzyme telomerase or by recombination-based mechanisms. On the other hand, G-quadruplex formation in telomeric DNA, as elsewhere in the genome, can form an impediment to DNA replication and a source of genome instability. This review summarizes recent evidence for the in vivo existence of G-quadruplexes at telomeres, with a focus on human telomeres, and highlights some of the many unanswered questions regarding the location, form, and functions of these structures.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
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27
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Paudel BP, Moye AL, Abou Assi H, El-Khoury R, Cohen SB, Holien JK, Birrento ML, Samosorn S, Intharapichai K, Tomlinson CG, Teulade-Fichou MP, González C, Beck JL, Damha MJ, van Oijen AM, Bryan TM. A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution. eLife 2020; 9:56428. [PMID: 32723475 PMCID: PMC7426096 DOI: 10.7554/elife.56428] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Telomeric G-quadruplexes (G4) were long believed to form a protective structure at telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this belief, we have previously demonstrated that parallel-stranded conformations of telomeric G4 can be extended by human and ciliate telomerase. However, a mechanistic understanding of the interaction of telomerase with structured DNA remained elusive. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) microscopy and bulk-phase enzymology to propose a mechanism for the resolution and extension of parallel G4 by telomerase. Binding is initiated by the RNA template of telomerase interacting with the G-quadruplex; nucleotide addition then proceeds to the end of the RNA template. It is only through the large conformational change of translocation following synthesis that the G-quadruplex structure is completely unfolded to a linear product. Surprisingly, parallel G4 stabilization with either small molecule ligands or by chemical modification does not always inhibit G4 unfolding and extension by telomerase. These data reveal that telomerase is a parallel G-quadruplex resolvase.
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Affiliation(s)
- Bishnu P Paudel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawara Health and Medical Research Institute, Wollongong, Australia
| | - Aaron Lavel Moye
- Children's Medical Research Institute, University of Sydney, Westmead, Australia
| | - Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, Canada
| | | | - Scott B Cohen
- Children's Medical Research Institute, University of Sydney, Westmead, Australia
| | - Jessica K Holien
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Australia
| | - Monica L Birrento
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawara Health and Medical Research Institute, Wollongong, Australia
| | - Siritron Samosorn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | - Kamthorn Intharapichai
- Department of Biobased Materials Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, Japan
| | | | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, Madrid, Spain
| | - Jennifer L Beck
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawara Health and Medical Research Institute, Wollongong, Australia
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawara Health and Medical Research Institute, Wollongong, Australia
| | - Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, Westmead, Australia
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