Plasmodium falciparum GBP2 is a telomere-associated protein that binds to G-quadruplex DNA and RNA

In the early-diverging protozoan parasite Plasmodium, few telomere-binding proteins have been identified and several are unique. Plasmodium telomeres, like those of most eukaryotes, contain guanine-rich repeats that can form G-quadruplex structures. In model systems, quadruplex-binding drugs can disrupt telomere maintenance and some quadruplex-binding drugs are potent anti-plasmodial agents. Therefore, telomere-interacting and quadruplex-interacting proteins may offer new targets for anti-malarial therapy. Here, we report that P. falciparum GBP2 is such a protein. It was identified via Proteomics of Isolated Chromatin fragments, applied here for the first time in Plasmodium. In vitro, PfGBP2 binds specifically to G-rich telomere repeats in quadruplex form and it can also bind to G-rich RNA. In vivo, PfGBP2 partially colocalises with the known telomeric protein HP1 but is also found in the cytoplasm, probably due to its affinity for RNA. Consistently, its interactome includes numerous RNA-associated proteins. PfGBP2 is evidently a multifunctional DNA/RNA-binding factor in Plasmodium.

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G-quadruplex DNA drives genomic instability and represents a targetable molecular abnormality in ATRX-deficient malignant glioma

10.1101/347542 ◽

2018 ◽

Author(s):

Yuxiang Wang ◽

Jie Yang ◽

Wei Wu ◽

Rachna Shah ◽

Carla Danussi ◽

...

Keyword(s):

Dna Damage ◽

Malignant Glioma ◽

Model Systems ◽

Copy Number Alterations ◽

Molecular Alteration ◽

Quadruplex Dna ◽

G4 Dna ◽

G Quadruplex

AbstractMutational inactivation of ATRX (α-thalassemia mental retardation X-linked) represents a defining molecular alteration in large subsets of malignant glioma. Yet the pathogenic consequences of ATRX deficiency remain unclear, as do tractable mechanisms for its therapeutic targeting. Here we report that ATRX loss in isogenic glioma model systems induces replication stress and DNA damage by way of G-quadruplex (G4) DNA secondary structure. Moreover, these effects are associated with the acquisition of disease-relevant copy number alterations over time. We then demonstrate, both in vitro and in vivo, that ATRX deficiency selectively enhances DNA damage and cell death following chemical G4 stabilization. Finally, we show that G4 stabilization synergizes with other DNA-damaging therapies, including ionizing radiation, in the ATRX-deficient context. Our findings reveal novel pathogenic mechanisms driven by ATRX deficiency in glioma, while also pointing to tangible strategies for drug development.

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G-quadruplex–R-loop interactions and the mechanism of anticancer G-quadruplex binders

Nucleic Acids Research ◽

10.1093/nar/gkaa944 ◽

2020 ◽

Vol 48 (21) ◽

pp. 11942-11957

Author(s):

Giulia Miglietta ◽

Marco Russo ◽

Giovanni Capranico

Keyword(s):

Selective Inhibition ◽

Telomere Maintenance ◽

Published Data ◽

Gene Promoters ◽

Untranslated Exon ◽

G Quadruplex ◽

Functional Consequences ◽

Hoogsteen Hydrogen Bonds

Abstract Genomic DNA and cellular RNAs can form a variety of non-B secondary structures, including G-quadruplex (G4) and R-loops. G4s are constituted by stacked guanine tetrads held together by Hoogsteen hydrogen bonds and can form at key regulatory sites of eukaryote genomes and transcripts, including gene promoters, untranslated exon regions and telomeres. R-loops are 3-stranded structures wherein the two strands of a DNA duplex are melted and one of them is annealed to an RNA. Specific G4 binders are intensively investigated to discover new effective anticancer drugs based on a common rationale, i.e.: the selective inhibition of oncogene expression or specific impairment of telomere maintenance. However, despite the high number of known G4 binders, such a selective molecular activity has not been fully established and several published data point to a different mode of action. We will review published data that address the close structural interplay between G4s and R-loops in vitro and in vivo, and how these interactions can have functional consequences in relation to G4 binder activity. We propose that R-loops can play a previously-underestimated role in G4 binder action, in relation to DNA damage induction, telomere maintenance, genome and epigenome instability and alterations of gene expression programs.

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Dissecting the Fine Details of Assembly of aT = 3 Phage Capsid

Journal of Theoretical Medicine ◽

10.1080/10273660500149869 ◽

2005 ◽

Vol 6 (2) ◽

pp. 119-125 ◽

Cited By ~ 9

Author(s):

P. G. Stockley ◽

A. E. Ashcroft ◽

S. Francese ◽

G. S. Thompson ◽

N. A. Ranson ◽

...

Keyword(s):

Rna Binding ◽

Protein Complexes ◽

Model Systems ◽

Replicase Gene ◽

Nmr Studies ◽

Partial Explanation ◽

Stem Loop ◽

Assembly Pathway

The RNA bacteriophages represent ideal model systems in which to probe the detailed assembly pathway for the formation of aT = 3 quasi-equivalent capsid. For MS2, the assembly reaction can be probedin vitrousing acid disassembled coat protein subunits and a short (19 nt) RNA stem-loop that acts as the translational operator of the replicase gene and leads to sequence-specific sequestration and packaging of the cognate phage RNAin vivo. Reassembly reactions can be initiated by mixing these components at neutral pH. The molecular basis of the sequence-specific RNA–protein interaction is now well understood. Recent NMR studies on the protein demonstrate extensive mobility in the loops of the polypeptide that alter their conformations to form the quasi-equivalent conformers of the final capsid. It seems reasonable to assume that RNA binding results in reduction of this flexibility. However, mass spectrometry suggests that these RNA–protein complexes may only provide one type of quasi-equivalent capsid building block competent to form five-fold axes but not the full shell. Work with longer RNAs suggests that the RNA may actively template the assembly pathway providing a partial explanation of how conformers are selected in the growing shell.

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Water-Soluble Ruthenium(II) Complexes with Chiral 4-(2,3-Dihydroxypropyl)-formamide Oxoaporphine (FOA): In Vitro and in Vivo Anticancer Activity by Stabilization of G-Quadruplex DNA, Inhibition of Telomerase Activity, and Induction of Tumor Cell Apoptosis

Journal of Medicinal Chemistry ◽

10.1021/acs.jmedchem.5b00444 ◽

2015 ◽

Vol 58 (11) ◽

pp. 4771-4789 ◽

Cited By ~ 76

Author(s):

Zhen-Feng Chen ◽

Qi-Pin Qin ◽

Jiao-Lan Qin ◽

Jie Zhou ◽

Yu-Lan Li ◽

...

Keyword(s):

Tumor Cell ◽

Anticancer Activity ◽

Cell Apoptosis ◽

Telomerase Activity ◽

Water Soluble ◽

Tumor Cell Apoptosis ◽

Quadruplex Dna ◽

G Quadruplex

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G-quadruplex unwinding helicases and their function in vivo

Biochemical Society Transactions ◽

10.1042/bst20170097 ◽

2017 ◽

Vol 45 (5) ◽

pp. 1173-1182 ◽

Cited By ~ 66

Author(s):

Markus Sauer ◽

Katrin Paeschke

Keyword(s):

Dna Replication ◽

Genome Instability ◽

Evolutionary Conservation ◽

Telomere Maintenance ◽

Cellular Functions ◽

G Quadruplex

The concept that G-quadruplex (G4) structures can form within DNA or RNA in vitro has been long known and extensively discussed. In recent years, accumulating evidences imply that G-quadruplex structures form in vivo. Initially, inefficient regulation of G-quadruplex structures was mainly associated with genome instability. However, due to the location of G-quadruplex motifs and their evolutionary conservation, different cellular functions of these structures have been postulated (e.g. in telomere maintenance, DNA replication, transcription, and translation). Regardless of their function, efficient and controlled formation and unwinding are very important, because ‘mis’-regulated G-quadruplex structures are detrimental for a given process, causing genome instability and diseases. Several helicases have been shown to target and regulate specific G-quadruplex structures. This mini-review focuses on the biological consequences of G4 disruption by different helicases in vivo.

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Identification of Ewing’s sarcoma protein as a G-quadruplex DNA- and RNA-binding protein

FEBS Journal ◽

10.1111/j.1742-4658.2011.08020.x ◽

2011 ◽

Vol 278 (6) ◽

pp. 988-998 ◽

Cited By ~ 41

Author(s):

Kentaro Takahama ◽

Katsuhito Kino ◽

Shigeki Arai ◽

Riki Kurokawa ◽

Takanori Oyoshi

Keyword(s):

Ewing’S Sarcoma ◽

Rna Binding ◽

Ewing's Sarcoma ◽

Binding Protein ◽

Rna Binding Protein ◽

Quadruplex Dna ◽

Dna And Rna ◽

G Quadruplex ◽

Dna And Rna Binding

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A Physical Interaction between Gar1p and Rnt1p Is Required for the Nuclear Import of H/ACA Small Nucleolar RNA-Associated Proteins

Molecular and Cellular Biology ◽

10.1128/mcb.22.13.4792-4802.2002 ◽

2002 ◽

Vol 22 (13) ◽

pp. 4792-4802 ◽

Cited By ~ 20

Author(s):

Annie Tremblay ◽

Bruno Lamontagne ◽

Mathieu Catala ◽

Yeung Yam ◽

Stephanie Larose ◽

...

Keyword(s):

Rna Processing ◽

Rna Binding ◽

Physical Interaction ◽

Double Stranded Rna ◽

Protein Substrates ◽

Associated Proteins ◽

Rrna Maturation ◽

Nucleolar Rna

ABSTRACT During rRNA biogenesis, multiple RNA and protein substrates are modified and assembled through the coordinated activity of many factors. In Saccharomyces cerevisiae, the double-stranded RNA nuclease Rnt1p and the H/ACA snoRNA pseudouridylase complex participate in the transformation of the nascent pre-rRNA transcript into 35S pre-rRNA. Here we demonstrate the binding of a component of the H/ACA complex (Gar1p) to Rnt1p in vivo and in vitro in the absence of other factors. In vitro, Rnt1p binding to Gar1p is mutually exclusive of its RNA binding and cleavage activities. Mutations in Rnt1p that disrupt Gar1p binding do not inhibit RNA cleavage in vitro but slow RNA processing, prevent nucleolar localization of H/ACA snoRNA-associated proteins, and reduce pre-rRNA pseudouridylation in vivo. These results demonstrate colocalization of various components of the rRNA maturation complex and suggest a mechanism that links rRNA pseudouridylation and cleavage factors.

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Characterization of G-Quadruplex DNA- and RNA-Binding Protein

Long Noncoding RNAs ◽

10.1007/978-4-431-55576-6_4 ◽

2015 ◽

pp. 57-65

Author(s):

Takanori Oyoshi

Keyword(s):

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Quadruplex Dna ◽

Dna And Rna ◽

G Quadruplex ◽

Dna And Rna Binding

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Mgs1 function at G-quadruplex structures during DNA replication

Current Genetics ◽

10.1007/s00294-020-01128-1 ◽

2020 ◽

Author(s):

Katrin Paeschke ◽

Peter Burkovics

Keyword(s):

Dna Replication ◽

Genome Stability ◽

Mechanistic Model ◽

Regulation Of Gene Expression ◽

Telomere Maintenance ◽

Dna Structures ◽

Genomic Deletions ◽

G Quadruplex

AbstractThe coordinated action of DNA polymerases and DNA helicases is essential at genomic sites that are hard to replicate. Among these are sites that harbour G-quadruplex DNA structures (G4). G4s are stable alternative DNA structures, which have been implicated to be involved in important cellular processes like the regulation of gene expression or telomere maintenance. G4 structures were shown to hinder replication fork progression and cause genomic deletions, mutations and recombination events. Many helicases unwind G4 structures and preserve genome stability, but a detailed understanding of G4 replication and the re-start of stalled replication forks around formed G4 structures is not clear, yet. In our recent study, we identified that Mgs1 preferentially binds to G4 DNA structures in vitro and is associated with putative G4-forming chromosomal regions in vivo. Mgs1 binding to G4 motifs in vivo is partially dependent on the helicase Pif1. Pif1 is the major G4-unwinding helicase in S. cerevisiae. In the absence of Mgs1, we determined elevated gross chromosomal rearrangement (GCR) rates in yeast, similar to Pif1 deletion. Here, we highlight the recent findings and set these into context with a new mechanistic model. We propose that Mgs1's functions support DNA replication at G4-forming regions.

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