Elsevier

Biochimie

Volume 90, Issue 8, August 2008, Pages 1250-1263
Biochimie

Review
In vivo veritas: Using yeast to probe the biological functions of G-quadruplexes

https://doi.org/10.1016/j.biochi.2008.02.013Get rights and content

Abstract

Certain guanine-rich sequences are capable of forming higher order structures known as G-quadruplexes. Moreover, particular genomic regions in a number of highly divergent organisms are enriched for such sequences, raising the possibility that G-quadruplexes form in vivo and affect cellular processes. While G-quadruplexes have been rigorously studied in vitro, whether these structures actually form in vivo and what their roles might be in the context of the cell have remained largely unanswered questions. Recent studies suggest that G-quadruplexes participate in the regulation of such varied processes as telomere maintenance, transcriptional regulation and ribosome biogenesis. Here we review studies aimed at elucidating the in vivo functions of quadruplex structures, with a particular focus on findings in yeast. In addition, we discuss the utility of yeast model systems in the study of the cellular roles of G-quadruplexes.

Introduction

The genomes and transcriptomes of many organisms, including those as diverse as E. coli and humans, contain a number of G-rich sequences that, at least in vitro and perhaps in vivo, are capable of forming structures known as G-quadruplexes (G4-DNA and G4-RNA, respectively). These structures are composed of stacked associations of G-quartets, which are planar assemblies of four Hoogsteen-bonded guanines (Fig. 1A and B) [1], [2]. G4 structures can arise through the interactions of guanines present on a single nucleic acid strand (intra-molecular) or multiple strands (inter-molecular). Beyond hydrogen bonding among guanines, the stability of quadruplexes derives from π-orbital interactions among stacked quartets as well as coordination by quartets of centrally located cations (e.g. Na+ or K+). Thus a minimum of two adjacent quartets, but ideally three or more, is required for stable quadruplex formation. G4 structures are stable under physiologic salt and pH conditions in vitro, and some have higher melting temperatures than the duplex DNA that would be formed by providing the complementary strand. There is a high degree of polymorphism among different G4 structures. In principal, 16 different quartet structures can form, which are distinguished by the patterns of glycosidic bond angles of the guanines [3]. Further, the number of stacked quartets, the number and polarity of the phosphodiester backbone strands from which the guanines extend, the type of coordinated cations, and the length, sequence and connectivity of intervening loops may vary [1].

Although the structures of G-quadruplexes have been well studied in vitro, if, when and where they form in vivo and how they might affect cell biology have remained key questions. The structural heterogeneity of quadruplexes makes it difficult to obtain universal rules to predict their formation or probes to test for their presence. Nonetheless, a good deal of information demonstrating or strongly suggesting their functions in vivo has emerged in recent years. For example, telomeric G4-DNA has been proven to exist in Stylonichia lemnae [4], [5], and sequences with intramolecular quadruplex-forming potential (QFP) have been shown to be highly overrepresented in the promoter regions of diverse organisms and to be connected with control of gene expression [6], [7], [8], [9], [10], [11], [12]. In addition, a number of small molecule ligands have been identified that bind to and stabilize quadruplexes (Fig. 1C) [13], [14], [15], [16], [17], [18], [19], [20], [21], and some of these have been found to affect expression from QFP-containing loci, indicating that QFP sequences can adopt G4 conformations.

Here we review findings pertaining to the in vivo functions of G-quadruplexes, with an emphasis on findings in yeast. We begin by highlighting the ways in which yeast model systems can help identify and dissect the cellular roles of quadruplex structures. For readers particularly interested in findings outside of yeast, we recommend these outstanding reviews [22], [23]. Yeast genetic tools have significant potential for revealing the full extent to which G-quadruplexes regulate biological processes, as well as for revealing underlying mechanisms.

Section snippets

Genetic systems for the analysis of G-quadruplexes in yeast

S. cerevisiae offers several genetic systems that could facilitate exploration of the in vivo functions of G-quadruplexes. Although none is unique to yeast, the ease with which they can be carried out in this single celled eukaryote make it an ideal choice for these studies. We first describe these systems, and in the second half of the review describe findings obtained from their use.

Evidence for G-quadruplex functions in vivo

Many observations suggest, and in some cases demonstrate, roles for G-quadruplexes in different aspects of cell biology. Each of the sections below describes one such aspect, beginning with general examples from several organisms and then focusing on findings from yeast. Table 1 provides a summary of various yeast proteins implicated in G-quadruplex metabolism.

Perspective

A combination of biophysical, bioinformatic, genetic and cell biological approaches have yielded a remarkable series of findings that argue for the relevance of G-quadruplexes to natural biology. However, more work is required to firmly establish the roles of G4-DNA and G4-RNA in nucleic acid functions and to decipher the mechanisms by which they operate. This knowledge might provide new approaches for selectively targeting processes ranging from transcription and translation, to DNA

Acknowledgements

We thank Li-San Wang, Steve Hershman and Qijun Chen for discussions, and Alex Chavez for insightful comments on the manuscript. This work was supported by the National Institute on Aging (5R01AG021521 to F.B.J).

References (120)

  • M. Fry et al.

    Human Werner syndrome DNA helicase unwinds tetrahelical structures of the fragile X syndrome repeat sequence d(CGG)n

    J. Biol. Chem.

    (1999)
  • H. Sun et al.

    The Bloom's syndrome helicase unwinds G4 DNA

    J. Biol. Chem.

    (1998)
  • D. Gomez et al.

    Telomestatin-induced telomere uncapping is modulated by POT1 through G-overhang extension in HT1080 human tumor cells

    J. Biol. Chem.

    (2006)
  • R.J. Wellinger et al.

    Evidence for a new step in telomere maintenance

    Cell

    (1996)
  • T.R. Hughes et al.

    The Est3 protein is a subunit of yeast telomerase

    Curr. Biol.

    (2000)
  • J.D. Frantz et al.

    A yeast gene product, G4p2, with a specific affinity for quadruplex nucleic acids

    J. Biol. Chem.

    (1995)
  • M.W. Van Dyke et al.

    Stm1p, a G4 quadruplex and purine motif triplex nucleic acid-binding protein, interacts with ribosomes and subtelomeric Y′ DNA in Saccharomyces cerevisiae

    J. Biol. Chem.

    (2004)
  • Y.C. Tsai et al.

    Protection of DNA ends by telomeric 3′ G-tail sequences

    J. Biol. Chem.

    (2007)
  • Y.C. Lin et al.

    Binding and partial denaturing of G-quartet DNA by Cdc13p of Saccharomyces cerevisiae

    J. Biol. Chem.

    (2001)
  • M. Downey et al.

    A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator

    Cell

    (2006)
  • L.A. Hanakahi et al.

    High affinity interactions of nucleolin with G-G-paired rDNA

    J. Biol. Chem.

    (1999)
  • T. Simonsson et al.

    c-myc Suppression in Burkitt's lymphoma cells

    Biochem. Biophys. Res. Commun.

    (2002)
  • M.S. Santisteban et al.

    Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes

    Cell

    (2000)
  • R.C. Fry et al.

    DNA damage and stress transcripts in Saccharomyces cerevisiae mutant sgs1

    Mech. Ageing Dev.

    (2003)
  • J.C. Darnell et al.

    Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function

    Cell

    (2001)
  • B. Li et al.

    Requirements for the nucleolytic processing of DNA ends by the Werner syndrome protein-Ku70/80 complex

    J. Biol. Chem.

    (2001)
  • A.S. Kamath-Loeb et al.

    Interactions between the Werner syndrome helicase and DNA polymerase delta specifically facilitate copying of tetraplex and hairpin structures of the d(CGG)n trinucleotide repeat sequence

    J. Biol. Chem.

    (2001)
  • D.D. Dudley et al.

    Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences

    Adv. Immunol.

    (2005)
  • E.D. Larson et al.

    MutSalpha binds to and promotes synapsis of transcriptionally activated immunoglobulin switch regions

    Curr. Biol.

    (2005)
  • Z. Liu et al.

    The yeast KEM1 gene encodes a nuclease specific for G4 tetraplex DNA: implication of in vivo functions for this novel DNA structure

    Cell

    (1994)
  • S. Burge et al.

    Quadruplex DNA: sequence, topology and structure

    Nucleic Acids Res.

    (2006)
  • D. Sen et al.

    Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis

    Nature

    (1988)
  • M. Webba da Silva

    Geometric formalism for DNA quadruplex folding

    Chemistry

    (2007)
  • K. Paeschke et al.

    Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo

    Nat. Struct. Mol. Biol.

    (2005)
  • C. Schaffitzel et al.

    In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei

    Proc. Natl. Acad. Sci. U.S.A.

    (2001)
  • J.L. Huppert et al.

    G-quadruplexes in promoters throughout the human genome

    Nucleic Acids Res.

    (2007)
  • J.L. Huppert et al.

    Prevalence of quadruplexes in the human genome

    Nucleic Acids Res.

    (2005)
  • P. Rawal et al.

    Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation

    Genome Res.

    (2006)
  • S.G. Hershman et al.

    Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae

    Nucleic Acids Res.

    (2007)
  • J. Eddy et al.

    Gene function correlates with potential for G4 DNA formation in the human genome

    Nucleic Acids Res.

    (2006)
  • A.K. Todd et al.

    Highly prevalent putative quadruplex sequence motifs in human DNA

    Nucleic Acids Res.

    (2005)
  • J.L. Mergny et al.

    Natural and pharmacological regulation of telomerase

    Nucleic Acids Res.

    (2002)
  • A. De Cian et al.

    Highly efficient G-quadruplex recognition by bisquinolinium compounds

    J. Am. Chem. Soc.

    (2007)
  • I.M. Dixon et al.

    A G-quadruplex ligand with 10000-fold selectivity over duplex DNA

    J. Am. Chem. Soc.

    (2007)
  • K. Shin-ya et al.

    Telomestatin, a novel telomerase inhibitor from Streptomyces anulatus

    J. Am. Chem. Soc.

    (2001)
  • J. Ren et al.

    Sequence and structural selectivity of nucleic acid binding ligands

    Biochemistry

    (1999)
  • A.D. Moorhouse et al.

    Stabilization of G-quadruplex DNA by highly selective ligands via click chemistry

    J. Am. Chem. Soc.

    (2006)
  • M. Bejugam et al.

    Trisubstituted isoalloxazines as a new class of G-quadruplex binding ligands: small molecule regulation of c-kit oncogene expression

    J. Am. Chem. Soc.

    (2007)
  • M. Fry

    Tetraplex DNA and its interacting proteins

    Front. Biosci.

    (2007)
  • N. Maizels

    Dynamic roles for G4 DNA in the biology of eukaryotic cells

    Nat. Struct. Mol. Biol.

    (2006)
  • Cited by (0)

    View full text