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Parekh VJ, Węgrzyn G, Arluison V, Sinden RR. Genomic Instability of G-Quadruplex Sequences in Escherichia coli: Roles of DinG, RecG, and RecQ Helicases. Genes (Basel) 2023; 14:1720. [PMID: 37761860 PMCID: PMC10530614 DOI: 10.3390/genes14091720] [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: 08/04/2023] [Revised: 08/23/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Guanine-rich DNA can fold into highly stable four-stranded DNA structures called G-quadruplexes (G4). Originally identified in sequences from telomeres and oncogene promoters, they can alter DNA metabolism. Indeed, G4-forming sequences represent obstacles for the DNA polymerase, with important consequences for cell life as they may lead to genomic instability. To understand their role in bacterial genomic instability, different G-quadruplex-forming repeats were cloned into an Escherichia coli genetic system that reports frameshifts and complete or partial deletions of the repeat when the G-tract comprises either the leading or lagging template strand during replication. These repeats formed stable G-quadruplexes in single-stranded DNA but not naturally supercoiled double-stranded DNA. Nevertheless, transcription promoted G-quadruplex formation in the resulting R-loop for (G3T)4 and (G3T)8 repeats. Depending on genetic background and sequence propensity for structure formation, mutation rates varied by five orders of magnitude. Furthermore, while in vitro approaches have shown that bacterial helicases can resolve G4, it is still unclear whether G4 unwinding is important in vivo. Here, we show that a mutation in recG decreased mutation rates, while deficiencies in the structure-specific helicases DinG and RecQ increased mutation rates. These results suggest that G-quadruplex formation promotes genetic instability in bacteria and that helicases play an important role in controlling this process in vivo.
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Affiliation(s)
- Virali J. Parekh
- Laboratory of DNA Structure and Mutagenesis, Department of Chemistry, Biology and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, 75006 Paris, France
| | - Richard R. Sinden
- Laboratory of DNA Structure and Mutagenesis, Department of Chemistry, Biology and Health Sciences, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
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Crucial Role of the C-Terminal Domain of Hfq Protein in Genomic Instability. Microorganisms 2020; 8:microorganisms8101598. [PMID: 33080799 PMCID: PMC7603069 DOI: 10.3390/microorganisms8101598] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 01/25/2023] Open
Abstract
G-rich DNA repeats that can form G-quadruplex structures are prevalent in bacterial genomes and are frequently associated with regulatory regions of genes involved in virulence, antigenic variation, and antibiotic resistance. These sequences are also inherently mutagenic and can lead to changes affecting cell survival and adaptation. Transcription of the G-quadruplex-forming repeat (G3T)n in E. coli, when mRNA comprised the G-rich strand, promotes G-quadruplex formation in DNA and increases rates of deletion of G-quadruplex-forming sequences. The genomic instability of G-quadruplex repeats may be a source of genetic variability that can influence alterations and evolution of bacteria. The DNA chaperone Hfq is involved in the genetic instability of these G-quadruplex sequences. Inactivation of the hfq gene decreases the genetic instability of G-quadruplex, demonstrating that the genomic instability of this regulatory element can be influenced by the E. coli highly pleiotropic Hfq protein, which is involved in small noncoding RNA regulation pathways, and DNA organization and packaging. We have shown previously that the protein binds to and stabilizes these sequences, increasing rates of their genomic instability. Here, we extend this analysis to characterize the role of the C-terminal domain of Hfq protein in interaction with G-quadruplex structures. This allows to better understand the function of this specific region of the Hfq protein in genomic instability.
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Parekh VJ, Niccum BA, Shah R, Rivera MA, Novak MJ, Geinguenaud F, Wien F, Arluison V, Sinden RR. Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli. Microorganisms 2019; 8:microorganisms8010028. [PMID: 31877879 PMCID: PMC7023247 DOI: 10.3390/microorganisms8010028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
Certain G-rich DNA repeats can form quadruplex in bacterial chromatin that can present blocks to DNA replication and, if not properly resolved, may lead to mutations. To understand the participation of quadruplex DNA in genomic instability in Escherichia coli (E. coli), mutation rates were measured for quadruplex-forming DNA repeats, including (G3T)4, (G3T)8, and a RET oncogene sequence, cloned as the template or nontemplate strand. We evidence that these alternative structures strongly influence mutagenesis rates. Precisely, our results suggest that G-quadruplexes form in E. coli cells, especially during transcription when the G-rich strand can be displaced by R-loop formation. Structure formation may then facilitate replication misalignment, presumably associated with replication fork blockage, promoting genomic instability. Furthermore, our results also evidence that the nucleoid-associated protein Hfq is involved in the genetic instability associated with these sequences. Hfq binds and stabilizes G-quadruplex structure in vitro and likely in cells. Collectively, our results thus implicate quadruplexes structures and Hfq nucleoid protein in the potential for genetic change that may drive evolution or alterations of bacterial gene expression.
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Affiliation(s)
- Virali J. Parekh
- Laboratory of DNA Structure and Mutagenesis, Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
| | - Brittany A. Niccum
- Department of Mathematics, Florida Institute of Technology, Melbourne, FL 32901, USA;
| | - Rachna Shah
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA; (R.S.); (M.A.R.)
| | - Marisa A. Rivera
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA; (R.S.); (M.A.R.)
| | - Mark J. Novak
- Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology; Rapid City, SD 57701, USA;
| | - Frederic Geinguenaud
- Plateforme CNanoMat & Inserm U1148, Laboratory for Vascular Translational Science, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, F-93017 Bobigny, France;
| | - Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Université de Paris, UFR Sciences du vivant, 35 rue Hélène Brion, 75205 Paris cedex, France
- Correspondence: (V.A.); (R.R.S.); Tel.: +1-605-394-1678 (R.R.S.)
| | - Richard R. Sinden
- Laboratory of DNA Structure and Mutagenesis, Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
- Correspondence: (V.A.); (R.R.S.); Tel.: +1-605-394-1678 (R.R.S.)
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Effects of Replication and Transcription on DNA Structure-Related Genetic Instability. Genes (Basel) 2017; 8:genes8010017. [PMID: 28067787 PMCID: PMC5295012 DOI: 10.3390/genes8010017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/21/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.
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Abstract
Repetitive genomic sequences can adopt a number of alternative DNA structures that differ from the canonical B-form duplex (i.e. non-B DNA). These non-B DNA-forming sequences have been shown to have many important biological functions related to DNA metabolic processes; for example, they may have regulatory roles in DNA transcription and replication. In addition to these regulatory functions, non-B DNA can stimulate genetic instability in the presence or absence of DNA damage, via replication-dependent and/or replication-independent pathways. This review focuses on the interactions of non-B DNA conformations with DNA repair proteins and how these interactions impact genetic instability.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
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Wang G, Gaddis S, Vasquez KM. Methods to detect replication-dependent and replication-independent DNA structure-induced genetic instability. Methods 2013; 64:67-72. [PMID: 23954565 DOI: 10.1016/j.ymeth.2013.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 08/02/2013] [Accepted: 08/07/2013] [Indexed: 10/26/2022] Open
Abstract
DNA can adopt a variety of alternative secondary (i.e., non-B DNA) conformations that play important roles in cellular metabolism, including genetic instability, disease etiology and evolution. While we still have much to learn, research in this field has expanded dramatically in the past decade. We have summarized in our previous Methods review (Wang et al., Methods, 2009) some commonly used techniques to determine non-B DNA structural conformations and non-B DNA-induced genetic instability in prokaryotes and eukaryotes. Since that time, we and others have further characterized mechanisms involved in DNA structure-induced mutagenesis and have proposed both replication-dependent and replication-independent models. Thus, in this review, we highlight some current methodologies to identify DNA replication-related and replication-independent mutations occurring at non-B DNA regions to allow for a better understanding of the mechanisms underlying DNA structure-induced genetic instability. We also describe a new web-based search engine to identify potential intramolecular triplex (H-DNA) and left-handed Z-DNA-forming motifs in entire genomes or at selected sequences of interest.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
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Wang G, Vasquez KM. Models for chromosomal replication-independent non-B DNA structure-induced genetic instability. Mol Carcinog 2009; 48:286-98. [PMID: 19123200 PMCID: PMC2766916 DOI: 10.1002/mc.20508] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Regions of genomic DNA containing repetitive nucleotide sequences can adopt a number of different structures in addition to the canonical B-DNA form: many of these non-B DNA structures are causative factors in genetic instability and human disease. Although chromosomal DNA replication through such repetitive sequences has been considered a major cause of non-B form DNA structure-induced genetic instability, it is also observed in non-proliferative tissues. In this review, we discuss putative mechanisms responsible for the mutagenesis induced by non-B DNA structures in the absence of chromosomal DNA replication.
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Affiliation(s)
- Guliang Wang
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, 1808 Park Road 1-C, Smithville, TX 78957
| | - Karen M. Vasquez
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, 1808 Park Road 1-C, Smithville, TX 78957
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Abstract
Accurate and complete replication of the genome in every cell division is a prerequisite of genomic stability. Thus, both prokaryotic and eukaryotic replication forks are extremely precise and robust molecular machines that have evolved to be up to the task. However, it has recently become clear that the replication fork is more of a hurdler than a runner: it must overcome various obstacles present on its way. Such obstacles can be called natural impediments to DNA replication, as opposed to external and genetic factors. Natural impediments to DNA replication are particular DNA binding proteins, unusual secondary structures in DNA, and transcription complexes that occasionally (in eukaryotes) or constantly (in prokaryotes) operate on replicating templates. This review describes the mechanisms and consequences of replication stalling at various natural impediments, with an emphasis on the role of replication stalling in genomic instability.
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Affiliation(s)
- Ekaterina V. Mirkin
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Sergei M. Mirkin
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60607
- Corresponding author. Present address: Department of Biology, Tufts University, Medford, MA 02155. Phone: (617) 627-4794. Fax: (617) 627-3805. E-mail:
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