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Juribašić Kulcsár M, Gabelica V, Plavec J. Solution-State Structure of a Long-Loop G-Quadruplex Formed Within Promoters of Plasmodium falciparum B var Genes. Chemistry 2024; 30:e202401190. [PMID: 38647110 DOI: 10.1002/chem.202401190] [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: 03/25/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
We report the high-resolution NMR solution-state structure of an intramolecular G-quadruplex with a diagonal loop of ten nucleotides. The G-quadruplex is formed by a 34-nt DNA sequence, d[CAG3T2A2G3TATA2CT3AG4T2AG3T2], named UpsB-Q-1. This sequence is found within promoters of the var genes of Plasmodium falciparum, which play a key role in malaria pathogenesis and evasion of the immune system. The [3+1]-hybrid G-quadruplex formed under physiologically relevant conditions exhibits a unique equilibrium between two structures, both stabilized by base stacking and non-canonical hydrogen bonding. Unique equilibrium of the two closely related 3D structures originates from a North-South repuckering of deoxyribose moiety of residue T27 in the lateral loop. Besides the 12 guanines involved in three G-quartets, most residues in loop regions are involved in interactions at both G-quartet-loop interfaces.
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Affiliation(s)
- Marina Juribašić Kulcsár
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Valérie Gabelica
- School of Pharmaceutical Sciences, University of Geneva, 1 rue Michel-Servet, CH-1211, Geneva 4, Switzerland
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg OF 13, SI-1000, Ljubljana, Slovenia
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2
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Craven HM, Nettesheim G, Cicuta P, Blagborough AM, Merrick CJ. Effects of the G-quadruplex-binding drugs quarfloxin and CX-5461 on the malaria parasite Plasmodium falciparum. Int J Parasitol Drugs Drug Resist 2023; 23:106-119. [PMID: 38041930 PMCID: PMC10711401 DOI: 10.1016/j.ijpddr.2023.11.007] [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: 08/15/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023]
Abstract
Plasmodium falciparum is the deadliest causative agent of human malaria. This parasite has historically developed resistance to most drugs, including the current frontline treatments, so new therapeutic targets are needed. Our previous work on guanine quadruplexes (G4s) in the parasite's DNA and RNA has highlighted their influence on parasite biology, and revealed G4 stabilising compounds as promising candidates for repositioning. In particular, quarfloxin, a former anticancer agent, kills blood-stage parasites at all developmental stages, with fast rates of kill and nanomolar potency. Here we explored the molecular mechanism of quarfloxin and its related derivative CX-5461. In vitro, both compounds bound to P. falciparum-encoded G4 sequences. In cellulo, quarfloxin was more potent than CX-5461, and could prevent establishment of blood-stage malaria in vivo in a murine model. CX-5461 showed clear DNA damaging activity, as reported in human cells, while quarfloxin caused weaker signatures of DNA damage. Both compounds caused transcriptional dysregulation in the parasite, but the affected genes were largely different, again suggesting different modes of action. Therefore, CX-5461 may act primarily as a DNA damaging agent in both Plasmodium parasites and mammalian cells, whereas the complete antimalarial mode of action of quarfloxin may be parasite-specific and remains somewhat elusive.
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Affiliation(s)
- Holly M Craven
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Guilherme Nettesheim
- Department of Physics, Cavendish Laboratory University of Cambridge, J.J. Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Pietro Cicuta
- Department of Physics, Cavendish Laboratory University of Cambridge, J.J. Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Andrew M Blagborough
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Catherine J Merrick
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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Thompson TA, Chahine Z, Le Roch KG. The role of long noncoding RNAs in malaria parasites. Trends Parasitol 2023; 39:517-531. [PMID: 37121862 DOI: 10.1016/j.pt.2023.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/02/2023]
Abstract
The human malaria parasites, including Plasmodium falciparum, persist as a major cause of global morbidity and mortality. The recent stalling of progress toward malaria elimination substantiates a need for novel interventions. Controlled gene expression is central to the parasite's numerous life cycle transformations and adaptation. With few specific transcription factors (TFs) identified, crucial roles for chromatin states and epigenetics in parasite transcription have become evident. Although many chromatin-modifying enzymes are known, less is known about which factors mediate their impacts on transcriptional variation. Like those of higher eukaryotes, long noncoding RNAs (lncRNAs) have recently been shown to have integral roles in parasite gene regulation. This review aims to summarize recent developments and key findings on the role of lncRNAs in P. falciparum.
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Affiliation(s)
- Trevor A Thompson
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA.
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4
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Diffendall GM, Barcons-Simon A, Baumgarten S, Dingli F, Loew D, Scherf A. Discovery of RUF6 ncRNA-interacting proteins involved in P. falciparum immune evasion. Life Sci Alliance 2022; 6:6/1/e202201577. [PMID: 36379669 PMCID: PMC9670795 DOI: 10.26508/lsa.202201577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are emerging regulators of immune evasion and transmission of Plasmodium falciparum RUF6 is an ncRNA gene family that is transcribed by RNA polymerase III but actively regulates the Pol II-transcribed var virulence gene family. Understanding how RUF6 ncRNA connects to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA-protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including RNA Pol II subunits, nucleosome assembly proteins, and a homologue of DEAD box helicase 5 (DDX5). Affinity purification of Pf-DDX5 identified proteins originally found by our RUF6-ChIRP protocol, validating the technique's robustness for identifying ncRNA interactomes in P. falciparum Inducible displacement of nuclear Pf-DDX5 resulted in significant down-regulation of the active var gene. Our work identifies a RUF6 ncRNA-protein complex that interacts with RNA Pol II to sustain the var gene expression, including a helicase that may resolve G-quadruplex secondary structures in var genes to facilitate transcriptional activation and progression.
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Affiliation(s)
- Gretchen M Diffendall
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France
| | - Anna Barcons-Simon
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Artur Scherf
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France
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5
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Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters. Int J Mol Sci 2022; 23:ijms231810873. [PMID: 36142782 PMCID: PMC9504043 DOI: 10.3390/ijms231810873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Eukaryotic and archaeal RNA polymerase II (POL II) machinery is highly conserved, regardless of the extreme changes in promoter sequences in different organisms. The goal of our work is to find the cause of this conservatism. The representative sets of aligned promoter sequences of fifteen organisms belonging to different evolutional stages were studied. Their textual profiles, as well as profiles of the indexes that characterize the secondary structure and the mechanical and physicochemical properties, were analyzed. The evolutionarily stable, extremely heterogeneous special secondary structure of POL II core promoters was revealed, which includes two singular regions—hexanucleotide “INR” around TSS and octanucleotide “TATA element” of about −28 bp upstream. Such structures may have developed at some stage of evolution. It turned out to be so well matched for the pre-initiation complex formation and the subsequent initiation of transcription for POL II machinery that in the course of evolution there were selected only those nucleotide sequences that were able to reproduce these structural properties. The individual features of specific sequences representing the singular region of the promoter of each gene can affect the kinetics of DNA-protein complex formation and facilitate strand separation in double-stranded DNA at the TSS position.
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Dumetz F, Chow EYC, Harris LM, Liew SW, Jensen A, Umar MI, Chung B, Chan TF, Merrick CJ, Kwok CK. G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum. Nucleic Acids Res 2021; 49:12486-12501. [PMID: 34792144 PMCID: PMC8643661 DOI: 10.1093/nar/gkab1095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.
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Affiliation(s)
- Franck Dumetz
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Eugene Yui-Ching Chow
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Lynne M Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Anders Jensen
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Betty Chung
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ting Fung Chan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Catherine J Merrick
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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Mishra S, Kota S, Chaudhary R, Misra HS. Guanine quadruplexes and their roles in molecular processes. Crit Rev Biochem Mol Biol 2021; 56:482-499. [PMID: 34162300 DOI: 10.1080/10409238.2021.1926417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The role of guanine quadruplexes (G4) in fundamental biological processes like DNA replication, transcription, translation and telomere maintenance is recognized. G4 structure dynamics is regulated by G4 structure binding proteins and is thought to be crucial for the maintenance of genome integrity in both prokaryotic and eukaryotic cells. Growing research over the last decade has expanded the existing knowledge of the functional diversity of G4 (DNA and RNA) structures across the working models. The control of G4 structure dynamics using G4 binding drugs has been suggested as the putative targets in the control of cancer and bacterial pathogenesis. This review has brought forth the collections of recent information that indicate G4 (mostly G4 DNA) roles in microbial pathogenesis, DNA damaging stress response in bacteria and mammalian cells. Studies in mitochondrial gene function regulation by G4s have also been underscored. Finally, the interdependence of G4s and epigenetic modifications and their speculated medical implications through G4 interacting proteins has been discussed.
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Affiliation(s)
- Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - H S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
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8
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Abiri A, Lavigne M, Rezaei M, Nikzad S, Zare P, Mergny JL, Rahimi HR. Unlocking G-Quadruplexes as Antiviral Targets. Pharmacol Rev 2021; 73:897-923. [PMID: 34045305 DOI: 10.1124/pharmrev.120.000230] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Guanine-rich DNA and RNA sequences can fold into noncanonical nucleic acid structures called G-quadruplexes (G4s). Since the discovery that these structures may act as scaffolds for the binding of specific ligands, G4s aroused the attention of a growing number of scientists. The versatile roles of G4 structures in viral replication, transcription, and translation suggest direct applications in therapy or diagnostics. G4-interacting molecules (proteins or small molecules) may also affect the balance between latent and lytic phases, and increasing evidence reveals that G4s are implicated in generally suppressing viral processes, such as replication, transcription, translation, or reverse transcription. In this review, we focus on the discovery of G4s in viruses and the role of G4 ligands in the antiviral drug discovery process. After assessing the role of viral G4s, we argue that host G4s participate in immune modulation, viral tumorigenesis, cellular pathways involved in virus maturation, and DNA integration of viral genomes, which can be potentially employed for antiviral therapeutics. Furthermore, we scrutinize the impediments and shortcomings in the process of studying G4 ligands and drug discovery. Finally, some unanswered questions regarding viral G4s are highlighted for prospective future projects. SIGNIFICANCE STATEMENT: G-quadruplexes (G4s) are noncanonical nucleic acid structures that have gained increasing recognition during the last few decades. First identified as relevant targets in oncology, their importance in virology is now increasingly clear. A number of G-quadruplex ligands are known: viral transcription and replication are the main targets of these ligands. Both viral and cellular G4s may be targeted; this review embraces the different aspects of G-quadruplexes in both host and viral contexts.
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Affiliation(s)
- Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Marc Lavigne
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Masoud Rezaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Sanaz Nikzad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Peyman Zare
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Jean-Louis Mergny
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
| | - Hamid-Reza Rahimi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (A.A., S.N.); Institut Pasteur, Department of Virology, UMR 3569 CNRS, Paris, France (M.L.); Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran (M.R.); Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland (P.Z.); Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland (P.Z.); Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex, France (J.-L.M.); Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran (H.-R.R.)
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9
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Structural insights into histone chaperone Asf1 and its characterization from Plasmodium falciparum. Biochem J 2021; 478:1117-1136. [PMID: 33501928 DOI: 10.1042/bcj20200891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Asf1 is a highly conserved histone chaperone that regulates tightly coupled nucleosome assembly/disassembly process. We observed that Plasmodium falciparum Asf1 (PfAsf1) is ubiquitously expressed in different stages of the life cycle of the parasite. To gain further insight into its biological activity, we solved the structure of N-terminal histone chaperone domain of PfAsf1 (1-159 amino acids) by X-ray crystallography to a resolution of 2.4 Å. The structure is composed of two beta-sheet to form a beta-sandwich, which resembles an immunoglobulin-like fold. The surface-charge distribution of PfAsf1 is distinct from yAsf1 and hAsf1 although the core-structure shows significant similarity. The crystal-structure indicated that PfAsf1 may exist in a dimeric-state which was further confirmed by solution cross-linking experiment. PfAsf1 was found to specifically interact with Plasmodium histone H3 and H4 and was able to deposit H3/H4 dimer onto DNA-template to form disomes, showing its characteristic histone chaperone activity. We mapped the critical residues of PfAsf1 involved in histone H3/H4 interaction and confirmed by site-directed mutagenesis. Further analysis indicates that histone interacting surface of Asf1 is highly conserved while the dimerization interface is variable. Our results identify the role of PfAsf1 as a mediator of chromatin assembly in Plasmodium falciparum, which is the causative agent of malignant malaria in humans.
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10
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Craven HM, Bonsignore R, Lenis V, Santi N, Berrar D, Swain M, Whiteland H, Casini A, Hoffmann KF. Identifying and validating the presence of Guanine-Quadruplexes (G4) within the blood fluke parasite Schistosoma mansoni. PLoS Negl Trop Dis 2021; 15:e0008770. [PMID: 33600427 PMCID: PMC7924807 DOI: 10.1371/journal.pntd.0008770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/02/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Schistosomiasis is a neglected tropical disease that currently affects over 250 million individuals worldwide. In the absence of an immunoprophylactic vaccine and the recognition that mono-chemotherapeutic control of schistosomiasis by praziquantel has limitations, new strategies for managing disease burden are urgently needed. A better understanding of schistosome biology could identify previously undocumented areas suitable for the development of novel interventions. Here, for the first time, we detail the presence of G-quadruplexes (G4) and putative quadruplex forming sequences (PQS) within the Schistosoma mansoni genome. We find that G4 are present in both intragenic and intergenic regions of the seven autosomes as well as the sex-defining allosome pair. Amongst intragenic regions, G4 are particularly enriched in 3´ UTR regions. Gene Ontology (GO) term analysis evidenced significant G4 enrichment in the wnt signalling pathway (p<0.05) and PQS oligonucleotides synthetically derived from wnt-related genes resolve into parallel and anti-parallel G4 motifs as elucidated by circular dichroism (CD) spectroscopy. Finally, utilising a single chain anti-G4 antibody called BG4, we confirm the in situ presence of G4 within both adult female and male worm nuclei. These results collectively suggest that G4-targeted compounds could be tested as novel anthelmintic agents and highlights the possibility that G4-stabilizing molecules could be progressed as candidates for the treatment of schistosomiasis.
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Affiliation(s)
- Holly M. Craven
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, United Kingdom
| | | | - Vasilis Lenis
- School of Health and Life Sciences, Teesside University, United Kingdom
| | - Nicolo Santi
- School of Chemistry, Cardiff University, Cardiff, United Kingdom
| | - Daniel Berrar
- Data Science Laboratory, Tokyo Institute of Technology, Tokyo, Japan
| | - Martin Swain
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, United Kingdom
| | - Helen Whiteland
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, United Kingdom
| | - Angela Casini
- Department of Chemistry, Technical University of Munich, Germany
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, United Kingdom
- * E-mail:
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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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Brázda V, Luo Y, Bartas M, Kaura P, Porubiaková O, Šťastný J, Pečinka P, Verga D, Da Cunha V, Takahashi TS, Forterre P, Myllykallio H, Fojta M, Mergny JL. G-Quadruplexes in the Archaea Domain. Biomolecules 2020; 10:biom10091349. [PMID: 32967357 PMCID: PMC7565180 DOI: 10.3390/biom10091349] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/26/2022] Open
Abstract
The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Yu Luo
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
| | - Otilia Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkyňova 464/118, 612 00 Brno, Czech Republic
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic
- Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Daniela Verga
- Institut Curie, CNRS UMR9187, INSERM U1196, Universite Paris Saclay, 91400 Orsay, France
| | - Violette Da Cunha
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Tomio S Takahashi
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Patrick Forterre
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, Université Paris-Saclay, CEDEX, 91198 Gif-sur-Yvette, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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Bartas M, Brázda V, Bohálová N, Cantara A, Volná A, Stachurová T, Malachová K, Jagelská EB, Porubiaková O, Červeň J, Pečinka P. In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles. Front Microbiol 2020; 11:1583. [PMID: 32719673 PMCID: PMC7347907 DOI: 10.3389/fmicb.2020.01583] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Non-canonical nucleic acid structures play important roles in the regulation of molecular processes. Considering the importance of the ongoing coronavirus crisis, we decided to evaluate genomes of all coronaviruses sequenced to date (stated more broadly, the order Nidovirales) to determine if they contain non-canonical nucleic acid structures. We discovered much evidence of putative G-quadruplex sites and even much more of inverted repeats (IRs) loci, which in fact are ubiquitous along the whole genomic sequence and indicate a possible mechanism for genomic RNA packaging. The most notable enrichment of IRs was found inside 5'UTR for IRs of size 12+ nucleotides, and the most notable enrichment of putative quadruplex sites (PQSs) was located before 3'UTR, inside 5'UTR, and before mRNA. This indicates crucial regulatory roles for both IRs and PQSs. Moreover, we found multiple G-quadruplex binding motifs in human proteins having potential for binding of SARS-CoV-2 RNA. Non-canonical nucleic acids structures in Nidovirales and in novel SARS-CoV-2 are therefore promising druggable structures that can be targeted and utilized in the future.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Alessio Cantara
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Tereza Stachurová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Kateřina Malachová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Eva B. Jagelská
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Otília Porubiaková
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
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