1
|
Singh A, Jain N, Shankar U, Sharma TK, Kumar A. Characterization of G-quadruplex structures in genes involved in survival and pathogenesis of Acinetobacter baumannii as a potential drug target. Int J Biol Macromol 2024; 269:131806. [PMID: 38670179 DOI: 10.1016/j.ijbiomac.2024.131806] [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: 12/13/2023] [Revised: 03/21/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024]
Abstract
Acinetobacter baumannii is a notorious pathogen that commonly thrives in hospital environments and is responsible for numerous nosocomial infections in humans. The burgeoning multi-drug resistance leaves relatively minimal options for treating the bacterial infection, posing a significant problem and prompting the identification of new approaches for tackling the same. This motivated us to focus on non-canonical nucleic acid structures, mainly G-quadruplexes, as drug targets. G-quadruplexes have recently been gaining attention due to their involvement in multiple bacterial and viral pathogenesis. Herein, we sought to explore conserved putative G-quadruplex motifs in A. baumannii. In silico analysis revealed the presence of eight conserved motifs in genes involved in bacterial survival and pathogenesis. The biophysical and biomolecular analysis confirmed stable G-quadruplex formation by the motifs and showed a high binding affinity with the well-reported G-quadruplex binding ligand, BRACO-19. BRACO-19 exposure also decreased the growth of bacteria and downregulated the expression of G-quadruplex-harboring genes. The biofilm-forming ability of the bacteria was also affected by BRACO-19 addition. Taking all these observations into account, we have shown here for the first time the potential of G-quadruplex structures as a promising drug target in Acinetobacter baumannii, for addressing the challenges posed by this infamous pathogen.
Collapse
Affiliation(s)
- Aakriti Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Department of Medical Biotechnology, Gujarat Biotechnology University, Gandhinagar 382355, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India.
| |
Collapse
|
2
|
Basu M, Mishra PP. G-quadruplex modulation by E. coli SSB: A comprehensive study on binding affinities and modes using single-molecule FRET. Int J Biol Macromol 2024; 266:131057. [PMID: 38522699 DOI: 10.1016/j.ijbiomac.2024.131057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
G-quadruplexes (GQs) are essential guanine-rich secondary structures found in DNA and RNA, playing crucial roles in genomic maintenance and stability. Recent studies have unveiled GQs in the intergenic regions of the E. coli genome, suggesting their biological significance and potential as anti-microbial targets. Here, we investigated the interaction between homo-tetrameric E. coli SSB and GQ-forming single-stranded DNA (ssDNA) sequence with varying lengths. Combining Microscale Thermophoresis (MST) and conventional spectroscopic techniques, we explored E. coli SSB binding to ssDNA and the structural changes of these secondary DNA structures upon protein binding. Subsequently, we have utilized smFRET to probe the conformational changes of GQ-ssDNA structures upon SSB binding. Our results provide detailed insights into SSB's access to various GQ-ssDNA sequencies and the wrapping of this homo-tetrameric protein around GQ-ssDNA in multiple distinct binding modalities. This study sheds light on the intricate details of E. coli SSB's interaction with ssDNA and the resulting widespread conformational changes within these oligonucleotide structures after protein binding. It offers a thorough insight into SSB's accesses to various GQ-ssDNA architectures. The finding demonstrates the multifaceted binding methods through which this homo-tetrameric protein envelops GQ-ssDNA and could prove valuable in deciphering biological processes that involve DNA G-quadruplexes.
Collapse
Affiliation(s)
- Manali Basu
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Mumbai, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Mumbai, India.
| |
Collapse
|
3
|
Chaudhuri R, Prasanth T, Biswas D, Mandal S, Dash J. Combating multidrug-resistance in S. pneumoniae: a G-quadruplex binding inhibitor of efflux pump and its bio-orthogonal assembly. NAR MOLECULAR MEDICINE 2024; 1:ugae005. [PMID: 38694210 PMCID: PMC11059089 DOI: 10.1093/narmme/ugae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Antibiotic resistance poses a significant global health threat, necessitating innovative strategies to combat multidrug-resistant bacterial infections. Streptococcus pneumoniae, a pathogen responsible for various infections, harbors highly conserved DNA quadruplexes in genes linked to its pathogenesis. In this study, we introduce a novel approach to counter antibiotic resistance by stabilizing G-quadruplex structures within the open reading frames of key resistance-associated genes (pmrA, recD and hsdS). We synthesized An4, a bis-anthracene derivative, using Cu(I)-catalyzed azide-alkyne cycloaddition, which exhibited remarkable binding and stabilization of the G-quadruplex in the pmrA gene responsible for drug efflux. An4 effectively permeated multidrug-resistant S. pneumoniae strains, leading to a substantial 12.5-fold reduction in ciprofloxacin resistance. Furthermore, An4 downregulated pmrA gene expression, enhancing drug retention within bacterial cells. Remarkably, the pmrA G-quadruplex cloned into the pET28a(+) plasmid transformed into Escherichia coli BL21 cells can template Cu-free bio-orthogonal synthesis of An4 from its corresponding alkyne and azide fragments. This study presents a pioneering strategy to combat antibiotic resistance by genetically reducing drug efflux pump expression through G-quadruplex stabilization, offering promising avenues for addressing antibiotic resistance.
Collapse
Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West-Bengal 700032, India
| | - Thumpati Prasanth
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West-Bengal 700032, India
| | - Debasmita Biswas
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West-Bengal 700032, India
| | - Subhranshu Mandal
- Laboratory Medicine, Chittaranjan National Cancer Institute, Kolkata, West Bengal 700156, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West-Bengal 700032, India
| |
Collapse
|
4
|
Misra HS, Rajpurohit YS. DNA damage response and cell cycle regulation in bacteria: a twist around the paradigm. Front Microbiol 2024; 15:1389074. [PMID: 38605710 PMCID: PMC11007091 DOI: 10.3389/fmicb.2024.1389074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
The co-protease activity in the RecA-ssDNA complex cleaves the autorepressor LexA, resulting in the derepression of a large number of genes under LexA control. This process is called the SOS response, and genes that are expressed in response to DNA damage are called SOS genes. The proteins encoded by the SOS genes are involved in both DNA repair and maintaining the functions of crucial cell division proteins (e.g., FtsZ) under check until the damaged DNA is presumably repaired. This mechanism of SOS response is the only known mechanism of DNA damage response and cell cycle regulation in bacteria. However, there are bacteria that do not obey this rule of DNA damage response and cell cycle regulation, yet they respond to DNA damage, repair it, and survive. That means such bacteria would have some alternate mechanism(s) of DNA damage response and cell cycle regulation beyond the canonical pathway of the SOS response. In this study, we present the perspectives that bacteria may have other mechanisms of DNA damage response and cell cycle regulation mediated by bacterial eukaryotic type Ser/Thr protein kinases as an alternate to the canonical SOS response and herewith elaborate on them with a well-studied example in the radioresistant bacterium Deinococcus radiodurans.
Collapse
Affiliation(s)
- Hari Sharan Misra
- School of Sciences, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| |
Collapse
|
5
|
Kumar A, Kamuju V, Vivekanandan P. RNA G-quadruplexes inhibit translation of the PE/PPE transcripts in Mycobacterium tuberculosis. J Biol Chem 2024; 300:105567. [PMID: 38103641 PMCID: PMC10801317 DOI: 10.1016/j.jbc.2023.105567] [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: 08/21/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023] Open
Abstract
The role of RNA G-quadruplexes (rG4s) in bacteria remains poorly understood. High G-quadruplex densities have been linked to organismal stress. Here we investigate rG4s in mycobacteria, which survive highly stressful conditions within the host. We show that rG4-enrichment is a unique feature exclusive to slow-growing pathogenic mycobacteria, and Mycobacterium tuberculosis (Mtb) transcripts contain an abundance of folded rG4s. Notably, the PE/PPE family of genes, unique to slow-growing pathogenic mycobacteria, contain over 50% of rG4s within Mtb transcripts. We found that RNA oligonucleotides of putative rG4s in PE/PPE genes form G-quadruplex structures in vitro, which are stabilized by the G-quadruplex ligand BRACO19. Furthermore, BRACO19 inhibits the transcription of PE/PPE genes and selectively suppresses the growth of Mtb but not Mycobacterium smegmatis or other rapidly growing bacteria. Importantly, the stabilization of rG4s inhibits the translation of Mtb PE/PPE genes (PPE56, PPE67, PPE68, PE_PGRS39, and PE_PGRS41) ectopically expressed in M. smegmatis or Escherichia coli. In addition, the rG4-mediated reduction in PE/PPE protein levels attenuates proinflammatory response upon infection of THP-1 cells. Our findings shed new light on the regulation of PE/PPE genes and highlight a pivotal role for rG4s in Mtb transcripts as regulators of post-transcriptional translational control. The rG4s in mycobacterial transcripts may represent potential drug targets for newer therapies.
Collapse
Affiliation(s)
- Ashish Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Vinay Kamuju
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India.
| |
Collapse
|
6
|
Pathak R. G-Quadruplexes in the Viral Genome: Unlocking Targets for Therapeutic Interventions and Antiviral Strategies. Viruses 2023; 15:2216. [PMID: 38005893 PMCID: PMC10674748 DOI: 10.3390/v15112216] [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: 09/01/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
G-quadruplexes (G4s) are unique non-canonical four-stranded nucleic acid secondary structures formed by guanine-rich DNA or RNA sequences. Sequences with the potential to form quadruplex motifs (pG4s) are prevalent throughout the genomes of all organisms, spanning from prokaryotes to eukaryotes, and are enriched within regions of biological significance. In the past few years, the identification of pG4s within most of the Baltimore group viruses has attracted increasing attention due to their occurrence in regulatory regions of the genome and the subsequent implications for regulating critical stages of viral life cycles. In this context, the employment of specific G4 ligands has aided in comprehending the intricate G4-mediated regulatory mechanisms in the viral life cycle, showcasing the potential of targeting viral G4s as a novel antiviral strategy. This review offers a thorough update on the literature concerning G4s in viruses, including their identification and functional significance across most of the human-infecting viruses. Furthermore, it delves into potential therapeutic avenues targeting G4s, encompassing various G4-binding ligands, G4-interacting proteins, and oligonucleotide-based strategies. Finally, the article highlights both progress and challenges in the field, providing valuable insights into leveraging this unusual nucleic acid structure for therapeutic purposes.
Collapse
Affiliation(s)
- Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| |
Collapse
|
7
|
De Mandal S, Srinivasan S, Jeon J. Complete genome sequence of Deinococcus rubellus Ant6 isolated from the fish muscle in the Antarctic Ocean. Front Bioeng Biotechnol 2023; 11:1257705. [PMID: 37908375 PMCID: PMC10614293 DOI: 10.3389/fbioe.2023.1257705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Affiliation(s)
- Surajit De Mandal
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio and Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul, Republic of Korea
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
8
|
Pradhan M, Kumar A, Kirti A, Pandey S, Rajaram H. NtcA, LexA and heptamer repeats involved in the multifaceted regulation of DNA repair genes recF, recO and recR in the cyanobacterium Nostoc PCC7120. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194907. [PMID: 36638863 DOI: 10.1016/j.bbagrm.2023.194907] [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: 11/07/2022] [Revised: 01/01/2023] [Accepted: 01/02/2023] [Indexed: 01/11/2023]
Abstract
Regulation of DNA repair genes in cyanobacteria is an unexplored field despite some of them exhibiting high radio-resistance. With RecF pathway speculated to be the major double strand break repair pathway in Nostoc sp. strain PCC7120, regulation of recF, recO and recR genes was investigated. Bioinformatic approach-based identification of promoter and regulatory elements was validated using qRT-PCR analysis, reporter gene and DNA binding assays. Different deletion constructs of the upstream regulatory regions of these genes were analysed in host Nostoc as well as heterologous system Escherichia coli. Studies revealed: (1) Positive regulation of all three genes by NtcA, (2) Negative regulation by LexA, (3) Involvement of contiguous heptamer repeats with/without its yet to be identified interacting partner in regulating (i) binding of NtcA and LexA to recO promoter and its translation, (ii) transcription or translation of recF, (4) Translational regulation of recF and recO through non-canonical and distant S.D. sequence and of recR through a rare initiation codon. Presence of NtcA either precludes binding of LexA to AnLexA-Box or negates its repressive action resulting in higher expression of these genes under nitrogen-fixing conditions in Nostoc. Thus, in Nostoc, expression of recF, recO and recR genes is intricately regulated through multiple regulatory elements/proteins. Contiguous heptamer repeats present across the Nostoc genome in the vicinity of start codon or promoter is likely to have a global regulatory role. This is the first report detailing regulation of DSB repair genes in any algae.
Collapse
Affiliation(s)
- Mitali Pradhan
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arvind Kumar
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Anurag Kirti
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Sarita Pandey
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Hema Rajaram
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
| |
Collapse
|
9
|
Chaudhary R, Kota S, Misra HS. DivIVA Phosphorylation Affects Its Dynamics and Cell Cycle in Radioresistant Deinococcus radiodurans. Microbiol Spectr 2023; 11:e0314122. [PMID: 36744915 PMCID: PMC10100863 DOI: 10.1128/spectrum.03141-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/06/2023] [Indexed: 02/07/2023] Open
Abstract
DivIVA is a member of the Min family of proteins that spatially regulates septum formation at the midcell position and cell pole determination in Bacillus subtilis. Deinococcus radiodurans, a Gram-positive coccus-shaped bacterium, is characterized by its extreme resistance to DNA-damaging agents, including radiation. D. radiodurans cells exposed to gamma radiation undergo cell division arrest by as-yet-uncharacterized mechanisms. divIVA is shown to be an essential cell division gene in this bacterium, and DivIVA of D. radiodurans (drDivIVA) interacts with genome segregation proteins through its N-terminal region. Earlier, RqkA, a gamma radiation-responsive Ser/Thr quinoprotein kinase, was characterized for its role in radioresistance in D. radiodurans. Here, we showed that RqkA phosphorylates drDivIVA at the threonine 19 (T19) residue. The phospho-mimetic mutant with a mutation of T19 to E19 in DivIVA (DivIVAT19E) is found to be functionally different from the phospho-ablative mutant (DivIVAT19A) or the wild-type drDivIVA. A DivIVAT19E-red fluorescent protein (RFP) fusion expressed in the wild-type background showed the arrest in the typical dynamics of drDivIVA and the loss of its interaction with the genome segregation protein ParA2. The allelic replacement of divIVA with divIVAT19E-rfp was not tolerated unless drDivIVA was expressed episomally, while there was no phenotypic change when the wild-type allele was replaced with either divIVAT19A-rfp or divIVA-rfp. These results suggested that the phosphorylation of T19 in drDivIVA by RqkA affected its in vivo functions, which may contribute to the cell cycle arrest in this bacterium. IMPORTANCE Deinococcus radiodurans, a radioresistant bacterium, lacks LexA/RecA-mediated DNA damage response and cell cycle regulation as known in other bacteria. However, it adjusts its transcriptome and proteome upon DNA damage. In eukaryotes, the DNA damage response and cell cycle are regulated by Ser/Thr protein kinases. In D. radiodurans, we characterized a gamma radiation-responsive Ser/Thr quinoprotein kinase (RqkA) that phosphorylated DNA repair and cell division proteins in this bacterium. In previous work, the effect of S/T phosphorylation by RqkA on activity improvement of the DNA repair proteins has been demonstrated. This study reports that Ser phosphorylation by RqkA attenuates the function of a cell polarity and plane of cell division-determining protein, DivIVA, and its cellular dynamics in response to DNA damage, which might help to understand the mechanism of cell cycle regulation in this bacterium.
Collapse
Affiliation(s)
- Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Hari S. Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Mumbai, India
- School of Science, GITAM, Visakhapatnam, Andhra Pradesh, India
| |
Collapse
|
10
|
Zheng BX, Yu J, Long W, Chan KH, Leung ASL, Wong WL. Structurally diverse G-quadruplexes as the noncanonical nucleic acid drug target for live cell imaging and antibacterial study. Chem Commun (Camb) 2023; 59:1415-1433. [PMID: 36636928 DOI: 10.1039/d2cc05945b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The formation of G-quadruplex structures (G4s) in vitro from guanine (G)-rich nucleic acid sequences of DNA and RNA stabilized with monovalent cations, typically K+ and Na+, under physiological conditions, has been verified experimentally and some of them have high-resolution NMR or X-ray crystal structures; however, the biofunction of these special noncanonical secondary structures of nucleic acids has not been fully understood and their existence in vivo is still controversial at present. It is generally believed that the folding and unfolding of G4s in vivo is a transient process. Accumulating evidence has shown that G4s may play a role in the regulation of certain important cellular functions including telomere maintenance, replication, transcription and translation. Therefore, both DNA and RNA G4s of human cancer hallmark genes are recognized as the potential anticancer drug target for the investigation in cancer biology, chemical biology and drug discovery. The relationship between the sequence, structure and stability of G4s, the interaction of G4s with small molecules, and insights into the rational design of G4-selective binding ligands have been intensively studied over the decade. At present, some G4-ligands have achieved a new milestone and successfully entered the human clinical trials for anticancer therapy. Over the past few decades, numerous efforts have been devoted to anticancer therapy; however, G4s for molecular recognition and live cell imaging and for application as antibacterial agents and antibiofilms against antibiotic resistance have been obviously underexplored. The recent advances in G4-ligands in these areas are thus selected and discussed concentratedly in this article in order to shed light on the emerging role of G4s in chemical biology and therapeutic prospects against bacterial infections. In addition, the recently published molecular scaffolds for designing small ligands selectively targeting G4s in live cell imaging, bacterial biofilm imaging, and antibacterial studies are discussed. Furthermore, a number of underexplored G4-targets from the cytoplasmic membrane-associated DNA, the conserved promoter region of K. pneumoniae genomes, the RNA G4-sites in the transcriptome of E. coli and P. aeruginosa, and the mRNA G4-sites in the sequence for coding the vital bacterial FtsZ protein are highlighted to further explore in G4-drug development against human diseases.
Collapse
Affiliation(s)
- Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Jie Yu
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Wei Long
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Ka Hin Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Alan Siu-Lun Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China. .,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| |
Collapse
|
11
|
Evans L, Kotar A, Valentini M, Filloux A, Jamshidi S, Plavec J, Rahman KM, Vilar R. Identification and characterisation of G-quadruplex DNA-forming sequences in the Pseudomonas aeruginosa genome. RSC Chem Biol 2023; 4:94-100. [PMID: 36685252 PMCID: PMC9811510 DOI: 10.1039/d2cb00205a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
Abstract
A number of Gram-negative bacteria such as Pseudomonas aeruginosa are becoming resistant to front-line antibiotics. Consequently, there is a pressing need to find alternative bio-molecular targets for the development of new drugs. Since non-canonical DNA structures such as guanine-quadruplexes (G4s) have been implicated in regulating transcription, we were interested in determining whether there are putative quadruplex-forming sequences (PQS) in the genome of Pseudomonas aeruginosa. Using bioinformatic tools, we screened 36 genes potentially relevant to drug resistance for the presence of PQS and 10 of these were selected for biophysical characterisation (i.e. circular dichroism and thermal difference UV/Vis spectroscopy). These studies showed that three of these G-rich sequences (linked to murE, ftsB and mexC genes) form stable guanine-quadruplexes which were studied by NMR spectroscopy; detailed analysis of one of the sequences (mexC) confirmed that it adopts a two-quartet antiparallel quadruplex structure in the presence of K+ ions. We also show by FRET melting assays that small molecules can stabilise these three new G4 DNA structures under physiological conditions. These initial results could be of future interest in the development of new antibiotics with alternative bio-molecular targets which in turn would help tackle antimicrobial resistance.
Collapse
Affiliation(s)
- Lindsay Evans
- Department of Chemistry, Imperial College London, White City CampusLondon W12 OBZUK
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 191000 LjubljanaSlovenia
| | - Martina Valentini
- Department of Life Sciences, MRC Centre for Molecular Microbiology and Infection, Imperial College London, South Kensington CampusLondon SW7 2AZUK
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Microbiology and Infection, Imperial College London, South Kensington CampusLondon SW7 2AZUK
| | - Shirin Jamshidi
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building150 Stamford StreetLondon SE1 9NHUK
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 191000 LjubljanaSlovenia
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building150 Stamford StreetLondon SE1 9NHUK
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, White City CampusLondon W12 OBZUK
| |
Collapse
|
12
|
Qin G, Zhao C, Yang J, Wang Z, Ren J, Qu X. Unlocking G-Quadruplexes as Targets and Tools against COVID-19. CHINESE J CHEM 2022; 41:CJOC202200486. [PMID: 36711116 PMCID: PMC9874442 DOI: 10.1002/cjoc.202200486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 02/01/2023]
Abstract
The applicability of G-quadruplexes (G4s) as antiviral targets, therapeutic agents and diagnostic tools for coronavirus disease 2019 (COVID-19) is currently being evaluated, which has drawn the extensive attention of the scientific community. During the COVID-19 pandemic, research in this field is rapidly accumulating. In this review, we summarize the latest achievements and breakthroughs in the use of G4s as antiviral targets, therapeutic agents and diagnostic tools for COVID-19, particularly using G4 ligands. Finally, strength and weakness regarding G4s in anti-SARS-CoV-2 field are highlighted for prospective future projects.
Collapse
Affiliation(s)
- Geng Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Jie Yang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Zhao Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource UtilizationChangchun Institute of Applied Chemistry Chinese Academy of ScienceChangchun, Jilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| |
Collapse
|
13
|
Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. G-Quadruplex Structures in Bacteria: Functional Properties and Prospects for Use as Biotargets. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2022. [DOI: 10.1134/s1990750822040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
14
|
Cueny RR, McMillan SD, Keck JL. G-quadruplexes in bacteria: insights into the regulatory roles and interacting proteins of non-canonical nucleic acid structures. Crit Rev Biochem Mol Biol 2022; 57:539-561. [PMID: 36999585 PMCID: PMC10336854 DOI: 10.1080/10409238.2023.2181310] [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: 08/04/2022] [Revised: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 04/01/2023]
Abstract
G-quadruplexes (G4s) are highly stable, non-canonical DNA or RNA structures that can form in guanine-rich stretches of nucleic acids. G4-forming sequences have been found in all domains of life, and proteins that bind and/or resolve G4s have been discovered in both bacterial and eukaryotic organisms. G4s regulate a variety of cellular processes through inhibitory or stimulatory roles that depend upon their positions within genomes or transcripts. These include potential roles as impediments to genome replication, transcription, and translation or, in other contexts, as activators of genome stability, transcription, and recombination. This duality suggests that G4 sequences can aid cellular processes but that their presence can also be problematic. Despite their documented importance in bacterial species, G4s remain understudied in bacteria relative to eukaryotes. In this review, we highlight the roles of bacterial G4s by discussing their prevalence in bacterial genomes, the proteins that bind and unwind G4s in bacteria, and the processes regulated by bacterial G4s. We identify limitations in our current understanding of the functions of G4s in bacteria and describe new avenues for studying these remarkable nucleic acid structures.
Collapse
Affiliation(s)
- Rachel R. Cueny
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Sarah D. McMillan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| |
Collapse
|
15
|
Chang T, Li G, Ding Z, Li W, Zhu P, Lei W, Shangguan D. Potential G-quadruplexes within the Promoter Nuclease Hypersensitive Sites of the Heat-responsive Genes in Rice. Chembiochem 2022; 23:e202200405. [PMID: 36006168 DOI: 10.1002/cbic.202200405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Indexed: 11/11/2022]
Abstract
G-quadruplexes (G4s) have been shown to be involved in the regulation of multiple cellular processes. Exploring putative G4-forming sequences (PQSs) in heat-responsive genes of rice and their folding structures under different conditions will help to understand the mechanism in response to heat stress. In this work, we discovered a prevalence of PQSs in nuclease hypersensitive sites within the promoters of heat-responsive genes. Moreover, 50% of the searched G3 PQSs ((G3+L1-7)3+G3+) locate in heat shock transcription factors. Circular dichroism spectroscopy, thermal difference spectroscopy, and UV melting analysis demonstrated the representative PQSs could adopt stable G4s at physiological temperature and potassium concentration. These PQSs were able to stall Klenow Fragment (KF) DNA polymerase by the formation of G4s. However, the G4s with Tm values around 50 - 60 oC could be increasingly unwound by KF with the increase of temperatures from 25 to 50 oC, implying these G4s could sense the changes in temperature by structural switch. This work offers fresh clue to understand the potential of G4-involved functions of PQSs and the molecular events in plants in the response to heat stress.
Collapse
Affiliation(s)
- Tianjun Chang
- Henan Polytechnic University, Institute of Enveiroment and Resoures, 2001 Shiji Avenue, 454003, Jiaozuo, CHINA
| | - Guangping Li
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Zhan Ding
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Weiguo Li
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Panpan Zhu
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Wei Lei
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Dihua Shangguan
- Institute of Chemistry Chinese Academy of Sciences, Beijing National Laboratory for Molecular Sciences, Key Labor-atory of Analytical Chemistry for Living Biosystems, CAS Re-search/Education Center for Excellence in Molecular Sciences, CHINA
| |
Collapse
|
16
|
Effects of G-Quadruplex-Binding Plant Secondary Metabolites on c-MYC Expression. Int J Mol Sci 2022; 23:ijms23169209. [PMID: 36012470 PMCID: PMC9409388 DOI: 10.3390/ijms23169209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 11/25/2022] Open
Abstract
Guanine-rich DNA sequences tending to adopt noncanonical G-quadruplex (G4) structures are over-represented in promoter regions of oncogenes. Ligands recognizing G4 were shown to stabilize these DNA structures and drive their formation regulating expression of corresponding genes. We studied the interaction of several plant secondary metabolites (PSMs) with G4s and their effects on gene expression in a cellular context. The binding of PSMs with G4s formed by the sequences of well-studied oncogene promoters and telomeric repeats was evaluated using a fluorescent indicator displacement assay. c-MYC G4 folding topology and thermal stability, as well as the PMS influence on these parameters, were demonstrated by UV-spectroscopy and circular dichroism. The effects of promising PSMs on c-MYC expression were assessed using luciferase reporter assay and qPR-PCR in cancer and immortalized cultured cells. The ability of PMS to multi-targeting cell signaling pathways was analyzed by the pathway-focused gene expression profiling with qRT-PCR. The multi-target activity of a number of PSMs was demonstrated by their interaction with a set of G4s mimicking those formed in the human genome. We have shown a direct G4-mediated down regulation of c-MYC expression by sanguinarine, quercetin, kaempferol, and thymoquinone; these effects being modulated by PSM’s indirect influence via cell signaling pathways.
Collapse
|
17
|
Ishiguro A, Ishihama A. Essential Roles and Risks of G-Quadruplex Regulation: Recognition Targets of ALS-Linked TDP-43 and FUS. Front Mol Biosci 2022; 9:957502. [PMID: 35898304 PMCID: PMC9309350 DOI: 10.3389/fmolb.2022.957502] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
A non-canonical DNA/RNA structure, G-quadruplex (G4), is a unique structure formed by two or more guanine quartets, which associate through Hoogsteen hydrogen bonding leading to form a square planar arrangement. A set of RNA-binding proteins specifically recognize G4 structures and play certain unique physiological roles. These G4-binding proteins form ribonucleoprotein (RNP) through a physicochemical phenomenon called liquid-liquid phase separation (LLPS). G4-containing RNP granules are identified in both prokaryotes and eukaryotes, but extensive studies have been performed in eukaryotes. We have been involved in analyses of the roles of G4-containing RNAs recognized by two G4-RNA-binding proteins, TDP-43 and FUS, which both are the amyotrophic lateral sclerosis (ALS) causative gene products. These RNA-binding proteins play the essential roles in both G4 recognition and LLPS, but they also carry the risk of agglutination. The biological significance of G4-binding proteins is controlled through unique 3D structure of G4, of which the risk of conformational stability is influenced by environmental conditions such as monovalent metals and guanine oxidation.
Collapse
|
18
|
Castelli M, Doria F, Freccero M, Colombo G, Moroni E. Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data. J Chem Theory Comput 2022; 18:4515-4528. [PMID: 35666124 PMCID: PMC9281369 DOI: 10.1021/acs.jctc.2c00291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Molecular dynamics
(MD) simulations are coming of age in the study
of nucleic acids, including specific tertiary structures such as G-quadruplexes.
While being precious for providing structural and dynamic information
inaccessible to experiments at the atomistic level of resolution,
MD simulations in this field may still be limited by several factors.
These include the force fields used, different models for ion parameters,
ionic strengths, and water models. We address various aspects of this
problem by analyzing and comparing microsecond-long atomistic simulations
of the G-quadruplex structure formed by the human immunodeficiency
virus long terminal repeat (HIV LTR)-III sequence for which nuclear
magnetic resonance (NMR) structures are available. The system is studied
in different conditions, systematically varying the ionic strengths,
ion numbers, and water models. We comparatively analyze the dynamic
behavior of the G-quadruplex motif in various conditions and assess
the ability of each simulation to satisfy the nuclear magnetic resonance
(NMR)-derived experimental constraints and structural parameters.
The conditions taking into account K+-ions to neutralize
the system charge, mimicking the intracellular ionic strength, and
using the four-atom water model are found to be the best in reproducing
the experimental NMR constraints and data. Our analysis also reveals
that in all of the simulated environments residues belonging to the
duplex moiety of HIV LTR-III exhibit the highest flexibility.
Collapse
Affiliation(s)
- Matteo Castelli
- Department of Chemistry, University of Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, V.le Taramelli 12, 27100 Pavia, Italy.,Institute of Chemical Sciences and Technologies SCITEC-CNR, Via Mario Bianco, 9, 20131 Milano, Italy
| | - Elisabetta Moroni
- Institute of Chemical Sciences and Technologies SCITEC-CNR, Via Mario Bianco, 9, 20131 Milano, Italy
| |
Collapse
|
19
|
Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. [G-quadruplex structures in bacteria: functional properties and prospects for use as biotargets]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:93-103. [PMID: 35485483 DOI: 10.18097/pbmc20226802093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
G-quadruplexes (G4), non-canonical secondary DNA structures, are intensively investigated for a long time. In eukaryotic organisms they play an important role in the regulation of gene expression and DNA repair. G4 have also been found in the genomes of numerous bacteria and archaea, but their functional role has not yet been fully explored. Nevertheless, their participation in the formation of antigenic variability, pathogenicity, antibiotic resistance and survival in extreme conditions has been established. Currently, many tools have been developed to detect potential G4 sequences and confirm their formation ability. Since the controlled formation and resolution of the quadruplex are significant means for the regulation of genes critical for survival, a promising direction is the search for ligands - compounds that can have a stabilizing effect on the quadruplex structure and thereby alter gene expression. Currently, a number of ligands are already known, their use stops the growth of pathogenic microorganisms. G4 ligands are of interest as potential antibiotics, which are extremely relevant due to the wide spread of drug resistant pathogens.
Collapse
Affiliation(s)
- E A Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D A Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I N Bodoev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - M V Zaychikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| |
Collapse
|
20
|
Haldar S, Zhang Y, Xia Y, Islam B, Liu S, Gervasio FL, Mulholland AJ, Waller ZAE, Wei D, Haider S. Mechanistic Insights into the Ligand-Induced Unfolding of an RNA G-Quadruplex. J Am Chem Soc 2022; 144:935-950. [PMID: 34989224 DOI: 10.1021/jacs.1c11248] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The cationic porphyrin TMPyP4 is a well-established DNA G-quadruplex (G4) binding ligand that can stabilize different topologies via multiple binding modes. However, TMPyP4 can have both a stabilizing and destabilizing effect on RNA G4 structures. The structural mechanisms that mediate RNA G4 unfolding remain unknown. Here, we report on the TMPyP4-induced RNA G4 unfolding mechanism studied by well-tempered metadynamics (WT-MetaD) with supporting biophysical experiments. The simulations predict a two-state mechanism of TMPyP4 interaction via a groove-bound and a top-face-bound conformation. The dynamics of TMPyP4 stacking on the top tetrad disrupts Hoogsteen H-bonds between guanine bases, resulting in the consecutive TMPyP4 intercalation from top-to-bottom G-tetrads. The results reveal a striking correlation between computational and experimental approaches and validate WT-MetaD simulations as a powerful tool for studying RNA G4-ligand interactions.
Collapse
Affiliation(s)
- Susanta Haldar
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, U.K
- D.E. Shaw India Private Ltd., Hyderabad, Telangana 500096, India
| | - Yashu Zhang
- State Key Laboratory of Agricultural Microbiology, College of Vetrinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Xia
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
| | - Barira Islam
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, U.K
| | - Sisi Liu
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Francesco L Gervasio
- Department of Chemistry, University College London, London, WC1H 0AJ, U.K
- Pharmaceutical Sciences, University of Geneva, Geneva CH-1211, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), Geneva CH-1211, Switzerland
| | | | - Zoë A E Waller
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Vetrinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- National Reference Laboratory of Veterinary Drug Residues and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London, WC1N 1AX, U.K
- UCL Centre for Advanced Research Computing, University College London, London, WC1H 9RN, U.K
| |
Collapse
|
21
|
Nishikawa T, Kuwano Y, Nakata M, Rokutan K, Nishida K. Multiple G-quadruplexes in the LMNA promoter regulate LMNA variant 6 transcription and promote colon cancer cell growth. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194746. [PMID: 34419630 DOI: 10.1016/j.bbagrm.2021.194746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/22/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
Lamin A/C proteins, major components of the nuclear lamina, are encoded by the LMNA gene. These proteins have multiple cellular functions, including DNA transcription and replication, chromatin organization, regulation of the cell cycle, and apoptosis. Mutations in LMNA are associated with a variety of diseases called laminopathies. LMNA has implications in cancer; however, its mechanisms of dysregulation in cancer cells are not yet fully understood. In this study, among the LMNA transcript variants, we focused on a transcriptional variant 6 (termed LMNA-V6), which contains unique 3 exons upstream of exon 1 of LMNA. The promoter region of LMNA-V6 formed multiple G-quadruplexes and increased its transcriptional activity. Moreover, LMNA-V6 negatively regulated other LMNA mRNA variants, lamin A and lamin C, via direct interaction with their promoter. Knockdown of LMNA-V6 decreased the proliferation of colon cancer cells, whereas overexpression of the unique 3 exons of LMNA-V6 increased cell growth. Furthermore, microarray gene expression profiling showed that alteration of LMNA-V6 levels influenced the expression of p53 in colon cancer cells. Taken together, the results suggest that LMNA-V6 may be a novel functional RNA whose expression is regulated through multiple G-quadruplexes in colon cancer cells.
Collapse
Affiliation(s)
- Tatsuya Nishikawa
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan; Department of Onco-cardiology, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan.
| | - Mayu Nakata
- Student Lab, Tokushima University Faculty of Medicine, Tokushima, Japan
| | - Kazuhito Rokutan
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Kensei Nishida
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Non-B DNA-Forming Motifs Promote Mfd-Dependent Stationary-Phase Mutagenesis in Bacillus subtilis. Microorganisms 2021; 9:microorganisms9061284. [PMID: 34204686 PMCID: PMC8231525 DOI: 10.3390/microorganisms9061284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 02/07/2023] Open
Abstract
Transcription-induced mutagenic mechanisms limit genetic changes to times when expression happens and to coding DNA. It has been hypothesized that intrinsic sequences that have the potential to form alternate DNA structures, such as non-B DNA structures, influence these mechanisms. Non-B DNA structures are promoted by transcription and induce genome instability in eukaryotic cells, but their impact in bacterial genomes is less known. Here, we investigated if G4 DNA- and hairpin-forming motifs influence stationary-phase mutagenesis in Bacillus subtilis. We developed a system to measure the influence of non-B DNA on B. subtilis stationary-phase mutagenesis by deleting the wild-type argF at its chromosomal position and introducing IPTG-inducible argF alleles differing in their ability to form hairpin and G4 DNA structures into an ectopic locus. Using this system, we found that sequences predicted to form non-B DNA structures promoted mutagenesis in B. subtilis stationary-phase cells; such a response did not occur in growing conditions. We also found that the transcription-coupled repair factor Mfd promoted mutagenesis at these predicted structures. In summary, we showed that non-B DNA-forming motifs promote genetic instability, particularly in coding regions in stressed cells; therefore, non-B DNA structures may have a spatial and temporal mutagenic effect in bacteria. This study provides insights into mechanisms that prevent or promote mutagenesis and advances our understanding of processes underlying bacterial evolution.
Collapse
|
24
|
G-Quadruplex Structures in Bacteria: Biological Relevance and Potential as an Antimicrobial Target. J Bacteriol 2021; 203:e0057720. [PMID: 33649149 DOI: 10.1128/jb.00577-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA strands consisting of multiple runs of guanines can adopt a noncanonical, four-stranded DNA secondary structure known as G-quadruplex or G4 DNA. G4 DNA is thought to play an important role in transcriptional and translational regulation of genes, DNA replication, genome stability, and oncogene expression in eukaryotic genomes. In other organisms, including several bacterial pathogens and some plant species, the biological roles of G4 DNA and G4 RNA are starting to be explored. Recent investigations showed that G4 DNA and G4 RNA are generally conserved across plant species. In silico analyses of several bacterial genomes identified putative guanine-rich, G4 DNA-forming sequences in promoter regions. The sequences were particularly abundant in certain gene classes, suggesting that these highly diverse structures can be employed to regulate the expression of genes involved in secondary metabolite synthesis and signal transduction. Furthermore, in the pathogen Mycobacterium tuberculosis, the distribution of G4 motifs and their potential role in the regulation of gene transcription advocate for the use of G4 ligands to develop novel antitubercular therapies. In this review, we discuss the various roles of G4 structures in bacterial DNA and the application of G4 DNA as inhibitors or therapeutic agents to address bacterial pathogens.
Collapse
|
25
|
Masud T, Soong C, Xu H, Biele J, Bjornson S, McKinney S, Aparicio S. Ubiquitin-mediated DNA damage response is synthetic lethal with G-quadruplex stabilizer CX-5461. Sci Rep 2021; 11:9812. [PMID: 33963218 PMCID: PMC8105411 DOI: 10.1038/s41598-021-88988-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 04/09/2021] [Indexed: 12/12/2022] Open
Abstract
CX-5461 is a G-quadruplex (G4) ligand currently in trials with initial indications of clinical activity in cancers with defects in homologous recombination repair. To identify more genetic defects that could sensitize tumors to CX-5461, we tested synthetic lethality for 480 DNA repair and genome maintenance genes to CX-5461, pyridostatin (PDS), a structurally unrelated G4-specific stabilizer, and BMH-21, which binds GC-rich DNA but not G4 structures. We identified multiple members of HRD, Fanconi Anemia pathways, and POLQ, a polymerase with a helicase domain important for G4 structure resolution. Significant synthetic lethality was observed with UBE2N and RNF168, key members of the DNA damage response associated ubiquitin signaling pathway. Loss-of-function of RNF168 and UBE2N resulted in significantly lower cell survival in the presence of CX-5461 and PDS but not BMH-21. RNF168 recruitment and histone ubiquitination increased with CX-5461 treatment, and nuclear ubiquitination response frequently co-localized with G4 structures. Pharmacological inhibition of UBE2N acted synergistically with CX-5461. In conclusion, we have uncovered novel genetic vulnerabilities to CX-5461 with potential significance for patient selection in future clinical trials.
Collapse
Affiliation(s)
- Tehmina Masud
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Charles Soong
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Hong Xu
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Justina Biele
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Saelin Bjornson
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Steven McKinney
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
| |
Collapse
|
26
|
Ketkar A, Smith L, Johnson C, Richey A, Berry M, Hartman JH, Maddukuri L, Reed MR, Gunderson JEC, Leung JWC, Eoff RL. Human Rev1 relies on insert-2 to promote selective binding and accurate replication of stabilized G-quadruplex motifs. Nucleic Acids Res 2021; 49:2065-2084. [PMID: 33555350 PMCID: PMC7913688 DOI: 10.1093/nar/gkab041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/06/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
We previously reported that human Rev1 (hRev1) bound to a parallel-stranded G-quadruplex (G4) from the c-MYC promoter with high affinity. We have extended those results to include other G4 motifs, finding that hRev1 exhibited stronger affinity for parallel-stranded G4 than either anti-parallel or hybrid folds. Amino acids in the αE helix of insert-2 were identified as being important for G4 binding. Mutating E466 and Y470 to alanine selectively perturbed G4 binding affinity. The E466K mutant restored wild-type G4 binding properties. Using a forward mutagenesis assay, we discovered that loss of hRev1 increased G4 mutation frequency >200-fold compared to the control sequence. Base substitutions and deletions occurred around and within the G4 motif. Pyridostatin (PDS) exacerbated this effect, as the mutation frequency increased >700-fold over control and deletions upstream of the G4 site more than doubled. Mutagenic replication of G4 DNA (±PDS) was partially rescued by wild-type and E466K hRev1. The E466A or Y470A mutants failed to suppress the PDS-induced increase in G4 mutation frequency. These findings have implications for the role of insert-2, a motif conserved in vertebrates but not yeast or plants, in Rev1-mediated suppression of mutagenesis during G4 replication.
Collapse
Affiliation(s)
- Amit Ketkar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Lane Smith
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Callie Johnson
- Arkansas School for Mathematics, Sciences, and the Arts, Hot Springs, AR 71901, USA
| | - Alyssa Richey
- Arkansas School for Mathematics, Sciences, and the Arts, Hot Springs, AR 71901, USA
| | - Makayla Berry
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jessica H Hartman
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Leena Maddukuri
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Megan R Reed
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | | | - Justin W C Leung
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| |
Collapse
|
27
|
Kumari N, Raghavan SC. G-quadruplex DNA structures and their relevance in radioprotection. Biochim Biophys Acta Gen Subj 2021; 1865:129857. [PMID: 33508382 DOI: 10.1016/j.bbagen.2021.129857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND DNA, the genetic material of most of the organisms, is the crucial element of life. Integrity of DNA needs to be maintained for transmission of genetic material from one generation to another. All organisms are constantly challenged by the environmental conditions which can lead to the induction of DNA damage. Ionizing radiation (IR) has been known to induce DNA damage and IR sensitivity varies among different organisms. The causes for differential radiosensitivity among various organisms have not been studied in great detail. SCOPE OF REVIEW We discuss DNA secondary structure formation, GC content of the genome, role of G-quadruplex formation, and its relationship with radiosensitivity of the genome. MAJOR CONCLUSION In Deinococcus radiodurans, the bacterium that exhibits maximum radio resistance, multiple G-quadruplex forming motifs are reported. In human cells, G-quadruplex formation led to differential radiosensitivity. In this article, we have discussed, the role of secondary DNA structure formation like G-quadruplex in shielding the genome from radiation and its implications in understanding evolution of radio protective effect of an organism. We also discuss role of GC content and its correlation with radio resistance. GENERAL SIGNIFICANCE This review provides an insight into the role of G-quadruplexes in providing differential radiosensitivity at different site of the genome and in different organisms. It further discusses the possibility of higher GC content contributing towards reduced radiosensitivity in different organisms, evolution of radiosensitivity, and regulation of multiple cellular processes.
Collapse
Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
28
|
Wu F, Niu K, Cui Y, Li C, Lyu M, Ren Y, Chen Y, Deng H, Huang L, Zheng S, Liu L, Wang J, Song Q, Xiang H, Feng Q. Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution. Commun Biol 2021; 4:98. [PMID: 33483610 PMCID: PMC7822830 DOI: 10.1038/s42003-020-01643-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/29/2020] [Indexed: 01/30/2023] Open
Abstract
G-quadruplex (G4) structures have been predicted in the genomes of many organisms and proven to play regulatory roles in diverse cellular activities. However, there is little information on the evolutionary history and distribution characteristics of G4s. Here, whole-genome characteristics of potential G4s were studied in 37 evolutionarily representative species. During evolution, the number, length, and density of G4s generally increased. Immunofluorescence in seven species confirmed G4s' presence and evolutionary pattern. G4s tended to cluster in chromosomes and were enriched in genetic regions. Short-loop G4s were conserved in most species, while loop-length diversity also existed, especially in mammals. The proportion of G4-bearing genes and orthologue genes, which appeared to be increasingly enriched in transcription factors, gradually increased. The antagonistic relationship between G4s and DNA methylation sites was detected. These findings imply that organisms may have evolutionarily developed G4 into a novel reversible and elaborate transcriptional regulatory mechanism benefiting multiple physiological activities of higher organisms.
Collapse
Affiliation(s)
- Feng Wu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yong Cui
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Cencen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mo Lyu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yandong Ren
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Yanfei Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huimin Deng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lihua Huang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sichun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| |
Collapse
|
29
|
Sengupta A, Roy SS, Chowdhury S. Non-duplex G-Quadruplex DNA Structure: A Developing Story from Predicted Sequences to DNA Structure-Dependent Epigenetics and Beyond. Acc Chem Res 2021; 54:46-56. [PMID: 33347280 DOI: 10.1021/acs.accounts.0c00431] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The story of the non-duplex DNA form known as the G-quadruplex (G4) has traversed a winding path. From initial skepticism followed by debate to a surge in interest, the G4 story intertwines many threads. Starting with computational predictions of a gene regulatory role, which now include epigenetic functions, our group was involved in many of these advances along with many other laboratories. Following a brief background, set in the latter half of the last century when the concept of the G4 as a structure took ground, here we account the developments. This is through a lens that though focused on our groups' research presents work from many other groups that played significant roles. Together these provide a broad perspective to the G4 story. Initially we were intrigued on seeing potential G4 (pG4)-forming sequences, then known to be found primarily at the telomeres and immunoglobin switch regions, occurring throughout the genome and being particularly prevalent in promoters of bacteria. We further observed that pG4s were not only prevalent but also conserved through evolution in promoters of human, chimpanzee, mouse and rat genomes. This was between 2005 and 2007. Encouraged by these partly and partly in response to the view held by many that genome-wide presence of G4s were genomic "accidents", the focus shifted to seeking experimental evidence.In the next year, 2008, two independent findings showed promise. First, on treating human cancer cells with G4-binding ligands, we observed widespread change in gene expression. Second, our search for the missing G4-specific transcription factor, without which, importantly, G4s in promoters posed only half the story, yielded results. We determined how NM23-H2 (also known as NME2 or NDPK-B) interacts with G4s and how interaction of NM23-H2 with a G4 in the promoter of the oncogene c-myc was important for regulation of c-myc transcription. NM23-H2, and subsequently many other similar factors discovered by multiple groups, is possibly giving shape to what might be the "G4-transcriptome". Later, a close look at NM23-H2-G4 interaction in regulation of the human reverse transcriptase gene (hTERT) revealed the role of G4s in local epigenetic modifications. Meanwhile work from others showed how G4s impact histone modifications following replication. Together these show the intrinsic role of DNA sequence, through formation of DNA structure, in epigenetics.More recent work, however, was waiting to reveal aspects that tend to bring forth a completely new understanding of G4s. We observed that the telomere-repeat-binding-factor-2 (TRF2), known canonically to be telomere-associated, binds extensively outside telomeres throughout the genome. Moreover, a large fraction of the non-telomeric TRF2 sites comprise G4s. Second, the extent of non-telomeric TRF2 binding at promoters was dependent on telomere length. Thereby TRF2-induced epigenetic gene regulation was telomere-dependent. Together these implicate underlying connections that show signs of addressing an intriguing unanswered question that takes us back to the beginning: Why are G4s prevalent in two distinct regions, the telomeres and gene promoters?
Collapse
Affiliation(s)
- Antara Sengupta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shuvra Shekhar Roy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shantanu Chowdhury
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
30
|
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.
Collapse
|
31
|
Kota S, Chaudhary R, Mishra S, Misra HS. Topoisomerase IB interacts with genome segregation proteins and is involved in multipartite genome maintenance in Deinococcus radiodurans. Microbiol Res 2020; 242:126609. [PMID: 33059113 DOI: 10.1016/j.micres.2020.126609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
Deinococcus radiodurans, an extremophile, resistant to many abiotic stresses including ionizing radiation, has 2 type I topoisomerases (drTopo IA and drTopo IB) and one type II topoisomerase (DNA gyrase). The role of drTopo IB in guanine quadruplex DNA (G4 DNA) metabolism was demonstrated earlier in vitro. Here, we report that D. radiodurans cells lacking drTopo IB (ΔtopoIB) show sensitivity to G4 DNA binding drug (NMM) under normal growth conditions. The activity of G4 motif containing promoters like mutL and recQ was reduced in the presence of NMM in mutant cells. In mutant, the percentage of anucleate cells was more while the copy number of genome elements were less as compared to wild type. Protein-protein interaction studies showed that drTopo IB interacts with genome segregation and DNA replication initiation (DnaA) proteins. The typical patterns of cellular localization of GFP-PprA were affected in the mutant cells. Microscopic examination of D. radiodurans cells expressing drTopo IB-RFP showed its localization on nucleoid forming a streak parallel to the old division septum and perpendicular to newly formed septum. These results together suggest the role of drTopo IB in genome maintenance in this bacterium.
Collapse
Affiliation(s)
- Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai, 400094, India.
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai, 400094, India
| | - Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai, 400094, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai, 400094, India.
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Jain N, Mishra SK, Shankar U, Jaiswal A, Sharma TK, Kodgire P, Kumar A. G-quadruplex stabilization in the ions and maltose transporters gene inhibit Salmonella enterica growth and virulence. Genomics 2020; 112:4863-4874. [PMID: 32898642 PMCID: PMC7474834 DOI: 10.1016/j.ygeno.2020.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/15/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022]
Abstract
The G-quadruplex structure is a highly conserved drug target for preventing infection of several human pathogens. We tried to explore G-quadruplex forming motifs as promising drug targets in the genome of Salmonella enterica that causes enteric fever in humans. Herein, we report three highly conserved G-quadruplex motifs (SE-PGQ-1, 2, and 3) in the genome of Salmonella enterica. Bioinformatics analysis inferred the presence of SE-PGQ-1 in the regulatory region of mgtA, SE-PGQ-2 in ORF of entA, and SE-PGQ-3 in the promoter region of malE and malK genes. The G-quadruplex forming sequences were confirmed by biophysical and biomolecular techniques. Cellular studies affirm the inhibitory effect of G-quadruplex specific ligands on Salmonella enterica growth. Further, PCR inhibition, reporter based assay, and RT-qPCR assays emphasize the biological relevance of G-quadruplexes in these genes. Thus, this study confirmed the presence of G-quadruplex motifs in Salmonella enterica and characterized them as a promising drug target.
Collapse
Affiliation(s)
- Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Ankit Jaiswal
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India.
| |
Collapse
|
34
|
Xue ZY, Wu WQ, Zhao XC, Kumar A, Ran X, Zhang XH, Zhang Y, Guo LJ. Single-molecule probing the duplex and G4 unwinding patterns of a RecD family helicase. Int J Biol Macromol 2020; 164:902-910. [PMID: 32693146 DOI: 10.1016/j.ijbiomac.2020.07.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 10/23/2022]
Abstract
RecD family helicases play an important role in prokaryotic genome stability and serve as the structural models for studying superfamily 1B (SF1B) helicases. However, RecD-catalyzed duplex DNA unwinding behavior and the underlying mechanism are still elusive. RecD family helicases share a common proto-helicase with eukaryotic Pif1 family helicases, which are well known for their outstanding G-quadruplex (G4) unwinding ability. However, there are still controversial points as to whether and how RecD helicases unfold G4 structures. Here, single-molecule fluorescence resonance energy transfer (smFRET) and magnetic tweezers (MT) were used to study Deinococcus radiodurans RecD2 (DrRecD2)-mediated duplex DNA unwinding and resolution of G4 structures. A symmetric, repetitive unwinding phenomenon was observed on duplex DNA, revealed from the strand switch and translocation of one monomer. Furthermore, we found that DrRecD2 was able to unwind both parallel and antiparallel G4 structures without obvious topological preferences. Surprisingly, the unwinding properties of RecD on duplex and G4 DNA are different from those of Pif1. The findings provide an example, in which the patterns of two molecules derived from a common ancestor deviate during evolution, and they are of significance for understanding the unwinding mechanism and function of SF1B helicases.
Collapse
Affiliation(s)
- Zhen-Yong Xue
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China
| | - Wen-Qiang Wu
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China.
| | - Xiao-Cong Zhao
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Arvind Kumar
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China
| | - Xia Ran
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Yu Zhang
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China
| | - Li-Jun Guo
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Physics and Electronics, Henan University, Kaifeng 475001, China.
| |
Collapse
|
35
|
Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
Collapse
Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| |
Collapse
|
36
|
Majee P, Shankar U, Pasadi S, Muniyappa K, Nayak D, Kumar A. Genome-wide analysis reveals a regulatory role for G-quadruplexes during Adenovirus multiplication. Virus Res 2020; 283:197960. [DOI: 10.1016/j.virusres.2020.197960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022]
|
37
|
Sontakke VA, Srivatsan SG. A dual-app nucleoside probe reports G-quadruplex formation and ligand binding in the long terminal repeat of HIV-1 proviral genome. Bioorg Med Chem Lett 2020; 30:127345. [PMID: 32631544 DOI: 10.1016/j.bmcl.2020.127345] [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: 05/09/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022]
Abstract
We have developed a dual-app nucleoside analog, 5-selenophene-modified 2'-deoxyuridine (SedU), to probe the structure and ligand-binding properties of a G-rich segment present in the long terminal repeat (LTR) of the HIV-1 proviral DNA promoter region. The nucleoside probe is made of an environment-responsive fluorophore and X-ray crystallography phasing label (Se atom). SedU incorporated into LTR-IV sequence, fluorescently reports the formation of G-quadruplex (GQ) structure without affecting the native fold. Further, using the environment sensitivity of the probe, a fluorescence assay was designed to estimate the binding affinity of small molecule ligands to the GQ motif. An added feature of this probe system is that it would enable direct correlation of structure and recognition properties in solution and atomic level by using a combination of fluorescence and X-ray crystallography techniques.
Collapse
Affiliation(s)
- Vyankat A Sontakke
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India.
| |
Collapse
|
38
|
Hwang J, Kim JY, Kim C, Park S, Joo S, Kim SK, Lee NK. Single-molecule observation of ATP-independent SSB displacement by RecO in Deinococcus radiodurans. eLife 2020; 9:50945. [PMID: 32297860 PMCID: PMC7200156 DOI: 10.7554/elife.50945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 04/15/2020] [Indexed: 12/27/2022] Open
Abstract
Deinococcus radiodurans (DR) survives in the presence of hundreds of double-stranded DNA (dsDNA) breaks by efficiently repairing such breaks. RecO, a protein that is essential for the extreme radioresistance of DR, is one of the major recombination mediator proteins in the RecA-loading process in the RecFOR pathway. However, how RecO participates in the RecA-loading process is still unclear. In this work, we investigated the function of drRecO using single-molecule techniques. We found that drRecO competes with the ssDNA-binding protein (drSSB) for binding to the freely exposed ssDNA, and efficiently displaces drSSB from ssDNA without consuming ATP. drRecO replaces drSSB and dissociates it completely from ssDNA even though drSSB binds to ssDNA approximately 300 times more strongly than drRecO does. We suggest that drRecO facilitates the loading of RecA onto drSSB-coated ssDNA by utilizing a small drSSB-free space on ssDNA that is generated by the fast diffusion of drSSB on ssDNA.
Collapse
Affiliation(s)
- Jihee Hwang
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jae-Yeol Kim
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, United States
| | - Cheolhee Kim
- Daegu National Science Museum, Daegu, Republic of Korea
| | - Soojin Park
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Sungmin Joo
- Department of Physics, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
39
|
Abstract
Guanine (G)-rich sequences in RNA can fold into diverse RNA G-quadruplex (rG4) structures to mediate various biological functions and cellular processes in eukaryotic organisms. However, the presence, locations, and functions of rG4s in prokaryotes are still elusive. We used QUMA-1, an rG4-specific fluorescent probe, to detect rG4 structures in a wide range of bacterial species both in vitro and in live cells and found rG4 to be an abundant RNA secondary structure across those species. Subsequently, to identify bacterial rG4 sites in the transcriptome, the model Escherichia coli strain and a major human pathogen, Pseudomonas aeruginosa, were subjected to recently developed high-throughput rG4 structure sequencing (rG4-seq). In total, 168 and 161 in vitro rG4 sites were found in E. coli and P. aeruginosa, respectively. Genes carrying these rG4 sites were found to be involved in virulence, gene regulation, cell envelope synthesis, and metabolism. More importantly, biophysical assays revealed the formation of a group of rG4 sites in mRNAs (such as hemL and bswR), and they were functionally validated in cells by genetic (point mutation and lux reporter assays) and phenotypic experiments, providing substantial evidence for the formation and function of rG4s in bacteria. Overall, our study uncovers important regulatory functions of rG4s in bacterial pathogenicity and metabolic pathways and strongly suggests that rG4s exist and can be detected in a wide range of bacterial species.IMPORTANCE G-quadruplex in RNA (rG4) mediates various biological functions and cellular processes in eukaryotic organisms. However, the presence, locations, and functions of rG4 are still elusive in prokaryotes. Here, we found that rG4 is an abundant RNA secondary structure across a wide range of bacterial species. Subsequently, the transcriptome-wide rG4 structure sequencing (rG4-seq) revealed that the model E. coli strain and a major human pathogen, P. aeruginosa, have 168 and 161 in vitro rG4 sites, respectively, involved in virulence, gene regulation, cell envelope, and metabolism. We further verified the regulatory functions of two rG4 sites in bacteria (hemL and bswR). Overall, this finding strongly suggests that rG4s play key regulatory roles in a wide range of bacterial species.
Collapse
|
40
|
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.
Collapse
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.)
| |
Collapse
|
41
|
Yett A, Lin LY, Beseiso D, Miao J, Yatsunyk LA. N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA. J PORPHYR PHTHALOCYA 2019; 23:1195-1215. [PMID: 34385812 PMCID: PMC8356643 DOI: 10.1142/s1088424619300179] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
N-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect - high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules (e.g. ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.
Collapse
Affiliation(s)
- Ariana Yett
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Linda Yingqi Lin
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Dana Beseiso
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Joanne Miao
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Liliya A. Yatsunyk
- Correspondence to: Liliya A. Yatsunyk, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA. tel.: 610-328-8558,
| |
Collapse
|
42
|
Mukherjee AK, Sharma S, Bagri S, Kutum R, Kumar P, Hussain A, Singh P, Saha D, Kar A, Dash D, Chowdhury S. Telomere repeat-binding factor 2 binds extensively to extra-telomeric G-quadruplexes and regulates the epigenetic status of several gene promoters. J Biol Chem 2019; 294:17709-17722. [PMID: 31575660 PMCID: PMC6879327 DOI: 10.1074/jbc.ra119.008687] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/18/2019] [Indexed: 12/22/2022] Open
Abstract
The role of the telomere repeat-binding factor 2 (TRF2) in telomere maintenance is well-established. However, recent findings suggest that TRF2 also functions outside telomeres, but relatively little is known about this function. Herein, using genome-wide ChIP-Seq assays of TRF2-bound chromatin from HT1080 fibrosarcoma cells, we identified thousands of TRF2-binding sites within the extra-telomeric genome. In light of this observation, we asked how TRF2 occupancy is organized within the genome. Interestingly, we found that extra-telomeric TRF2 sites throughout the genome are enriched in potential G-quadruplex-forming DNA sequences. Furthermore, we validated TRF2 occupancy at several promoter G-quadruplex motifs, which did adopt quadruplex forms in solution. TRF2 binding altered expression and the epigenetic state of several target promoters, indicated by histone modifications resulting in transcriptional repression of eight of nine genes investigated here. Furthermore, TRF2 occupancy and target gene expression were also sensitive to the well-known intracellular G-quadruplex-binding ligand 360A. Together, these results reveal an extensive genome-wide association of TRF2 outside telomeres and that it regulates gene expression in a G-quadruplex-dependent fashion.
Collapse
Affiliation(s)
- Ananda Kishore Mukherjee
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Shalu Sharma
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Rintu Kutum
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,CSIR Ayurgenomics Unit-TRISUTRA, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Pankaj Kumar
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Asgar Hussain
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Prateek Singh
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Dhurjhoti Saha
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Anirban Kar
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Debasis Dash
- Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,CSIR Ayurgenomics Unit-TRISUTRA, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India .,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India.,G.N.R. Knowledge Centre for Genome Informatics, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| |
Collapse
|
43
|
Wang W, Ma Y, He J, Qi H, Xiao F, He S. Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans. Gene 2019; 715:144008. [DOI: 10.1016/j.gene.2019.144008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023]
|
44
|
Prister LL, Ozer EA, Cahoon LA, Seifert HS. Transcriptional initiation of a small RNA, not R-loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae. Mol Microbiol 2019; 112:1219-1234. [PMID: 31338863 PMCID: PMC6800796 DOI: 10.1111/mmi.14356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2019] [Indexed: 02/06/2023]
Abstract
Neisseria gonorrhoeae, the sole causative agent of gonorrhea, constitutively undergoes diversification of the Type IV pilus. Gene conversion occurs between one of the several donor silent copies located in distinct loci and the recipient pilE gene, encoding the major pilin subunit of the pilus. A guanine quadruplex (G4) DNA structure and a cis-acting sRNA (G4-sRNA) are located upstream of the pilE gene and both are required for pilin antigenic variation (Av). We show that the reduced sRNA transcription lowers pilin Av frequencies. Extended transcriptional elongation is not required for Av, since limiting the transcript to 32 nt allows for normal Av frequencies. Using chromatin immunoprecipitation (ChIP) assays, we show that cellular G4s are less abundant when sRNA transcription is lower. In addition, using ChIP, we demonstrate that the G4-sRNA forms a stable RNA:DNA hybrid (R-loop) with its template strand. However, modulating R-loop levels by controlling RNase HI expression does not alter G4 abundance quantified through ChIP. Since pilin Av frequencies were not altered when modulating R-loop levels by controlling RNase HI expression, we conclude that transcription of the sRNA is necessary, but stable R-loops are not required to promote pilin Av.
Collapse
Affiliation(s)
- Lauren L Prister
- Department of Microbiology-Immunology, DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
| | - Egon A Ozer
- Department of Microbiology-Immunology, DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
- Department of Medicine, Division of Infectious DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
| | - Laty A Cahoon
- Department of Microbiology-Immunology, DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
| | - H Steven Seifert
- Department of Microbiology-Immunology, DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
| |
Collapse
|
45
|
Guanine Quadruplex DNA Regulates Gamma Radiation Response of Genome Functions in the Radioresistant Bacterium Deinococcus radiodurans. J Bacteriol 2019; 201:JB.00154-19. [PMID: 31235513 DOI: 10.1128/jb.00154-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022] Open
Abstract
Guanine quadruplex (G4) DNA/RNA are secondary structures that regulate the various cellular processes in both eukaryotes and bacteria. Deinococcus radiodurans, a Gram-positive bacterium known for its extraordinary radioresistance, shows a genomewide occurrence of putative G4 DNA-forming motifs in its GC-rich genome. N-Methyl mesoporphyrin (NMM), a G4 DNA structure-stabilizing drug, did not affect bacterial growth under normal conditions but inhibited the postirradiation recovery of gamma-irradiated cells. Transcriptome sequencing analysis of cells treated with both radiation and NMM showed repression of gamma radiation-responsive gene expression, which was observed in the absence of NMM. Notably, this effect of NMM on the expression of housekeeping genes involved in other cellular processes was not observed. Stabilization of G4 DNA structures mapped at the upstream of recA and in the encoding region of DR_2199 had negatively affected promoter activity in vivo, DNA synthesis in vitro and protein translation in Escherichia coli host. These results suggested that G4 DNA plays an important role in DNA damage response and in the regulation of expression of the DNA repair proteins required for radioresistance in D. radiodurans IMPORTANCE Deinococcus radiodurans can recover from extensive DNA damage caused by many genotoxic agents. It lacks LexA/RecA-mediated canonical SOS response. Therefore, the molecular mechanisms underlying the regulation of DNA damage response would be worth investigating in this bacterium. D. radiodurans genome is GC-rich and contains numerous islands of putative guanine quadruplex (G4) DNA structure-forming motifs. Here, we showed that in vivo stabilization of G4 DNA structures can impair DNA damage response processes in D. radiodurans Essential cellular processes such as transcription, DNA synthesis, and protein translation, which are also an integral part of the double-strand DNA break repair pathway, are affected by the arrest of G4 DNA structure dynamics. Thus, the role of DNA secondary structures in DNA damage response and radioresistance is demonstrated.
Collapse
|
46
|
HnRNPA1 interacts with G-quadruplex in the TRA2B promoter and stimulates its transcription in human colon cancer cells. Sci Rep 2019; 9:10276. [PMID: 31311954 PMCID: PMC6635519 DOI: 10.1038/s41598-019-46659-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 04/24/2019] [Indexed: 12/15/2022] Open
Abstract
The human TRA2B gene consists of 10 exons and 9 introns and produces 5 splice isoforms (TRA2β1 to TRA2β5). TRA2B exon 2 encodes multiple premature termination codons. TRA2β1 lacks exon 2 and is translated into a functional transformer 2β (Tra2β) protein, whereas TRA2β4 contains 10 exons and works as a functional RNA. Overexpressed Tra2β and ectopic expression of TRA2β4 may be oncogenic. We found that heterogeneous nuclear ribonucleoprotein (hnRNP)A1 and hnRNPU interacted with TRA2β4 exon 2. Minigene assays revealed that hnRNPA1 facilitated inclusion of exon 2, whereas hnRNPU promoted its skipping. However, knockdown of hnRNPA1 or hnRNPU reduced both TRA2β1 and TRA2β4 levels, and overexpression of these hnRNPs increased levels of both isoforms, suggesting that hnRNPA1 and hnRNPU mainly regulate the transcription of TRA2B. In fact, hnRNPA1 and hnRNPU positively regulated the promoter activity of TRA2B. Circular dichroism analyses, electrophoretic mobility shift assays and chromatin immunoprecipitation assays demonstrated the presence of G-quadruplex (G4) formation in the promoter of TRA2B. Formation of G4 suppressed TRA2B transcription, whereas hnRNPA1, but not hnRNPU, interacted with the G4 to facilitate transcription. Our results suggest that hnRNPA1 may modulate TRA2B transcription through its regulation of G4 formation in its promoter in colon cancer cells.
Collapse
|
47
|
Khairnar NP, Maurya GK, Pandey N, Das A, Misra HS. DrRecQ regulates guanine quadruplex DNA structure dynamics and its impact on radioresistance in
Deinococcus radiodurans. Mol Microbiol 2019; 112:854-865. [DOI: 10.1111/mmi.14321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2019] [Indexed: 11/30/2022]
Affiliation(s)
| | - Ganesh Kumar Maurya
- Molecular Biology Division Bhabha Atomic Research Centre Mumbai 400085India
- Life Sciences Homi Bhabha National Institute Mumbai 400094India
| | - Neha Pandey
- Molecular Biology Division Bhabha Atomic Research Centre Mumbai 400085India
| | - Anubrata Das
- Molecular Biology Division Bhabha Atomic Research Centre Mumbai 400085India
| | - Hari S. Misra
- Molecular Biology Division Bhabha Atomic Research Centre Mumbai 400085India
- Life Sciences Homi Bhabha National Institute Mumbai 400094India
| |
Collapse
|
48
|
Bartas M, Čutová M, Brázda V, Kaura P, Šťastný J, Kolomazník J, Coufal J, Goswami P, Červeň J, Pečinka P. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. Molecules 2019; 24:molecules24091711. [PMID: 31052562 PMCID: PMC6539912 DOI: 10.3390/molecules24091711] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/09/2023] Open
Abstract
The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
Collapse
Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Michaela Čutová
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.
| | - Václav Brázda
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic.
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic.
- Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic.
| | - Jan Kolomazník
- Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic.
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Pratik Goswami
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jiří Červeň
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| |
Collapse
|
49
|
Hotoda's Sequence and Anti-HIV Activity: Where Are We Now? Molecules 2019; 24:molecules24071417. [PMID: 30974914 PMCID: PMC6479790 DOI: 10.3390/molecules24071417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 01/24/2023] Open
Abstract
The pharmacological relevance of ODNs forming G-quadruplexes as anti-HIV agents has been extensively reported in the literature over the last few years. Recent detailed studies have elucidated the peculiar arrangement adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. In this review, we have reported the history of a strong anti-HIV agent: the 6-mer d(TGGGAG) sequence, commonly called "Hotoda's sequence". In particular, all findings reported on this sequence and its modified sequences have been discussed considering the following research phases: (i) discovery of the first 5'-modified active d(TGGGAG) sequences; (ii) synthesis of a variety of end-modified d(TGGGAG) sequences; (iii) biophysical and NMR investigations of natural and modified Hotoda's sequences; (iv); kinetic studies on the most active 5'-modified d(TGGGAG) sequences; and (v) extensive anti-HIV screening of G-quadruplexes formed by d(TGGGAG) sequences. This review aims to clarify all results obtained over the years on Hotoda's sequence, revealing its potentiality as a strong anti-HIV agent (EC50 = 14 nM).
Collapse
|
50
|
Ge F, Wang Y, Li H, Zhang R, Wang X, Li Q, Liang Z, Yang L. Plant-GQ: An Integrative Database of G-Quadruplex in Plant. J Comput Biol 2019; 26:1013-1019. [PMID: 30958698 DOI: 10.1089/cmb.2019.0010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
G-quadruplex (G-Q) is advanced DNA or RNA secondary structures frequently found in plant and involved in important biological processes such as transcription, translation, and telomere maintenance. Although some databases and tools were developed for predicting and studying G-Q, none of them was for plant. With the development of next-generation sequencing technology, a large number of plant genomes have been assembled and annotated to provide opportunities for mining G-Q. Plant G-quadruplex database (Plant-GQ) was constructed for predicting G-Q in 195 plants. It has a total of 626,341,645 predicted G-Qs. The database contains four major parts: Search, Tools, JBrowse, and Download. Not only G-Q information but also online forecasting tool can be retrieved and obtained from Plant-GQ. It can also browse and analyze G-Q information by JBrowse in a graph visualization interface. Considering the key role of G-Q in plant, this database will play an important status in the study of the structure, function, and biological relevance of G-Q in plant.
Collapse
Affiliation(s)
- Fangfang Ge
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Huayang Li
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Rui Zhang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Xiaotong Wang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Qingyun Li
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Long Yang
- Agricultural Big-Data Research Center and College of Plant Protection, Shandong Agricultural University, Taian, China
| |
Collapse
|