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Westover KR, Jin P, Yao B. Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. Epigenomics 2024; 16:589-608. [PMID: 38530068 PMCID: PMC11160457 DOI: 10.2217/epi-2023-0379] [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: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
R-loops, intricate three-stranded structures formed by RNA-DNA hybrids and an exposed non-template DNA strand, are fundamental to various biological phenomena. They carry out essential and contrasting functions within cellular mechanisms, underlining their critical role in maintaining cellular homeostasis. The specific cellular context that dictates R-loop formation determines their function, particularly emphasizing the necessity for their meticulous genomic regulation. Notably, the aberrant formation or misregulation of R-loops is implicated in numerous neurological disorders. This review focuses on the complex interactions between R-loops and double-strand DNA breaks, exploring how R-loop dysregulation potentially contributes to the pathogenesis of various brain disorders, which could provide novel insights into the molecular mechanisms underpinning neurological disease progression and identify potential therapeutic targets by highlighting these aspects.
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Affiliation(s)
- Katherine R Westover
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
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2
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Pan C, Li YX, Yang K, Famous E, Ma Y, He X, Geng Q, Liu M, Tian J. The Molecular Mechanism of Perillaldehyde Inducing Cell Death in Aspergillus flavus by Inhibiting Energy Metabolism Revealed by Transcriptome Sequencing. Int J Mol Sci 2020; 21:ijms21041518. [PMID: 32102190 PMCID: PMC7073185 DOI: 10.3390/ijms21041518] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 01/01/2023] Open
Abstract
Perillaldehyde (PAE), an essential oil in Perilla plants, serves as a safe flavor ingredient in foods, and shows an effectively antifungal activity. Reactive oxygen species (ROS) accumulation in Aspergillus flavus plays a critical role in initiating a metacaspase-dependent apoptosis. However, the reason for ROS accumulation in A. flavus is not yet clear. Using transcriptome sequencing of A. flavus treated with different concentrations of PAE, our data showed that the ROS accumulation might have been as a result of an inhibition of energy metabolism with less production of reducing power. By means of GO and KEGG enrichment analysis, we screened four key pathways, which were divided into two distinct groups: a downregulated group that was made up of the glycolysis and pentose phosphate pathway, and an upregulated group that consisted of MAPK signaling pathway and GSH metabolism pathway. The inhibition of dehydrogenase gene expression in two glycometabolism pathways might play a crucial role in antifungal mechanism of PAE. Also, in our present study, we systematically showed a gene interaction network of how genes of four subsets are effected by PAE stress on glycometabolism, oxidant damage repair, and cell cycle control. This research may contribute to explaining an intrinsic antifungal mechanism of PAE against A. flavus.
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Affiliation(s)
- Chao Pan
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
| | - Yong-Xin Li
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
| | - Kunlong Yang
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
| | - Erhunmwunsee Famous
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
| | - Yan Ma
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
| | - Xiaona He
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
| | - Qingru Geng
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
| | - Man Liu
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
- Correspondence: (M.L.); (J.T.); Tel.: +86-516-83403172 (J.T.)
| | - Jun Tian
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, China; (C.P.); (Y.-X.L.); (K.Y.); (E.F.)
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing100048, China
- Correspondence: (M.L.); (J.T.); Tel.: +86-516-83403172 (J.T.)
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Sariki SK, Kumawat R, Singh V, Tomar RS. Flocculation ofSaccharomyces cerevisiaeis dependent on activation of Slt2 and Rlm1 regulated by the cell wall integrity pathway. Mol Microbiol 2019; 112:1350-1369. [DOI: 10.1111/mmi.14375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Santhosh Kumar Sariki
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Ramesh Kumawat
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations. Nat Commun 2018; 9:533. [PMID: 29416069 PMCID: PMC5803260 DOI: 10.1038/s41467-018-02894-w] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/05/2018] [Indexed: 12/21/2022] Open
Abstract
Ataxia with oculomotor apraxia 2 (AOA-2) and amyotrophic lateral sclerosis (ALS4) are neurological disorders caused by mutations in the gene encoding for senataxin (SETX), a putative RNA:DNA helicase involved in transcription and in the maintenance of genome integrity. Here, using ChIP followed by high throughput sequencing (ChIP-seq), we report that senataxin is recruited at DNA double-strand breaks (DSBs) when they occur in transcriptionally active loci. Genome-wide mapping unveiled that RNA:DNA hybrids accumulate on DSB-flanking chromatin but display a narrow, DSB-induced, depletion near DNA ends coinciding with senataxin binding. Although neither required for resection nor for timely repair of DSBs, senataxin was found to promote Rad51 recruitment, to minimize illegitimate rejoining of distant DNA ends and to sustain cell viability following DSB production in active genes. Our data suggest that senataxin functions at DSBs in order to limit translocations and ensure cell viability, providing new insights on AOA2/ALS4 neuropathies.
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5
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Golla U, Swagatika S, Chauhan S, Tomar RS. A systematic assessment of chemical, genetic, and epigenetic factors influencing the activity of anticancer drug KP1019 (FFC14A). Oncotarget 2017; 8:98426-98454. [PMID: 29228701 PMCID: PMC5716741 DOI: 10.18632/oncotarget.21416] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/28/2017] [Indexed: 12/11/2022] Open
Abstract
KP1019 ([trans-RuCl4(1H-indazole)2]; FFC14A) is one of the promising ruthenium-based anticancer drugs undergoing clinical trials. Despite the pre-clinical and clinical success of KP1019, the mode of action and various factors capable of modulating its effects are largely unknown. Here, we used transcriptomics and genetic screening approaches in budding yeast model and deciphered various genetic targets and plethora of cellular pathways including cellular signaling, metal homeostasis, vacuolar transport, and lipid homeostasis that are primarily targeted by KP1019. We also demonstrated that KP1019 modulates the effects of TOR (target of rapamycin) signaling pathway and induces accumulation of neutral lipids (lipid droplets) in both yeast and HeLa cells. Interestingly, KP1019-mediated effects were found augmented with metal ions (Al3+/Ca2+/Cd2+/Cu2+/Mn2+/Na+/Zn2+), and neutralized by Fe2+, antioxidants, osmotic stabilizer, and ethanolamine. Additionally, our comprehensive screening of yeast histone H3/H4 mutant library revealed several histone residues that could significantly modulate the KP1019-induced toxicity. Altogether, our findings in both the yeast and HeLa cells provide molecular insights into mechanisms of action of KP1019 and various factors (chemical/genetic/epigenetic) that can alter the therapeutic efficiency of this clinically important anticancer drug.
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Affiliation(s)
- Upendarrao Golla
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
| | - Swati Swagatika
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
| | - Sakshi Chauhan
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
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Choudhury SD, Vs A, Mushtaq Z, Kumar V. Altered translational repression of an RNA-binding protein, Elav by AOA2-causative Senataxin mutation. Synapse 2017; 71. [PMID: 28245518 DOI: 10.1002/syn.21969] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/20/2017] [Accepted: 02/22/2017] [Indexed: 11/09/2022]
Abstract
Mutations in Senataxin (SETX) gene causes two types of neurological disorders, Amyotrophic Lateral Sclerosis (ALS4) and Ataxia with Oculomotor Apraxia type 2 (AOA2). Recent studies in cultured cells suggest that SETX plays a crucial role at the interface of transcription and the DNA damage response. Whether SETX can alter translational of specific RNA is not known. In this study, we report that expressing AOA2-causative truncated form of human SETX in Drosophila neurons alters the development of neuromuscular junction (NMJ) synapses. Interestingly, we found that expressing this truncated form of SETX in Drosophila muscles resulted in an alteration of translational repression of an RNA-binding protein, Embryonic Lethal Abnormal Vision (Elav). Elav is transcribed in all tissues but remains translationally repressed except in neurons. Thus, our data suggest that an altered repression profile of RNA by SETX mutants could be one of the mechanisms underlying ALS4 or AOA2 pathogenesis.
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Affiliation(s)
- Saumitra Dey Choudhury
- Department of Biological Sciences, Laboratory of Neurogenetics, Indian Institute of Science Education and Research (IISER) Bhopal, Bhouri, Bhopal, Madhya Pradesh, India, 462 066
| | - Ancy Vs
- Department of Biological Sciences, Laboratory of Neurogenetics, Indian Institute of Science Education and Research (IISER) Bhopal, Bhouri, Bhopal, Madhya Pradesh, India, 462 066
| | - Zeeshan Mushtaq
- Department of Biological Sciences, Laboratory of Neurogenetics, Indian Institute of Science Education and Research (IISER) Bhopal, Bhouri, Bhopal, Madhya Pradesh, India, 462 066
| | - Vimlesh Kumar
- Department of Biological Sciences, Laboratory of Neurogenetics, Indian Institute of Science Education and Research (IISER) Bhopal, Bhouri, Bhopal, Madhya Pradesh, India, 462 066
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Sariki SK, Sahu PK, Golla U, Singh V, Azad GK, Tomar RS. Sen1, the homolog of human Senataxin, is critical for cell survival through regulation of redox homeostasis, mitochondrial function, and the TOR pathway inSaccharomyces cerevisiae. FEBS J 2016; 283:4056-4083. [DOI: 10.1111/febs.13917] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/30/2016] [Accepted: 10/05/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Santhosh Kumar Sariki
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Pushpendra Kumar Sahu
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Upendarrao Golla
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Vikash Singh
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Gajendra Kumar Azad
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
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8
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Groh M, Albulescu LO, Cristini A, Gromak N. Senataxin: Genome Guardian at the Interface of Transcription and Neurodegeneration. J Mol Biol 2016; 429:3181-3195. [PMID: 27771483 DOI: 10.1016/j.jmb.2016.10.021] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 12/12/2022]
Abstract
R-loops comprise an RNA/DNA hybrid and a displaced single-stranded DNA. They play crucial biological functions and are implicated in neurological diseases, including ataxias, amyotrophic lateral sclerosis, nucleotide expansion disorders (Friedreich ataxia and fragile X syndrome), and cancer. Currently, it is unclear which mechanisms cause R-loop structures to become pathogenic. The RNA/DNA helicase senataxin (SETX) is one of the best characterised R-loop-binding factors in vivo. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). SETX is known to play a role in transcription, neurogenesis, and antiviral response. Here, we review the causes of R-loop dysregulation in neurodegenerative diseases and how these structures contribute to pathomechanisms. We will discuss the importance of SETX as a genome guardian in suppressing aberrant R-loop formation and analyse how SETX mutations can lead to neurodegeneration in AOA2/ALS4. Finally, we will discuss the implications for other R-loop-associated neurodegenerative diseases and point to future therapeutic approaches to treat these disorders.
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Affiliation(s)
- Matthias Groh
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Laura Oana Albulescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Agnese Cristini
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK.
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Combined Transcriptomics and Chemical-Genetics Reveal Molecular Mode of Action of Valproic acid, an Anticancer Molecule using Budding Yeast Model. Sci Rep 2016; 6:35322. [PMID: 27734932 PMCID: PMC5062167 DOI: 10.1038/srep35322] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/28/2016] [Indexed: 12/16/2022] Open
Abstract
Valproic acid (VA) is a pharmacologically important histone deacetylase inhibitor that recently garnered attention as an anticancer agent. Since the molecular mechanisms behind the multiple effects of VA are unclear, this study was aimed to unravel the comprehensive cellular processes affected by VA and its molecular targets in vivo using budding yeast as a model organism. Interestingly, genome-wide transcriptome analysis of cells treated with VA showed differential regulation of 30% of the genome. Functional enrichment analysis of VA transcriptome evidenced alteration of various cellular processes including cell cycle, cell wall biogenesis, DNA repair, ion homeostasis, metabolism, stress response, transport and ribosomal biogenesis, etc. Moreover, our genetic screening analysis revealed VA molecular targets belonging to oxidative and osmotic stress, DNA repair, cell wall integrity, and iron homeostasis. Further, our results demonstrated the activation of mitogen-activated protein kinases (MAPKs) Hog1 (p38) and Slt2 (p44/42) upon VA treatment. Our results also exhibited that VA acts through alteration of mitochondrial, ER architecture and functions. Especially, VA effects were neutralized in cells lacking lipid particles. Altogether, our results deciphered the novel molecular insights and mechanistic links to strengthen our knowledge on diverse cellular effects of VA along with its probable therapeutic targets and detoxification approaches.
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Azad GK, Tomar RS. Partial purification of histone H3 proteolytic activity from the budding yeastSaccharomyces cerevisiae. Yeast 2016; 33:217-26. [DOI: 10.1002/yea.3153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 11/06/2022] Open
Affiliation(s)
- Gajendra Kumar Azad
- Laboratory of Chromatin Biology; Department of Biological Sciences, Indian Institute of Science Education and Research; Bhopal India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology; Department of Biological Sciences, Indian Institute of Science Education and Research; Bhopal India
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Flocculation inSaccharomyces cerevisiaeis regulated by RNA/DNA helicase Sen1p. FEBS Lett 2015; 589:3165-74. [DOI: 10.1016/j.febslet.2015.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 12/13/2022]
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12
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Golla U, Bandi G, Tomar RS. Molecular Cytotoxicity Mechanisms of Allyl Alcohol (Acrolein) in Budding Yeast. Chem Res Toxicol 2015; 28:1246-64. [DOI: 10.1021/acs.chemrestox.5b00071] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Upendarrao Golla
- Laboratory of Chromatin Biology,
Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal-462023, India
| | - Goutham Bandi
- Laboratory of Chromatin Biology,
Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal-462023, India
| | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology,
Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal-462023, India
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Mitogen-activated protein kinase Hog1 is activated in response to curcumin exposure in the budding yeast Saccharomyces cerevisiae. BMC Microbiol 2014; 14:317. [PMID: 25523922 PMCID: PMC4275933 DOI: 10.1186/s12866-014-0317-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/05/2014] [Indexed: 11/28/2022] Open
Abstract
Background Curcumin (CUR), an active polyphenol derived from the spice turmeric, has been traditionally used for centuries in ancient Indian medicine to treat a number of diseases. The physiological effects of CUR have been shown to be diverse; however, the target molecules and pathways that CUR affects have yet to be fully described. Results Here, we demonstrate for the first time that the budding yeast mitogen-activated protein kinase (MAPK) Hog1 is essential for the response to CUR. Moreover, CUR-induced Hog1 phosphorylation was rescued by supplementation of iron to the growth medium. Hog1 was rapidly phosphorylated upon CUR treatment, but unlike the response to hyperosmotic shock (0.8 M NaCl), it remains activated for an extended period of time. A detailed analysis of HOG pathway mutants revealed that Pbs2p, Ptc2p, and Ssk2p are required for optimal CUR-induced Hog1 phosphorylation. We also observed a Hog1 dependent transcriptional response to CUR treatment that involved the up-regulation of glycerol-3-phosphate dehydrogenase 1 (GPD1), a factor that is essential for the hyperosmotic stress response. Conclusions Our present finding revealed the role of Hog1 MAPK in regulation of CUR-induced transcriptional response. We anticipate that our finding will enhance the understanding on the molecular mode of action of CUR on S. cerevisiae.
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Azad GK, Singh V, Baranwal S, Thakare MJ, Tomar RS. The transcription factor Rap1p is required for tolerance to cell-wall perturbing agents and for cell-wall maintenance inSaccharomyces cerevisiae. FEBS Lett 2014; 589:59-67. [DOI: 10.1016/j.febslet.2014.11.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 11/13/2014] [Accepted: 11/17/2014] [Indexed: 11/28/2022]
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Baranwal S, Azad GK, Singh V, Tomar RS. Signaling of chloroquine-induced stress in the yeast Saccharomyces cerevisiae requires the Hog1 and Slt2 mitogen-activated protein kinase pathways. Antimicrob Agents Chemother 2014; 58:5552-66. [PMID: 25022582 PMCID: PMC4135872 DOI: 10.1128/aac.02393-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 06/28/2014] [Indexed: 01/24/2023] Open
Abstract
Chloroquine (CQ) has been under clinical use for several decades, and yet little is known about CQ sensing and signaling mechanisms or about their impact on various biological pathways. We employed the budding yeast Saccharomyces cerevisiae as a model organism to study the pathways targeted by CQ. Our screening with yeast mutants revealed that it targets histone proteins and histone deacetylases (HDACs). Here, we also describe the novel role of mitogen-activated protein kinases Hog1 and Slt2, which aid in survival in the presence of CQ. Cells deficient in Hog1 or Slt2 are found to be CQ hypersensitive, and both proteins were phosphorylated in response to CQ exposure. CQ-activated Hog1p is translocated to the nucleus and facilitates the expression of GPD1 (glycerol-3-phosphate dehydrogenase), which is required for the synthesis of glycerol (one of the major osmolytes). Moreover, cells treated with CQ exhibited an increase in intracellular reactive oxygen species (ROS) levels and the effects were rescued by addition of reduced glutathione to the medium. The deletion of SOD1, the superoxide dismutase in yeast, resulted in hypersensitivity to CQ. We have also observed P38 as well as P42/44 phosphorylation in HEK293T human cells upon exposure to CQ, indicating that the kinds of responses generated in yeast and human cells are similar. In summary, our findings define the multiple biological pathways targeted by CQ that might be useful for understanding the toxicity modulated by this pharmacologically important molecule.
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Affiliation(s)
- Shivani Baranwal
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Gajendra Kumar Azad
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Raghuvir S Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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Anti-cancer drug KP1019 induces Hog1 phosphorylation and protein ubiquitylation in Saccharomyces cerevisiae. Eur J Pharmacol 2014; 736:77-85. [DOI: 10.1016/j.ejphar.2014.04.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 01/29/2023]
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17
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Mechanisms of genome instability induced by RNA-processing defects. Trends Genet 2014; 30:245-53. [PMID: 24794811 DOI: 10.1016/j.tig.2014.03.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/20/2022]
Abstract
The role of normal transcription and RNA processing in maintaining genome integrity is becoming increasingly appreciated in organisms ranging from bacteria to humans. Several mutations in RNA biogenesis factors have been implicated in human cancers, but the mechanisms and potential connections to tumor genome instability are not clear. Here, we discuss how RNA-processing defects could destabilize genomes through mutagenic R-loop structures and by altering expression of genes required for genome stability. A compelling body of evidence now suggests that researchers should be directly testing these mechanisms in models of human cancer.
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18
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Azad GK, Singh V, Tomar RS. Assessment of the biological pathways targeted by isocyanate using N-succinimidyl N-methylcarbamate in budding yeast Saccharomyces cerevisiae. PLoS One 2014; 9:e92993. [PMID: 24664350 PMCID: PMC3963962 DOI: 10.1371/journal.pone.0092993] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/27/2014] [Indexed: 02/05/2023] Open
Abstract
Isocyanates, a group of low molecular weight aromatic and aliphatic compounds possesses the functional isocyanate group. They are highly toxic in nature hence; we used N-succinimidyl N-methylcarbamate (NSNM), a surrogate chemical containing a functional isocyanate group to understand the mode of action of this class of compounds. We employed budding yeast Saccharomyces cerevisiae as a model organism to study the pathways targeted by NSNM. Our screening with yeast mutants revealed that it affects chromatin, DNA damage response, protein-ubiquitylation and chaperones, oxidative stress, TOR pathway and DNA repair processes. We also show that NSNM acts as an epigenetic modifier as its treatment causes reduction in global histone acetylation and formation of histone adducts. Cells treated with NSNM exhibited increase in mitochondrial membrane potential as well as intracellular ROS levels and the effects were rescued by addition of reduced glutathione to the medium. We also report that deletion of SOD1 and SOD2, the superoxide dismutase in Saccharomyces cerevisiae displayed hypersensitivity to NSNM. Furthermore, NSNM treatment causes rapid depletion of total glutathione and reduced glutathione. We also demonstrated that NSNM induces degradation of Sml1, a ribonucleotide reductase inhibitor involved in regulating dNTPs production. In summary, we define the various biological pathways targeted by isocyanates.
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Affiliation(s)
- Gajendra Kumar Azad
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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19
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Anti-cancer drug KP1019 modulates epigenetics and induces DNA damage response inSaccharomyces cerevisiae. FEBS Lett 2014; 588:1044-52. [DOI: 10.1016/j.febslet.2014.02.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 01/28/2014] [Accepted: 02/05/2014] [Indexed: 12/11/2022]
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Azad G, Singh V, Mandal P, Singh P, Golla U, Baranwal S, Chauhan S, Tomar RS. Ebselen induces reactive oxygen species (ROS)-mediated cytotoxicity in Saccharomyces cerevisiae with inhibition of glutamate dehydrogenase being a target. FEBS Open Bio 2014; 4:77-89. [PMID: 24490132 PMCID: PMC3907691 DOI: 10.1016/j.fob.2014.01.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 01/03/2014] [Accepted: 01/03/2014] [Indexed: 12/12/2022] Open
Abstract
Ebselen is a synthetic, lipid-soluble seleno-organic compound. The high electrophilicity of ebselen enables it to react with multiple cysteine residues of various proteins. Despite extensive research on ebselen, its target molecules and mechanism of action remains less understood. We performed biochemical as well as in vivo experiments employing budding yeast as a model organism to understand the mode of action of ebselen. The growth curve analysis and FACS (florescence activated cell sorting) assays revealed that ebselen exerts growth inhibitory effects on yeast cells by causing a delay in cell cycle progression. We observed that ebselen exposure causes an increase in intracellular ROS levels and mitochondrial membrane potential, and that these effects were reversed by addition of antioxidants such as reduced glutathione (GSH) or N-acetyl-l-cysteine (NAC). Interestingly, a significant increase in ROS levels was noticed in gdh3-deleted cells compared to wild-type cells. Furthermore, we showed that ebselen inhibits GDH function by interacting with its cysteine residues, leading to the formation of inactive hexameric GDH. Two-dimensional gel electrophoresis revealed protein targets of ebselen including CPR1, the yeast homolog of Cyclophilin A. Additionally, ebselen treatment leads to the inhibition of yeast sporulation. These results indicate a novel direct connection between ebselen and redox homeostasis.
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Key Words
- CypA, Cyclophilin A
- DCFH-DA, 2,7-dichlorodihydrofluorescein diacetate
- Ebselen
- FACS, florescence activated cell sorting
- GDH, glutamate dehydrogenase
- GSH, glutathione
- Glutamate dehydrogenase
- Histone clipping
- Mitochondrial membrane potential
- NAC, N-acetyl-l-cysteine
- Ni-NTA, nickel-nitrilotriacetic acid
- ROS levels
- ROS, reactive oxygen species
- SOD, superoxide dismutase
- Yeast sporulation
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Affiliation(s)
| | | | | | | | | | | | | | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462023, India
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