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Dinh N, Bonnefoy N. Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks. IUBMB Life 2024; 76:397-419. [PMID: 38117001 DOI: 10.1002/iub.2801] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
Schizosaccharomyces pombe (fission yeast) is an attractive model for mitochondrial research. The organism resembles human cells in terms of mitochondrial inheritance, mitochondrial transport, sugar metabolism, mitogenome structure and dependence of viability on the mitogenome (the petite-negative phenotype). Transcriptions of these genomes produce only a few polycistronic transcripts, which then undergo processing as per the tRNA punctuation model. In general, the machinery for mitochondrial gene expression is structurally and functionally conserved between fission yeast and humans. Furthermore, molecular research on S. pombe is supported by a considerable number of experimental techniques and database resources. Owing to these advantages, fission yeast has significantly contributed to biomedical and fundamental research. Here, we review the current state of knowledge regarding S. pombe mitochondrial gene expression, and emphasise the pertinence of fission yeast as both a model and tool, especially for studies on mitochondrial translation.
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Affiliation(s)
- Nhu Dinh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
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2
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Lam UTF, Nguyen TTT, Raechell R, Yang J, Singer H, Chen ES. A Normalization Protocol Reduces Edge Effect in High-Throughput Analyses of Hydroxyurea Hypersensitivity in Fission Yeast. Biomedicines 2023; 11:2829. [PMID: 37893202 PMCID: PMC10604075 DOI: 10.3390/biomedicines11102829] [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: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Edge effect denotes better growth of microbial organisms situated at the edge of the solid agar media. Although the precise reason underlying edge effect is unresolved, it is generally attributed to greater nutrient availability with less competing neighbors at the edge. Nonetheless, edge effect constitutes an unavoidable confounding factor that results in misinterpretation of cell fitness, especially in high-throughput screening experiments widely employed for genome-wide investigation using microbial gene knockout or mutant libraries. Here, we visualize edge effect in high-throughput high-density pinning arrays and report a normalization approach based on colony growth rate to quantify drug (hydroxyurea)-hypersensitivity in fission yeast strains. This normalization procedure improved the accuracy of fitness measurement by compensating cell growth rate discrepancy at different locations on the plate and reducing false-positive and -negative frequencies. Our work thus provides a simple and coding-free solution for a struggling problem in robotics-based high-throughput screening experiments.
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Affiliation(s)
- Ulysses Tsz-Fung Lam
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Raechell Raechell
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Jay Yang
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Harry Singer
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
- NUS Center for Cancer Research, National University of Singapore, Singapore 117599, Singapore
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI), Life Science Institute, National University of Singapore, Singapore 117456, Singapore
- National University Health System (NUHS), Singapore 119228, Singapore
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3
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Lim KK, Koh NZH, Zeng YB, Chuan JK, Raechell R, Chen ES. Resistance to Chemotherapeutic 5-Fluorouracil Conferred by Modulation of Heterochromatic Integrity through Ino80 Function in Fission Yeast. Int J Mol Sci 2023; 24:10687. [PMID: 37445861 DOI: 10.3390/ijms241310687] [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: 05/25/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
5-Fluorouracil (5-FU) is a conventional chemotherapeutic drug widely used in clinics worldwide, but development of resistance that compromises responsiveness remains a major hurdle to its efficacy. The mechanism underlying 5-FU resistance is conventionally attributed to the disruption of nucleotide synthesis, even though research has implicated other pathways such as RNA processing and chromatin dysregulation. Aiming to clarify resistance mechanisms of 5-FU, we tested the response of a collection of fission yeast (Schizosaccharomyces pombe) null mutants, which confer multiple environmental factor responsiveness (MER). Our screen identified disruption of membrane transport, chromosome segregation and mitochondrial oxidative phosphorylation to increase cellular susceptibility towards 5-FU. Conversely, we revealed several null mutants of Ino80 complex factors exhibited resistance to 5-FU. Furthermore, attenuation of Ino80 function via deleting several subunit genes reversed loss of chromosome-segregation fidelity in 5-FU in the loss-of-function mutant of the Argonaute protein, which regulates RNA interference (RNAi)-dependent maintenance of pericentromeric heterochromatin. Our study thus uncovered a critical role played by chromatin remodeling Ino80 complex factors in 5-FU resistance, which may constitute a possible target to modulate in reversing 5-FU resistance.
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Affiliation(s)
- Kim Kiat Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Nathaniel Zhi Hao Koh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Yi Bing Zeng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Jun Kai Chuan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Raechell Raechell
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- National University Health System (NUHS), Singapore 119228, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- NUS Graduate School-Integrative Sciences & Engineering Programme, National University of Singapore, Singapore 119077, Singapore
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4
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GRANT Motif Regulates CENP-A Incorporation and Restricts RNA Polymerase II Accessibility at Centromere. Genes (Basel) 2022; 13:genes13101697. [PMID: 36292582 PMCID: PMC9602348 DOI: 10.3390/genes13101697] [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: 07/22/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/24/2022] Open
Abstract
Precise chromosome segregation is essential for maintaining genomic stability, and its proper execution centers on the centromere, a chromosomal locus that mounts the kinetochore complex to mediate attachment of chromosomes to the spindle microtubules. The location of the centromere is epigenetically determined by a centromere-specific histone H3 variant, CENP-A. Many human cancers exhibit overexpression of CENP-A, which correlates with occurrence of aneuploidy in these malignancies. Centromeric targeting of CENP-A depends on its histone fold, but recent studies showed that the N-terminal tail domain (NTD) also plays essential roles. Here, we investigated implications of NTD in conferring aneuploidy formation when CENP-A is overexpressed in fission yeast. A series of mutant genes progressively lacking one amino acid of the NTD have been constructed for overexpression in wild-type cells using the intermediate strength nmt41 promoter. Constructs hosting disrupted GRANT (Genomic stability-Regulating site within CENP-A N-Terminus) motif in NTD results in growth retardation, aneuploidy, increased localization to the centromere, upregulated RNA polymerase II accessibility and transcriptional derepression of the repressive centromeric chromatin, suggesting that GRANT residues fine-tune centromeric CENP-A incorporation and restrict RNA polymerase II accessibility. This work highlighted the importance of CENP-A NTD, particularly the GRANT motif, in aneuploidy formation of overexpressed CENP-A in fission yeast.
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Fission Yeast Methylenetetrahydrofolate Reductase Ensures Mitotic and Meiotic Chromosome Segregation Fidelity. Int J Mol Sci 2021; 22:ijms22020639. [PMID: 33440639 PMCID: PMC7827777 DOI: 10.3390/ijms22020639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in the folate metabolic pathway, and its loss of function through polymorphisms is often associated with human conditions, including cancer, congenital heart disease, and Down syndrome. MTHFR is also required in the maintenance of heterochromatin, a crucial determinant of genomic stability and precise chromosomal segregation. Here, we characterize the function of a fission yeast gene met11+, which encodes a protein that is highly homologous to the mammalian MTHFR. We show that, although met11+ is not essential for viability, its disruption increases chromosome missegregation and destabilizes constitutive heterochromatic regions at pericentromeric, sub-telomeric and ribosomal DNA (rDNA) loci. Transcriptional silencing at these sites were disrupted, which is accompanied by the reduction in enrichment of histone H3 lysine 9 dimethylation (H3K9me2) and binding of the heterochromatin protein 1 (HP1)-like Swi6. The met11 null mutant also dominantly disrupts meiotic fidelity, as displayed by reduced sporulation efficiency and defects in proper partitioning of the genetic material during meiosis. Interestingly, the faithful execution of these meiotic processes is synergistically ensured by cooperation among Met11, Rec8, a meiosis-specific cohesin protein, and the shugoshin protein Sgo1, which protects Rec8 from untimely cleavage. Overall, our results suggest a key role for Met11 in maintaining pericentromeric heterochromatin for precise genetic inheritance during mitosis and meiosis.
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Santos SM, Hartman JL. A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin. Cancer Metab 2019; 7:9. [PMID: 31660150 PMCID: PMC6806529 DOI: 10.1186/s40170-019-0201-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/03/2019] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. METHODS Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. RESULTS Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. We analyzed human homologs of yeast genes exhibiting gene-doxorubicin interaction in cancer pharmacogenomics data to predict causality for differential gene expression associated with doxorubicin cytotoxicity in cancer cells. This analysis suggested conserved cellular responses to doxorubicin due to influences of homologous recombination, sphingolipid homeostasis, telomere tethering at nuclear periphery, actin cortical patch localization, and other gene functions. CONCLUSIONS Warburg status alters the genetic network required for yeast to buffer doxorubicin toxicity. Integration of yeast phenomic and cancer pharmacogenomics data suggests evolutionary conservation of gene-drug interaction networks and provides a new experimental approach to model their influence on chemotherapy response. Thus, yeast phenomic models could aid the development of precision oncology algorithms to predict efficacious cytotoxic drugs for cancer, based on genetic and metabolic profiles of individual tumors.
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Affiliation(s)
- Sean M. Santos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL USA
| | - John L. Hartman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL USA
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7
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Ren B, Tan HL, Nguyen TTT, Sayed AMM, Li Y, Mok YK, Yang H, Chen ES. Regulation of transcriptional silencing and chromodomain protein localization at centromeric heterochromatin by histone H3 tyrosine 41 phosphorylation in fission yeast. Nucleic Acids Res 2019; 46:189-202. [PMID: 29136238 PMCID: PMC5758876 DOI: 10.1093/nar/gkx1010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/13/2017] [Indexed: 12/29/2022] Open
Abstract
Heterochromatin silencing is critical for genomic integrity and cell survival. It is orchestrated by chromodomain (CD)-containing proteins that bind to methylated histone H3 lysine 9 (H3K9me), a hallmark of heterochromatin. Here, we show that phosphorylation of tyrosine 41 (H3Y41p)—a novel histone H3 modification—participates in the regulation of heterochromatin in fission yeast. We show that a loss-of-function mutant of H3Y41 can suppress heterochromatin de-silencing in the centromere and subtelomere repeat regions, suggesting a de-silencing role for H3Y41p on heterochromatin. Furthermore, we show both in vitro and in vivo that H3Y41p differentially regulates two CD-containing proteins without the change in the level of H3K9 methylation: it promotes the binding of Chp1 to histone H3 and the exclusion of Swi6. H3Y41p is preferentially enriched on centromeric heterochromatin during M- to early S phase, which coincides with the localization switch of Swi6/Chp1. The loss-of-function H3Y41 mutant could suppress the hypersensitivity of the RNAi mutants towards hydroxyurea (HU), which arrests replication in S phase. Overall, we describe H3Y41p as a novel histone modification that differentially regulates heterochromatin silencing in fission yeast via the binding of CD-containing proteins.
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Affiliation(s)
- Bingbing Ren
- Department of Biochemistry, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Hwei Ling Tan
- Department of Biochemistry, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | | | - Ying Li
- Cancer Science Institute, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Yu-Keung Mok
- Department of Biological Sciences, National University of Singapore
| | - Henry Yang
- Cancer Science Institute, National University of Singapore, Yong Loo Lin School of Medicine, Singapore.,National University Health System (NUHS), Singapore
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Yong Loo Lin School of Medicine, Singapore.,National University Health System (NUHS), Singapore
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8
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A Rahaman SN, Mat Yusop J, Mohamed-Hussein ZA, Aizat WM, Ho KL, Teh AH, Waterman J, Tan BK, Tan HL, Li AY, Chen ES, Ng CL. Crystal structure and functional analysis of human C1ORF123. PeerJ 2018; 6:e5377. [PMID: 30280012 PMCID: PMC6166629 DOI: 10.7717/peerj.5377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/14/2018] [Indexed: 12/12/2022] Open
Abstract
Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast Schizosaccharomyces pombe (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation.
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Affiliation(s)
| | - Jastina Mat Yusop
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.,Center for Frontier Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Jitka Waterman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, England, United Kingdom
| | - Boon Keat Tan
- Division of Human Biology, School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Hwei Ling Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Adelicia Yongling Li
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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9
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Chen ES. Targeting epigenetics using synthetic lethality in precision medicine. Cell Mol Life Sci 2018; 75:3381-3392. [PMID: 30003270 PMCID: PMC11105276 DOI: 10.1007/s00018-018-2866-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/30/2018] [Accepted: 07/03/2018] [Indexed: 12/31/2022]
Abstract
Technological breakthroughs in genomics have had a significant impact on clinical therapy for human diseases, allowing us to use patient genetic differences to guide medical care. The "synthetic lethal approach" leverages on cancer-specific genetic rewiring to deliver a therapeutic regimen that preferentially targets malignant cells while sparing normal cells. The utility of this system is evident in several recent studies, particularly in poor prognosis cancers with loss-of-function mutations that become "treatable" when two otherwise discrete and unrelated genes are targeted simultaneously. This review focuses on the chemotherapeutic targeting of epigenetic alterations in cancer cells and consolidates a network that outlines the interplay between epigenetic and genetic regulators in DNA damage repair. This network consists of numerous synergistically acting relationships that are druggable, even in recalcitrant triple-negative breast cancer. This collective knowledge points to the dawn of a new era of personalized medicine.
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Affiliation(s)
- Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- National University Health System (NUHS), Singapore, 119228, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117456, Singapore.
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10
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SAHA and cisplatin sensitize gastric cancer cells to doxorubicin by induction of DNA damage, apoptosis and perturbation of AMPK-mTOR signalling. Exp Cell Res 2018; 370:283-291. [PMID: 29959912 DOI: 10.1016/j.yexcr.2018.06.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 06/21/2018] [Accepted: 06/26/2018] [Indexed: 12/23/2022]
Abstract
Chemotherapy remains the most prescribed anti-cancer therapy, despite patients suffering severe side effects and frequently developing chemoresistance. These complications can be partially overcome by combining different chemotherapeutic agents that target multiple biological pathways. However, selecting efficacious drug combinations remains challenging. We previously used fission yeast Schizosaccharomycespombe as a surrogate model to predict drug combinations, and showed that suberoylanilide hydroxamic acid (SAHA) and cisplatin can sensitise gastric adenocarcinoma cells toward the cytotoxic effects of doxorubicin. Yet, how this combination undermines cell viability is unknown. Here, we show that SAHA and doxorubicin markedly enhance the cleavage of two apoptosis markers, caspase 3 and poly-ADP ribose polymerase (PARP-1), and increase the phosphorylation of γH2AX, a marker of DNA damage. Further, we found a prominent reduction in Ser485 phosphorylation of AMP-dependent protein kinase (AMPK), and reductions in its target mTOR and downstream ribosomal protein S6 phosphorylation. We show that SAHA contributes most of the effect, as confirmed using another histone deacetylase inhibitor, trichostatin A. Overall, our results show that the combination of SAHA and doxorubicin can induce apoptosis in gastric adenocarcinoma in a synthetically lethal manner, and that fission yeast offers an efficient tool for identifying potent drug combinations against human cancer cells.
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11
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Lim K, Nguyen T, Li AY, Yeo Y, Chen E. Histone H3 lysine 36 methyltransferase mobilizes NER factors to regulate tolerance against alkylation damage in fission yeast. Nucleic Acids Res 2018; 46:5061-5074. [PMID: 29635344 PMCID: PMC6007430 DOI: 10.1093/nar/gky245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 03/17/2018] [Accepted: 03/22/2018] [Indexed: 11/30/2022] Open
Abstract
The Set2 methyltransferase and its target, histone H3 lysine 36 (H3K36), affect chromatin architecture during the transcription and repair of DNA double-stranded breaks. Set2 also confers resistance against the alkylating agent, methyl methanesulfonate (MMS), through an unknown mechanism. Here, we show that Schizosaccharomyces pombe (S. pombe) exhibit MMS hypersensitivity when expressing a set2 mutant lacking the catalytic histone methyltransferase domain or a H3K36R mutant (reminiscent of a set2-null mutant). Set2 acts synergistically with base excision repair factors but epistatically with nucleotide excision repair (NER) factors, and determines the timely nuclear accumulation of the NER initiator, Rhp23, in response to MMS. Set2 facilitates Rhp23 recruitment to chromatin at the brc1 locus, presumably to repair alkylating damage and regulate the expression of brc1+ in response to MMS. Set2 also show epistasis with DNA damage checkpoint proteins; regulates the activation of Chk1, a DNA damage response effector kinase; and acts in a similar functional group as proteins involved in homologous recombination. Consistently, Set2 and H3K36 ensure the dynamicity of Rhp54 in DNA repair foci formation after MMS treatment. Overall, our results indicate a novel role for Set2/H3K36me in coordinating the recruitment of DNA repair machineries to timely manage alkylating damage.
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Affiliation(s)
- Kim Kiat Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Adelicia Yongling Li
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee Phan Yeo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
- NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore
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12
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Lee SQE, Tan TS, Kawamukai M, Chen ES. Cellular factories for coenzyme Q 10 production. Microb Cell Fact 2017; 16:39. [PMID: 28253886 PMCID: PMC5335738 DOI: 10.1186/s12934-017-0646-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/10/2017] [Indexed: 04/20/2023] Open
Abstract
Coenzyme Q10 (CoQ10), a benzoquinone present in most organisms, plays an important role in the electron-transport chain, and its deficiency is associated with various neuropathies and muscular disorders. CoQ10 is the only lipid-soluble antioxidant found in humans, and for this, it is gaining popularity in the cosmetic and healthcare industries. To meet the growing demand for CoQ10, there has been considerable interest in ways to enhance its production, the most effective of which remains microbial fermentation. Previous attempts to increase CoQ10 production to an industrial scale have thus far conformed to the strategies used in typical metabolic engineering endeavors. However, the emergence of new tools in the expanding field of synthetic biology has provided a suite of possibilities that extend beyond the traditional modes of metabolic engineering. In this review, we cover the various strategies currently undertaken to upscale CoQ10 production, and discuss some of the potential novel areas for future research.
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Affiliation(s)
- Sean Qiu En Lee
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Tsu Soo Tan
- School of Chemical & Life Sciences, Nanyang Polytechnic, Singapore, Singapore
| | - Makoto Kawamukai
- Faculty of Life and Environmental Science, Shimane University, Matsue, 690-8504, Japan
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore, Singapore. .,National University Health System (NUHS), Singapore, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore. .,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore.
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13
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Jackson RA, Chen ES. Synthetic lethal approaches for assessing combinatorial efficacy of chemotherapeutic drugs. Pharmacol Ther 2016; 162:69-85. [DOI: 10.1016/j.pharmthera.2016.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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14
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Nguyen TTT, Lim YJ, Fan MHM, Jackson RA, Lim KK, Ang WH, Ban KHK, Chen ES. Calcium modulation of doxorubicin cytotoxicity in yeast and human cells. Genes Cells 2016; 21:226-40. [DOI: 10.1111/gtc.12346] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/29/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Thi Thuy Trang Nguyen
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- National University Health System; Singapore
| | - Ying Jun Lim
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- National University Health System; Singapore
| | - Melanie Hui Min Fan
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- National University Health System; Singapore
| | - Rebecca A. Jackson
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - Kim Kiat Lim
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- National University Health System; Singapore
| | - Wee Han Ang
- Department of Chemistry; Faculty of Science; National University of Singapore; Singapore
| | - Kenneth Hon Kim Ban
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- National University Health System; Singapore
| | - Ee Sin Chen
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- National University Health System; Singapore
- NUS Graduate School of Science & Engineering; National University of Singapore; Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI); Life Sciences Institute; National University of Singapore; Singapore
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15
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Nguyen TTT, Chua JKK, Seah KS, Koo SH, Yee JY, Yang EG, Lim KK, Pang SYW, Yuen A, Zhang L, Ang WH, Dymock B, Lee EJD, Chen ES. Predicting chemotherapeutic drug combinations through gene network profiling. Sci Rep 2016; 6:18658. [PMID: 26791325 PMCID: PMC4726371 DOI: 10.1038/srep18658] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 11/23/2015] [Indexed: 12/29/2022] Open
Abstract
Contemporary chemotherapeutic treatments incorporate the use of several agents in combination. However, selecting the most appropriate drugs for such therapy is not necessarily an easy or straightforward task. Here, we describe a targeted approach that can facilitate the reliable selection of chemotherapeutic drug combinations through the interrogation of drug-resistance gene networks. Our method employed single-cell eukaryote fission yeast (Schizosaccharomyces pombe) as a model of proliferating cells to delineate a drug resistance gene network using a synthetic lethality workflow. Using the results of a previous unbiased screen, we assessed the genetic overlap of doxorubicin with six other drugs harboring varied mechanisms of action. Using this fission yeast model, drug-specific ontological sub-classifications were identified through the computation of relative hypersensitivities. We found that human gastric adenocarcinoma cells can be sensitized to doxorubicin by concomitant treatment with cisplatin, an intra-DNA strand crosslinking agent, and suberoylanilide hydroxamic acid, a histone deacetylase inhibitor. Our findings point to the utility of fission yeast as a model and the differential targeting of a conserved gene interaction network when screening for successful chemotherapeutic drug combinations for human cells.
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Affiliation(s)
- Thi Thuy Trang Nguyen
- Department of Biochemistry, National University of Singapore, Singapore.,National University Health System (NUHS), Singapore
| | - Jacqueline Kia Kee Chua
- Department of Biochemistry, National University of Singapore, Singapore.,Department of Chemistry, Faculty of Science, National University of Singapore, Singapore
| | - Kwi Shan Seah
- Department of Biochemistry, National University of Singapore, Singapore.,National University Health System (NUHS), Singapore
| | - Seok Hwee Koo
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Changi General Hospital, Ministry of Health, Singapore
| | - Jie Yin Yee
- National University Health System (NUHS), Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Eugene Guorong Yang
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Kim Kiat Lim
- Department of Biochemistry, National University of Singapore, Singapore.,National University Health System (NUHS), Singapore
| | | | - Audrey Yuen
- School of Chemical and Life Sciences, Singapore Polytechnic, Singapore
| | - Louxin Zhang
- Department of Mathematics, Faculty of Science, National University of Singapore, Singapore
| | - Wee Han Ang
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.,Department of Chemistry, Faculty of Science, National University of Singapore, Singapore
| | - Brian Dymock
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore
| | - Edmund Jon Deoon Lee
- National University Health System (NUHS), Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore.,National University Health System (NUHS), Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
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16
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Tang MYR, Guo H, Nguyen TTT, Low LS, Jackson RA, Yamada T, Chen ES. Two fission yeast high mobility group box proteins in the maintenance of genomic integrity following doxorubicin insult. Gene 2015; 562:70-5. [DOI: 10.1016/j.gene.2015.02.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 02/15/2015] [Indexed: 11/30/2022]
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17
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Nguyen TTT, Lim JSL, Tang RMY, Zhang L, Chen ES. Fitness profiling links topoisomerase II regulation of centromeric integrity to doxorubicin resistance in fission yeast. Sci Rep 2015; 5:8400. [PMID: 25669599 PMCID: PMC4323662 DOI: 10.1038/srep08400] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/14/2015] [Indexed: 01/18/2023] Open
Abstract
Doxorubicin, a chemotherapeutic agent, inhibits the religation step of topoisomerase II (Top2). However, the downstream ramifications of this action are unknown. Here we performed epistasis analyses of top2 with 63 genes representing doxorubicin resistance (DXR) genes in fission yeast and revealed a subset that synergistically collaborate with Top2 to confer DXR. Our findings show that the chromatin-regulating RSC and SAGA complexes act with Top2 in a cluster that is functionally distinct from the Ino80 complex. In various DXR mutants, doxorubicin hypersensitivity was unexpectedly suppressed by a concomitant top2 mutation. Several DXR proteins showed centromeric localization, and their disruption resulted in centromeric defects and chromosome missegregation. An additional top2 mutation could restore centromeric chromatin integrity, suggesting a counterbalance between Top2 and these DXR factors in conferring doxorubicin resistance. Overall, this molecular basis for mitotic catastrophe associated with doxorubicin treatment will help to facilitate drug combinatorial usage in doxorubicin-related chemotherapeutic regimens.
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Affiliation(s)
- Thi Thuy Trang Nguyen
- 1] Department of Biochemistry, National University of Singapore, Singapore 117597 [2] National University Health System (NUHS), Singapore
| | - Julia Sze Lynn Lim
- 1] Department of Biochemistry, National University of Singapore, Singapore 117597 [2] National University Health System (NUHS), Singapore
| | - Richard Ming Yi Tang
- 1] Department of Biochemistry, National University of Singapore, Singapore 117597 [2] National University Health System (NUHS), Singapore
| | - Louxin Zhang
- 1] NUS Graduate School for Integrative Sciences and Engineering [2] Department of Mathematics, National University of Singapore, Singapore 119076
| | - Ee Sin Chen
- 1] Department of Biochemistry, National University of Singapore, Singapore 117597 [2] National University Health System (NUHS), Singapore [3] Synthetic Biology Research Consortium, National University of Singapore [4] NUS Graduate School for Integrative Sciences and Engineering
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18
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Allan CM, Awad AM, Johnson JS, Shirasaki DI, Wang C, Blaby-Haas CE, Merchant SS, Loo JA, Clarke CF. Identification of Coq11, a new coenzyme Q biosynthetic protein in the CoQ-synthome in Saccharomyces cerevisiae. J Biol Chem 2015; 290:7517-34. [PMID: 25631044 DOI: 10.1074/jbc.m114.633131] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Coenzyme Q (Q or ubiquinone) is a redox active lipid composed of a fully substituted benzoquinone ring and a polyisoprenoid tail and is required for mitochondrial electron transport. In the yeast Saccharomyces cerevisiae, Q is synthesized by the products of 11 known genes, COQ1-COQ9, YAH1, and ARH1. The function of some of the Coq proteins remains unknown, and several steps in the Q biosynthetic pathway are not fully characterized. Several of the Coq proteins are associated in a macromolecular complex on the matrix face of the inner mitochondrial membrane, and this complex is required for efficient Q synthesis. Here, we further characterize this complex via immunoblotting and proteomic analysis of tandem affinity-purified tagged Coq proteins. We show that Coq8, a putative kinase required for the stability of the Q biosynthetic complex, is associated with a Coq6-containing complex. Additionally Q6 and late stage Q biosynthetic intermediates were also found to co-purify with the complex. A mitochondrial protein of unknown function, encoded by the YLR290C open reading frame, is also identified as a constituent of the complex and is shown to be required for efficient de novo Q biosynthesis. Given its effect on Q synthesis and its association with the biosynthetic complex, we propose that the open reading frame YLR290C be designated COQ11.
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Affiliation(s)
- Christopher M Allan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Agape M Awad
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Jarrett S Johnson
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Dyna I Shirasaki
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Charles Wang
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Crysten E Blaby-Haas
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute
| | - Sabeeha S Merchant
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, the UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Joseph A Loo
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, the Department of Biological Chemistry, and the UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Catherine F Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute,
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19
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Functional conservation of coenzyme Q biosynthetic genes among yeasts, plants, and humans. PLoS One 2014; 9:e99038. [PMID: 24911838 PMCID: PMC4049637 DOI: 10.1371/journal.pone.0099038] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/09/2014] [Indexed: 12/11/2022] Open
Abstract
Coenzyme Q (CoQ) is an essential factor for aerobic growth and oxidative phosphorylation in the electron transport system. The biosynthetic pathway for CoQ has been proposed mainly from biochemical and genetic analyses of Escherichia coli and Saccharomyces cerevisiae; however, the biosynthetic pathway in higher eukaryotes has been explored in only a limited number of studies. We previously reported the roles of several genes involved in CoQ synthesis in the fission yeast Schizosaccharomyces pombe. Here, we expand these findings by identifying ten genes (dps1, dlp1, ppt1, and coq3–9) that are required for CoQ synthesis. CoQ10-deficient S. pombe coq deletion strains were generated and characterized. All mutant fission yeast strains were sensitive to oxidative stress, produced a large amount of sulfide, required an antioxidant to grow on minimal medium, and did not survive at the stationary phase. To compare the biosynthetic pathway of CoQ in fission yeast with that in higher eukaryotes, the ability of CoQ biosynthetic genes from humans and plants (Arabidopsis thaliana) to functionally complement the S. pombe coq deletion strains was determined. With the exception of COQ9, expression of all other human and plant COQ genes recovered CoQ10 production by the fission yeast coq deletion strains, although the addition of a mitochondrial targeting sequence was required for human COQ3 and COQ7, as well as A. thaliana COQ6. In summary, this study describes the functional conservation of CoQ biosynthetic genes between yeasts, humans, and plants.
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