1
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Kar A, Degtyareva NP, Doetsch PW. Human NTHL1 expression and subcellular distribution determines cisplatin sensitivity in human lung epithelial and non-small cell lung cancer cells. NAR Cancer 2024; 6:zcae006. [PMID: 38384388 PMCID: PMC10880605 DOI: 10.1093/narcan/zcae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/11/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024] Open
Abstract
Base excision repair is critical for maintaining genomic stability and for preventing malignant transformation. NTHL1 is a bifunctional DNA glycosylase/AP lyase that initiates repair of oxidatively damaged pyrimidines. Our recent work established that transient over-expression of NTHL1 leads to acquisition of several hallmarks of cancer in non-tumorigenic immortalized cells likely through interaction with nucleotide excision repair protein XPG. Here, we investigate how NTHL1 expression levels impact cellular sensitivity to cisplatin in non-tumorigenic immortalized cells and five non-small cell lung carcinomas cell lines. The cell line with lowest expression of NTHL1 (H522) shows the highest resistance to cisplatin indicating that decrease in NTHL1 levels may modulate resistance to crosslinking agents in NSCLC tumors. In a complementation study, overexpression of NTHL1 in H522 cell line sensitized it to cisplatin. Using NTHL1 N-terminal deletion mutants defective in nuclear localization we show that cisplatin treatment can alter NTHL1 subcellular localization possibly leading to altered protein-protein interactions and affecting cisplatin sensitivity. Experiments presented in this study reveal a previously unknown link between NTHL1 expression levels and cisplatin sensitivity of NSCLC tumor cells. These findings provide an opportunity to understand how altered NTHL1 expression levels and subcellular distribution can impact cisplatin sensitivity in NSCLC tumor cells.
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Affiliation(s)
- Anirban Kar
- Mutagenesis & DNA Repair Regulation Group, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Durham, NC 27709, USA
| | - Natalya P Degtyareva
- Mutagenesis & DNA Repair Regulation Group, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Durham, NC 27709, USA
| | - Paul W Doetsch
- Mutagenesis & DNA Repair Regulation Group, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Durham, NC 27709, USA
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2
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Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst 2023; 14:447-463.e8. [PMID: 37220749 PMCID: PMC10330685 DOI: 10.1016/j.cels.2023.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/30/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
The DNA damage response (DDR) ensures error-free DNA replication and transcription and is disrupted in numerous diseases. An ongoing challenge is to determine the proteins orchestrating DDR and their organization into complexes, including constitutive interactions and those responding to genomic insult. Here, we use multi-conditional network analysis to systematically map DDR assemblies at multiple scales. Affinity purifications of 21 DDR proteins, with/without genotoxin exposure, are combined with multi-omics data to reveal a hierarchical organization of 605 proteins into 109 assemblies. The map captures canonical repair mechanisms and proposes new DDR-associated proteins extending to stress, transport, and chromatin functions. We find that protein assemblies closely align with genetic dependencies in processing specific genotoxins and that proteins in multiple assemblies typically act in multiple genotoxin responses. Follow-up by DDR functional readouts newly implicates 12 assembly members in double-strand-break repair. The DNA damage response assemblies map is available for interactive visualization and query (ccmi.org/ddram/).
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Affiliation(s)
- Anton Kratz
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Minkyu Kim
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA; University of Texas Health Science Center San Antonio, Department of Biochemistry and Structural Biology, San Antonio, TX 78229, USA
| | - Marcus R Kelly
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Fan Zheng
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Christopher A Koczor
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Jianfeng Li
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Keiichiro Ono
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Yue Qin
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Christopher Churas
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jing Chen
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Rudolf T Pillich
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jisoo Park
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Maya Modak
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Rachel Collier
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Kate Licon
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Dexter Pratt
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Robert W Sobol
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA; Brown University, Department of Pathology and Laboratory Medicine and Legorreta Cancer Center, Providence, RI 02903, USA.
| | - Nevan J Krogan
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
| | - Trey Ideker
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
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3
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Zhang X, Li D, Zhu J, Zheng J, Li H, He Q, Peng J, Chen S, Chen XL, Wang W. RNAPII Degradation Factor Def1 Is Required for Development, Stress Response, and Full Virulence of Magnaporthe oryzae. J Fungi (Basel) 2023; 9:jof9040467. [PMID: 37108921 PMCID: PMC10145571 DOI: 10.3390/jof9040467] [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: 02/15/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The RNA polymerase II degradation factor Degradation Factor 1 (Def1) is important for DNA damage repair and plays various roles in eukaryotes; however, the biological role in plant pathogenic fungi is still unknown. In this study, we investigated the role of Def1 during the development and infection of the rice blast fungus Magnaporthe oryzae. The deletion mutant of Def1 displayed slower mycelial growth, less conidial production, and abnormal conidial morphology. The appressoria of Δdef1 was impaired in the penetration into host cells, mainly due to blocking in the utilization of conidial storages, such as glycogen and lipid droplets. The invasive growth of the Δdef1 mutant was also retarded and accompanied with the accumulation of reactive oxygen species (ROS) inside the host cells. Furthermore, compared with the wild type, Δdef1 was more sensitive to multiple stresses, such as oxidative stress, high osmotic pressure, and alkaline/acidic pH. Interestingly, we found that Def1 was modified by O-GlcNAcylation at Ser232, which was required for the stability of Def1 and its function in pathogenicity. Taken together, the O-GlcNAc modified Def1 is required for hyphae growth, conidiation, pathogenicity, and stress response in M. oryzae. This study reveals a novel regulatory mechanism of O-GlcNAc-mediated Def1 in plant pathogenic fungi.
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Affiliation(s)
- Xinrong Zhang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dong Li
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Jun Zhu
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Zheng
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongye Li
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qixuan He
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Jun Peng
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Shen Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiao-Lin Chen
- State Key Laboratory of Agricultural Microbiology, Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weixiang Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
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4
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Karpov DS, Spasskaya DS, Tutyaeva VV, Karpov VL. Rpn4p without the DNA-Binding Domain Provides Saccharomyces cerevisiae Resistance to Oxidative Stress and Cycloheximide. Mol Biol 2022. [DOI: 10.1134/s0026893322040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Schizosaccharomyces pombe Fzo1 is subjected to the ubiquitin-proteasome-mediated degradation during the stationary phase. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:397-404. [PMID: 35075549 DOI: 10.1007/s10123-022-00231-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/13/2021] [Accepted: 12/23/2021] [Indexed: 02/01/2023]
Abstract
Mitochondria are highly dynamic organelles that undergo fission and fusion to adapt to the metabolic needs of the cell. Mitofusins are dynamin-like GTPases that play a key role in the regulation of mitochondrial fusion and metabolism. In Saccharomyces cerevisiae, mitofusin Fzo1 levels are controlled by post-translational ubiquitination and degradation. However, it is not clear whether the levels of the Schizosaccharomyces pombe mitofusin Fzo1 are similarly regulated. In this study, we examined the expression S. pombe Fzo1 during normal growth. We showed that Fzo1 protein levels but not mRNA expression levels were reduced during the stationary phase. The protein was stabilized by the proteasome inhibitor bortezomib. Disruption of ubc8 encoding a ubiquitin-conjugating enzyme and rsv2 encoding an S. pombe homolog of S. cerevisiae RPN4 known for activating the expression of genes required for proteasomal biogenesis suppresses the proteasomal degradation of Fzo1 during the stationary phase. Overexpression of fzo1 prevents its degradation. Our results suggest that like S. pombe Fzo1 expression is not regulated by transcription but rather by proteolytic degradation during the stationary phase. Our findings also suggest that although S. cerevisiae and S. pombe Fzo1 proteins are regulated by ubiquitin-proteasomal degradation, different ubiquitin-conjugating enzymes (E2) and ubiquitin ligases (E3) are involved in their degradation.
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6
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Milano L, Charlier CF, Andreguetti R, Cox T, Healing E, Thomé MP, Elliott RM, Samson LD, Masson JY, Lenz G, Henriques JAP, Nohturfft A, Meira LB. A DNA repair-independent role for alkyladenine DNA glycosylase in alkylation-induced unfolded protein response. Proc Natl Acad Sci U S A 2022; 119:e2111404119. [PMID: 35197283 PMCID: PMC8892324 DOI: 10.1073/pnas.2111404119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/08/2022] [Indexed: 01/25/2023] Open
Abstract
Alkylating agents damage DNA and proteins and are widely used in cancer chemotherapy. While cellular responses to alkylation-induced DNA damage have been explored, knowledge of how alkylation affects global cellular stress responses is sparse. Here, we examined the effects of the alkylating agent methylmethane sulfonate (MMS) on gene expression in mouse liver, using mice deficient in alkyladenine DNA glycosylase (Aag), the enzyme that initiates the repair of alkylated DNA bases. MMS induced a robust transcriptional response in wild-type liver that included markers of the endoplasmic reticulum (ER) stress/unfolded protein response (UPR) known to be controlled by XBP1, a key UPR effector. Importantly, this response is significantly reduced in the Aag knockout. To investigate how AAG affects alkylation-induced UPR, the expression of UPR markers after MMS treatment was interrogated in human glioblastoma cells expressing different AAG levels. Alkylation induced the UPR in cells expressing AAG; conversely, AAG knockdown compromised UPR induction and led to a defect in XBP1 activation. To verify the requirements for the DNA repair activity of AAG in this response, AAG knockdown cells were complemented with wild-type Aag or with an Aag variant producing a glycosylase-deficient AAG protein. As expected, the glycosylase-defective Aag does not fully protect AAG knockdown cells against MMS-induced cytotoxicity. Remarkably, however, alkylation-induced XBP1 activation is fully complemented by the catalytically inactive AAG enzyme. This work establishes that, besides its enzymatic activity, AAG has noncanonical functions in alkylation-induced UPR that contribute to cellular responses to alkylation.
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Affiliation(s)
- Larissa Milano
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom
- Center of Biotechnology, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Center, Quebec City, QC G1V 0A6, Canada
| | - Clara F Charlier
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom
| | - Rafaela Andreguetti
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom
| | - Thomas Cox
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom
| | - Eleanor Healing
- Department of Nutritional Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, United Kingdom
| | - Marcos P Thomé
- Department of Biophysics, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
| | - Ruan M Elliott
- Department of Nutritional Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, United Kingdom
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Center, Quebec City, QC G1V 0A6, Canada
| | - Guido Lenz
- Center of Biotechnology, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
- Department of Biophysics, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
| | - João Antonio P Henriques
- Center of Biotechnology, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
- Department of Biophysics, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
| | - Axel Nohturfft
- Molecular and Clinical Sciences Research Institute, St. George's University of London, SW17 0RE London, United Kingdom
| | - Lisiane B Meira
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom;
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7
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Onchieku NM, Kumari S, Pandey R, Sharma V, Kumar M, Deshmukh A, Kaur I, Mohmmed A, Gupta D, Kiboi D, Gaur N, Malhotra P. Artemisinin Binds and Inhibits the Activity of Plasmodium falciparum Ddi1, a Retroviral Aspartyl Protease. Pathogens 2021; 10:pathogens10111465. [PMID: 34832620 PMCID: PMC8621276 DOI: 10.3390/pathogens10111465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 01/10/2023] Open
Abstract
Reduced sensitivity of the human malaria parasite, Plasmodium falciparum, to Artemisinin and its derivatives (ARTs) threatens the global efforts towards eliminating malaria. ARTs have been shown to cause ubiquitous cellular and genetic insults, which results in the activation of the unfolded protein response (UPR) pathways. The UPR restores protein homeostasis, which otherwise would be toxic to cellular survival. Here, we interrogated the role of DNA-damage inducible protein 1 (PfDdi1), a unique proteasome-interacting retropepsin in mediating the actions of the ARTs. We demonstrate that PfDdi1 is an active A2 family protease that hydrolyzes ubiquitinated proteasome substrates. Treatment of P. falciparum parasites with ARTs leads to the accumulation of ubiquitinated proteins in the parasites and blocks the destruction of ubiquitinated proteins by inhibiting the PfDdi1 protease activity. Besides, whereas the PfDdi1 is predominantly localized in the cytoplasm, exposure of the parasites to ARTs leads to DNA fragmentation and increased recruitment of the PfDdi1 into the nucleus. Furthermore, we show that Ddi1 knock-out Saccharomycescerevisiae cells are more susceptible to ARTs and the PfDdI1 protein robustly restores the corresponding functions in the knock-out cells. Together, these results show that ARTs act in multiple ways; by inducing DNA and protein damage and might be impairing the damage recovery by inhibiting the activity of PfDdi1, an essential ubiquitin-proteasome retropepsin.
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Affiliation(s)
- Noah Machuki Onchieku
- Malaria Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India or (N.M.O.); (V.S.); (A.D.); (I.K.)
| | - Sonam Kumari
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.K.); (M.K.); (N.G.)
| | - Rajan Pandey
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (R.P.); (D.G.)
| | - Vaibhav Sharma
- Malaria Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India or (N.M.O.); (V.S.); (A.D.); (I.K.)
| | - Mohit Kumar
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.K.); (M.K.); (N.G.)
| | - Arunaditya Deshmukh
- Malaria Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India or (N.M.O.); (V.S.); (A.D.); (I.K.)
| | - Inderjeet Kaur
- Malaria Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India or (N.M.O.); (V.S.); (A.D.); (I.K.)
| | - Asif Mohmmed
- Parasite Cell Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (R.P.); (D.G.)
| | - Daniel Kiboi
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya;
| | - Naseem Gaur
- Yeast Biofuel Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.K.); (M.K.); (N.G.)
| | - Pawan Malhotra
- Malaria Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India or (N.M.O.); (V.S.); (A.D.); (I.K.)
- Correspondence: or
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8
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Cao C, Xue C. More Than Just Cleaning: Ubiquitin-Mediated Proteolysis in Fungal Pathogenesis. Front Cell Infect Microbiol 2021; 11:774613. [PMID: 34858882 PMCID: PMC8631298 DOI: 10.3389/fcimb.2021.774613] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022] Open
Abstract
Ubiquitin-proteasome mediated protein turnover is an important regulatory mechanism of cellular function in eukaryotes. Extensive studies have linked the ubiquitin-proteasome system (UPS) to human diseases, and an array of proteasome inhibitors have been successfully developed for cancer therapy. Although still an emerging field, research on UPS regulation of fungal development and virulence has been rapidly advancing and has generated considerable excitement in its potential as a target for novel drugs. In this review, we summarize UPS composition and regulatory function in pathogenic fungi, especially in stress responses, host adaption, and fungal pathogenesis. Emphasis will be given to UPS regulation of pathogenic factors that are important for fungal pathogenesis. We also discuss future potential therapeutic strategies for fungal infections based on targeting UPS pathways.
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Affiliation(s)
- Chengjun Cao
- Public Health Research Institute, Rutgers University, New Brunswick, NJ, United States
| | - Chaoyang Xue
- Public Health Research Institute, Rutgers University, New Brunswick, NJ, United States
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ, United States
- Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ, United States
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9
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Akinniyi OT, Reese JC. DEF1: Much more than an RNA polymerase degradation factor. DNA Repair (Amst) 2021; 107:103202. [PMID: 34419700 PMCID: PMC8879385 DOI: 10.1016/j.dnarep.2021.103202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 01/14/2023]
Abstract
Degradation Factor 1 was discovered 20 years ago as a yeast protein copurifying with Rad26, a helicase involved in transcription-coupled DNA repair. It was subsequently shown to control the ubiquitylation and destruction of the large subunit of DNA damage-arrested RNA Polymerase II. Since that time, much has been learned about Def1's role in polymerase destruction and new functions of the protein have been revealed. We now understand that Def1 is involved in more than just RNA polymerase II regulation. Most of its known functions are associated with maintaining chromosome and genomic integrity, but other exciting activities outside this realm have been suggested. Here we review this fascinating protein, describe its regulation and present a hypothesis that Def1 is a central coordinator of ubiquitin signaling pathways in cells.
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Affiliation(s)
- Oluwasegun T Akinniyi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Joseph C Reese
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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10
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Wang Y, Tan Y, Zhang F, Lu X, Shao L, Liu Y, Liu Z. Characterizing the role of the zinc finger transcription factor AcrpnR in governing development in Aspergillus cristatus. J Basic Microbiol 2021; 61:1035-1047. [PMID: 34596896 DOI: 10.1002/jobm.202100305] [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: 06/28/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 11/05/2022]
Abstract
Filamentous fungi reproduce sexually or asexually, and the developmental processes are strictly regulated by a variety of transcription factors. In this study, we characterized a zinc finger transcription factor, called AcrpnR, in Aspergillus cristatus (GME2916). The ∆AcrpnR strain exhibited decreased asexual reproduction and increased cleistothecium production. The complementation strain showed restoration of these phenotypic differences. Overexpression of AcrpnR resulted in enhanced asexual development and delayed and inhibited sexual reproduction, suggesting that AcrpnR is required for proper asexual and sexual development in A. cristatus. In addition, AcrpnR positively regulated the expression of genes of the central regulatory pathway of conidiation and negatively regulated the expression of sex-related genes. Overall, these results demonstrate that AcrpnR is essential for maintaining a balance between asexual and sexual development.
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Affiliation(s)
- Yaping Wang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Yumei Tan
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China.,Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Fuqian Zhang
- School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolin Lu
- School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou, China
| | - Lei Shao
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Yongxiang Liu
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China.,Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Zuoyi Liu
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China.,Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China.,Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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11
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Bharati AP, Kumari S, Akhtar MS. Proteome analysis of Saccharomyces cerevisiae after methyl methane sulfonate (MMS) treatment. Biochem Biophys Rep 2020; 24:100820. [PMID: 33072891 PMCID: PMC7548944 DOI: 10.1016/j.bbrep.2020.100820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 11/27/2022] Open
Abstract
The treatment of methyl methane sulfonate (MMS) increases sensitivity to the DNA damage which, further leads to the cell death followed by a cell cycle delay. Delay in the cell cycle is because of the change in global transcription regulation which results into proteome change. There are several microarray studies on the transcriptome changes after MMS treatment, but very few studies are reported related to proteome change. The proteome analysis in this report identified subgroups of proteins, belonging to known cell cycle regulators, metabolic pathways and protein folding. About 53 proteins were identified by MS/MS and found that 36 of them were induced, 10 were repressed and few of them showed insignificant change. Our results indicated the change in the interactome as well as phosphorylation status of carboxy terminal domain (CTD) of RNA Polymerase II (RNAP-II) after MMS treatment. The RNAP-II complex was affinity purified and ~1640 peptides were identified using nano LC/MS corresponding to 27 interacting proteins along with the twelve RNAP-II subunit. These identified proteins participated in the repair of the damage, changes the function of the main energetic pathways and the carbon flux in various end products. The main metabolic enzymes in the glycolysis, pyruvate phosphate and amino acid biosynthesis pathways showed significant change. Our results indicate that DNA damage is somehow related to these pathways and is co-regulated simultaneously.
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Affiliation(s)
- Akhilendra Pratap Bharati
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
- Molecular and Structural Biology Division, CSIR-CDRI, Sector 10, Jankipuram Extension, Lucknow, PIN 226 031, India
| | - Sunita Kumari
- ICAR-Indian Institute of Seed Science, Mau, Uttar Pradesh, 275103, India
| | - Md Sohail Akhtar
- Molecular and Structural Biology Division, CSIR-CDRI, Sector 10, Jankipuram Extension, Lucknow, PIN 226 031, India
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12
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Spasskaya DS, Nadolinskaia NI, Tutyaeva VV, Lysov YP, Karpov VL, Karpov DS. Yeast Rpn4 Links the Proteasome and DNA Repair via RAD52 Regulation. Int J Mol Sci 2020; 21:ijms21218097. [PMID: 33143019 PMCID: PMC7672625 DOI: 10.3390/ijms21218097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
Environmental and intracellular factors often damage DNA, but multiple DNA repair pathways maintain genome integrity. In yeast, the 26S proteasome and its transcriptional regulator and substrate Rpn4 are involved in DNA damage resistance. Paradoxically, while proteasome dysfunction may induce hyper-resistance to DNA-damaging agents, Rpn4 malfunction sensitizes yeasts to these agents. Previously, we proposed that proteasome inhibition causes Rpn4 stabilization followed by the upregulation of Rpn4-dependent DNA repair genes and pathways. Here, we aimed to elucidate the key Rpn4 targets responsible for DNA damage hyper-resistance in proteasome mutants. We impaired the Rpn4-mediated regulation of candidate genes using the CRISPR/Cas9 system and tested the sensitivity of mutant strains to 4-NQO, MMS and zeocin. We found that the separate or simultaneous deregulation of 19S or 20S proteasome subcomplexes induced MAG1, DDI1, RAD23 and RAD52 in an Rpn4-dependent manner. Deregulation of RAD23, DDI1 and RAD52 sensitized yeast to DNA damage. Genetic, epigenetic or dihydrocoumarin-mediated RAD52 repression restored the sensitivity of the proteasome mutants to DNA damage. Our results suggest that the Rpn4-mediated overexpression of DNA repair genes, especially RAD52, defines the DNA damage hyper-resistant phenotype of proteasome mutants. The developed yeast model is useful for characterizing drugs that reverse the DNA damage hyper-resistance phenotypes of cancers.
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Affiliation(s)
- Daria S. Spasskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia; (D.S.S.); (V.V.T.)
| | - Nonna I. Nadolinskaia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.I.N.); (Y.P.L.); (V.L.K.)
| | - Vera V. Tutyaeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia; (D.S.S.); (V.V.T.)
| | - Yuriy P. Lysov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.I.N.); (Y.P.L.); (V.L.K.)
| | - Vadim L. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (N.I.N.); (Y.P.L.); (V.L.K.)
| | - Dmitry S. Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, 119991 Moscow, Russia; (D.S.S.); (V.V.T.)
- Correspondence: ; Tel.: +7-499-135-98-01
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13
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De-Souza EA, Pimentel FSA, De-Queiroz ALFV, Camara H, Felix-Formiga ML, Machado CM, Pinto S, Galina A, Mori MA, Montero-Lomeli M, Masuda CA. The yeast protein Ubx4p contributes to mitochondrial respiration and lithium-galactose-mediated activation of the unfolded protein response. J Biol Chem 2020; 295:3773-3782. [PMID: 31996377 PMCID: PMC7086034 DOI: 10.1074/jbc.ra119.011271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
In the presence of galactose, lithium ions activate the unfolded protein response (UPR) by inhibiting phosphoglucomutase activity and causing the accumulation of galactose-related metabolites, including galactose-1-phosphate. These metabolites also accumulate in humans who have the disease classic galactosemia. Here, we demonstrate that Saccharomyces cerevisiae yeast strains harboring a deletion of UBX4, a gene encoding a partner of Cdc48p in the endoplasmic reticulum-associated degradation (ERAD) pathway, exhibit delayed UPR activation after lithium and galactose exposure because the deletion decreases galactose-1-phosphate levels. The delay in UPR activation did not occur in yeast strains in which key ERAD or proteasomal pathway genes had been disrupted, indicating that the ubx4Δ phenotype is ERAD-independent. We also observed that the ubx4Δ strain displays decreased oxygen consumption. The inhibition of mitochondrial respiration was sufficient to diminish galactose-1-phosphate levels and, consequently, affects UPR activation. Finally, we show that the deletion of the AMP-activated protein kinase ortholog-encoding gene SNF1 can restore the oxygen consumption rate in ubx4Δ strain, thereby reestablishing galactose metabolism, UPR activation, and cellular adaption to lithium-galactose challenge. Our results indicate a role for Ubx4p in yeast mitochondrial function and highlight that mitochondrial and endoplasmic reticulum functions are intertwined through galactose metabolism. These findings also shed new light on the mechanisms of lithium action and on the pathophysiology of galactosemia.
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Affiliation(s)
- Evandro A De-Souza
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Felipe S A Pimentel
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Ana Luiza F V De-Queiroz
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Henrique Camara
- Department of Biochemistry and Tissue Biology, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP, 13083-970, Brazil
| | - Mikaella L Felix-Formiga
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Caio M Machado
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Silas Pinto
- Department of Biochemistry and Tissue Biology, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP, 13083-970, Brazil
| | - Antonio Galina
- Programa de Bioquímica e Biofísica Celular, Instituto de Bioquímica M[c33c]zpi;●dica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP, 13083-970, Brazil
| | - Monica Montero-Lomeli
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Claudio A Masuda
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
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Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy. Appl Microbiol Biotechnol 2020; 104:4027-4041. [PMID: 32157425 DOI: 10.1007/s00253-020-10518-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/15/2020] [Accepted: 03/01/2020] [Indexed: 12/18/2022]
Abstract
Distilled spirits production using Saccharomyces cerevisiae requires understanding of the mechanisms of yeast cell response to alcohol stress. Reportedly, specific mutations in genes of the ubiquitin-proteasome system, e.g., RPN4, may result in strains exhibiting hyper-resistance to different alcohols. To study the Rpn4-dependent yeast response to short-term ethanol exposure, we performed a comparative analysis of the wild-type (WT) strain, strain with RPN4 gene deletion (rpn4-Δ), and a mutant strain with decreased proteasome activity and consequent Rpn4 accumulation due to PRE1 deregulation (YPL). The stress resistance tests demonstrated an increased sensitivity of mutant strains to ethanol compared with WT. Comparative proteomics analysis revealed significant differences in molecular responses to ethanol between these strains. GO analysis of proteins upregulated in WT showed enrichments represented by oxidative and heat responses, protein folding/unfolding, and protein degradation. Enrichment of at least one of these responses was not observed in the mutant strains. Moreover, activity of autophagy was not increased in the RPN4 deletion strain upon ethanol stress which agrees with changes in mRNA levels of ATG7 and PRB1 genes of the autophagy system. Activity of the autophagic system was clearly induced and accompanied with PRB1 overexpression in the YPL strain upon ethanol stress. We demonstrated that Rpn4 stabilization contributes to the PRB1 upregulation. CRISPR-Cas9-mediated repression of PACE-core Rpn4 binding sites in the PRB1 promoter inhibits PRB1 induction in the YPL strain upon ethanol treatment and results in YPL hypersensitivity to ethanol. Our data suggest that Rpn4 affects the autophagic system activity upon ethanol stress through the PRB1 regulation. These findings can be a basis for creating genetically modified yeast strains resistant to high levels of alcohol, being further used for fermentation in ethanol production.
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15
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Finley D, Prado MA. The Proteasome and Its Network: Engineering for Adaptability. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033985. [PMID: 30833452 DOI: 10.1101/cshperspect.a033985] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteasome, the most complex protease known, degrades proteins that have been conjugated to ubiquitin. It faces the unique challenge of acting enzymatically on hundreds and perhaps thousands of structurally diverse substrates, mechanically unfolding them from their native state and translocating them vectorially from one specialized compartment of the enzyme to another. Moreover, substrates are modified by ubiquitin in myriad configurations of chains. The many unusual design features of the proteasome may have evolved in part to endow this enzyme with a robust ability to process substrates regardless of their identity. The proteasome plays a major role in preserving protein homeostasis in the cell, which requires adaptation to a wide variety of stress conditions. Modulation of proteasome function is achieved through a large network of proteins that interact with it dynamically, modify it enzymatically, or fine-tune its levels. The resulting adaptability of the proteasome, which is unique among proteases, enables cells to control the output of the ubiquitin-proteasome pathway on a global scale.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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16
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Yang TH. Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast. BMC Bioinformatics 2019; 20:630. [PMID: 31881824 PMCID: PMC6933673 DOI: 10.1186/s12859-019-3212-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Current technologies for understanding the transcriptional reprogramming in cells include the transcription factor (TF) chromatin immunoprecipitation (ChIP) experiments and the TF knockout experiments. The ChIP experiments show the binding targets of TFs against which the antibody directs while the knockout techniques find the regulatory gene targets of the knocked-out TFs. However, it was shown that these two complementary results contain few common targets. Researchers have used the concept of TF functional redundancy to explain the low overlap between these two techniques. But the detailed molecular mechanisms behind TF functional redundancy remain unknown. Without knowing the possible molecular mechanisms, it is hard for biologists to fully unravel the cause of TF functional redundancy. RESULTS To mine out the molecular mechanisms, a novel algorithm to extract TF regulatory modules that help explain the observed TF functional redundancy effect was devised and proposed in this research. The method first searched for candidate TF sets from the TF binding data. Then based on these candidate sets the method utilized the modified Steiner Tree construction algorithm to construct the possible TF regulatory modules from protein-protein interaction data and finally filtered out the noise-induced results by using confidence tests. The mined-out regulatory modules were shown to correlate to the concept of functional redundancy and provided testable hypotheses of the molecular mechanisms behind functional redundancy. And the biological significance of the mined-out results was demonstrated in three different biological aspects: ontology enrichment, protein interaction prevalence and expression coherence. About 23.5% of the mined-out TF regulatory modules were literature-verified. Finally, the biological applicability of the proposed method was shown in one detailed example of a verified TF regulatory module for pheromone response and filamentous growth in yeast. CONCLUSION In this research, a novel method that mined out the potential TF regulatory modules which elucidate the functional redundancy observed among TFs is proposed. The extracted TF regulatory modules not only correlate the molecular mechanisms to the observed functional redundancy among TFs, but also show biological significance in inferring TF functional binding target genes. The results provide testable hypotheses for biologists to further design subsequent research and experiments.
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Affiliation(s)
- Tzu-Hsien Yang
- Department of Information Management, National University of Kaohsiung, 700, Kaohsiung University Rd, Kaohsiung, 81148, Taiwan.
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17
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Silva E, Ideker T. Transcriptional responses to DNA damage. DNA Repair (Amst) 2019; 79:40-49. [PMID: 31102970 PMCID: PMC6570417 DOI: 10.1016/j.dnarep.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/20/2019] [Accepted: 05/04/2019] [Indexed: 12/31/2022]
Abstract
In response to the threat of DNA damage, cells exhibit a dramatic and multi-factorial response spanning from transcriptional changes to protein modifications, collectively known as the DNA damage response (DDR). Here, we review the literature surrounding the transcriptional response to DNA damage. We review differences in observed transcriptional responses as a function of cell cycle stage and emphasize the importance of experimental design in these transcriptional response studies. We additionally consider topics including structural challenges in the transcriptional response to DNA damage as well as the connection between transcription and protein abundance.
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Affiliation(s)
- Erica Silva
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA.
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Biomedical Sciences Program, University of California San Diego, La Jolla, California, USA; Program in Bioinformatics, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.
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18
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Wendler P, Enenkel C. Nuclear Transport of Yeast Proteasomes. Front Mol Biosci 2019; 6:34. [PMID: 31157235 PMCID: PMC6532418 DOI: 10.3389/fmolb.2019.00034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/26/2019] [Indexed: 11/13/2022] Open
Abstract
Proteasomes are key proteases in regulating protein homeostasis. Their holo-enzymes are composed of 40 different subunits which are arranged in a proteolytic core (CP) flanked by one to two regulatory particles (RP). Proteasomal proteolysis is essential for the degradation of proteins which control time-sensitive processes like cell cycle progression and stress response. In dividing yeast and human cells, proteasomes are primarily nuclear suggesting that proteasomal proteolysis is mainly required in the nucleus during cell proliferation. In yeast, which have a closed mitosis, proteasomes are imported into the nucleus as immature precursors via the classical import pathway. During quiescence, the reversible absence of proliferation induced by nutrient depletion or growth factor deprivation, proteasomes move from the nucleus into the cytoplasm. In the cytoplasm of quiescent yeast, proteasomes are dissociated into CP and RP and stored in membrane-less cytoplasmic foci, named proteasome storage granules (PSGs). With the resumption of growth, PSGs clear and mature proteasomes are transported into the nucleus by Blm10, a conserved 240 kDa protein and proteasome-intrinsic import receptor. How proteasomes are exported from the nucleus into the cytoplasm is unknown.
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Affiliation(s)
- Petra Wendler
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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19
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Schmidt RM, Schessner JP, Borner GH, Schuck S. The proteasome biogenesis regulator Rpn4 cooperates with the unfolded protein response to promote ER stress resistance. eLife 2019; 8:43244. [PMID: 30865586 PMCID: PMC6415940 DOI: 10.7554/elife.43244] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/27/2019] [Indexed: 12/27/2022] Open
Abstract
Misfolded proteins in the endoplasmic reticulum (ER) activate the unfolded protein response (UPR), which enhances protein folding to restore homeostasis. Additional pathways respond to ER stress, but how they help counteract protein misfolding is incompletely understood. Here, we develop a titratable system for the induction of ER stress in yeast to enable a genetic screen for factors that augment stress resistance independently of the UPR. We identify the proteasome biogenesis regulator Rpn4 and show that it cooperates with the UPR. Rpn4 abundance increases during ER stress, first by a post-transcriptional, then by a transcriptional mechanism. Induction of RPN4 transcription is triggered by cytosolic mislocalization of secretory proteins, is mediated by multiple signaling pathways and accelerates clearance of misfolded proteins from the cytosol. Thus, Rpn4 and the UPR are complementary elements of a modular cross-compartment response to ER stress.
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Affiliation(s)
- Rolf M Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Heidelberg, Germany
| | - Julia P Schessner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Georg Hh Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, Heidelberg, Germany
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20
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FlbA-Regulated Gene rpnR Is Involved in Stress Resistance and Impacts Protein Secretion when Aspergillus niger Is Grown on Xylose. Appl Environ Microbiol 2019; 85:AEM.02282-18. [PMID: 30413474 DOI: 10.1128/aem.02282-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/20/2018] [Indexed: 11/20/2022] Open
Abstract
Proteins are secreted throughout the mycelium of Aspergillus niger except for the sporulating zone. A link between sporulation and repression of protein secretion was underlined by the finding that inactivation of the sporulation gene flbA results in mycelial colonies that secrete proteins throughout the colony. However, ΔflbA strain hyphae also lyse and have thinner cell walls. This pleiotropic phenotype is associated with differential expression of 36 predicted transcription factor genes, one of which, rpnR, was inactivated in this study. Sporulation, biomass, and secretome complexity were not affected in the ΔrpnR deletion strain of the fungus. In contrast, ribosomal subunit expression and protein secretion into the medium were reduced when A. niger was grown on xylose. Moreover, the ΔrpnR strain showed decreased resistance to H2O2 and the proteotoxic stress-inducing agent dithiothreitol. Taking the data together, RpnR is involved in proteotoxic stress resistance and impacts protein secretion when A. niger is grown on xylose.IMPORTANCE Aspergillus niger secretes a large amount and diversity of industrially relevant enzymes into the culture medium. This makes the fungus a widely used industrial cell factory. For instance, carbohydrate-active enzymes of A. niger are used in biofuel production from lignocellulosic feedstock. These enzymes represent a major cost factor in this process. Higher production yields could substantially reduce these costs and therefore contribute to a more sustainable economy and less dependence on fossil fuels. Enzyme secretion is inhibited in A. niger by asexual reproduction. The sporulation protein FlbA is involved in this process by impacting the expression of 36 predicted transcription factor genes. Here, we show that one of these predicted transcriptional regulators, RpnR, regulates protein secretion and proteotoxic stress resistance. The gene is thus an interesting target to improve enzyme production in A. niger.
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21
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Karpov DS, Spasskaya DS, Nadolinskaia NI, Tutyaeva VV, Lysov YP, Karpov VL. Deregulation of the 19S proteasome complex increases yeast resistance to 4-NQO and oxidative stress via upregulation of Rpn4- and proteasome-dependent stress responsive genes. FEMS Yeast Res 2019; 19:5281435. [DOI: 10.1093/femsyr/foz002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/05/2019] [Indexed: 01/07/2023] Open
Affiliation(s)
- Dmitry S Karpov
- Department of Intracellular proteolysis regulation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
- Laboratory of Medicinal Proteomics, Orekhovich Institute of Biomedical Chemistry, Pogodinskaya str. 10, Moscow 119121, Russia
| | - Daria S Spasskaya
- Department of Intracellular proteolysis regulation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
| | - Nonna I Nadolinskaia
- Department of Intracellular proteolysis regulation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
| | - Vera V Tutyaeva
- Department of Intracellular proteolysis regulation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
| | - Yuriy P Lysov
- Department of Intracellular proteolysis regulation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
| | - Vadim L Karpov
- Department of Intracellular proteolysis regulation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
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22
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Pais P, Galocha M, Teixeira MC. Genome-Wide Response to Drugs and Stress in the Pathogenic Yeast Candida glabrata. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:155-193. [PMID: 30911893 DOI: 10.1007/978-3-030-13035-0_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Candida glabrata is the second most common cause of candidemia worldwide and its prevalence has continuously increased over the last decades. C. glabrata infections are especially worrisome in immunocompromised patients, resulting in serious systemic infections, associated to high mortality rates. Intrinsic resistance to azole antifungals, widely used drugs in the clinical setting, and the ability to efficiently colonize the human host and medical devices, withstanding stress imposed by the immune system, are thought to underlie the emergence of C. glabrata. There is a clear clinical need to understand drug and stress resistance in C. glabrata. The increasing prevalence of multidrug resistant isolates needs to be addressed in order to overcome the decrease of viable therapeutic strategies and find new therapeutic targets. Likewise, the understanding of the mechanisms underlying its impressive ability thrive under oxidative, nitrosative, acidic and metabolic stresses, is crucial to design drugs that target these pathogenesis features. The study of the underlying mechanisms that translate C. glabrata plasticity and its competence to evade the immune system, as well as survive host stresses to establish infection, will benefit from extensive scrutiny. This chapter provides a review on the contribution of genome-wide studies to uncover clinically relevant drug resistance and stress response mechanisms in the human pathogenic yeast C. glabrata.
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Affiliation(s)
- Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,Biological Sciences Research Group, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Mónica Galocha
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,Biological Sciences Research Group, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Cacho Teixeira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal. .,Biological Sciences Research Group, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
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23
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Weisshaar N, Welsch H, Guerra-Moreno A, Hanna J. Phospholipase Lpl1 links lipid droplet function with quality control protein degradation. Mol Biol Cell 2017; 28:716-725. [PMID: 28100635 PMCID: PMC5349779 DOI: 10.1091/mbc.e16-10-0717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 11/11/2022] Open
Abstract
Protein misfolding is toxic to cells and is believed to underlie many human diseases, including many neurodegenerative diseases. Accordingly, cells have developed stress responses to deal with misfolded proteins. The transcription factor Rpn4 mediates one such response and is best known for regulating the abundance of the proteasome, the complex multisubunit protease that destroys proteins. Here we identify Lpl1 as an unexpected target of the Rpn4 response. Lpl1 is a phospholipase and a component of the lipid droplet. Lpl1 has dual functions: it is required for both efficient proteasome-mediated protein degradation and the dynamic regulation of lipid droplets. Lpl1 shows a synthetic genetic interaction with Hac1, the master regulator of a second proteotoxic stress response, the unfolded protein response (UPR). The UPR has long been known to regulate phospholipid metabolism, and Lpl1's relationship with Hac1 appears to reflect Hac1's role in stimulating phospholipid synthesis under stress. Thus two distinct proteotoxic stress responses control phospholipid metabolism. Furthermore, these results provide a direct link between the lipid droplet and proteasomal protein degradation and suggest that dynamic regulation of lipid droplets is a key aspect of some proteotoxic stress responses.
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Affiliation(s)
- Nina Weisshaar
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Hendrik Welsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Angel Guerra-Moreno
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - John Hanna
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
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Mms21 SUMO Ligase Activity Promotes Nucleolar Function in Saccharomyces cerevisiae. Genetics 2016; 204:645-658. [PMID: 27510371 PMCID: PMC5068852 DOI: 10.1534/genetics.115.181750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 07/12/2016] [Indexed: 01/26/2023] Open
Abstract
The budding yeast E3 SUMO ligase Mms21, also known as Nse2, is a component of the Smc5/6 complex, which regulates sister chromatid cohesion, DNA replication, and repair. Our study shows that the mms21RINGΔ mutant exhibits (1) reduced ribosomal RNA production; (2) nuclear accumulation of ribosomal proteins; (3) elevated Gcn4 translation, indicating translational stress; and (4) upregulation of Gcn4 targets. Genes involved in ribosome biogenesis and translation are downregulated in the mms21RINGΔ mutant. We identified RPL19A as a novel genetic suppressor of the mms21RINGΔ mutant. Deletion of RPL19A partially suppresses growth defects in both smc5-6 and mms21RINGΔ mutants as well as nuclear accumulation of ribosome subunits in the mms21RINGΔ mutant. Deletion of a previously identified strong suppressor, MPH1, rescues both the accumulation of ribosome subunits and translational stress. This study suggests that the Smc5/6 complex supports nucleolar function.
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25
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Session 5: Signalling Networks in Tumorigenesis. Toxicol Pathol 2016. [DOI: 10.1080/01926230490882457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Aspen Cancer Conference Fellows. Toxicol Pathol 2016. [DOI: 10.1080/01926230490882358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Genetic determinants for enhanced glycerol growth of Saccharomyces cerevisiae. Metab Eng 2016; 36:68-79. [DOI: 10.1016/j.ymben.2016.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/12/2016] [Accepted: 03/10/2016] [Indexed: 11/21/2022]
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28
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Guerra-Moreno A, Hanna J. Tmc1 Is a Dynamically Regulated Effector of the Rpn4 Proteotoxic Stress Response. J Biol Chem 2016; 291:14788-95. [PMID: 27226598 DOI: 10.1074/jbc.m116.726398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome system represents the major pathway of selective intracellular protein degradation in eukaryotes. Misfolded proteins represent an important class of substrates for this pathway, and the failure to destroy misfolded proteins is associated with a number of human diseases. The transcription factor Rpn4 mediates a key proteotoxic stress response whose best known function is to control proteasome abundance by a homeostatic feedback mechanism. Here we identify the uncharacterized zinc finger protein Tmc1 as a dynamically regulated stress-responsive protein. Rpn4 induces TMC1 transcription in response to misfolded proteins. However, this response is counteracted by rapid proteasome-dependent degradation of Tmc1, which serves to normalize Tmc1 protein levels after induction. Precise control of Tmc1 levels is needed in vivo to survive multiple stressors related to proteostasis. Thus, Tmc1 represents a novel effector and substrate of the Rpn4 proteotoxic stress response.
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Affiliation(s)
- Angel Guerra-Moreno
- From the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - John Hanna
- From the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
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29
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Gupta DK, Patra AT, Zhu L, Gupta AP, Bozdech Z. DNA damage regulation and its role in drug-related phenotypes in the malaria parasites. Sci Rep 2016; 6:23603. [PMID: 27033103 PMCID: PMC4817041 DOI: 10.1038/srep23603] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/10/2016] [Indexed: 11/29/2022] Open
Abstract
DNA of malaria parasites, Plasmodium falciparum, is subjected to extraordinary high levels of genotoxic insults during its complex life cycle within both the mosquito and human host. Accordingly, most of the components of DNA repair machinery are conserved in the parasite genome. Here, we investigated the genome-wide responses of P. falciparum to DNA damaging agents and provided transcriptional evidence of the existence of the double strand break and excision repair system. We also showed that acetylation at H3K9, H4K8, and H3K56 play a role in the direct and indirect response to DNA damage induced by an alkylating agent, methyl methanesulphonate (MMS). Artemisinin, the first line antimalarial chemotherapeutics elicits a similar response compared to MMS which suggests its activity as a DNA damaging agent. Moreover, in contrast to the wild-type P. falciparum, two strains (Dd2 and W2) previously shown to exhibit a mutator phenotype, fail to induce their DNA repair upon MMS-induced DNA damage. Genome sequencing of the two mutator strains identified point mutations in 18 DNA repair genes which may contribute to this phenomenon.
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Affiliation(s)
- Devendra Kumar Gupta
- School of Biological Sciences, Nanyang Technological University, 639798, Singapore
| | - Alok Tanala Patra
- School of Biological Sciences, Nanyang Technological University, 639798, Singapore
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, 639798, Singapore
| | - Archana Patkar Gupta
- School of Biological Sciences, Nanyang Technological University, 639798, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 639798, Singapore
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30
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Li Z, Long Y, Zhong L, Song G, Zhang X, Yuan L, Cui Z, Dai H. RNA sequencing provides insights into the toxicogenomic response of ZF4 cells to methyl methanesulfonate. J Appl Toxicol 2015; 36:94-104. [DOI: 10.1002/jat.3147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/10/2015] [Accepted: 02/10/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Zhouquan Li
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
- University of Chinese Academy of Sciences; Yuquan Road 19A Beijing 100039 People's Republic of China
| | - Yong Long
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Liqiao Zhong
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
- University of Chinese Academy of Sciences; Yuquan Road 19A Beijing 100039 People's Republic of China
| | - Guili Song
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Xiaohua Zhang
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Li Yuan
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Zongbin Cui
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Heping Dai
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
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31
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Meas R, Smerdon MJ, Wyrick JJ. The amino-terminal tails of histones H2A and H3 coordinate efficient base excision repair, DNA damage signaling and postreplication repair in Saccharomyces cerevisiae. Nucleic Acids Res 2015; 43:4990-5001. [PMID: 25897129 PMCID: PMC4446432 DOI: 10.1093/nar/gkv372] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/07/2015] [Indexed: 11/19/2022] Open
Abstract
Histone amino-terminal tails (N-tails) are required for cellular resistance to DNA damaging agents; therefore, we examined the role of histone N-tails in regulating DNA damage response pathways in Saccharomyces cerevisiae. Combinatorial deletions reveal that the H2A and H3 N-tails are important for the removal of MMS-induced DNA lesions due to their role in regulating the basal and MMS-induced expression of DNA glycosylase Mag1. Furthermore, overexpression of Mag1 in a mutant lacking the H2A and H3 N-tails rescues base excision repair (BER) activity but not MMS sensitivity. We further show that the H3 N-tail functions in the Rad9/Rad53 DNA damage signaling pathway, but this function does not appear to be the primary cause of MMS sensitivity of the double tailless mutants. Instead, epistasis analyses demonstrate that the tailless H2A/H3 phenotypes are in the RAD18 epistasis group, which regulates postreplication repair. We observed increased levels of ubiquitylated PCNA and significantly lower mutation frequency in the tailless H2A/H3 mutant, indicating a defect in postreplication repair. In summary, our data identify novel roles of the histone H2A and H3 N-tails in (i) regulating the expression of a critical BER enzyme (Mag1), (ii) supporting efficient DNA damage signaling and (iii) facilitating postreplication repair.
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Affiliation(s)
- Rithy Meas
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Michael J Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
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32
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Chan CTY, Deng W, Li F, DeMott MS, Babu IR, Begley TJ, Dedon PC. Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes. Chem Res Toxicol 2015; 28:978-88. [PMID: 25772370 PMCID: PMC4438938 DOI: 10.1021/acs.chemrestox.5b00004] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Cells respond to stress by controlling
gene expression at several
levels, with little known about the role of translation. Here, we
demonstrate a coordinated translational stress response system involving
stress-specific reprogramming of tRNA wobble modifications that leads
to selective translation of codon-biased mRNAs representing different
classes of critical response proteins. In budding yeast exposed to
four oxidants and five alkylating agents, tRNA modification patterns
accurately distinguished among chemically similar stressors, with
14 modified ribonucleosides forming the basis for a data-driven model
that predicts toxicant chemistry with >80% sensitivity and specificity.
tRNA modification subpatterns also distinguish SN1 from
SN2 alkylating agents, with SN2-induced increases
in m3C in tRNA mechanistically linked to selective translation
of threonine-rich membrane proteins from genes enriched with ACC and
ACT degenerate codons for threonine. These results establish tRNA
modifications as predictive biomarkers of exposure and illustrate
a novel regulatory mechanism for translational control of cell stress
response.
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Affiliation(s)
| | | | | | | | | | - Thomas J Begley
- ∥College of Nanoscale Science, State University of New York, Albany, New York 12203, United States
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33
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Shirozu R, Yashiroda H, Murata S. Identification of minimum Rpn4-responsive elements in genes related to proteasome functions. FEBS Lett 2015; 589:933-40. [PMID: 25747386 DOI: 10.1016/j.febslet.2015.02.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 12/29/2022]
Abstract
The proteasome is an essential, 66-subunit protease that mediates ubiquitin-dependent proteolysis. The transcription factor Rpn4 regulates concerted expression of proteasome subunits to increase the proteasome by recognizing nonamer proteasome-associated control element (PACE) elements on the promoter regions. However, the genes for proteasome assembly chaperones and some of the subunits have no PACEs. Here we identified a minimal hexamer "PACE-core" sequence that responds to Rpn4. PACE-cores are found in many genes related to proteasome function including the assembly chaperones, but cannot substitute for PACE of the subunits. Our results add a new layer of complexity in transcriptional regulation of genes involved in protein degradation.
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Affiliation(s)
- Ryohei Shirozu
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hideki Yashiroda
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
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34
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Deryabina Y, Isakova E, Sekova V, Antipov A, Saris NEL. Inhibition of free radical scavenging enzymes affects mitochondrial membrane permeability transition during growth and aging of yeast cells. J Bioenerg Biomembr 2014; 46:479-92. [DOI: 10.1007/s10863-014-9582-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/14/2014] [Indexed: 10/24/2022]
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35
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O'Duibhir E, Lijnzaad P, Benschop JJ, Lenstra TL, van Leenen D, Groot Koerkamp MJA, Margaritis T, Brok MO, Kemmeren P, Holstege FCP. Cell cycle population effects in perturbation studies. Mol Syst Biol 2014; 10:732. [PMID: 24952590 PMCID: PMC4265054 DOI: 10.15252/msb.20145172] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 05/08/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022] Open
Abstract
Growth condition perturbation or gene function disruption are commonly used strategies to study cellular systems. Although it is widely appreciated that such experiments may involve indirect effects, these frequently remain uncharacterized. Here, analysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common gene expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response (ESR), an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response in single cells, both the slow growth signature and ESR mainly reflect a redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed.
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Affiliation(s)
- Eoghan O'Duibhir
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Philip Lijnzaad
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joris J Benschop
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Tineke L Lenstra
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dik van Leenen
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Thanasis Margaritis
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mariel O Brok
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrick Kemmeren
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
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36
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Dos Santos SC, Teixeira MC, Dias PJ, Sá-Correia I. MFS transporters required for multidrug/multixenobiotic (MD/MX) resistance in the model yeast: understanding their physiological function through post-genomic approaches. Front Physiol 2014; 5:180. [PMID: 24847282 PMCID: PMC4021133 DOI: 10.3389/fphys.2014.00180] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/19/2014] [Indexed: 12/03/2022] Open
Abstract
Multidrug/Multixenobiotic resistance (MDR/MXR) is a widespread phenomenon with clinical, agricultural and biotechnological implications, where MDR/MXR transporters that are presumably able to catalyze the efflux of multiple cytotoxic compounds play a key role in the acquisition of resistance. However, although these proteins have been traditionally considered drug exporters, the physiological function of MDR/MXR transporters and the exact mechanism of their involvement in resistance to cytotoxic compounds are still open to debate. In fact, the wide range of structurally and functionally unrelated substrates that these transporters are presumably able to export has puzzled researchers for years. The discussion has now shifted toward the possibility of at least some MDR/MXR transporters exerting their effect as the result of a natural physiological role in the cell, rather than through the direct export of cytotoxic compounds, while the hypothesis that MDR/MXR transporters may have evolved in nature for other purposes than conferring chemoprotection has been gaining momentum in recent years. This review focuses on the drug transporters of the Major Facilitator Superfamily (MFS; drug:H+ antiporters) in the model yeast Saccharomyces cerevisiae. New insights into the natural roles of these transporters are described and discussed, focusing on the knowledge obtained or suggested by post-genomic research. The new information reviewed here provides clues into the unexpectedly complex roles of these transporters, including a proposed indirect regulation of the stress response machinery and control of membrane potential and/or internal pH, with a special emphasis on a genome-wide view of the regulation and evolution of MDR/MXR-MFS transporters.
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Affiliation(s)
- Sandra C Dos Santos
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa Lisbon, Portugal
| | - Miguel C Teixeira
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa Lisbon, Portugal
| | - Paulo J Dias
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa Lisbon, Portugal
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37
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Spasskaya DS, Karpov DS, Mironov AS, Karpov VL. Transcription factor Rpn4 promotes a complex antistress response in Saccharomyces cerevisiae cells exposed to methyl methanesulfonate. Mol Biol 2014. [DOI: 10.1134/s0026893314010130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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A Synthetic Interaction between CDC20 and RAD4 in Saccharomyces cerevisiae upon UV Irradiation. Mol Biol Int 2014; 2014:519290. [PMID: 24707403 PMCID: PMC3953430 DOI: 10.1155/2014/519290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/12/2014] [Accepted: 01/13/2014] [Indexed: 12/25/2022] Open
Abstract
Regulation of DNA repair can be achieved through ubiquitin-mediated degradation of transiently induced proteins. In Saccharomyces cerevisiae, Rad4 is involved in damage recognition during nucleotide excision repair (NER) and, in conjunction with Rad23, recruits other proteins to the site of damage. We identified a synthetic interaction upon UV exposure between Rad4 and Cdc20, a protein that modulates the activity of the anaphase promoting complex (APC/C), a multisubunit E3 ubiquitin ligase complex. The moderately UV sensitive Δrad4 strain became highly sensitive when cdc20-1 was present, and was rescued by overexpression of CDC20. The double mutant is also deficient in elicting RNR3-lacZ transcription upon exposure to UV irradiation or 4-NQO compared with the Δrad4 single mutant. We demonstrate that the Δrad4/cdc20-1 double mutant is defective in double strand break repair by way of a plasmid end-joining assay, indicating that Rad4 acts to ensure that damaged DNA is repaired via a Cdc20-mediated mechanism. This study is the first to present evidence that Cdc20 may play a role in the degradation of proteins involved in nucleotide excision repair.
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39
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Yang TH, Wu WS. Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 6:S13. [PMID: 24565265 PMCID: PMC4029220 DOI: 10.1186/1752-0509-7-s6-s13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Chromatin immunoprecipitation (ChIP) experiments are now the most comprehensive experimental approaches for mapping the binding of transcription factors (TFs) to their target genes. However, ChIP data alone is insufficient for identifying functional binding target genes of TFs for two reasons. First, there is an inherent high false positive/negative rate in ChIP-chip or ChIP-seq experiments. Second, binding signals in the ChIP data do not necessarily imply functionality. Methods It is known that ChIP-chip data and TF knockout (TFKO) data reveal complementary information on gene regulation. While ChIP-chip data can provide TF-gene binding pairs, TFKO data can provide TF-gene regulation pairs. Therefore, we propose a novel network approach for identifying functional TF-gene binding pairs by integrating the ChIP-chip data with the TFKO data. In our method, a TF-gene binding pair from the ChIP-chip data is regarded to be functional if it also has high confident curated TFKO TF-gene regulatory relation or deduced hypostatic TF-gene regulatory relation. Results and conclusions We first validated our method on a gathered ground truth set. Then we applied our method to the ChIP-chip data to identify functional TF-gene binding pairs. The biological significance of our identified functional TF-gene binding pairs was shown by assessing their functional enrichment, the prevalence of protein-protein interaction, and expression coherence. Our results outperformed the results of three existing methods across all measures. And our identified functional targets of TFs also showed statistical significance over the randomly assigned TF-gene pairs. We also showed that our method is dataset independent and can apply to ChIP-seq data and the E. coli genome. Finally, we provided an example showing the biological applicability of our notion.
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40
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Zhang C, Hong Z, Ma W, Ma D, Qian Y, Xie W, Tie F, Fang M. Drosophila UTX coordinates with p53 to regulate ku80 expression in response to DNA damage. PLoS One 2013; 8:e78652. [PMID: 24265704 PMCID: PMC3827076 DOI: 10.1371/journal.pone.0078652] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/13/2013] [Indexed: 01/08/2023] Open
Abstract
UTX is known as a general factor that activates gene transcription during development. Here, we demonstrate an additional essential role of UTX in the DNA damage response, in which it upregulates the expression of ku80 in Drosophila, both in cultured cells and in third instar larvae. We further showed that UTX mediates the expression of ku80 by the demethylation of H3K27me3 at the ku80 promoter upon exposure to ionizing radiation (IR) in a p53-dependent manner. UTX interacts physically with p53, and both UTX and p53 are recruited to the ku80 promoter following IR exposure in an interdependent manner. In contrast, the loss of utx has little impact on the expression of ku70, mre11, hid and reaper, suggesting the specific regulation of ku80 expression by UTX. Thus, our findings further elucidate the molecular function of UTX.
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Affiliation(s)
- Chengwan Zhang
- Institute of Life Sciences, Southeast University, State Ministry of Education Key Laboratory of Developmental Genes and Human Diseases, Nanjing, China
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41
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Oppikofer M, Kueng S, Gasser SM. SIR–nucleosome interactions: Structure–function relationships in yeast silent chromatin. Gene 2013; 527:10-25. [DOI: 10.1016/j.gene.2013.05.088] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 05/27/2013] [Accepted: 05/30/2013] [Indexed: 01/09/2023]
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42
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Schmidt M, Finley D. Regulation of proteasome activity in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:13-25. [PMID: 23994620 DOI: 10.1016/j.bbamcr.2013.08.012] [Citation(s) in RCA: 337] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 12/13/2022]
Abstract
The ubiquitin-proteasome system (UPS) is the primary selective degradation system in the nuclei and cytoplasm of eukaryotic cells, required for the turnover of myriad soluble proteins. The hundreds of factors that comprise the UPS include an enzymatic cascade that tags proteins for degradation via the covalent attachment of a poly-ubiquitin chain, and a large multimeric enzyme that degrades ubiquitinated proteins, the proteasome. Protein degradation by the UPS regulates many pathways and is a crucial component of the cellular proteostasis network. Dysfunction of the ubiquitination machinery or the proteolytic activity of the proteasome is associated with numerous human diseases. In this review we discuss the contributions of the proteasome to human pathology, describe mechanisms that regulate the proteolytic capacity of the proteasome, and discuss strategies to modulate proteasome function as a therapeutic approach to ameliorate diseases associated with altered UPS function. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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Affiliation(s)
- Marion Schmidt
- Albert Einstein College of Medicine, Department of Biochemistry, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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43
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Karpov DS, Spasskaya DS, Tutyaeva VV, Mironov AS, Karpov VL. Proteasome inhibition enhances resistance to DNA damage via upregulation of Rpn4-dependent DNA repair genes. FEBS Lett 2013; 587:3108-14. [DOI: 10.1016/j.febslet.2013.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/19/2013] [Accepted: 08/03/2013] [Indexed: 10/26/2022]
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44
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Mazumder A, Pesudo LQ, McRee S, Bathe M, Samson LD. Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae. Nucleic Acids Res 2013; 41:9310-24. [PMID: 23935119 PMCID: PMC3814357 DOI: 10.1093/nar/gkt715] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An effective response to DNA damaging agents involves modulating numerous facets of cellular homeostasis in addition to DNA repair and cell-cycle checkpoint pathways. Fluorescence microscopy-based imaging offers the opportunity to simultaneously interrogate changes in both protein level and subcellular localization in response to DNA damaging agents at the single-cell level. We report here results from screening the yeast Green Fluorescent Protein (GFP)-fusion library to investigate global cellular protein reorganization on exposure to the alkylating agent methyl methanesulfonate (MMS). Broad groups of induced, repressed, nucleus- and cytoplasm-enriched proteins were identified. Gene Ontology and interactome analyses revealed the underlying cellular processes. Transcription factor (TF) analysis identified principal regulators of the response, and targets of all major stress-responsive TFs were enriched amongst the induced proteins. An unexpected partitioning of biological function according to the number of TFs targeting individual genes was revealed. Finally, differential modulation of ribosomal proteins depending on methyl methanesulfonate dose was shown to correlate with cell growth and with the translocation of the Sfp1 TF. We conclude that cellular responses can navigate different routes according to the extent of damage, relying on both expression and localization changes of specific proteins.
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Affiliation(s)
- Aprotim Mazumder
- Department of Biological Engineering, Center for Environmental Health Sciences, Laboratory for Computational Biology and Biophysics, Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Zhang N, Quan Z, Rash B, Oliver SG. Synergistic effects of TOR and proteasome pathways on the yeast transcriptome and cell growth. Open Biol 2013; 3:120137. [PMID: 23697803 PMCID: PMC3866871 DOI: 10.1098/rsob.120137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The proteasome has been implicated in gene transcription through a variety of mechanisms. How the proteasome regulates genome-wide transcription in relation to nutrient signalling pathways is largely unknown. Using chemical inhibitors to compromise the functions of the proteasome and/or TORC1, we reveal that the proteasome and TORC1 synergistically promote the expression of de novo purine and amino acid biosynthetic genes, and restrict the transcription of those associated with proteolysis, starvation and stress responses. Genetic analysis demonstrates that TORC1 negatively regulates both the Yak1 and Rim15 kinases to modulate starvation-specific gene expression mediated by the Msn2/4 and Gis1 transcription factors. Compromising proteasome function induces starvation-specific gene transcription in exponential-phase cells and abrogates the strict control of such expression by Yak1 and Rim15 in rapamycin-treated cells, confirming that the proteasome functions to ensure stringent control of the starvation response by the TOR pathway. Synergy between the two pathways is also exhibited on cell growth control. Rpn4-dependent upregulation of proteasomal genes and a catalytically competent 20S proteasome are essential for yeast cells to respond to reduced TORC1 activity. These data suggest that the proteasome and the TOR signalling pathway synergistically regulate a significant portion of the genome to coordinate cell growth and starvation response.
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Affiliation(s)
- Nianshu Zhang
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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46
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Tennen RI, Haye JE, Wijayatilake HD, Arlow T, Ponzio D, Gammie AE. Cell-cycle and DNA damage regulation of the DNA mismatch repair protein Msh2 occurs at the transcriptional and post-transcriptional level. DNA Repair (Amst) 2013; 12:97-109. [PMID: 23261051 PMCID: PMC3749301 DOI: 10.1016/j.dnarep.2012.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 10/03/2012] [Accepted: 11/06/2012] [Indexed: 12/13/2022]
Abstract
DNA mismatch repair during replication is a conserved process essential for maintaining genomic stability. Mismatch repair is also implicated in cell-cycle arrest and apoptosis after DNA damage. Because yeast and human mismatch repair systems are well conserved, we have employed the budding yeast Saccharomyces cerevisiae to understand the regulation and function of the mismatch repair gene MSH2. Using a luciferase-based transcriptional reporter, we defined a 218-bp region upstream of MSH2 that contains cell-cycle and DNA damage responsive elements. The 5' end of the MSH2 transcript was mapped by primer extension and was found to encode a small upstream open reading frame (uORF). Mutagenesis of the uORF start codon or of the uORF stop codon, which creates a continuous reading frame with MSH2, increased Msh2 steady-state protein levels ∼2-fold. Furthermore, we found that the cell-cycle transcription factors Swi6, Swi4, and Mbp1-along with SCB/MCB cell-cycle binding sites upstream of MSH2-are all required for full basal expression of MSH2. Mutagenesis of the cell-cycle boxes resulted in a minor reduction in basal Msh2 levels and a 3-fold defect in mismatch repair. Disruption of the cell-cycle boxes also affected growth in a DNA polymerase-defective strain background where mismatch repair is essential, particularly in the presence of the DNA damaging agent methyl methane sulfonate (MMS). Promoter replacements conferring constitutive expression of MSH2 revealed that the transcriptional induction in response to MMS is required to maintain induced levels of Msh2. Turnover experiments confirmed an elevated rate of degradation in the presence of MMS. Taken together, the data show that the DNA damage regulation of Msh2 occurs at the transcriptional and post-transcriptional levels. The transcriptional and translational control elements identified are conserved in mammalian cells, underscoring the use of yeast as a model system to examine the regulation of MSH2.
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Affiliation(s)
- Ruth I. Tennen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, United States
| | - Joanna E. Haye
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, United States
| | | | - Tim Arlow
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, United States
| | - Danielle Ponzio
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, United States
| | - Alison E. Gammie
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, United States
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The fate of the messenger is pre-determined: a new model for regulation of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:643-53. [PMID: 23337853 DOI: 10.1016/j.bbagrm.2013.01.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 02/08/2023]
Abstract
Recent years have seen a rise in publications demonstrating coupling between transcription and mRNA decay. This coupling most often accompanies cellular processes that involve transitions in gene expression patterns, for example during mitotic division and cellular differentiation and in response to cellular stress. Transcription can affect the mRNA fate by multiple mechanisms. The most novel finding is the process of co-transcriptional imprinting of mRNAs with proteins, which in turn regulate cytoplasmic mRNA stability. Transcription therefore is not only a catalyst of mRNA synthesis but also provides a platform that enables imprinting, which coordinates between transcription and mRNA decay. Here we present an overview of the literature, which provides the evidence of coupling between transcription and decay, review the mechanisms and regulators by which the two processes are coupled, discuss why such coupling is beneficial and present a new model for regulation of gene expression. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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48
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Fujiwara H, Kawai S, Murata K. Significance of sulfiredoxin/peroxiredoxin and mitochondrial respiratory chain in response to and protection from 100% O(2) in Saccharomyces cerevisiae. Mitochondrion 2013; 13:52-8. [PMID: 23291433 DOI: 10.1016/j.mito.2012.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 10/01/2012] [Accepted: 12/20/2012] [Indexed: 11/26/2022]
Abstract
The mechanisms underlying organisms respond to and protect from hyperoxia remain elusive. We establish a system for cultivating the yeast Saccharomyces cerevisiae cells in liquid medium under 100% O(2) and revealed that SRX1, encoding sulfiredoxin, is significantly induced by 100% O(2) dependently on transcription factors Yap1 and Skn7. Sulfiredoxin has a role in restoring the abundant peroxiredoxin, Tsa1. Tsa1 was indispensable for protection from 100% O(2) in the presence of antimycin A, an inhibitor of complex III in the mitochondrial respiratory chain, collectively emphasizing the significance of sulfiredoxin, peroxiredoxin, and mitochondrial respiratory chain to respond to and to protect from 100% O(2).
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Affiliation(s)
- Hiroki Fujiwara
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food and Biological Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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Svensson JP, Fry RC, Wang E, Somoza LA, Samson LD. Identification of novel human damage response proteins targeted through yeast orthology. PLoS One 2012; 7:e37368. [PMID: 22615993 PMCID: PMC3353887 DOI: 10.1371/journal.pone.0037368] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 04/21/2012] [Indexed: 01/09/2023] Open
Abstract
Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rules were implemented to identify 45 candidates for human toxicity-modulating proteins. The corresponding transcripts were targeted by RNA interference in human cells. The cell lines with depleted target expression were challenged with three DNA damaging agents: the alkylating agents MMS and 4-NQO, and the oxidizing agent t-BuOOH. A comparison of the survival revealed that the majority (74%) of proteins conferred either sensitivity or resistance. The identified human toxicity-modulating proteins represent a variety of biological functions: autophagy, chromatin modifications, RNA and protein metabolism, and telomere maintenance. Further studies revealed that MMS-induced autophagy increase the survival of cells treated with DNA damaging agents. In summary, we show that damage recovery proteins in humans can be identified through homology to S. cerevisiae and that many of the same pathways are represented among the toxicity modulators.
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Affiliation(s)
- J. Peter Svensson
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rebecca C. Fry
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Computation and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Emma Wang
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Luis A. Somoza
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Leona D. Samson
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Computation and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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50
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Mwai L, Diriye A, Masseno V, Muriithi S, Feltwell T, Musyoki J, Lemieux J, Feller A, Mair GR, Marsh K, Newbold C, Nzila A, Carret CK. Genome wide adaptations of Plasmodium falciparum in response to lumefantrine selective drug pressure. PLoS One 2012; 7:e31623. [PMID: 22384044 PMCID: PMC3288012 DOI: 10.1371/journal.pone.0031623] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 01/16/2012] [Indexed: 01/08/2023] Open
Abstract
The combination therapy of the Artemisinin-derivative Artemether (ART) with Lumefantrine (LM) (Coartem®) is an important malaria treatment regimen in many endemic countries. Resistance to Artemisinin has already been reported, and it is feared that LM resistance (LMR) could also evolve quickly. Therefore molecular markers which can be used to track Coartem® efficacy are urgently needed. Often, stable resistance arises from initial, unstable phenotypes that can be identified in vitro. Here we have used the Plasmodium falciparum multidrug resistant reference strain V1S to induce LMR in vitro by culturing the parasite under continuous drug pressure for 16 months. The initial IC50 (inhibitory concentration that kills 50% of the parasite population) was 24 nM. The resulting resistant strain V1SLM, obtained after culture for an estimated 166 cycles under LM pressure, grew steadily in 378 nM of LM, corresponding to 15 times the IC50 of the parental strain. However, after two weeks of culturing V1SLM in drug-free medium, the IC50 returned to that of the initial, parental strain V1S. This transient drug tolerance was associated with major changes in gene expression profiles: using the PFSANGER Affymetrix custom array, we identified 184 differentially expressed genes in V1SLM. Among those are 18 known and putative transporters including the multidrug resistance gene 1 (pfmdr1), the multidrug resistance associated protein and the V-type H+ pumping pyrophosphatase 2 (pfvp2) as well as genes associated with fatty acid metabolism. In addition we detected a clear selective advantage provided by two genomic loci in parasites grown under LM drug pressure, suggesting that all, or some of those genes contribute to development of LM tolerance – they may prove useful as molecular markers to monitor P. falciparum LM susceptibility.
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Affiliation(s)
- Leah Mwai
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Abdi Diriye
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
| | - Victor Masseno
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
| | - Steven Muriithi
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
| | - Theresa Feltwell
- Pathogen Microarrays group, The Welcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Jennifer Musyoki
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
| | - Jacob Lemieux
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Avi Feller
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Gunnar R. Mair
- Molecular Parasitology Unit, Instituto de Medicina Molecular, Lisboa, Portugal
| | - Kevin Marsh
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Chris Newbold
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alexis Nzila
- Kenya Medical Research Institute, Welcome Trust Research Programme, Kilifi, Kenya
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Céline K. Carret
- Molecular Parasitology Unit, Instituto de Medicina Molecular, Lisboa, Portugal
- * E-mail:
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