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Takallou S, Hajikarimlou M, Al-Gafari M, Wang J, Jagadeesan SK, Kazmirchuk TDD, Moteshareie H, Indrayanti AM, Azad T, Holcik M, Samanfar B, Smith M, Golshani A. Hydrogen peroxide sensitivity connects the activity of COX5A and NPR3 to the regulation of YAP1 expression. FASEB J 2024; 38:e23439. [PMID: 38416461 DOI: 10.1096/fj.202300978rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 02/29/2024]
Abstract
Reactive oxygen species (ROS) are among the most severe types of cellular stressors with the ability to damage essential cellular biomolecules. Excess levels of ROS are correlated with multiple pathophysiological conditions including neurodegeneration, diabetes, atherosclerosis, and cancer. Failure to regulate the severely imbalanced levels of ROS can ultimately lead to cell death, highlighting the importance of investigating the molecular mechanisms involved in the detoxification procedures that counteract the effects of these compounds in living organisms. One of the most abundant forms of ROS is H2 O2 , mainly produced by the electron transport chain in the mitochondria. Numerous genes have been identified as essential to the process of cellular detoxification. Yeast YAP1, which is homologous to mammalian AP-1 type transcriptional factors, has a key role in oxidative detoxification by upregulating the expression of antioxidant genes in yeast. The current study reveals novel functions for COX5A and NPR3 in H2 O2 -induced stress by demonstrating that their deletions result in a sensitive phenotype. Our follow-up investigations indicate that COX5A and NPR3 regulate the expression of YAP1 through an alternative mode of translation initiation. These novel gene functions expand our understanding of the regulation of gene expression and defense mechanism of yeast against oxidative stress.
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Affiliation(s)
- Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mustafa Al-Gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jiashu Wang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Sasi Kumar Jagadeesan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Thomas David Daniel Kazmirchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Houman Moteshareie
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | | | - Taha Azad
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Research Center of the Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, Quebec, Canada
| | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Bahram Samanfar
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada
| | - Myron Smith
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
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2
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Takallou S, Hajikarimlou M, Al-Gafari M, Wang J, Kazmirchuk TDD, Said KB, Samanfar B, Golshani A. The Involvement of YNR069C in Protein Synthesis in the Baker's Yeast, Saccharomyces cerevisiae. Biology (Basel) 2024; 13:138. [PMID: 38534408 DOI: 10.3390/biology13030138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
Maintaining translation fidelity is a critical step within the process of gene expression. It requires the involvement of numerous regulatory elements to ensure the synthesis of functional proteins. The efficient termination of protein synthesis can play a crucial role in preserving this fidelity. Here, we report on investigating a protein of unknown function, YNR069C (also known as BSC5), for its activity in the process of translation. We observed a significant increase in the bypass of premature stop codons upon the deletion of YNR069C. Interestingly, the genomic arrangement of this ORF suggests a compatible mode of expression reliant on translational readthrough, incorporating the neighboring open reading frame. We also showed that the deletion of YNR069C results in an increase in the rate of translation. Based on our results, we propose that YNR069C may play a role in translation fidelity, impacting the overall quantity and quality of translation. Our genetic interaction analysis supports our hypothesis, associating the role of YNR069C to the regulation of protein synthesis.
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Affiliation(s)
- Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mustafa Al-Gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiashu Wang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Thomas David Daniel Kazmirchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Kamaledin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Hail 55476, Saudi Arabia
| | - Bahram Samanfar
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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Hajikarimlou M, Hooshyar M, Sunba N, Nazemof N, Moutaoufik MT, Phanse S, Said KB, Babu M, Holcik M, Samanfar B, Smith M, Golshani A. A Correlation between 3'-UTR of OXA1 Gene and Yeast Mitochondrial Translation. J Fungi (Basel) 2023; 9:jof9040445. [PMID: 37108900 PMCID: PMC10143089 DOI: 10.3390/jof9040445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/27/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
Mitochondria possess their own DNA (mtDNA) and are capable of carrying out their transcription and translation. Although protein synthesis can take place in mitochondria, the majority of the proteins in mitochondria have nuclear origin. 3' and 5' untranslated regions of mRNAs (3'-UTR and 5'-UTR, respectively) are thought to play key roles in directing and regulating the activity of mitochondria mRNAs. Here we investigate the association between the presence of 3'-UTR from OXA1 gene on a prokaryotic reporter mRNA and mitochondrial translation in yeast. OXA1 is a nuclear gene that codes for mitochondrial inner membrane insertion protein and its 3'-UTR is shown to direct its mRNA toward mitochondria. It is not clear, however, if this mRNA may also be translated by mitochondria. In the current study, using a β-galactosidase reporter gene, we provide genetic evidence for a correlation between the presence of 3'-UTR of OXA1 on an mRNA and mitochondrial translation in yeast.
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Affiliation(s)
- Maryam Hajikarimlou
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mohsen Hooshyar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Noor Sunba
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Nazila Nazemof
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mohamed Taha Moutaoufik
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sadhena Phanse
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - Kamaledin B Said
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Hail P.O. Box 2240, Saudi Arabia
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K2H 8S2, Canada
| | - Myron Smith
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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Jagadeesan SK, Al-gafari M, Wang J, Takallou S, Allard D, Hajikarimlou M, Kazmirchuk TDD, Moteshareie H, Said KB, Nokhbeh R, Smith M, Samanfar B, Golshani A. DBP7 and YRF1-6 Are Involved in Cell Sensitivity to LiCl by Regulating the Translation of PGM2 mRNA. Int J Mol Sci 2023; 24:ijms24021785. [PMID: 36675300 PMCID: PMC9864399 DOI: 10.3390/ijms24021785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/17/2023] Open
Abstract
Lithium chloride (LiCl) has been widely researched and utilized as a therapeutic option for bipolar disorder (BD). Several pathways, including cell signaling and signal transduction pathways in mammalian cells, are shown to be regulated by LiCl. LiCl can negatively control the expression and activity of PGM2, a phosphoglucomutase that influences sugar metabolism in yeast. In the presence of galactose, when yeast cells are challenged by LiCl, the phosphoglucomutase activity of PGM2p is decreased, causing an increase in the concentration of toxic galactose metabolism intermediates that result in cell sensitivity. Here, we report that the null yeast mutant strains DBP7∆ and YRF1-6∆ exhibit increased LiCl sensitivity on galactose-containing media. Additionally, we demonstrate that DBP7 and YRF1-6 modulate the translational level of PGM2 mRNA, and the observed alteration in translation seems to be associated with the 5'-untranslated region (UTR) of PGM2 mRNA. Furthermore, we observe that DBP7 and YRF1-6 influence, to varying degrees, the translation of other mRNAs that carry different 5'-UTR secondary structures.
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Affiliation(s)
- Sasi Kumar Jagadeesan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mustafa Al-gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiashu Wang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Danielle Allard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Thomas David Daniel Kazmirchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Houman Moteshareie
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Kamaledin B. Said
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Hail 55476, Saudi Arabia
| | - Reza Nokhbeh
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Myron Smith
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Correspondence:
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5
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Jagadeesan SK, Potter T, Al-Gafari M, Hooshyar M, Hewapathirana CM, Takallou S, Hajikarimlou M, Burnside D, Samanfar B, Moteshareie H, Smith M, Golshani A. Discovery and identification of genes involved in DNA damage repair in yeast. Gene 2022; 831:146549. [PMID: 35569766 DOI: 10.1016/j.gene.2022.146549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/16/2022] [Accepted: 05/06/2022] [Indexed: 11/04/2022]
Abstract
DNA repair defects are common in tumour cells and can lead to misrepair of double-strand breaks (DSBs), posing a significant challenge to cellular integrity. The overall mechanisms of DSB have been known for decades. However, the list of the genes that affect the efficiency of DSB repair continues to grow. Additional factors that play a role in DSB repair pathways have yet to be identified. In this study, we present a computational approach to identify novel gene functions that are involved in DNA damage repair in Saccharomyces cerevisiae. Among the primary candidates, GAL7, YMR130W, and YHI9 were selected for further analysis since they had not previously been identified as being active in DNA repair pathways. Originally, GAL7 was linked to galactose metabolism. YHI9 and YMR130W encode proteins of unknown functions. Laboratory testing of deletion strains gal7Δ, ymr130wΔ, and yhi9Δ implicated all 3 genes in Homologous Recombination (HR) and/or Non-Homologous End Joining (NHEJ) repair pathways, and enhanced sensitivity to DNA damage-inducing drugs suggested involvement in the broader DNA damage repair machinery. A subsequent genetic interaction analysis revealed interconnections of these three genes, most strikingly through SIR2, SIR3 and SIR4 that are involved in chromatin regulation and DNA damage repair network.
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Affiliation(s)
- Sasi Kumar Jagadeesan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Taylor Potter
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Mustafa Al-Gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Mohsen Hooshyar
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | | | - Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Daniel Burnside
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada.
| | - Houman Moteshareie
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Myron Smith
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada.
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
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Hajikarimlou M, Hooshyar M, Moutaoufik M, Aly K, Azad T, Takallou S, Jagadeesan S, Phanse S, Said K, Samanfar B, Bell J, Dehne F, Babu M, Golshani A. A computational approach to rapidly design peptides that detect SARS-CoV-2 surface protein S. NAR Genom Bioinform 2022; 4:lqac058. [PMID: 36004308 PMCID: PMC9394169 DOI: 10.1093/nargab/lqac058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/10/2022] [Accepted: 08/01/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
The coronavirus disease 19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prompted the development of diagnostic and therapeutic frameworks for timely containment of this pandemic. Here, we utilized our non-conventional computational algorithm, InSiPS, to rapidly design and experimentally validate peptides that bind to SARS-CoV-2 spike (S) surface protein. We previously showed that this method can be used to develop peptides against yeast proteins, however, the applicability of this method to design peptides against other proteins has not been investigated. In the current study, we demonstrate that two sets of peptides developed using InSiPS method can detect purified SARS-CoV-2 S protein via ELISA and Surface Plasmon Resonance (SPR) approaches, suggesting the utility of our strategy in real time COVID-19 diagnostics. Mass spectrometry-based salivary peptidomics shortlist top SARS-CoV-2 peptides detected in COVID-19 patients’ saliva, rendering them attractive SARS-CoV-2 diagnostic targets that, when subjected to our computational platform, can streamline the development of potent peptide diagnostics of SARS-CoV-2 variants of concern. Our approach can be rapidly implicated in diagnosing other communicable diseases of immediate threat.
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Affiliation(s)
- Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa , Health Science Campus, Ottawa , Ontario , Canada
- Department of Biology, Carleton University , Ottawa , Ontario , Canada
| | - Mohsen Hooshyar
- Ottawa Institute of Systems Biology, University of Ottawa , Health Science Campus, Ottawa , Ontario , Canada
- Department of Biology, Carleton University , Ottawa , Ontario , Canada
| | - Mohamed Taha Moutaoufik
- Department of Biochemistry, Research and Innovation Centre, University of Regina , Regina , Canada
| | - Khaled A Aly
- Department of Biochemistry, Research and Innovation Centre, University of Regina , Regina , Canada
| | - Taha Azad
- The Ottawa Hospital Research Institute 501 Smyth Road , Ottawa , Ontario , Canada
| | - Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa , Health Science Campus, Ottawa , Ontario , Canada
- Department of Biology, Carleton University , Ottawa , Ontario , Canada
| | - Sasi Jagadeesan
- Ottawa Institute of Systems Biology, University of Ottawa , Health Science Campus, Ottawa , Ontario , Canada
- Department of Biology, Carleton University , Ottawa , Ontario , Canada
| | - Sadhna Phanse
- Department of Biochemistry, Research and Innovation Centre, University of Regina , Regina , Canada
| | - Kamaledin B Said
- Department of Biology, Carleton University , Ottawa , Ontario , Canada
- Department of Pathology and Microbiology, College of Medicine, University of Hail , Saudi Arabia
| | - Bahram Samanfar
- Ottawa Institute of Systems Biology, University of Ottawa , Health Science Campus, Ottawa , Ontario , Canada
- Department of Biology, Carleton University , Ottawa , Ontario , Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC) , Ottawa , Ontario , Canada
| | - John C Bell
- The Ottawa Hospital Research Institute 501 Smyth Road , Ottawa , Ontario , Canada
| | - Frank Dehne
- School of Computer Science, Carleton University , Ottawa , Ontario , Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina , Regina , Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa , Health Science Campus, Ottawa , Ontario , Canada
- Department of Biology, Carleton University , Ottawa , Ontario , Canada
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Hajikarimlou M, Hunt K, Kirby G, Takallou S, Jagadeesan SK, Omidi K, Hooshyar M, Burnside D, Moteshareie H, Babu M, Smith M, Holcik M, Samanfar B, Golshani A. Lithium Chloride Sensitivity in Yeast and Regulation of Translation. Int J Mol Sci 2020; 21:ijms21165730. [PMID: 32785068 PMCID: PMC7461102 DOI: 10.3390/ijms21165730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022] Open
Abstract
For decades, lithium chloride (LiCl) has been used as a treatment option for those living with bipolar disorder (BD). As a result, many studies have been conducted to examine its mode of action, toxicity, and downstream cellular responses. We know that LiCl is able to affect cell signaling and signaling transduction pathways through protein kinase C and glycogen synthase kinase-3, which are considered to be important in regulating gene expression at the translational level. However, additional downstream effects require further investigation, especially in translation pathway. In yeast, LiCl treatment affects the expression, and thus the activity, of PGM2, a phosphoglucomutase involved in sugar metabolism. Inhibition of PGM2 leads to the accumulation of intermediate metabolites of galactose metabolism causing cell toxicity. However, it is not fully understood how LiCl affects gene expression in this matter. In this study, we identified three genes, NAM7, PUS2, and RPL27B, which increase yeast LiCl sensitivity when deleted. We further demonstrate that NAM7, PUS2, and RPL27B influence translation and exert their activity through the 5′-Untranslated region (5′-UTR) of PGM2 mRNA in yeast.
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Affiliation(s)
- Maryam Hajikarimlou
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Kathryn Hunt
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Grace Kirby
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Sarah Takallou
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Sasi Kumar Jagadeesan
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Katayoun Omidi
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Mohsen Hooshyar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Daniel Burnside
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Houman Moteshareie
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada;
| | - Myron Smith
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
| | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1Y 4X2, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (M.H.); (K.H.); (G.K.); (S.T.); (S.K.J.); (K.O.); (M.H.); (D.B.); (H.M.); (M.S.); (B.S.)
- Correspondence:
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8
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Hajikarimlou M, Moteshareie H, Omidi K, Hooshyar M, Shaikho S, Kazmirchuk T, Burnside D, Takallou S, Zare N, Jagadeesan SK, Puchacz N, Babu M, Smith M, Holcik M, Samanfar B, Golshani A. Sensitivity of yeast to lithium chloride connects the activity of YTA6 and YPR096C to translation of structured mRNAs. PLoS One 2020; 15:e0235033. [PMID: 32639961 PMCID: PMC7343135 DOI: 10.1371/journal.pone.0235033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/08/2020] [Indexed: 11/18/2022] Open
Abstract
Lithium Chloride (LiCl) toxicity, mode of action and cellular responses have been the subject of active investigations over the past decades. In yeast, LiCl treatment is reported to reduce the activity and alters the expression of PGM2, a gene that encodes a phosphoglucomutase involved in sugar metabolism. Reduced activity of phosphoglucomutase in the presence of galactose causes an accumulation of intermediate metabolites of galactose metabolism leading to a number of phenotypes including growth defect. In the current study, we identify two understudied yeast genes, YTA6 and YPR096C that when deleted, cell sensitivity to LiCl is increased when galactose is used as a carbon source. The 5’-UTR of PGM2 mRNA is structured. Using this region, we show that YTA6 and YPR096C influence the translation of PGM2 mRNA.
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Affiliation(s)
- Maryam Hajikarimlou
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Houman Moteshareie
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Katayoun Omidi
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mohsen Hooshyar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Sarah Shaikho
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Tom Kazmirchuk
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Daniel Burnside
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Sarah Takallou
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Narges Zare
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Sasi Kumar Jagadeesan
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Nathalie Puchacz
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Canada
| | - Myron Smith
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
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9
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Burnside D, Schoenrock A, Moteshareie H, Hooshyar M, Basra P, Hajikarimlou M, Dick K, Barnes B, Kazmirchuk T, Jessulat M, Pitre S, Samanfar B, Babu M, Green JR, Wong A, Dehne F, Biggar KK, Golshani A. In Silico Engineering of Synthetic Binding Proteins from Random Amino Acid Sequences. iScience 2018; 11:375-387. [PMID: 30660105 PMCID: PMC6348295 DOI: 10.1016/j.isci.2018.11.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/19/2018] [Accepted: 11/28/2018] [Indexed: 12/29/2022] Open
Abstract
Synthetic proteins with high affinity and selectivity for a protein target can be used as research tools, biomarkers, and pharmacological agents, but few methods exist to design such proteins de novo. To this end, the In-Silico Protein Synthesizer (InSiPS) was developed to design synthetic binding proteins (SBPs) that bind pre-determined targets while minimizing off-target interactions. InSiPS is a genetic algorithm that refines a pool of random sequences over hundreds of generations of mutation and selection to produce SBPs with pre-specified binding characteristics. As a proof of concept, we design SBPs against three yeast proteins and demonstrate binding and functional inhibition of two of three targets in vivo. Peptide SPOT arrays confirm binding sites, and a permutation array demonstrates target specificity. Our foundational approach will support the field of de novo design of small binding polypeptide motifs and has robust applicability while offering potential advantages over the limited number of techniques currently available. InSiPS engineers synthetic binding proteins (SBPs) using primary protein sequence SBPs are designed to a bind a target protein and avoid “off-target” interactions Binding and functional inhibition of two of three target proteins in yeast is demonstrated Our new approach offers advantages over alternative tools that rely on 3D models
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Affiliation(s)
- Daniel Burnside
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Andrew Schoenrock
- School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Houman Moteshareie
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Mohsen Hooshyar
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Prabh Basra
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Maryam Hajikarimlou
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Kevin Dick
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Brad Barnes
- School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Tom Kazmirchuk
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Matthew Jessulat
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sylvain Pitre
- School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C5, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Kyle K Biggar
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Institute of Biochemistry, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S5B6, Canada; Institute of Biochemistry, Carleton University, Ottawa, ON K1S5B6, Canada.
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10
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Omidi K, Jessulat M, Hooshyar M, Burnside D, Schoenrock A, Kazmirchuk T, Hajikarimlou M, Daniel M, Moteshareie H, Bhojoo U, Sanders M, Ramotar D, Dehne F, Samanfar B, Babu M, Golshani A. Uncharacterized ORF HUR1 influences the efficiency of non-homologous end-joining repair in Saccharomyces cerevisiae. Gene 2018; 639:128-136. [DOI: 10.1016/j.gene.2017.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/25/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
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11
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Kazmirchuk T, Dick K, Burnside DJ, Barnes B, Moteshareie H, Hajikarimlou M, Omidi K, Ahmed D, Low A, Lettl C, Hooshyar M, Schoenrock A, Pitre S, Babu M, Cassol E, Samanfar B, Wong A, Dehne F, Green JR, Golshani A. Designing anti-Zika virus peptides derived from predicted human-Zika virus protein-protein interactions. Comput Biol Chem 2017; 71:180-187. [DOI: 10.1016/j.compbiolchem.2017.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/03/2017] [Accepted: 10/27/2017] [Indexed: 01/22/2023]
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12
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Samanfar B, Shostak K, Moteshareie H, Hajikarimlou M, Shaikho S, Omidi K, Hooshyar M, Burnside D, Márquez IG, Kazmirchuk T, Naing T, Ludovico P, York-Lyon A, Szereszewski K, Leung C, Jin JY, Megarbane R, Smith ML, Babu M, Holcik M, Golshani A. The sensitivity of the yeast, Saccharomyces cerevisiae, to acetic acid is influenced by DOM34 and RPL36A. PeerJ 2017; 5:e4037. [PMID: 29158977 PMCID: PMC5691786 DOI: 10.7717/peerj.4037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
The presence of acetic acid during industrial alcohol fermentation reduces the yield of fermentation by imposing additional stress on the yeast cells. The biology of cellular responses to stress has been a subject of vigorous investigations. Although much has been learned, details of some of these responses remain poorly understood. Members of heat shock chaperone HSP proteins have been linked to acetic acid and heat shock stress responses in yeast. Both acetic acid and heat shock have been identified to trigger different cellular responses including reduction of global protein synthesis and induction of programmed cell death. Yeast HSC82 and HSP82 code for two important heat shock proteins that together account for 1–2% of total cellular proteins. Both proteins have been linked to responses to acetic acid and heat shock. In contrast to the overall rate of protein synthesis which is reduced, the expression of HSC82 and HSP82 is induced in response to acetic acid stress. In the current study we identified two yeast genes DOM34 and RPL36A that are linked to acetic acid and heat shock sensitivity. We investigated the influence of these genes on the expression of HSP proteins. Our observations suggest that Dom34 and RPL36A influence translation in a CAP-independent manner.
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Affiliation(s)
- Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Agriculture and Ari-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada
| | - Kristina Shostak
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Agriculture and Ari-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada
| | - Houman Moteshareie
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Maryam Hajikarimlou
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Sarah Shaikho
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada
| | - Katayoun Omidi
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mohsen Hooshyar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Ottawa Hospital Research Institute, Center for Cancer Therapeutics, Ottawa, Ontario, Canada
| | - Daniel Burnside
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Imelda Galván Márquez
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Tom Kazmirchuk
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Thet Naing
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Portugal
| | - Anna York-Lyon
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Kama Szereszewski
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.,Department of Chemistry, Carleton University, Ottawa, Ontario, Canada
| | - Cindy Leung
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jennifer Yixin Jin
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Rami Megarbane
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Myron L Smith
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Martin Holcik
- Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics , University of Ottawa, Ottawa, Ontario, Canada.,Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
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