1
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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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3
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Hooker JC, Smith M, Zapata G, Charette M, Luckert D, Mohr RM, Daba KA, Warkentin TD, Hadinezhad M, Barlow B, Hou A, Lefebvre F, Golshani A, Cober ER, Samanfar B. Differential gene expression provides leads to environmentally regulated soybean seed protein content. Front Plant Sci 2023; 14:1260393. [PMID: 37790790 PMCID: PMC10544915 DOI: 10.3389/fpls.2023.1260393] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023]
Abstract
Soybean is an important global source of plant-based protein. A persistent trend has been observed over the past two decades that soybeans grown in western Canada have lower seed protein content than soybeans grown in eastern Canada. In this study, 10 soybean genotypes ranging in average seed protein content were grown in an eastern location (control) and three western locations (experimental) in Canada. Seed protein and oil contents were measured for all lines in each location. RNA-sequencing and differential gene expression analysis were used to identify differentially expressed genes that may account for relatively low protein content in western-grown soybeans. Differentially expressed genes were enriched for ontologies and pathways that included amino acid biosynthesis, circadian rhythm, starch metabolism, and lipid biosynthesis. Gene ontology, pathway mapping, and quantitative trait locus (QTL) mapping collectively provide a close inspection of mechanisms influencing nitrogen assimilation and amino acid biosynthesis between soybeans grown in the East and West. It was found that western-grown soybeans had persistent upregulation of asparaginase (an asparagine hydrolase) and persistent downregulation of asparagine synthetase across 30 individual differential expression datasets. This specific difference in asparagine metabolism between growing environments is almost certainly related to the observed differences in seed protein content because of the positive correlation between seed protein content at maturity and free asparagine in the developing seed. These results provided pointed information on seed protein-related genes influenced by environment. This information is valuable for breeding programs and genetic engineering of geographically optimized soybeans.
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Affiliation(s)
- Julia C. Hooker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Myron Smith
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - Martin Charette
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Doris Luckert
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Ramona M. Mohr
- Brandon Research Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Mehri Hadinezhad
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anfu Hou
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | | | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Elroy R. Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Bahram Samanfar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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4
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Haidar S, Lackey S, Charette M, Yoosefzadeh-Najafabadi M, Gahagan AC, Hotte T, Belzile F, Rajcan I, Golshani A, Morrison MJ, Cober ER, Samanfar B. Genome-wide analysis of cold imbibition stress in soybean, Glycine max. Front Plant Sci 2023; 14:1221644. [PMID: 37670866 PMCID: PMC10476531 DOI: 10.3389/fpls.2023.1221644] [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] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/07/2023]
Abstract
In Canada, the length of the frost-free season necessitates planting crops as early as possible to ensure that the plants have enough time to reach full maturity before they are harvested. Early planting carries inherent risks of cold water imbibition (specifically less than 4°C) affecting seed germination. A marker dataset developed for a previously identified Canadian soybean GWAS panel was leveraged to investigate the effect of cold water imbibition on germination. Seed from a panel of 137 soybean elite cultivars, grown in the field at Ottawa, ON, over three years, were placed on filter paper in petri dishes and allowed to imbibe water for 16 hours at either 4°C or 20°C prior to being transferred to a constant 20°C. Observations on seed germination, defined as the presence of a 1 cm radicle, were done from day two to seven. A three-parameter exponential rise to a maximum equation (3PERM) was fitted to estimate germination, time to the one-half maximum germination, and germination uniformity for each cultivar. Genotype-by-sequencing was used to identify SNPs in 137 soybean lines, and using genome-wide association studies (GWAS - rMVP R package, with GLM, MLM, and FarmCPU as methods), haplotype block analysis, and assumed linkage blocks of ±100 kbp, a threshold for significance was established using the qvalue package in R, and five significant SNPs were identified on chromosomes 1, 3, 4, 6, and 13 for maximum germination after cold water imbibition. Percent of phenotypic variance explained (PVE) and allele substitution effect (ASE) eliminated two of the five candidate SNPs, leaving three QTL regions on chromosomes 3, 6, and 13 (Chr3-3419152, Chr6-5098454, and Chr13-29649544). Based on the gene ontology (GO) enrichment analysis, 14 candidate genes whose function is predicted to include germination and cold tolerance related pathways were identified as candidate genes. The identified QTLs can be used to select future soybean cultivars tolerant to cold water imbibition and mitigate risks associated with early soybean planting.
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Affiliation(s)
- Siwar Haidar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Simon Lackey
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | | | - A. Claire Gahagan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Thomas Hotte
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Francois Belzile
- Department of Phytology, Institut de Biologie Intégrative et des Systèmes (IBIS), Université de Laval, Quebec City, QC, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Malcolm J. Morrison
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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5
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Nissan N, Hooker J, Arezza E, Dick K, Golshani A, Mimee B, Cober E, Green J, Samanfar B. Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode. Front Bioinform 2023; 3:1199675. [PMID: 37409347 PMCID: PMC10319130 DOI: 10.3389/fbinf.2023.1199675] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
The soybean cyst nematode (SCN) [Heterodera glycines Ichinohe] is a devastating pathogen of soybean [Glycine max (L.) Merr.] that is rapidly becoming a global economic issue. Two loci conferring SCN resistance have been identified in soybean, Rhg1 and Rhg4; however, they offer declining protection. Therefore, it is imperative that we identify additional mechanisms for SCN resistance. In this paper, we develop a bioinformatics pipeline to identify protein-protein interactions related to SCN resistance by data mining massive-scale datasets. The pipeline combines two leading sequence-based protein-protein interaction predictors, the Protein-protein Interaction Prediction Engine (PIPE), PIPE4, and Scoring PRotein INTeractions (SPRINT) to predict high-confidence interactomes. First, we predicted the top soy interacting protein partners of the Rhg1 and Rhg4 proteins. Both PIPE4 and SPRINT overlap in their predictions with 58 soybean interacting partners, 19 of which had GO terms related to defense. Beginning with the top predicted interactors of Rhg1 and Rhg4, we implement a "guilt by association" in silico proteome-wide approach to identify novel soybean genes that may be involved in SCN resistance. This pipeline identified 1,082 candidate genes whose local interactomes overlap significantly with the Rhg1 and Rhg4 interactomes. Using GO enrichment tools, we highlighted many important genes including five genes with GO terms related to response to the nematode (GO:0009624), namely, Glyma.18G029000, Glyma.11G228300, Glyma.08G120500, Glyma.17G152300, and Glyma.08G265700. This study is the first of its kind to predict interacting partners of known resistance proteins Rhg1 and Rhg4, forming an analysis pipeline that enables researchers to focus their search on high-confidence targets to identify novel SCN resistance genes in soybean.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Julia Hooker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Eric Arezza
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Kevin Dick
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jeansur-Richelieu, QC, Canada
| | - Elroy Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - James Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, ON, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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6
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Kazmirchuk TDD, Bradbury-Jost C, Withey TA, Gessese T, Azad T, Samanfar B, Dehne F, Golshani A. Peptides of a Feather: How Computation Is Taking Peptide Therapeutics under Its Wing. Genes (Basel) 2023; 14:1194. [PMID: 37372372 DOI: 10.3390/genes14061194] [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: 03/30/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Leveraging computation in the development of peptide therapeutics has garnered increasing recognition as a valuable tool to generate novel therapeutics for disease-related targets. To this end, computation has transformed the field of peptide design through identifying novel therapeutics that exhibit enhanced pharmacokinetic properties and reduced toxicity. The process of in-silico peptide design involves the application of molecular docking, molecular dynamics simulations, and machine learning algorithms. Three primary approaches for peptide therapeutic design including structural-based, protein mimicry, and short motif design have been predominantly adopted. Despite the ongoing progress made in this field, there are still significant challenges pertaining to peptide design including: enhancing the accuracy of computational methods; improving the success rate of preclinical and clinical trials; and developing better strategies to predict pharmacokinetics and toxicity. In this review, we discuss past and present research pertaining to the design and development of in-silico peptide therapeutics in addition to highlighting the potential of computation and artificial intelligence in the future of disease therapeutics.
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Affiliation(s)
- Thomas David Daniel Kazmirchuk
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Calvin Bradbury-Jost
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Taylor Ann Withey
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Tadesse Gessese
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Taha Azad
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC J1H 5N4, Canada
| | - Bahram Samanfar
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Ashkan Golshani
- Department of Biology, and the Ottawa Institute of Systems Biology (OISB), Carleton University, Ottawa, ON K1S 5B6, Canada
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7
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Azad T, Rezaei R, Singaravelu R, Pelin A, Boulton S, Petryk J, Onsu KA, Martin NT, Hoskin V, Ghahremani M, Marotel M, Marius R, He X, Crupi MJF, Hoang HD, Nik-Akhtar A, Ahmadi M, Zamani NK, Golshani A, Alain T, Greer P, Ardolino M, Dickinson BC, Tai LH, Ilkow CS, Bell JC. Synthetic virology approaches to improve the safety and efficacy of oncolytic virus therapies. Nat Commun 2023; 14:3035. [PMID: 37236967 DOI: 10.1038/s41467-023-38651-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The large coding potential of vaccinia virus (VV) vectors is a defining feature. However, limited regulatory switches are available to control viral replication as well as timing and dosing of transgene expression in order to facilitate safe and efficacious payload delivery. Herein, we adapt drug-controlled gene switches to enable control of virally encoded transgene expression, including systems controlled by the FDA-approved rapamycin and doxycycline. Using ribosome profiling to characterize viral promoter strength, we rationally design fusions of the operator element of different drug-inducible systems with VV promoters to produce synthetic promoters yielding robust inducible expression with undetectable baseline levels. We also generate chimeric synthetic promoters facilitating additional regulatory layers for VV-encoded synthetic transgene networks. The switches are applied to enable inducible expression of fusogenic proteins, dose-controlled delivery of toxic cytokines, and chemical regulation of VV replication. This toolbox enables the precise modulation of transgene circuitry in VV-vectored oncolytic virus design.
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Affiliation(s)
- Taha Azad
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
- Centre de Recherche du CHUS, Sherbrooke, QC, J1H 5N4, Canada
| | - Reza Rezaei
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Ragunath Singaravelu
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, CA 94158, USA
| | - Stephen Boulton
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Julia Petryk
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | | | | | - Victoria Hoskin
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Mina Ghahremani
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Marie Marotel
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, K1H, Canada
| | - Ricardo Marius
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Xiaohong He
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Mathieu J F Crupi
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Huy-Dung Hoang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Abolfazl Nik-Akhtar
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Mahsa Ahmadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Nika Kooshki Zamani
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Tommy Alain
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Peter Greer
- Department of Pathology and Molecular Medicine, Queens University, Kingston, ON, K7L 3N6, Canada
| | - Michele Ardolino
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, K1H, Canada
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Lee-Hwa Tai
- Centre de Recherche du CHUS, Sherbrooke, QC, J1H 5N4, Canada
- Department of Immunology & Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Carolina S Ilkow
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - John C Bell
- Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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8
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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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9
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Takallou S, Puchacz N, Allard D, Said KB, Nokhbeh MR, Samanfar B, Golshani A. IRES-mediated translation in bacteria. Biochem Biophys Res Commun 2023; 641:110-115. [PMID: 36527744 DOI: 10.1016/j.bbrc.2022.12.022] [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: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Despite the similarity in fundamental goals of translation initiation between different domains of life, it is one of the most phylogenetically diverse steps of the central dogma of molecular biology. In a classical view, the translation signals for prokaryotes and eukaryotes are distinct from each other. This idea was challenged by the finding that the Internal Ribosome Entry Site (IRES) belonging to Plautia stali intestine virus (PSIV) could bypass the domain-specific boundaries and effectively initiate translation in E. coli. This finding led us to investigate whether the ability of PSIV IRES to initiate translation in E. coli is specific to this IRES and also to study features that allow this viral IRES to mediate prokaryotic translation initiation. We observed that certain IRESs may also possess the ability to initiate E. coli translation. Our results also indicated that the structural integrity of the PSIV IRES in translation in prokaryotes does not appear to be as critical as it is in eukaryotes. We also demonstrated that two regions of the PSIV IRES with complementarity to 16S ribosomal RNA are important for the ability of this IRES to initiate translation in E. coli.
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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.
| | - Nathalie Puchacz
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Danielle Allard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Kamaledin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Saudi Arabia.
| | | | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, Ontario, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), 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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10
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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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11
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Ajila V, Colley L, Ste-Croix DT, Nissan N, Golshani A, Cober ER, Mimee B, Samanfar B, Green JR. P-TarPmiR accurately predicts plant-specific miRNA targets. Sci Rep 2023; 13:332. [PMID: 36609461 PMCID: PMC9822942 DOI: 10.1038/s41598-022-27283-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
microRNAs (miRNAs) are small non-coding ribonucleic acids that post-transcriptionally regulate gene expression through the targeting of messenger RNA (mRNAs). Most miRNA target predictors have focused on animal species and prediction performance drops substantially when applied to plant species. Several rule-based miRNA target predictors have been developed in plant species, but they often fail to discover new miRNA targets with non-canonical miRNA-mRNA binding. Here, the recently published TarDB database of plant miRNA-mRNA data is leveraged to retrain the TarPmiR miRNA target predictor for application on plant species. Rigorous experiment design across four plant test species demonstrates that animal-trained predictors fail to sustain performance on plant species, and that the use of plant-specific training data improves accuracy depending on the quantity of plant training data used. Surprisingly, our results indicate that the complete exclusion of animal training data leads to the most accurate plant-specific miRNA target predictor indicating that animal-based data may detract from miRNA target prediction in plants. Our final plant-specific miRNA prediction method, dubbed P-TarPmiR, is freely available for use at http://ptarpmir.cu-bic.ca . The final P-TarPmiR method is used to predict targets for all miRNA within the soybean genome. Those ranked predictions, together with GO term enrichment, are shared with the research community.
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Affiliation(s)
- Victoria Ajila
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
| | - Laura Colley
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
| | - Dave T. Ste-Croix
- grid.55614.330000 0001 1302 4958Saint-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5 Canada
| | - Nour Nissan
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada ,grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - Ashkan Golshani
- grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - Elroy R. Cober
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada
| | - Benjamin Mimee
- grid.55614.330000 0001 1302 4958Saint-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5 Canada
| | - Bahram Samanfar
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada ,grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - James R. Green
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
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12
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Hooker JC, Nissan N, Luckert D, Charette M, Zapata G, Lefebvre F, Mohr RM, Daba KA, Warkentin TD, Hadinezhad M, Barlow B, Hou A, Golshani A, Cober ER, Samanfar B. A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean ( Glycine max). Int J Mol Sci 2022; 24:ijms24010222. [PMID: 36613666 PMCID: PMC9820483 DOI: 10.3390/ijms24010222] [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: 11/05/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low protein soybean varieties, we performed differential expression analysis on high and low total protein soybean varieties and high and low 11S soybean varieties grown in four locations across Eastern and Western Canada over three years (2018-2020). Simultaneously, ten individual differential expression datasets for high vs. low total protein soybeans and ten individual differential expression datasets for high vs. low 11S soybeans were assessed, for a total of 20 datasets. The top 15 most upregulated and the 15 most downregulated genes were extracted from each differential expression dataset and cross-examination was conducted to create shortlists of the most consistently differentially expressed genes. Shortlisted genes were assessed for gene ontology to gain a global appreciation of the commonly differentially expressed genes. Genes with roles in the lipid metabolic pathway and carbohydrate metabolic pathway were differentially expressed in high total protein and high 11S soybeans in comparison to their low total protein and low 11S counterparts. Expression differences were consistent between East and West locations with the exception of one, Glyma.03G054100. These data are important for uncovering the genes and biological pathways responsible for the difference in seed protein between high and low total protein or 11S cultivars.
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Affiliation(s)
- Julia C. Hooker
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Nour Nissan
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Doris Luckert
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, 740 Dr. Penfield Ave, Montréal, QC H3A 0G1, Canada
| | - François Lefebvre
- Canadian Centre for Computational Genomics, 740 Dr. Penfield Ave, Montréal, QC H3A 0G1, Canada
| | - Ramona M. Mohr
- Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB R7A 5Y3, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Thomas D. Warkentin
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Mehri Hadinezhad
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Anfu Hou
- Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada
- Correspondence:
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13
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Hooker JC, Nissan N, Luckert D, Zapata G, Hou A, Mohr RM, Glenn AJ, Barlow B, Daba KA, Warkentin TD, Lefebvre F, Golshani A, Cober ER, Samanfar B. GmSWEET29 and Paralog GmSWEET34 Are Differentially Expressed between Soybeans Grown in Eastern and Western Canada. Plants 2022; 11:plants11182337. [PMID: 36145738 PMCID: PMC9502396 DOI: 10.3390/plants11182337] [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] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022]
Abstract
Over the past two decades soybeans grown in western Canada have persistently had lower seed protein than those grown in eastern Canada. To understand the discrepancy in seed protein content between eastern- and western-grown soybeans, RNA-seq and differential expression analysis have been investigated. Ten soybean genotypes, ranging from low to high in seed protein content, were grown in four locations across eastern (Ottawa) and western (Morden, Brandon, and Saskatoon) Canada. Differential expression analysis revealed 34 differentially expressed genes encoding Glycine max Sugars Will Eventually be Exported Transporters (GmSWEETs), including paralogs GmSWEET29 and GmSWEET34 (AtSWEET2 homologs) that were consistently upregulated across all ten genotypes in each of the western locations over three years. GmSWEET29 and GmSWEET34 are likely candidates underlying the lower seed protein content of western soybeans. GmSWEET20 (AtSWEET12 homolog) was downregulated in the western locations and may also play a role in lower seed protein content. These findings are valuable for improving soybean agriculture in western growing regions, establishing more strategic and efficient agricultural practices.
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Affiliation(s)
- Julia C. Hooker
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Doris Luckert
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada
| | - Anfu Hou
- Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada
| | - Ramona M. Mohr
- Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada
| | - Aaron J. Glenn
- Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Thomas D. Warkentin
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - François Lefebvre
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Correspondence:
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14
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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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15
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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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16
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Nissan N, Hooker J, Pattang A, Charette M, Morrison M, Yu K, Hou A, Golshani A, Molnar SJ, Cober ER, Samanfar B. Novel QTL for Low Seed Cadmium Accumulation in Soybean. Plants (Basel) 2022; 11:1146. [PMID: 35567147 PMCID: PMC9102923 DOI: 10.3390/plants11091146] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022]
Abstract
Soybean is a valuable crop, used in animal feed and for human consumption. Selecting soybean cultivars with low seed cadmium (Cd) concentration is important for the purpose of minimizing the transfer of Cd into the human body. To ensure international trade, farmers need to produce soybean that meets the European Union (EU) Cd limit of 0.2 mg kg-1. In this study, we evaluated two populations of recombinant inbred lines (RILs), X5154 and X4050, for seed Cd accumulation. Linkage maps were constructed with 325 and 280 polymorphic simple sequence repeat (SSR) markers, respectively, and used to identify a novel minor quantitative trait locus (QTL) on chromosome 13 in the X4050 population between SSR markers Satt522 and Satt218. Based on a gene ontology search within the QTL region, seven genes were identified as candidates responsible for low seed Cd accumulation, including Glyma.13G308700 and Glyma.13G309100. In addition, we confirmed the known major gene, Cda1, in the X5154 population and developed KASP and CAPS/dCAPS allele-specific markers for efficient marker-assisted breeding for Cda1.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Julia Hooker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Arezo Pattang
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Martin Charette
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
| | - Malcolm Morrison
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
| | - Kangfu Yu
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON N0R 1G0, Canada;
| | - Anfu Hou
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada;
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Stephen J. Molnar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada; (N.N.); (J.H.); (A.P.); (M.C.); (M.M.); (S.J.M.); (E.R.C.)
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
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17
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Nissan N, Mimee B, Cober ER, Golshani A, Smith M, Samanfar B. A Broad Review of Soybean Research on the Ongoing Race to Overcome Soybean Cyst Nematode. Biology (Basel) 2022; 11:211. [PMID: 35205078 PMCID: PMC8869295 DOI: 10.3390/biology11020211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
Plant pathogens greatly impact food security of the ever-growing human population. Breeding resistant crops is one of the most sustainable strategies to overcome the negative effects of these biotic stressors. In order to efficiently breed for resistant plants, the specific plant-pathogen interactions should be understood. Soybean is a short-day legume that is a staple in human food and animal feed due to its high nutritional content. Soybean cyst nematode (SCN) is a major soybean stressor infecting soybean worldwide including in China, Brazil, Argentina, USA and Canada. There are many Quantitative Trait Loci (QTLs) conferring resistance to SCN that have been identified; however, only two are widely used: rhg1 and Rhg4. Overuse of cultivars containing these QTLs/genes can lead to SCN resistance breakdown, necessitating the use of additional strategies. In this manuscript, a literature review is conducted on research related to soybean resistance to SCN. The main goal is to provide a current understanding of the mechanisms of SCN resistance and list the areas of research that could be further explored.
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Affiliation(s)
- Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada;
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Myron Smith
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1Y 4X2, Canada; (N.N.); (E.R.C.)
- Ottawa Institute of Systems Biology and Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.G.); (M.S.)
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18
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Hernández RB, de Souza-Pinto NC, Kleinjans J, van Herwijnen M, Piepers J, Moteshareie H, Burnside D, Golshani A. Manganese-Induced Neurotoxicity through Impairment of Cross-Talk Pathways in Human Neuroblastoma Cell Line SH-SY5Y Differentiated with Retinoic Acid. Toxics 2021; 9:toxics9120348. [PMID: 34941782 PMCID: PMC8704659 DOI: 10.3390/toxics9120348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 01/29/2023]
Abstract
Manganese (Mn) is an important element; yet acute and/or chronic exposure to this metal has been linked to neurotoxicity and neurodegenerative illnesses such as Parkinson’s disease and others via an unknown mechanism. To better understand it, we exposed a human neuroblastoma cell model (SH-SY5Y) to two Mn chemical species, MnCl2 and Citrate of Mn(II) (0–2000 µM), followed by a cell viability assay, transcriptomics, and bioinformatics. Even though these cells have been chemically and genetically modified, which may limit the significance of our findings, we discovered that by using RA-differentiated cells instead of undifferentiated SH-SY5Y cell line, both chemical species induce a similar toxicity, potentially governed by disruption of protein metabolism, with some differences. The MnCl2 altered amino acid metabolism, which affects RNA metabolism and protein synthesis. Citrate of Mn(II), however, inhibited the E3 ubiquitin ligases–target protein degradation pathway, which can lead to the buildup of damaged/unfolded proteins, consistent with histone modification. Finally, we discovered that Mn(II)-induced cytotoxicity in RA-SH-SY5Y cells shared 84 percent of the pathways involved in neurodegenerative diseases.
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Affiliation(s)
- Raúl Bonne Hernández
- Laboratory of Bioinorganic and Environmental Toxicology—LABITA, Department of Chemistry, Federal University of São Paulo, Rua Prof. Artur Riedel, 275, Diadema 09972-270, SP, Brazil
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
- Correspondence: ; Tel.: +55-11-3385-4137 (ext. 3522)
| | - Nadja C. de Souza-Pinto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes, 748, Butantã, São Paulo 05508-900, SP, Brazil;
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Marcel van Herwijnen
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Jolanda Piepers
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER Maastricht, The Netherlands; (J.K.); (M.v.H.); (J.P.)
| | - Houman Moteshareie
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
| | - Daniel Burnside
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
| | - Ashkan Golshani
- Department of Biology, Carleton University, 209 Nesbitt Biology Building, 1125 Colonel by Drive, Ottawa, ON K1S 5B6, Canada; (H.M.); (D.B.); (A.G.)
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19
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Ahmed D, Humphrey A, Roy D, Sheridan ME, Versey Z, Jaworski A, Edwards A, Donner J, Abizaid A, Willmore W, Kumar A, Golshani A, Cassol E. HIF-1α Regulation of Cytokine Production following TLR3 Engagement in Murine Bone Marrow-Derived Macrophages Is Dependent on Viral Nucleic Acid Length and Glucose Availability. J Immunol 2021; 207:2813-2827. [PMID: 34740958 DOI: 10.4049/jimmunol.2001282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 09/16/2021] [Indexed: 12/24/2022]
Abstract
Hypoxia-inducible factor-1α (HIF-1α) is an important regulator of glucose metabolism and inflammatory cytokine production in innate immune responses. Viruses modulate HIF-1α to support viral replication and the survival of infected cells, but it is unclear if this transcription factor also plays an important role in regulating antiviral immune responses. In this study, we found that short and long dsRNA differentially engage TLR3, inducing distinct levels of proinflammatory cytokine production (TNF-α and IL-6) in bone marrow-derived macrophages from C57BL/6 mice. These responses are associated with differential accumulation of HIF-1α, which augments NF-κB activation. Unlike TLR4 responses, increased HIF-1α following TLR3 engagement is not associated with significant alterations in glycolytic activity and was more pronounced in low glucose conditions. We also show that the mechanisms supporting HIF-1α stabilization may differ following stimulation with short versus long dsRNA and that pyruvate kinase M2 and mitochondrial reactive oxygen species play a central role in these processes. Collectively, this work suggests that HIF-1α may fine-tune proinflammatory cytokine production during early antiviral immune responses, particularly when there is limited glucose availability or under other conditions of stress. Our findings also suggest we may be able to regulate the magnitude of proinflammatory cytokine production during antiviral responses by targeting proteins or molecules that contribute to HIF-1α stabilization.
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Affiliation(s)
- Duale Ahmed
- Department of Biology, Carleton University, Ottawa, Ontario, Canada.,Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Allan Humphrey
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada.,Apoptosis Research Centre, The Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - David Roy
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | | | - Zoya Versey
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Allison Jaworski
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Alex Edwards
- Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada
| | - James Donner
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Alfonso Abizaid
- Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada
| | - William Willmore
- Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Ashok Kumar
- Department of Pathology, The Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; and.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada;
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20
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Dick K, Pattang A, Hooker J, Nissan N, Sadowski M, Barnes B, Tan LH, Burnside D, Phanse S, Aoki H, Babu M, Dehne F, Golshani A, Cober ER, Green JR, Samanfar B. Human-Soybean Allergies: Elucidation of the Seed Proteome and Comprehensive Protein-Protein Interaction Prediction. J Proteome Res 2021; 20:4925-4947. [PMID: 34582199 DOI: 10.1021/acs.jproteome.1c00138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The soybean crop, Glycine max (L.) Merr., is consumed by humans, Homo sapiens, worldwide. While the respective bodies of literature and -omics data for each of these organisms are extensive, comparatively few studies investigate the molecular biological processes occurring between the two. We are interested in elucidating the network of protein-protein interactions (PPIs) involved in human-soybean allergies. To this end, we leverage state-of-the-art sequence-based PPI predictors amenable to predicting the enormous comprehensive interactome between human and soybean. A network-based analytical approach is proposed, leveraging similar interaction profiles to identify candidate allergens and proteins involved in the allergy response. Interestingly, the predicted interactome can be explored from two complementary perspectives: which soybean proteins are predicted to interact with specific human proteins and which human proteins are predicted to interact with specific soybean proteins. A total of eight proteins (six specific to the human proteome and two to the soy proteome) have been identified and supported by the literature to be involved in human health, specifically related to immunological and neurological pathways. This study, beyond generating the most comprehensive human-soybean interactome to date, elucidated a soybean seed interactome and identified several proteins putatively consequential to human health.
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Affiliation(s)
- Kevin Dick
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Arezo Pattang
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada K1A 0C6
- Department of Biology and Institute of Biochemistry, and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Julia Hooker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada K1A 0C6
- Department of Biology and Institute of Biochemistry, and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Nour Nissan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada K1A 0C6
- Department of Biology and Institute of Biochemistry, and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Michael Sadowski
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada K1A 0C6
- Department of Biology and Institute of Biochemistry, and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Bradley Barnes
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Le Hoa Tan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada K1A 0C6
- Department of Biology and Institute of Biochemistry, and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Daniel Burnside
- Department of Biology and Institute of Biochemistry, and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada S4S 0A2
| | - Hiroyuki Aoki
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada S4S 0A2
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada S4S 0A2
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Ashkan Golshani
- Department of Biology and Institute of Biochemistry, and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Elroy R Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada K1A 0C6
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada K1A 0C6
- Department of Biology and Institute of Biochemistry, and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
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21
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Micalizzi EW, Golshani A, Smith ML. Propionic acid disrupts endocytosis, cell cycle, and cellular respiration in yeast. BMC Res Notes 2021; 14:335. [PMID: 34454571 PMCID: PMC8403364 DOI: 10.1186/s13104-021-05752-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/13/2021] [Accepted: 08/20/2021] [Indexed: 12/28/2022] Open
Abstract
Objective We previously identified propionic acid as a microbially-produced volatile organic compound with fungicidal activity against several pathogenic fungi. The purpose of this work is to better understand how propionic acid affects fungi by examining some of the effects of this compound on the yeast cell. Results We show that propionic acid causes a dramatic increase in the uptake of lucifer yellow in yeast cells, which is consistent with enhanced endocytosis. Additionally, using a propidium iodide assay, we show that propionic acid treatment causes a significant increase in the proportion of yeast cells in G1 and a significant decrease in the proportion of cells in G2, suggesting that propionic acid causes a cell cycle arrest in yeast. Finally, we show that the reduction of MTT is attenuated in yeast cells treated with propionic acid, indicating that propionic acid disrupts cellular respiration. Understanding the effects of propionic acid on the yeast cell may aid in assessing the broader utility of this compound. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05752-z.
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Affiliation(s)
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Myron L Smith
- Department of Biology, Carleton University, Ottawa, ON, Canada
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22
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Jessulat M, Amin S, Hooshyar M, Malty R, Moutaoufik MT, Zilocchi M, Istace Z, Phanse S, Aoki H, Omidi K, Burnside D, Samanfar B, Aly KA, Golshani A, Babu M. The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLF. Nucleic Acids Res 2021; 49:8145-8160. [PMID: 34244791 PMCID: PMC8373142 DOI: 10.1093/nar/gkab585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 06/13/2021] [Accepted: 06/24/2021] [Indexed: 02/03/2023] Open
Abstract
The yeast cyclic AMP-dependent protein kinase A (PKA) is a ubiquitous serine-threonine kinase, encompassing three catalytic (Tpk1-3) and one regulatory (Bcy1) subunits. Evidence suggests PKA involvement in DNA damage checkpoint response, but how DNA repair pathways are regulated by PKA subunits remains inconclusive. Here, we report that deleting the tpk1 catalytic subunit reduces non-homologous end joining (NHEJ) efficiency, whereas tpk2-3 and bcy1 deletion does not. Epistatic analyses revealed that tpk1, as well as the DNA damage checkpoint kinase (dun1) and NHEJ factor (nej1), co-function in the same pathway, and parallel to the NHEJ factor yku80. Chromatin immunoprecipitation and resection data suggest that tpk1 deletion influences repair protein recruitments and DNA resection. Further, we show that Tpk1 phosphorylation of Nej1 at S298 (a Dun1 phosphosite) is indispensable for NHEJ repair and nuclear targeting of Nej1 and its binding partner Lif1. In mammalian cells, loss of PRKACB (human homolog of Tpk1) also reduced NHEJ efficiency, and similarly, PRKACB was found to phosphorylate XLF (a Nej1 human homolog) at S263, a corresponding residue of the yeast Nej1 S298. Together, our results uncover a new and conserved mechanism for Tpk1 and PRKACB in phosphorylating Nej1 (or XLF), which is critically required for NHEJ repair.
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Affiliation(s)
- Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Shahreen Amin
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohsen Hooshyar
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Ramy Malty
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | | | - Mara Zilocchi
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Zoe Istace
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Katayoun Omidi
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Daniel Burnside
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1S5 B6, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
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23
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Nissan N, Cober ER, Sadowski M, Charette M, Golshani A, Samanfar B. Identifying new variation at the J locus, previously identified as e6, in long juvenile 'Paranagoiana' soybean. Theor Appl Genet 2021; 134:1007-1014. [PMID: 33386860 PMCID: PMC7973924 DOI: 10.1007/s00122-020-03746-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/05/2020] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE A previously identified soybean maturity locus, E6, is discovered to be J, with the long juvenile allele in Paranagoiana now deemed j-x. Soybean grown at latitudes of ~20° or lower can produce lower grain yields due to the short days. This limitation can be overcome by using the long juvenile trait (LJ) which delays flowering under short day conditions. Two LJ loci have been mapped to the same location on Gm04, J and E6. The objective of this research was to investigate the e6 allele in 'Paranagoiana' and determine if E6 and J are the same locus or linked loci. KASP markers showed that e6 lines did not have the j-1 allele of LJ PI 159925. A population fixed for E1 but segregating for E6, with e6 introgressed from Paranagoiana, showed single gene control for flowering and maturity under short days. Sequencing Glyma.04G050200, the J gene, with long amplification Taq found that the e6 line 'Paranagoiana' contains a Ty1-copia retrotransposon of ~10,000 bp, inserted within exon 4. PCR amplification of the cDNA of Glyma.04G050200 also showed differences between the mRNA sequences (presence of insertion in j-x). Hence, we conclude that the loci E6 and J are one locus and deem this new variation found in Paranagoiana as j-x.
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Affiliation(s)
- Nour Nissan
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Elroy R Cober
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michael Sadowski
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Martin Charette
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Bahram Samanfar
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada.
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24
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Hooshyar M, Jessulat M, Burnside D, Kluew A, Babu M, Golshani A. Deletion of yeast TPK1 reduces the efficiency of non-homologous end joining DNA repair. Biochem Biophys Res Commun 2020; 533:899-904. [DOI: 10.1016/j.bbrc.2020.09.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 12/12/2022]
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Hernández RB, Carrascal M, Abian J, Michalke B, Farina M, Gonzalez YR, Iyirhiaro GO, Moteshareie H, Burnside D, Golshani A, Suñol C. Manganese-induced neurotoxicity in cerebellar granule neurons due to perturbation of cell network pathways with potential implications for neurodegenerative disorders. Metallomics 2020; 12:1656-1678. [PMID: 33206086 DOI: 10.1039/d0mt00085j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Manganese (Mn) is essential for living organisms, playing an important role in nervous system function. Nevertheless, chronic and/or acute exposure to this metal, especially during early life stages, can lead to neurotoxicity and dementia by unclear mechanisms. Thus, based on previous works of our group with yeast and zebrafish, we hypothesized that the mechanisms mediating manganese-induced neurotoxicity can be associated with the alteration of protein metabolism. These mechanisms may also depend on the chemical speciation of manganese. Therefore, the current study aimed at investigating the mechanisms mediating the toxic effects of manganese in primary cultures of cerebellar granule neurons (CGNs). By exposing cultured CGNs to different chemical species of manganese ([[2-[(dithiocarboxy)amino]ethyl]carbamodithioato]](2-)-kS,kS']manganese, named maneb (MB), and [[1,2-ethanediylbis[carbamodithioato]](2-)]manganese mixture with [[1,2-ethanediylbis[carbamodithioato]](2-)]zinc, named mancozeb (MZ), and manganese chloride (MnCl2)), and using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, we observed that both MB and MZ induced similar cytotoxicity (LC50∼ 7-9 μM), which was higher than that of MnCl2 (LC50∼ 27 μM). Subsequently, we applied systems biology approaches, including metallomics, proteomics, gene expression and bioinformatics, and revealed that independent of chemical speciation, for non-cytotoxic concentrations (0.3-3 μM), Mn-induced neurotoxicity in CGNs is associated with metal dyshomeostasis and impaired protein metabolism. In this way, we verified that MB induced more post-translational alterations than MnCl2, which can be a plausible explanation for cytotoxic differences between both chemical species. The metabolism of proteins is one of the most energy consuming cellular processes and its impairment appears to be a key event of some cellular stress processes reported separately in other studies such as cell cycle arrest, energy impairment, cell signaling, excitotoxicity, immune response, potential protein accumulation and apoptosis. Interestingly, we verified that Mn-induced neurotoxicity shares pathways associated with the development of Alzheimer's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, and Parkinson's disease. This has been observed in baker's yeast and zebrafish suggesting that the mode of action of Mn may be evolutionarily conserved.
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Affiliation(s)
- Raúl Bonne Hernández
- Laboratory of Bioinorganic and Environmental Toxicology - LABITA, Department of Exact and Earth Sciences, Federal University of São Paulo, Rua Prof. Artur Riedel, 275, CEP 09972-270, Diadema, SP, Brazil.
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26
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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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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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28
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Dick K, Samanfar B, Barnes B, Cober ER, Mimee B, Tan LH, Molnar SJ, Biggar KK, Golshani A, Dehne F, Green JR. PIPE4: Fast PPI Predictor for Comprehensive Inter- and Cross-Species Interactomes. Sci Rep 2020; 10:1390. [PMID: 31996697 PMCID: PMC6989690 DOI: 10.1038/s41598-019-56895-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
The need for larger-scale and increasingly complex protein-protein interaction (PPI) prediction tasks demands that state-of-the-art predictors be highly efficient and adapted to inter- and cross-species predictions. Furthermore, the ability to generate comprehensive interactomes has enabled the appraisal of each PPI in the context of all predictions leading to further improvements in classification performance in the face of extreme class imbalance using the Reciprocal Perspective (RP) framework. We here describe the PIPE4 algorithm. Adaptation of the PIPE3/MP-PIPE sequence preprocessing step led to upwards of 50x speedup and the new Similarity Weighted Score appropriately normalizes for window frequency when applied to any inter- and cross-species prediction schemas. Comprehensive interactomes for three prediction schemas are generated: (1) cross-species predictions, where Arabidopsis thaliana is used as a proxy to predict the comprehensive Glycine max interactome, (2) inter-species predictions between Homo sapiens-HIV1, and (3) a combined schema involving both cross- and inter-species predictions, where both Arabidopsis thaliana and Caenorhabditis elegans are used as proxy species to predict the interactome between Glycine max (the soybean legume) and Heterodera glycines (the soybean cyst nematode). Comparing PIPE4 with the state-of-the-art resulted in improved performance, indicative that it should be the method of choice for complex PPI prediction schemas.
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Affiliation(s)
- Kevin Dick
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, K1S 5B6, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, K1A 0C6, Canada
- Department of Biology, Carleton University, Ottawa, K1S 5B6, Ontario, Canada
| | - Bradley Barnes
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, K1S 5B6, Canada
| | - Elroy R Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, K1A 0C6, Canada
| | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, Saint-Jean-sur-Richelieu, J3B 3E6, Quebec, Canada
| | - Le Hoa Tan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, K1A 0C6, Canada
| | - Stephen J Molnar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, K1A 0C6, Canada
| | - Kyle K Biggar
- Department of Biology, Carleton University, Ottawa, K1S 5B6, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, K1S 5B6, Ontario, Canada
- Ottawa Institute of Systems Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, Ontario, K1S 5B6, Canada
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, K1S 5B6, Canada.
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29
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Ahmed D, Roy D, Jaworski A, Edwards A, Abizaid A, Kumar A, Golshani A, Cassol E. Differential remodeling of the electron transport chain is required to support TLR3 and TLR4 signaling and cytokine production in macrophages. Sci Rep 2019; 9:18801. [PMID: 31827178 PMCID: PMC6906364 DOI: 10.1038/s41598-019-55295-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 09/03/2019] [Accepted: 11/25/2019] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence suggests that mitochondria play a critical role in driving innate immune responses against bacteria and viruses. However, it is unclear if differential reprogramming of mitochondrial function contributes to the fine tuning of pathogen specific immune responses. Here, we found that TLR3 and TLR4 engagement on murine bone marrow derived macrophages was associated with differential remodeling of electron transport chain complex expression. This remodeling was associated with differential accumulation of mitochondrial and cytosolic ROS, which were required to support ligand specific inflammatory and antiviral cytokine production. We also found that the magnitude of TLR3, but not TLR4, responses were modulated by glucose availability. Under conditions of low glucose, TLR3 engagement was associated with increased ETC complex III expression, increased mitochondrial and cytosolic ROS and increased inflammatory and antiviral cytokine production. This amplification was selectively reversed by targeting superoxide production from the outer Q-binding site of the ETC complex III. These results suggest that ligand specific modulation of the ETC may act as a rheostat that fine tunes innate immune responses via mitochondrial ROS production. Modulation of these processes may represent a novel mechanism to modulate the nature as well as the magnitude of antiviral vs. inflammatory immune responses.
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Affiliation(s)
- Duale Ahmed
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - David Roy
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Allison Jaworski
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Alexander Edwards
- Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada
| | - Alfonso Abizaid
- Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada
| | - Ashok Kumar
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,The Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada.
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Abstract
Nisin is a class I polycyclic bacteriocin produced by the bacterium Lactococcus lactis, which is used extensively as a food additive to inhibit the growth of foodborne Gram-positive bacteria. Nisin also inhibits growth of Gram-negative bacteria when combined with membrane-disrupting chelators such as citric acid. To gain insight into nisin's mode of action, we analyzed chemical-genetic interactions and identified nisin-sensitive Escherichia coli strains in the Keio library of knockout mutants. The most sensitive mutants fell into two main groups. The first group accords with the previously proposed mode of action based on studies with Gram-positive bacteria, whereby nisin interacts with factors involved in cell wall, membrane, envelope biogenesis. We identified an additional, novel mode of action for nisin based on the second group of sensitive mutants that involves cell cycle and DNA replication, recombination, and repair. Further analyses supported these two distinct modes of action.
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Affiliation(s)
- Imelda J Galván Márquez
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Bruce McKay
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Alex Wong
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - James J Cheetham
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Cody Bean
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Ashkan Golshani
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Myron L Smith
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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31
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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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Bentley‐DeSousa A, Moteshareie H, Holinier C, Tseng Y, Bondy‐Chorney E, Davey N, Golshani A, Downey M. A screen for novel targets casts polyphosphorylation of lysine as a common post‐translational modification. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.791.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Amanda Bentley‐DeSousa
- Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
- Ottawa Institute of Systems BiologyOttawaONCanada
| | | | - Charlotte Holinier
- Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
- Ottawa Institute of Systems BiologyOttawaONCanada
| | - Yi‐Chieh Tseng
- Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
- Ottawa Institute of Systems BiologyOttawaONCanada
| | - Emma Bondy‐Chorney
- Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
- Ottawa Institute of Systems BiologyOttawaONCanada
| | - Norman Davey
- Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublinIreland
| | | | - Michael Downey
- Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
- Ottawa Institute of Systems BiologyOttawaONCanada
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33
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Galván Márquez I, Ghiyasvand M, Massarsky A, Babu M, Samanfar B, Omidi K, Moon TW, Smith ML, Golshani A. Zinc oxide and silver nanoparticles toxicity in the baker's yeast, Saccharomyces cerevisiae. PLoS One 2018; 13:e0193111. [PMID: 29554091 PMCID: PMC5858749 DOI: 10.1371/journal.pone.0193111] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/05/2018] [Indexed: 12/18/2022] Open
Abstract
Engineered nanomaterials (ENMs) are increasingly incorporated into a variety of commercial applications and consumer products; however, ENMs may possess cytotoxic properties due to their small size. This study assessed the effects of two commonly used ENMs, zinc oxide nanoparticles (ZnONPs) and silver nanoparticles (AgNPs), in the model eukaryote Saccharomyces cerevisiae. A collection of ≈4600 S. cerevisiae deletion mutant strains was used to deduce the genes, whose absence makes S. cerevisiae more prone to the cytotoxic effects of ZnONPs or AgNPs. We demonstrate that S. cerevisiae strains that lack genes involved in transmembrane and membrane transport, cellular ion homeostasis, and cell wall organization or biogenesis exhibited the highest sensitivity to ZnONPs. In contrast, strains that lack genes involved in transcription and RNA processing, cellular respiration, and endocytosis and vesicular transport exhibited the highest sensitivity to AgNPs. Secondary assays confirmed that ZnONPs affected cell wall function and integrity, whereas AgNPs exposure decreased transcription, reduced endocytosis, and led to a dysfunctional electron transport system. This study supports the use of S. cerevisiae Gene Deletion Array as an effective high-throughput technique to determine cellular targets of ENM toxicity.
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Affiliation(s)
- Imelda Galván Márquez
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Mergan Ghiyasvand
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Andrey Massarsky
- Department of Biology, Centre for Advanced Research in Environmental Genomics and the Collaborative Program in Chemical and Environmental Toxicology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, 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
| | - Katayoun Omidi
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Thomas W. Moon
- Department of Biology, Centre for Advanced Research in Environmental Genomics and the Collaborative Program in Chemical and Environmental Toxicology, University of Ottawa, Ottawa, Ontario, Canada
| | - Myron L. Smith
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
- * E-mail: (MLS); (AG)
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
- * E-mail: (MLS); (AG)
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34
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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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35
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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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36
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Gagarinova A, Stewart G, Samanfar B, Phanse S, White CA, Aoki H, Deineko V, Beloglazova N, Yakunin AF, Golshani A, Brown ED, Babu M, Emili A. Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery. Cell Rep 2017; 17:904-916. [PMID: 27732863 DOI: 10.1016/j.celrep.2016.09.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 09/24/2014] [Revised: 07/30/2016] [Accepted: 09/14/2016] [Indexed: 12/20/2022] Open
Abstract
Bacterial protein synthesis is an essential, conserved, and environmentally responsive process. Yet, many of its components and dependencies remain unidentified. To address this gap, we used quantitative synthetic genetic arrays to map functional relationships among >48,000 gene pairs in Escherichia coli under four culture conditions differing in temperature and nutrient availability. The resulting data provide global functional insights into the roles and associations of genes, pathways, and processes important for efficient translation, growth, and environmental adaptation. We predict and independently verify the requirement of unannotated genes for normal translation, including a previously unappreciated role of YhbY in 30S biogenesis. Dynamic changes in the patterns of genetic dependencies across the four growth conditions and data projections onto other species reveal overarching functional and evolutionary pressures impacting the translation system and bacterial fitness, underscoring the utility of systematic screens for investigating protein synthesis, adaptation, and evolution.
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Affiliation(s)
- Alla Gagarinova
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Geordie Stewart
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Bahram Samanfar
- Department of Biology and the Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Sadhna Phanse
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - Carl A White
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - Viktor Deineko
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK S4S 0A2, Canada
| | - Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Ashkan Golshani
- Department of Biology and the Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Mohan Babu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Andrew Emili
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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37
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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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38
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Mehranfar A, Ghadiri N, Kouhsar M, Golshani A. A Type-2 fuzzy data fusion approach for building reliable weighted protein interaction networks with application in protein complex detection. Comput Biol Med 2017; 88:18-31. [DOI: 10.1016/j.compbiomed.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 06/04/2017] [Accepted: 06/19/2017] [Indexed: 02/02/2023]
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39
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Schoenrock A, Burnside D, Moteshareie H, Pitre S, Hooshyar M, Green JR, Golshani A, Dehne F, Wong A. Evolution of protein-protein interaction networks in yeast. PLoS One 2017; 12:e0171920. [PMID: 28248977 PMCID: PMC5382968 DOI: 10.1371/journal.pone.0171920] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 01/28/2017] [Indexed: 01/04/2023] Open
Abstract
Interest in the evolution of protein-protein and genetic interaction networks has been rising in recent years, but the lack of large-scale high quality comparative datasets has acted as a barrier. Here, we carried out a comparative analysis of computationally predicted protein-protein interaction (PPI) networks from five closely related yeast species. We used the Protein-protein Interaction Prediction Engine (PIPE), which uses a database of known interactions to make sequence-based PPI predictions, to generate high quality predicted interactomes. Simulated proteomes and corresponding PPI networks were used to provide null expectations for the extent and nature of PPI network evolution. We found strong evidence for conservation of PPIs, with lower than expected levels of change in PPIs for about a quarter of the proteome. Furthermore, we found that changes in predicted PPI networks are poorly predicted by sequence divergence. Our analyses identified a number of functional classes experiencing fewer PPI changes than expected, suggestive of purifying selection on PPIs. Our results demonstrate the added benefit of considering predicted PPI networks when studying the evolution of closely related organisms.
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Affiliation(s)
| | | | | | - Sylvain Pitre
- School of Computer Science, Carleton University, Ottawa, Canada
| | | | - James R. Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada
| | | | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Canada
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40
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Samanfar B, Molnar SJ, Charette M, Schoenrock A, Dehne F, Golshani A, Belzile F, Cober ER. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. Theor Appl Genet 2017; 130:377-390. [PMID: 27832313 DOI: 10.1007/s00122-016-2819-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/27/2016] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE E10 is a new maturity locus in soybean and FT4 is the predicted/potential functional gene underlying the locus. Flowering and maturity time traits play crucial roles in economic soybean production. Early maturity is critical for north and west expansion of soybean in Canada. To date, 11 genes/loci have been identified which control time to flowering and maturity; however, the molecular bases of almost half of them are not yet clear. We have identified a new maturity locus called "E10" located at the end of chromosome Gm08. The gene symbol E10e10 has been approved by the Soybean Genetics Committee. The e10e10 genotype results in 5-10 days earlier maturity than E10E10. A set of presumed E10E10 and e10e10 genotypes was used to identify contrasting SSR and SNP haplotypes. These haplotypes, and their association with maturity, were maintained through five backcross generations. A functional genomics approach using a predicted protein-protein interaction (PPI) approach (Protein-protein Interaction Prediction Engine, PIPE) was used to investigate approximately 75 genes located in the genomic region that SSR and SNP analyses identified as the location of the E10 locus. The PPI analysis identified FT4 as the most likely candidate gene underlying the E10 locus. Sequence analysis of the two FT4 alleles identified three SNPs, in the 5'UTR, 3'UTR and fourth exon in the coding region, which result in differential mRNA structures. Allele-specific markers were developed for this locus and are available for soybean breeders to efficiently develop earlier maturing cultivars using molecular marker assisted breeding.
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Affiliation(s)
- Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Stephen J Molnar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Andrew Schoenrock
- School of Computer Science, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Frank Dehne
- School of Computer Science, 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
| | - François Belzile
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Elroy R Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada.
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41
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Shaikho S, Dobson CC, Naing T, Samanfar B, Moteshareie H, Hajikarimloo M, Golshani A, Holcik M. Elevated levels of ribosomal proteins eL36 and eL42 control expression of Hsp90 in rhabdomyosarcoma. ACTA ACUST UNITED AC 2016; 4:e1244395. [PMID: 28090422 DOI: 10.1080/21690731.2016.1244395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 06/28/2016] [Revised: 09/13/2016] [Accepted: 09/28/2016] [Indexed: 01/08/2023]
Abstract
Mammalian 90 kDa heat shock protein (Hsp90) is a ubiquitous molecular chaperone whose expression is selectively upregulated during stress, although the precise control mechanism of this increase is yet to be fully elucidated. We used polysome profiling to show that Hsp90α mRNA is selectively translated, while global translation is inhibited during heat stress. Furthermore, we have identified 2 ribosomal proteins, eL36 and eL42 that modulate Hsp90α expression under both normal and heat shock conditions. Importantly, we noted that expression of eL36 and eL42 is elevated in a panel of human rhabdomyosarcomas where it drives high expression of Hsp90 and modulates sensitivity of these cells to an Hsp90 inhibitor 17-AAG.
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Affiliation(s)
- Sarah Shaikho
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Christine C Dobson
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Thet Naing
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
| | - Bahram Samanfar
- 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
| | - Maryam Hajikarimloo
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University , Ottawa, Ontario, Canada
| | - Martin Holcik
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute , Ottawa, Ontario, Canada
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42
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Pelin A, Moteshareie H, Sak B, Selman M, Naor A, Eyahpaise MÈ, Farinelli L, Golshani A, Kvac M, Corradi N. The genome of an Encephalitozoon cuniculi type III strain reveals insights into the genetic diversity and mode of reproduction of a ubiquitous vertebrate pathogen. Heredity (Edinb) 2016; 116:458-65. [PMID: 26837273 DOI: 10.1038/hdy.2016.4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/10/2015] [Accepted: 12/18/2015] [Indexed: 02/07/2023] Open
Abstract
Encephalitozoon cuniculi is a model microsporidian species with a mononucleate nucleus and a genome that has been extensively studied. To date, analyses of genome diversity have revealed the existence of four genotypes in E. cuniculi (EcI, II, III and IV). Genome sequences are available for EcI, II and III, and are all very divergent, possibly diploid and genetically homogeneous. The mechanisms that cause low genetic diversity in E. cuniculi (for example, selfing, inbreeding or a combination of both), as well as the degree of genetic variation in their natural populations, have been hard to assess because genome data have been so far gathered from laboratory-propagated strains. In this study, we aim to tackle this issue by analyzing the complete genome sequence of a natural strain of E. cuniculi isolated in 2013 from a steppe lemming. The strain belongs to the EcIII genotype and has been designated EcIII-L. The EcIII-L genome sequence harbors genomic features intermediate to known genomes of II and III lab strains, and we provide primers that differentiate the three E. cuniculi genotypes using a single PCR. Surprisingly, the EcIII-L genome is also highly homogeneous, harbors signatures of heterozygosity and also one strain-specific single-nucleotide polymorphism (SNP) that introduces a stop codon in a key meiosis gene, Spo11. Functional analyses using a heterologous system demonstrate that this SNP leads to a deficient meiosis in a model fungus. This indicates that EcIII-L meiotic machinery may be presently broken. Overall, our findings reveal previously unsuspected genome diversity in E. cuniculi, some of which appears to affect genes of primary importance for the biology of this pathogen.
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Affiliation(s)
- A Pelin
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - H Moteshareie
- Department of Biology, Carleton University, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - B Sak
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - M Selman
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - A Naor
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - M-È Eyahpaise
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - L Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, Plan-les-Ouates, Switzerland
| | - A Golshani
- Department of Biology, Carleton University, Ottawa, Ontario, Canada.,Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - M Kvac
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - N Corradi
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
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43
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Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli. Cell Rep 2016; 14:648-661. [PMID: 26774489 DOI: 10.1016/j.celrep.2015.12.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/08/2015] [Accepted: 12/10/2015] [Indexed: 11/27/2022] Open
Abstract
As antibiotic resistance is increasingly becoming a public health concern, an improved understanding of the bacterial DNA damage response (DDR), which is commonly targeted by antibiotics, could be of tremendous therapeutic value. Although the genetic components of the bacterial DDR have been studied extensively in isolation, how the underlying biological pathways interact functionally remains unclear. Here, we address this by performing systematic, unbiased, quantitative synthetic genetic interaction (GI) screens and uncover widespread changes in the GI network of the entire genomic integrity apparatus of Escherichia coli under standard and DNA-damaging growth conditions. The GI patterns of untreated cultures implicated two previously uncharacterized proteins (YhbQ and YqgF) as nucleases, whereas reorganization of the GI network after DNA damage revealed DDR roles for both annotated and uncharacterized genes. Analyses of pan-bacterial conservation patterns suggest that DDR mechanisms and functional relationships are near universal, highlighting a modular and highly adaptive genomic stress response.
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Affiliation(s)
- Ashwani Kumar
- Department of Computer Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Cedoljub Bundalovic-Torma
- Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G OX4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sadhna Phanse
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Viktor Deineko
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Alla Gagarinova
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Gabriel Musso
- Department of Medicine, Harvard Medical School and Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James Vlasblom
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Mohsen Hooshyar
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Zoran Minic
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada
| | - Omar Wagih
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Roberto Mosca
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 10-12, Barcelona, 08028, Catalonia, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 10-12, Barcelona, 08028, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Catalonia, Spain
| | - Ashkan Golshani
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - John Parkinson
- Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G OX4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andrew Emili
- Terrence Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK S4S 0A2, Canada.
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Baldock TE, Golshani A, Atkinson A, Shimamoto T, Wu S, Callaghan DP, Mumby PJ. Impact of sea-level rise on cross-shore sediment transport on fetch-limited barrier reef island beaches under modal and cyclonic conditions. Mar Pollut Bull 2015; 97:188-198. [PMID: 26093817 DOI: 10.1016/j.marpolbul.2015.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
A one-dimensional wave model is combined with an analytical sediment transport model to investigate the likely influence of sea-level rise on net cross-shore sediment transport on fetch-limited barrier reef and lagoon island beaches. The modelling considers if changes in the nearshore wave height and wave period in the lagoon induced by different water levels over the reef flat are likely to lead to net offshore or onshore movement of sediment. The results indicate that the effects of SLR on net sediment movement are highly variable and controlled by the bathymetry of the reef and lagoon. A significant range of reef-lagoon bathymetry, and notably shallow and narrow reefs, appears to lead hydrodynamic conditions and beaches that are likely to be stable or even accrete under SLR. Loss of reef structural complexity, particularly on the reef flat, increases the chance of sediment transport away from beaches and offshore.
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Affiliation(s)
- T E Baldock
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia.
| | - A Golshani
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia
| | - A Atkinson
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia
| | - T Shimamoto
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia
| | - S Wu
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia
| | - D P Callaghan
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia
| | - P J Mumby
- Marine Spatial Ecology Lab, School of Biological Sciences, Goddard Building, The University of Queensland, St Lucia, Qld 4072, Australia
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Newsted D, Fallahi F, Golshani A, Azizi A. Advances and challenges in mucosal adjuvant technology. Vaccine 2015; 33:2399-405. [PMID: 25865473 DOI: 10.1016/j.vaccine.2015.03.096] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [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: 12/10/2014] [Revised: 03/17/2015] [Accepted: 03/26/2015] [Indexed: 12/23/2022]
Abstract
Adjuvants play attractive roles in enhancement of immune response during vaccination; however, due to several challenges, only a limited number of adjuvants are licensed by health authorities. The lack of an effective mucosal adjuvant is even more significant as none of the licensed adjuvants revealed a strong enhancement in immune system after mucosal administration. Over the past two decades, several mucosal adjuvants have been developed to deliver antigens to the target cells in the mucosal immune system and increase specific immune responses. However, the safety and efficacy of these adjuvants for testing in human trials is still an important issue, requiring further study. In this article, we briefly review the challenges associated with most common mucosal adjuvants and discuss potential strategies for targeting the mucosal immune system.
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Affiliation(s)
- Daniel Newsted
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St W, Hamilton, ON, Canada
| | | | - Ashkan Golshani
- Department of Biology, Carleton University, 1125 Colonel by Drive, Ottawa, ON, Canada
| | - Ali Azizi
- Department of Pathology and Laboratory Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, ON, Canada; Department of Biotechnology, University of Ontario Institute of Technology, Toronto, ON, Canada.
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Schoenrock A, Samanfar B, Pitre S, Hooshyar M, Jin K, Phillips CA, Wang H, Phanse S, Omidi K, Gui Y, Alamgir M, Wong A, Barrenäs F, Babu M, Benson M, Langston MA, Green JR, Dehne F, Golshani A. Efficient prediction of human protein-protein interactions at a global scale. BMC Bioinformatics 2014; 15:383. [PMID: 25492630 PMCID: PMC4272565 DOI: 10.1186/s12859-014-0383-1] [Citation(s) in RCA: 20] [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: 03/06/2014] [Accepted: 11/12/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. RESULTS On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments. CONCLUSIONS The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.
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Affiliation(s)
| | | | - Sylvain Pitre
- School of Computer Science, Carleton University, Ottawa, Canada.
| | | | - Ke Jin
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
| | - Charles A Phillips
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, USA.
| | - Hui Wang
- Department of Pediatrics, Gothenburg University, Gothenburg, Sweden. .,The Centre for Individualized Medication, Linköping University, Linköping, Sweden.
| | - Sadhna Phanse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
| | - Katayoun Omidi
- Department of Biology, Carleton University, Ottawa, Canada.
| | - Yuan Gui
- Department of Biology, Carleton University, Ottawa, Canada.
| | - Md Alamgir
- Department of Biology, Carleton University, Ottawa, Canada.
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Canada.
| | - Fredrik Barrenäs
- Department of Pediatrics, Gothenburg University, Gothenburg, Sweden. .,The Centre for Individualized Medication, Linköping University, Linköping, Sweden.
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada.
| | - Mikael Benson
- Department of Pediatrics, Gothenburg University, Gothenburg, Sweden. .,The Centre for Individualized Medication, Linköping University, Linköping, Sweden.
| | - Michael A Langston
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, USA.
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada.
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, Canada.
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Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, Emili A, Morris Q, Bader G, Babu M. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. ACTA ACUST UNITED AC 2014; 31:306-10. [PMID: 25316676 DOI: 10.1093/bioinformatics/btu671] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
MOTIVATION The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli. RESULTS We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron-sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses. CONTACT gary.bader@utoronto.ca; mohan.babu@uregina.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- James Vlasblom
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Khalid Zuberi
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Harold Rodriguez
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Roland Arnold
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Alla Gagarinova
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Viktor Deineko
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Ashwani Kumar
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Kamran Rizzolo
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Bahram Samanfar
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Luke Chang
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Ashkan Golshani
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Jack F Greenblatt
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Andrew Emili
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Quaid Morris
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Gary Bader
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, Univ
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Computer Science, University of Regina, Regina, Saskatchewan S4S0A2, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada, Department of Biology, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
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Baldock TE, Golshani A, Callaghan DP, Saunders MI, Mumby PJ. Impact of sea-level rise and coral mortality on the wave dynamics and wave forces on barrier reefs. Mar Pollut Bull 2014; 83:155-164. [PMID: 24768171 DOI: 10.1016/j.marpolbul.2014.03.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/14/2014] [Accepted: 03/29/2014] [Indexed: 06/03/2023]
Abstract
A one-dimensional wave model was used to investigate the reef top wave dynamics across a large suite of idealized reef-lagoon profiles, representing barrier coral reef systems under different sea-level rise (SLR) scenarios. The modeling shows that the impacts of SLR vary spatially and are strongly influenced by the bathymetry of the reef and coral type. A complex response occurs for the wave orbital velocity and forces on corals, such that the changes in the wave dynamics vary reef by reef. Different wave loading regimes on massive and branching corals also leads to contrasting impacts from SLR. For many reef bathymetries, wave orbital velocities increase with SLR and cyclonic wave forces are reduced for certain coral species. These changes may be beneficial to coral health and colony resilience and imply that predicting SLR impacts on coral reefs requires careful consideration of the reef bathymetry and the mix of coral species.
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Affiliation(s)
- T E Baldock
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia.
| | - A Golshani
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia.
| | - D P Callaghan
- School of Civil Engineering, University of Queensland, St Lucia, Qld 4072, Australia.
| | - M I Saunders
- Marine Spatial Ecology Lab, School of Biological Sciences, University of Queensland, St Lucia, Qld 4072, Australia; Global Change Institute, University of Queensland, St Lucia, Qld 4072, Australia.
| | - P J Mumby
- Marine Spatial Ecology Lab, School of Biological Sciences, University of Queensland, St Lucia, Qld 4072, Australia.
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Chepelev N, Chepelev L, Alamgir M, Golshani A. Large-Scale Protein-Protein Interaction Detection Approaches: Past, Present and Future. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2008.10817505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Kumar A, Stewart G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, Emili A. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet 2014; 10:e1004120. [PMID: 24586182 PMCID: PMC3930520 DOI: 10.1371/journal.pgen.1004120] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 12/03/2013] [Indexed: 02/02/2023] Open
Abstract
Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems. Genome-wide genetic interaction (GI) screens have been performed in yeast, but no analogous large-scale studies have yet been reported for bacteria. Here, we have used E. coli synthetic genetic array (eSGA) technology developed by our group to quantitatively map GIs to reveal epistatic dependencies and functional cross-talk among ∼600,000 digenic mutant combinations. By combining this epistasis information with functional modules derived by our group's earlier efforts from proteomic and genomic context (GC)-based methods, we identify several unexpected pathway-level dependencies, functional links between protein complexes, and biological roles of uncharacterized bacterial gene products. As part of the study, two of our pathway predictions from GI screens were validated experimentally, where we confirmed the role of these new components in iron-sulphur biogenesis and ribosome integrity. We also extrapolated the epistatic connectivity diagram of E. coli to 233 distantly related γ-proteobacterial species lacking GI information, and identified co-conserved genes and functional modules important for bacterial pathogenesis. Overall, this study describes the first genome-scale map of GIs in gram-negative bacterium, and through integrative analysis with previously derived protein-protein and GC-based interaction networks presents a number of novel insights into the architecture of bacterial pathways that could not have been discerned through either network alone.
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Affiliation(s)
- Mohan Babu
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
- * E-mail: (MB); (AE)
| | - Roland Arnold
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Cedoljub Bundalovic-Torma
- Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alla Gagarinova
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Keith S. Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ashwani Kumar
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Geordie Stewart
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Omar Wagih
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - James Vlasblom
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Sadhna Phanse
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Krunal Lad
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | | | - Christopher Graham
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Ke Jin
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Eric Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ashkan Golshani
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada
| | - Philip Kim
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | | | - Jack Greenblatt
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - John Parkinson
- Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (MB); (AE)
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