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Perdomo JA, Scales JC, Lee W, Kanyuka K, Carmo‐Silva E. Down-regulation of wheat Rubisco activase isoforms expression by virus-induced gene silencing. Plant Direct 2024; 8:e583. [PMID: 38628621 PMCID: PMC11018489 DOI: 10.1002/pld3.583] [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] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024]
Abstract
Rubisco activase (Rca) is an essential photosynthetic enzyme that removes inhibitors from the catalytic sites of the carboxylating enzyme Rubisco. In wheat, Rca is composed of one longer 46 kDa α-isoform and two shorter 42 kDa β-isoforms encoded by the genes TaRca1 and TaRca2. TaRca1 produces a single transcript from which a short 1β-isoform is expressed, whereas two alternative transcripts are generated from TaRca2 directing expression of either a long 2α-isoform or a short 2β-isoform. The 2β isoform is similar but not identical to 1β. Here, virus-induced gene silencing (VIGS) was used to silence the different TaRca transcripts. Abundance of the transcripts and the respective protein isoforms was then evaluated in the VIGS-treated and control plants. Remarkably, treatment with the construct specifically targeting TaRca1 efficiently decreased expression not only of TaRca1 but also of the two alternative TaRca2 transcripts. Similarly, specific targeting of the TaRca2 transcript encoding a long isoform TaRca2α resulted in silencing of both TaRca2 alternative transcripts. The corresponding protein isoforms decreased in abundance. These findings indicate concomitant down-regulation of TaRca1 and TaRca2 at both transcript and protein levels and may impact the feasibility of altering the relative abundance of Rca isoforms in wheat.
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Affiliation(s)
- Juan Alejandro Perdomo
- Lancaster Environment CentreLancaster UniversityLancasterUK
- School of Pharmacy and Biomedical SciencesUniversity of Central LancashirePrestonUK
| | | | - Wing‐Sham Lee
- Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
| | - Kostya Kanyuka
- Biointeractions and Crop ProtectionRothamsted ResearchHarpendenUK
- NIABCambridgeUK
| | - Elizabete Carmo‐Silva
- Lancaster Environment CentreLancaster UniversityLancasterUK
- Plant Biology and Crop SciencesRothamsted ResearchHarpendenUK
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Lee S, Zhang C, Liu Z, Klevstig M, Mukhopadhyay B, Bergentall M, Cinar R, Ståhlman M, Sikanic N, Park JK, Deshmukh S, Harzandi AM, Kuijpers T, Grøtli M, Elsässer SJ, Piening BD, Snyder M, Smith U, Nielsen J, Bäckhed F, Kunos G, Uhlen M, Boren J, Mardinoglu A. Network analyses identify liver-specific targets for treating liver diseases. Mol Syst Biol 2017; 13:938. [PMID: 28827398 PMCID: PMC5572395 DOI: 10.15252/msb.20177703] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [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: 04/21/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 01/02/2023] Open
Abstract
We performed integrative network analyses to identify targets that can be used for effectively treating liver diseases with minimal side effects. We first generated co-expression networks (CNs) for 46 human tissues and liver cancer to explore the functional relationships between genes and examined the overlap between functional and physical interactions. Since increased de novo lipogenesis is a characteristic of nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC), we investigated the liver-specific genes co-expressed with fatty acid synthase (FASN). CN analyses predicted that inhibition of these liver-specific genes decreases FASN expression. Experiments in human cancer cell lines, mouse liver samples, and primary human hepatocytes validated our predictions by demonstrating functional relationships between these liver genes, and showing that their inhibition decreases cell growth and liver fat content. In conclusion, we identified liver-specific genes linked to NAFLD pathogenesis, such as pyruvate kinase liver and red blood cell (PKLR), or to HCC pathogenesis, such as PKLR, patatin-like phospholipase domain containing 3 (PNPLA3), and proprotein convertase subtilisin/kexin type 9 (PCSK9), all of which are potential targets for drug development.
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Affiliation(s)
- Sunjae Lee
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Zhengtao Liu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Martina Klevstig
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bani Mukhopadhyay
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Mattias Bergentall
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Resat Cinar
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Marcus Ståhlman
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Natasha Sikanic
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Joshua K Park
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Sumit Deshmukh
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Azadeh M Harzandi
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Tim Kuijpers
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Simon J Elsässer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Brian D Piening
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ulf Smith
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jens Nielsen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - George Kunos
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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