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Wang L, Tonsager AJ, Zheng W, Wang Y, Stessman D, Fang W, Stenback KE, Campbell A, Tanvir R, Zhang J, Cothron S, Wan D, Meng Y, Spalding MH, Nikolau BJ, Li L. Single-cell genetic models to evaluate orphan gene function: The case of QQS regulating carbon and nitrogen allocation. Front Plant Sci 2023; 14:1126139. [PMID: 37051080 PMCID: PMC10084940 DOI: 10.3389/fpls.2023.1126139] [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: 12/17/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
We demonstrate two synthetic single-cell systems that can be used to better understand how the acquisition of an orphan gene can affect complex phenotypes. The Arabidopsis orphan gene, Qua-Quine Starch (QQS) has been identified as a regulator of carbon (C) and nitrogen (N) partitioning across multiple plant species. QQS modulates this important biotechnological trait by replacing NF-YB (Nuclear Factor Y, subunit B) in its interaction with NF-YC. In this study, we expand on these prior findings by developing Chlamydomonas reinhardtii and Saccharomyces cerevisiae strains, to refactor the functional interactions between QQS and NF-Y subunits to affect modulations in C and N allocation. Expression of QQS in C. reinhardtii modulates C (i.e., starch) and N (i.e., protein) allocation by affecting interactions between NF-YC and NF-YB subunits. Studies in S. cerevisiae revealed similar functional interactions between QQS and the NF-YC homolog (HAP5), modulating C (i.e., glycogen) and N (i.e., protein) allocation. However, in S. cerevisiae both the NF-YA (HAP2) and NF-YB (HAP3) homologs appear to have redundant functions to enable QQS and HAP5 to affect C and N allocation. The genetically tractable systems that developed herein exhibit the plasticity to modulate highly complex phenotypes.
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Affiliation(s)
- Lei Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Andrew J. Tonsager
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Wenguang Zheng
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Yingjun Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Dan Stessman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Wei Fang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Kenna E. Stenback
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Alexis Campbell
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Rezwan Tanvir
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Jinjiang Zhang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
- Mississippi School for Mathematics and Science, Columbus, MS, United States
| | - Samuel Cothron
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Dongli Wan
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yan Meng
- Department of Agriculture, Alcorn State University, Lorman, MS, United States
| | - Martin H. Spalding
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
- Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
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Xu Y, Cheng HF, Kong CH, Meiners SJ. Intra-specific kin recognition contributes to inter-specific allelopathy: A case study of allelopathic rice interference with paddy weeds. Plant Cell Environ 2021; 44:3479-3491. [PMID: 33993534 DOI: 10.1111/pce.14083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/10/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Species interactions and mechanisms affect plant coexistence and community assembly. Despite increasing knowledge of kin recognition and allelopathy in regulating inter-specific and intra-specific interactions among plants, little is known about whether kin recognition mediates allelopathic interference. We used allelopathic rice cultivars with the ability for kin recognition grown in kin versus non-kin mixtures to determine their impacts on paddy weeds in field trials and a series of controlled experiments. We experimentally tested potential mechanisms of the interaction via altered root behaviour, allelochemical production and resource partitioning in the dominant weed competitor, as well as soil microbial communities. We consistently found that the establishment and growth of paddy weeds were more inhibited by kin mixtures compared to non-kin mixtures. The effect was driven by kin recognition that induced changes in root placement, altered weed carbon and nitrogen partitioning, but was associated with similar soil microbial communities. Importantly, genetic relatedness enhanced the production of intrusive roots towards weeds and reduced the production of rice allelochemicals. These findings suggest that relatedness allows allelopathic plants to discriminate their neighbouring collaborators (kin) or competitors and adjust their growth, competitiveness and chemical defense accordingly.
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Affiliation(s)
- You Xu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Hui-Fang Cheng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Chui-Hua Kong
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Scott J Meiners
- Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois, USA
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Qi M, Zheng W, Zhao X, Hohenstein JD, Kandel Y, O'Conner S, Wang Y, Du C, Nettleton D, MacIntosh GC, Tylka GL, Wurtele ES, Whitham SA, Li L. QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. Plant Biotechnol J 2019; 17:252-263. [PMID: 29878511 PMCID: PMC6330549 DOI: 10.1111/pbi.12961] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/04/2018] [Indexed: 05/19/2023]
Abstract
Enhancing the nutritional quality and disease resistance of crops without sacrificing productivity is a key issue for developing varieties that are valuable to farmers and for simultaneously improving food security and sustainability. Expression of the Arabidopsis thaliana species-specific AtQQS (Qua-Quine Starch) orphan gene or its interactor, NF-YC4 (Nuclear Factor Y, subunit C4), has been shown to increase levels of leaf/seed protein without affecting the growth and yield of agronomic species. Here, we demonstrate that overexpression of AtQQS and NF-YC4 in Arabidopsis and soybean enhances resistance/reduces susceptibility to viruses, bacteria, fungi, aphids and soybean cyst nematodes. A series of Arabidopsis mutants in starch metabolism were used to explore the relationships between QQS expression, carbon and nitrogen partitioning, and defense. The enhanced basal defenses mediated by QQS were independent of changes in protein/carbohydrate composition of the plants. We demonstrate that either AtQQS or NF-YC4 overexpression in Arabidopsis and in soybean reduces susceptibility of these plants to pathogens/pests. Transgenic soybean lines overexpressing NF-YC4 produce seeds with increased protein while maintaining healthy growth. Pull-down studies reveal that QQS interacts with human NF-YC, as well as with Arabidopsis NF-YC4, and indicate two QQS binding sites near the NF-YC-histone-binding domain. A new model for QQS interaction with NF-YC is speculated. Our findings illustrate the potential of QQS and NF-YC4 to increase protein and improve defensive traits in crops, overcoming the normal growth-defense trade-offs.
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Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Wenguang Zheng
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
| | - Xuefeng Zhao
- Laurence H. Baker Center for Bioinformatics and Biological StatisticsIowa State UniversityAmesIAUSA
| | - Jessica D. Hohenstein
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIAUSA
| | - Yuba Kandel
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Seth O'Conner
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Department of Biological SciencesMississippi State UniversityStarkvilleMSUSA
| | - Yifan Wang
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Chuanlong Du
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Dan Nettleton
- Department of StatisticsIowa State UniversityAmesIAUSA
| | - Gustavo C. MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIAUSA
| | - Gregory L. Tylka
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Center for Metabolic BiologyIowa State UniversityAmesIAUSA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Ling Li
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIAUSA
- Department of Biological SciencesMississippi State UniversityStarkvilleMSUSA
- Center for Metabolic BiologyIowa State UniversityAmesIAUSA
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