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Qiao H, Zhou X, Yi Y, Wei L, Xu X, Jin P, Su W, Weng Y, Yu D, He S, Fu M, Hou C, Pan X, Wang W, Zhang YY, Ming R, Ye C, Li QQ, Shen Y. Molecular mechanism of vivipary as revealed by the genomes of viviparous mangroves and non-viviparous relatives. Curr Biol 2024; 34:3707-3721.e7. [PMID: 39079534 DOI: 10.1016/j.cub.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/31/2024] [Accepted: 07/01/2024] [Indexed: 08/22/2024]
Abstract
Vivipary is a prominent feature of mangroves, allowing seeds to complete germination while attached to the mother plant, and equips propagules to endure and flourish in challenging coastal intertidal wetlands. However, vivipary-associated genetic mechanisms remain largely elusive. Genomes of two viviparous mangrove species and a non-viviparous inland relative were sequenced and assembled at the chromosome level. Comparative genomic analyses between viviparous and non-viviparous genomes revealed that DELAY OF GERMINATION 1 (DOG1) family genes (DFGs), the proteins from which are crucial for seed dormancy, germination, and reserve accumulation, are either lost or dysfunctional in the entire lineage of true viviparous mangroves but are present and functional in their inland, non-viviparous relatives. Transcriptome dynamics at key stages of vivipary further highlighted the roles of phytohormonal homeostasis, proteins stored in mature seeds, and proanthocyanidins in vivipary under conditions lacking DFGs. Population genomic analyses elucidate dynamics of syntenic regions surrounding the missing DFGs. Our findings demonstrated the genetic foundation of constitutive vivipary in Rhizophoraceae mangroves.
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Affiliation(s)
- Hongmei Qiao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiaoxuan Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Yuchong Yi
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Liufeng Wei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Pengfei Jin
- Novogene Co. Ltd, Building 301, Zone A10 Jiuxianqiao North Road, Chaoyang District, Beijing 100006, China
| | - Wenyue Su
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Yulin Weng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Dingtian Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Shanshan He
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Meiping Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Chengcheng Hou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiaobao Pan
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China.
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China; Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA.
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China.
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Xu S, Shao S, Feng X, Li S, Zhang L, Wu W, Liu M, Tracy ME, Zhong C, Guo Z, Wu CI, Shi S, He Z. Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May-Wigner Theory. Mol Biol Evol 2024; 41:msae059. [PMID: 38507653 PMCID: PMC10991078 DOI: 10.1093/molbev/msae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
Although gene loss is common in evolution, it remains unclear whether it is an adaptive process. In a survey of seven major mangrove clades that are woody plants in the intertidal zones of daily environmental perturbations, we noticed that they generally evolved reduced gene numbers. We then focused on the largest clade of Rhizophoreae and observed the continual gene set reduction in each of the eight species. A great majority of gene losses are concentrated on environmental interaction processes, presumably to cope with the constant fluctuations in the tidal environments. Genes of the general processes for woody plants are largely retained. In particular, fewer gene losses are found in physiological traits such as viviparous seeds, high salinity, and high tannin content. Given the broad and continual genome reductions, we propose the May-Wigner theory (MWT) of system stability as a possible mechanism. In MWT, the most effective solution for buffering continual perturbations is to reduce the size of the system (or to weaken the total genic interactions). Mangroves are unique as immovable inhabitants of the compound environments in the land-sea interface, where environmental gradients (such as salinity) fluctuate constantly, often drastically. Extending MWT to gene regulatory network (GRN), computer simulations and transcriptome analyses support the stabilizing effects of smaller gene sets in mangroves vis-à-vis inland plants. In summary, we show the adaptive significance of gene losses in mangrove plants, including the specific role of promoting phenotype innovation and a general role in stabilizing GRN in unstable environments as predicted by MWT.
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Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Sen Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Lingjie Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Miles E Tracy
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cairong Zhong
- Institute of Wetland Research, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
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Kasianchuk N, Rzymski P, Kaczmarek Ł. The biomedical potential of tardigrade proteins: A review. Biomed Pharmacother 2023; 158:114063. [PMID: 36495665 DOI: 10.1016/j.biopha.2022.114063] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Tardigrades are ubiquitous microinvertebrates exhibiting extreme tolerance to various environmental stressors like low and high temperatures, lack of water, or high radiation. Although exact pathways behind the tardigrade extremotolerance are yet to be elucidated, some molecules involved have been identified. Their evidenced properties may lead to novel opportunities in biomedical and pharmacological development. This review aims to present the general characteristics of tardigrade intrinsically disordered proteins (TDPs: Dsup, CAHS, SAHS, MAHS) and late embryogenesis-abundant proteins (LEA) and provide an updated overview of their features and relevance for potential use in biomedicine and pharmacology. The Dsup reveals a promising action in attenuating oxidative stress, DNA damage, and pyrimidine dimerization, as well as increasing radiotolerance in transfected human cells. Whether Dsup can perform these functions when delivered externally is yet to be understood by in vivo preclinical testing. In turn, CAHS and SAHS demonstrate properties that could benefit the preservation of pharmaceuticals (e.g., vaccines) and biomaterials (e.g., cells). Selected CAHS proteins can also serve as inspiration for designing novel anti-apoptotic agents. The LEA proteins also reveal promising properties to preserve desiccated biomaterials and can act as anti-osmotic agents. In summary, tardigrade molecules reveal several potential biomedical applications advocating further research and development. The challenge of extracting larger amounts of these molecules can be solved with genetic engineering and synthetic biology tools. With new species identified each year and ongoing studies on their extremotolerance, progress in the medical use of tardigrade proteins is expected shortly.
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Affiliation(s)
- Nadiia Kasianchuk
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland; Faculty of Pharmacy, Bogomolets Nationals Medical University, Kyiv, Ukraine.
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznan, Poland; Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), Poznań, Poland
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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Yu T, Sun Z, Cao X, Pang Q, Deng H. Recent trends in T7 phage application in diagnosis and treatment of various diseases. Int Immunopharmacol 2022; 110:109071. [DOI: 10.1016/j.intimp.2022.109071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/25/2022] [Accepted: 07/14/2022] [Indexed: 11/05/2022]
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Li L, Zhou X, Chen Z, Cao Y, Zhao G. The group 3 LEA protein of Artemia franciscana for cryopreservation. Cryobiology 2022; 106:1-12. [DOI: 10.1016/j.cryobiol.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 11/03/2022]
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Dirk LMA, Abdel CG, Ahmad I, Neta ICS, Pereira CC, Pereira FECB, Unêda-Trevisoli SH, Pinheiro DG, Downie AB. Late Embryogenesis Abundant Protein-Client Protein Interactions. PLANTS (BASEL, SWITZERLAND) 2020; 9:E814. [PMID: 32610443 PMCID: PMC7412488 DOI: 10.3390/plants9070814] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
The intrinsically disordered proteins belonging to the LATE EMBRYOGENESIS ABUNDANT protein (LEAP) family have been ascribed a protective function over an array of intracellular components. We focus on how LEAPs may protect a stress-susceptible proteome. These examples include instances of LEAPs providing a shield molecule function, possibly by instigating liquid-liquid phase separations. Some LEAPs bind directly to their client proteins, exerting a holdase-type chaperonin function. Finally, instances of LEAP-client protein interactions have been documented, where the LEAP modulates (interferes with) the function of the client protein, acting as a surreptitious rheostat of cellular homeostasis. From the examples identified to date, it is apparent that client protein modulation also serves to mitigate stress. While some LEAPs can physically bind and protect client proteins, some apparently bind to assist the degradation of the client proteins with which they associate. Documented instances of LEAP-client protein binding, even in the absence of stress, brings to the fore the necessity of identifying how the LEAPs are degraded post-stress to render them innocuous, a first step in understanding how the cell regulates their abundance.
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Affiliation(s)
- Lynnette M. A. Dirk
- Department of Horticulture, University of Kentucky Seed Biology Program, Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546-0312, USA;
| | - Caser Ghaafar Abdel
- Agriculture College, Al-Muthanna University, Samawah, Al-Muthanna 66001, Iraq;
| | - Imran Ahmad
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan;
| | | | - Cristiane Carvalho Pereira
- Departamento de Agricultura—Setor de Sementes, Federal University of Lavras, Lavras, Minas Gerais CEP: 37200-000, Brazil;
| | | | - Sandra Helena Unêda-Trevisoli
- Department of Vegetable Production, (UNESP) National University of São Paulo, Jaboticabal, São Paulo CEP: 14884-900, Brazil;
| | - Daniel Guariz Pinheiro
- Department of Biology, Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo CEP: 14040-901, Brazil;
| | - Allan Bruce Downie
- Department of Horticulture, University of Kentucky Seed Biology Program, Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546-0312, USA;
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Griffiths JS, Šola K, Kushwaha R, Lam P, Tateno M, Young R, Voiniciuc C, Dean G, Mansfield SD, DeBolt S, Haughn GW. Unidirectional movement of cellulose synthase complexes in Arabidopsis seed coat epidermal cells deposit cellulose involved in mucilage extrusion, adherence, and ray formation. PLANT PHYSIOLOGY 2015; 168:502-20. [PMID: 25926481 PMCID: PMC4453796 DOI: 10.1104/pp.15.00478] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 04/28/2015] [Indexed: 05/17/2023]
Abstract
Cellulose synthase5 (CESA5) synthesizes cellulose necessary for seed mucilage adherence to seed coat epidermal cells of Arabidopsis (Arabidopsis thaliana). The involvement of additional CESA proteins in this process and details concerning the manner in which cellulose is deposited in the mucilage pocket are unknown. Here, we show that both CESA3 and CESA10 are highly expressed in this cell type at the time of mucilage synthesis and localize to the plasma membrane adjacent to the mucilage pocket. The isoxaben resistant1-1 and isoxaben resistant1-2 mutants affecting CESA3 show defects consistent with altered mucilage cellulose biosynthesis. CESA3 can interact with CESA5 in vitro, and green fluorescent protein-tagged CESA5, CESA3, and CESA10 proteins move in a linear, unidirectional fashion around the cytoplasmic column of the cell, parallel with the surface of the seed, in a pattern similar to that of cortical microtubules. Consistent with this movement, cytological evidence suggests that the mucilage is coiled around the columella and unwinds during mucilage extrusion to form a linear ray. Mutations in CESA5 and CESA3 affect the speed of mucilage extrusion and mucilage adherence. These findings imply that cellulose fibrils are synthesized in an ordered helical array around the columella, providing a distinct structure to the mucilage that is important for both mucilage extrusion and adherence.
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Affiliation(s)
- Jonathan S Griffiths
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Krešimir Šola
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Rekha Kushwaha
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Patricia Lam
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Mizuki Tateno
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Robin Young
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Cătălin Voiniciuc
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Gillian Dean
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Shawn D Mansfield
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - Seth DeBolt
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
| | - George W Haughn
- Department of Botany (J.S.G., K.Š., P.L., R.Y., C.V., G.D., G.W.H.) and Department of Wood Science (S.D.M.), University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Horticulture Plant Physiology/Biochemistry/Molecular Biology Program (R.K., M.T., S.D.) and University of Kentucky Seed Biology Group (R.K., M.T., S.D.), University of Kentucky, Lexington, Kentucky 40546
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Kushwaha R, Schäfermeyer KR, Downie AB. A protocol for phage display and affinity selection using recombinant protein baits. J Vis Exp 2014:e50685. [PMID: 24637694 DOI: 10.3791/50685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Using recombinant phage as a scaffold to present various protein portions encoded by a directionally cloned cDNA library to immobilized bait molecules is an efficient means to discover interactions. The technique has largely been used to discover protein-protein interactions but the bait molecule to be challenged need not be restricted to proteins. The protocol presented here has been optimized to allow a modest number of baits to be screened in replicates to maximize the identification of independent clones presenting the same protein. This permits greater confidence that interacting proteins identified are legitimate interactors of the bait molecule. Monitoring the phage titer after each affinity selection round provides information on how the affinity selection is progressing as well as on the efficacy of negative controls. One means of titering the phage, and how and what to prepare in advance to allow this process to progress as efficiently as possible, is presented. Attributes of amplicons retrieved following isolation of independent plaque are highlighted that can be used to ascertain how well the affinity selection has progressed. Trouble shooting techniques to minimize false positives or to bypass persistently recovered phage are explained. Means of reducing viral contamination flare up are discussed.
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Cuevas-Velazquez CL, Rendón-Luna DF, Covarrubias AA. Dissecting the cryoprotection mechanisms for dehydrins. FRONTIERS IN PLANT SCIENCE 2014; 5:583. [PMID: 25400649 PMCID: PMC4212605 DOI: 10.3389/fpls.2014.00583] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/09/2014] [Indexed: 05/10/2023]
Abstract
One of the common responses of plants to water deficit is the accumulation of the so-called late embryogenesis abundant (LEA) proteins. In vitro studies suggest that these proteins can protect other macromolecules and cellular structural components from the impairments caused by water limitation. Their binding to phospholipids, nucleic acids and/or to divalent cations has suggested multi-functionality. Genetic analyses indicate that these proteins are required for an optimal adjustment of plants to this insult. This diverse information has conducted to propose different models for LEA proteins action mechanisms. Many of these properties are shared by group 2 LEA proteins or dehydrins (DHNs), one of the LEA protein families for which large amount of data is available. This manuscript focuses on the different mechanisms proposed for this LEA protein group by analyzing published data derived from in vitro cryoprotection assays. We compared the molar ratio of protectant:enzyme needed to preserve 50% of the initial activity per enzyme monomer to assess different mechanisms of action. Our results add evidence for protein-protein interaction as a protection mechanism but also indicate that some DHNs might protect by different means. The strength and weakness of the proposed protection mechanisms are discussed.
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Affiliation(s)
| | | | - Alejandra A. Covarrubias
- *Correspondence: Alejandra A. Covarrubias, Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210 Cuernavaca, Morelos, México e-mail:
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Kushwaha R, Downie AB, Payne CM. Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:470390. [PMID: 23956788 PMCID: PMC3727180 DOI: 10.1155/2013/470390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/02/2013] [Indexed: 11/17/2022]
Abstract
A group of intrinsically disordered, hydrophilic proteins-Late Embryogenesis Abundant (LEA) proteins-has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.
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Affiliation(s)
- Rekha Kushwaha
- Agricultural Science Center, Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA
- Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
| | - A. Bruce Downie
- Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
- Plant Science Building, Department of Horticulture, University of Kentucky, Lexington, KY 40546, USA
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
- Center for Computational Sciences, University of Kentucky, Lexington, KY 40506, USA
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Nayak NR, Putnam AA, Addepalli B, Lowenson JD, Chen T, Jankowsky E, Perry SE, Dinkins RD, Limbach PA, Clarke SG, Downie AB. An Arabidopsis ATP-dependent, DEAD-box RNA helicase loses activity upon IsoAsp formation but is restored by PROTEIN ISOASPARTYL METHYLTRANSFERASE. THE PLANT CELL 2013; 25:2573-86. [PMID: 23903319 PMCID: PMC3753384 DOI: 10.1105/tpc.113.113456] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Orthodox seeds are capable of withstanding severe dehydration. However, in the dehydrated state, Asn and Asp residues in proteins can convert to succinimide residues that can further react to predominantly form isomerized isoAsp residues upon rehydration (imbibition). IsoAsp residues can impair protein function and can render seeds nonviable, but PROTEIN ISOASPARTYL METHYLTRANSFERASE (PIMT) can initiate isoAsp conversion to Asp residues. The proteins necessary for translation upon imbibition in orthodox seeds may be particularly important to maintain in an active state. One such protein is the large, multidomain protein, Arabidopsis thaliana PLANT RNA HELICASE75 (PRH75), a DEAD-box helicase known to be susceptible to isoAsp residue accumulation. However, the consequences of such isomerization on PRH75 catalysis and for the plant are unknown. Here, it is demonstrated that PRH75 is necessary for successful seed development. It acquires isoAsp rapidly during heat stress, which eliminates RNA unwinding (but not rewinding) competence. The repair by PIMT is able to restore PRH75's complex biochemical activity provided isoAsp formation has not led to subsequent, destabilizing conformational alterations. For PRH75, an important enzymatic activity associated with translation would be eliminated unless rapidly repaired by PIMT prior to additional, deleterious conformational changes that would compromise seed vitality and germination.
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Affiliation(s)
- Nihar R. Nayak
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40546-0312
- Seed Biology Group, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Andrea A. Putnam
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | | | - Jonathan D. Lowenson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
| | - Tingsu Chen
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40546-0312
- Seed Biology Group, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106
| | - Sharyn E. Perry
- Seed Biology Group, University of Kentucky, Lexington, Kentucky 40546-0312
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Randy D. Dinkins
- U.S. Department of Agriculture–Agricultural Research Service Forage Animal Production Research Unit, N220C Agriculture Science Center North, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Patrick A. Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
| | - A. Bruce Downie
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40546-0312
- Seed Biology Group, University of Kentucky, Lexington, Kentucky 40546-0312
- Address correspondence to
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12
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Kushwaha R, Payne CM, Downie AB. Uses of phage display in agriculture: a review of food-related protein-protein interactions discovered by biopanning over diverse baits. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:653759. [PMID: 23710253 PMCID: PMC3655605 DOI: 10.1155/2013/653759] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/02/2013] [Indexed: 12/24/2022]
Abstract
This review highlights discoveries made using phage display that impact the use of agricultural products. The contribution phage display made to our fundamental understanding of how various protective molecules serve to safeguard plants and seeds from herbivores and microbes is discussed. The utility of phage display for directed evolution of enzymes with enhanced capacities to degrade the complex polymers of the cell wall into molecules useful for biofuel production is surveyed. Food allergies are often directed against components of seeds; this review emphasizes how phage display has been employed to determine the seed component(s) contributing most to the allergenic reaction and how it has played a central role in novel approaches to mitigate patient response. Finally, an overview of the use of phage display in identifying the mature seed proteome protection and repair mechanisms is provided. The identification of specific classes of proteins preferentially bound by such protection and repair proteins leads to hypotheses concerning the importance of safeguarding the translational apparatus from damage during seed quiescence and environmental perturbations during germination. These examples, it is hoped, will spur the use of phage display in future plant science examining protein-ligand interactions.
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Affiliation(s)
- Rekha Kushwaha
- Department of Horticulture, Agricultural Science Center North, University of Kentucky, Room 308J, Lexington, KY 40546, USA
- Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Room 159, F. Paul Anderson Tower, Lexington, KY 40546, USA
- Center for Computational Sciences, University of Kentucky, Lexington, KY 40506, USA
| | - A. Bruce Downie
- Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
- Department of Horticulture, University of Kentucky, Room 401A, Plant Science Building, Lexington, KY 40546, USA
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