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Unêda-Trevisoli SH, Dirk LMA, Carlos Bezerra Pereira FE, Chakrabarti M, Hao G, Campbell JM, Bassetti Nayakwadi SD, Morrison A, Joshi S, Perry SE, Sharma V, Mensah C, Willard B, de Lorenzo L, Afroza B, Hunt AG, Kawashima T, Vaillancourt L, Pinheiro DG, Downie AB. Dehydrin Client Proteins Identified Using Phage Display Affinity Selected Libraries Processed With Paired-End Phage Sequencing. Mol Cell Proteomics 2024; 23:100867. [PMID: 39442694 PMCID: PMC11612773 DOI: 10.1016/j.mcpro.2024.100867] [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: 02/07/2024] [Revised: 09/26/2024] [Accepted: 10/17/2024] [Indexed: 10/25/2024] Open
Abstract
The late embryogenesis abundant proteins (LEAPs) are a class of noncatalytic, intrinsically disordered proteins with a malleable structure. Some LEAPs exhibit a protein and/or membrane binding capacity and LEAP binding to various targets has been positively correlated with abiotic stress tolerance. Regarding the LEAPs' presumptive role in protein protection, identifying client proteins (CtPs) to which LEAPs bind is one practicable means of revealing the mechanism by which they exert their function. To this end, we used phage display affinity selection to screen libraries derived from Arabidopsis thaliana seed mRNA with recombinant orthologous LEAPs from Arabidopsis and soybean (Glycine max). Subsequent high-throughput sequencing of DNA from affinity-purified phage was performed to characterize the entire subpopulation of phage retained by each LEAP ortholog. This entailed cataloging in-frame fusions, elimination of false positives, and aligning the hits on the CtP scaffold to reveal domains of respective CtPs that bound to orthologous LEAPs. This approach (paired-end phage sequencing) revealed a subpopulation of the proteome constituting the CtP repertoire in common between the two dehydrin orthologs (LEA14 and GmPm12) compared to bovine serum albumin (unrelated binding control). The veracity of LEAP:CtP binding for one of the CtPs (LEA14 and GmPM12 self-association) was independently assessed using temperature-related intensity change analysis. Moreover, LEAP:CtP interactions for four other CtPs were confirmed in planta using bimolecular fluorescence complementation assays. The results provide insights into the involvement of the dehydrin Y-segments and K-domains in protein binding.
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Affiliation(s)
- Sandra Helena Unêda-Trevisoli
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; Department of Crop Production, São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, São Paulo, Brazil
| | - Lynnette M A Dirk
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA
| | - Francisco Elder Carlos Bezerra Pereira
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; Department of Crop Production, São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, São Paulo, Brazil; Pastotech Pasture Seeds, Campo Grande, Mato Grosso do Sul, Brazil
| | - Manohar Chakrabarti
- School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Guijie Hao
- Department of Plant and Soil Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Catalent Pharma Solution, Baltimore, Maryland, USA
| | - James M Campbell
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; University of Kentucky Agricultural and Medical Biotechnology Program, Lexington, Kentucky, USA; Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Sai Deepshikha Bassetti Nayakwadi
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; University of Kentucky Agricultural and Medical Biotechnology Program, Lexington, Kentucky, USA
| | - Ashley Morrison
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; University of Kentucky Agricultural and Medical Biotechnology Program, Lexington, Kentucky, USA
| | - Sanjay Joshi
- Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; Department of Plant and Soil Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Kentucky Tobacco Research and Development Center, Lexington, Kentucky, USA
| | - Sharyn E Perry
- Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; Department of Plant and Soil Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Vijyesh Sharma
- Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; Department of Plant and Soil Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Caleb Mensah
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; Carter G. Woodson Academy, Fayette County Public Schools (FCPS), Lexington, Kentucky, USA
| | - Barbara Willard
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA
| | - Laura de Lorenzo
- Department of Plant and Soil Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Department of Biochemistry and Molecular Biology, University of New Mexico, School of Medicine, Albuquerque, New Mexico, USA
| | - Baseerat Afroza
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; Division of Vegetable Science, SKUAST- Kashmir, Srinagar, Kashmir, India
| | - Arthur G Hunt
- Department of Plant and Soil Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Tomokazu Kawashima
- Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA; Department of Plant and Soil Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Lisa Vaillancourt
- Department of Plant Pathology, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Daniel Guariz Pinheiro
- Department of Crop Production, São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, São Paulo, Brazil; Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, São Paulo, Brazil
| | - A Bruce Downie
- Department of Horticulture, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA; Seed Biology Program, University of Kentucky, Lexington, Kentucky, USA.
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Zhang H, Wu J, Fu D, Zhang M, Wang L, Gong M. Prokaryotic expression, purification, and the in vitro and in vivo protection study of dehydrin WDHN2 from Triticum aestivum. PROTOPLASMA 2024; 261:771-781. [PMID: 38342804 DOI: 10.1007/s00709-024-01933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
Dehydrins proteins accumulate and play important protective roles in most plants during abiotic stresses. The objective of this study was to characterize a YSK2-type dehydrin gene, WDHN2, isolated from Triticum aestivum previously. In this work, wheat dehydrin WDHN2 was expressed in Escherichia coli and purified by immobilized metal affinity chromatography, which exhibited as a single band by sodium dodecyl sulfonate polyacrylamide gel electrophoresis and western blotting. We show that WDHN2 is capable of alleviating lactate dehydrogenase inactivation from heat and desiccation in vitro enzyme activity protection assay. In vivo assay of Escherichia coli viability demonstrates the enhancement of cell survival by the overexpression of WDHN2. The protein aggregation prevention assay explores that WDHN2 has a broad protective effect on the cellular proteome. The results show that WDHN2 is mainly accumulated in the nucleus and cytosol, suggesting that this dehydrin may exert its function in both cellular compartments. Our data suggest that WDHN2 acts as a chaperone molecular in vivo.
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Affiliation(s)
- Hongmei Zhang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
- Key Laboratory of Microbial Resources Exploitation and Utilization, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Jiafa Wu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
- Key Laboratory of Microbial Resources Exploitation and Utilization, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Dandan Fu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Min Zhang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Lunji Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Minggui Gong
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, Henan, China.
- Key Laboratory of Microbial Resources Exploitation and Utilization, Henan University of Science and Technology, Luoyang, 471023, Henan, China.
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Hernández‐Sánchez I, Rindfleisch T, Alpers J, Dulle M, Garvey CJ, Knox‐Brown P, Miettinen MS, Nagy G, Pusterla JM, Rekas A, Shou K, Stadler AM, Walther D, Wolff M, Zuther E, Thalhammer A. Functional in vitro diversity of an intrinsically disordered plant protein during freeze-thawing is encoded by its structural plasticity. Protein Sci 2024; 33:e4989. [PMID: 38659213 PMCID: PMC11043620 DOI: 10.1002/pro.4989] [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: 10/25/2023] [Revised: 03/09/2024] [Accepted: 03/31/2024] [Indexed: 04/26/2024]
Abstract
Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration-sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra- and inter-monomeric helix-helix interactions, demonstrate how oligomerization is driven by an α-helical molecular recognition feature (α-MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right-handed coiled-coils might be a recurring theme for homo- and hetero-oligomerization of LEA proteins.
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Affiliation(s)
- Itzell Hernández‐Sánchez
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
Center for Desert Agriculture, Biological and Environmental Science and Engineering DivisionKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Tobias Rindfleisch
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
- Department of ChemistryUniversity of BergenBergenNorway
- Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway
| | - Jessica Alpers
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Martin Dulle
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
| | | | - Patrick Knox‐Brown
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
- Present address:
Department of Discovery Pharmaceutical SciencesMerck & Co., Inc.South San FranciscoCaliforniaUSA
| | - Markus S. Miettinen
- Department of ChemistryUniversity of BergenBergenNorway
- Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway
- Department of Theory and Bio‐SystemsMax Planck Institute of Colloids and InterfacesPotsdamGermany
| | - Gergely Nagy
- Neutron Scattering DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Julio M. Pusterla
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
| | - Agata Rekas
- Australian Nuclear Science and Technology Organization (ANSTO)KirraweeNew South WalesAustralia
| | - Keyun Shou
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
- Australian Nuclear Science and Technology Organization (ANSTO)KirraweeNew South WalesAustralia
- Institute of Physical Chemistry, RWTH Aachen UniversityAachenGermany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS‐1) and Institute of Biological Information Processing (IBI‐8: Neutron Scattering and Biological Matter)Forschungszentrum Jülich GmbHJülichGermany
- Institute of Physical Chemistry, RWTH Aachen UniversityAachenGermany
| | - Dirk Walther
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Martin Wolff
- Physical BiochemistryUniversity of PotsdamPotsdamGermany
| | - Ellen Zuther
- Max‐Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Present address:
Center of Artificial Intelligence in Public Health Research (ZKI‐PH)Robert Koch InstituteBerlinGermany
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Ghanmi S, Smith MA, Zaidi I, Drira M, Graether SP, Hanin M. Isolation and molecular characterization of an FSK 2-type dehydrin from Atriplex halimus. PHYTOCHEMISTRY 2023:113783. [PMID: 37406790 DOI: 10.1016/j.phytochem.2023.113783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
Dehydrins form the group II LEA protein family and are known to play multiple roles in plant stress tolerance and enzyme protection. They harbor a variable number of conserved lysine rich motifs (K-segments) and may also contain three additional conserved motifs (Y-, F- and S-segments). In this work, we report the isolation and characterization of an FSK2-type dehydrin from the halophytic species Atriplex halimus, which we designate as AhDHN1. In silico analysis of the protein sequence revealed that AhDHN1 contains large number of hydrophilic residues, and is predicted to be intrinsically disordered. In addition, it has an FSK2 architecture with one F-segment, one S-segment, and two K-segments. The expression analysis showed that the AhDHN1 transcript is induced by salt and water stress treatments in the leaves of Atriplex seedlings. Moreover, circular dichroism spectrum performed on recombinant AhDHN1 showed that the dehydrin lacks any secondary structure, confirming its intrinsic disorder nature. However, there is a gain of α-helicity in the presence of membrane-like SDS micelles. In vitro assays revealed that AhDHN1 is able to effectively protect enzymatic activity of the lactate dehydrogenase against cold, heat and dehydration stresses. Our findings strongly suggest that AhDHN1 can be involved in the adaptation mechanisms of halophytes to adverse environments.
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Affiliation(s)
- Siwar Ghanmi
- Plant Physiology & Functional Genomics Research Unit, Institute of Biotechnology, University of Sfax, 3038 Sfax, Tunisia
| | - Margaret A Smith
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Ikram Zaidi
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, BP "1177", University of Sfax, 3018 Sfax, Tunisia
| | - Marwa Drira
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, BP "1177", University of Sfax, 3018 Sfax, Tunisia
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Moez Hanin
- Plant Physiology & Functional Genomics Research Unit, Institute of Biotechnology, University of Sfax, 3038 Sfax, Tunisia.
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