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Panzade KP, Vishwakarma H, Kharate PS, Azameti MK. Genome-wide analysis and expression profile of TCP gene family under drought and salinity stress condition in cowpea ( Vigna unguiculata (L.) Walp.). 3 Biotech 2024; 14:138. [PMID: 38682097 PMCID: PMC11052985 DOI: 10.1007/s13205-024-03976-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/13/2024] [Indexed: 05/01/2024] Open
Abstract
TCP transcription factors are known to regulate abiotic stress condition, but their role in V. unguiculata remains unexplored. So, in silico analysis and expression profile of the TCP gene family were performed in V. unguiculata to understand its role in response to heat and drought stress. A genome-wide search detected 28 TCPs (designated as VuTCPs) that were grouped into three subclasses by phylogenetic analysis. Gene structure, synteny, and phylogeny analyses of VuTCPs have shown a typical evolutionary path. One tandem and eight segmental duplication events were identified. Furthermore, identified duplicated, and orthologous VuTCP genes were under strong purifying selection pressure. A total of 15 SSRs were identified in the 12 VuTCPs, while 10 VuTCP genes were regulated by different miRNAs having a major role in abiotic stress tolerance. Analysed physicochemical properties, cis-acting elements, and gene ontology suggested that VuTCPs play various roles, including salinity and drought stress tolerance. qRT-PCR analysis showed that 11 and 15 VuTCPs were upregulated under drought and salinity stress conditions, respectively. Our findings provide comprehensive insights into the genomic characterization of the VuTCPs gene family in V. unguiculata, offering a foundation for understanding their structure, evolution, and role in abiotic stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03976-x.
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Affiliation(s)
- Kishor Prabhakar Panzade
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Chh. Sambhaji Nagar (Aurangabad), Maharashtra, 431002 India
| | - Harinder Vishwakarma
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012 India
| | - Pawankumar S. Kharate
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Chh. Sambhaji Nagar (Aurangabad), Maharashtra, 431002 India
| | - Mawuli K. Azameti
- Department of Applied Biology, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Upper East Region Ghana
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Hatzianestis IH, Mountourakis F, Stavridou S, Moschou PN. Plant condensates: no longer membrane-less? TRENDS IN PLANT SCIENCE 2023; 28:1101-1112. [PMID: 37183142 DOI: 10.1016/j.tplants.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023]
Abstract
Cellular condensation is a reinvigorated area of study in biology, with scientific discussions focusing mainly on the forces that drive condensate formation, properties, and functions. Usually, condensates are called 'membrane-less' to highlight the absence of a surrounding membrane and the lack of associated contacts. In this opinion article we take a different direction, focusing on condensates that may be interfacing with membranes and their possible functions. We also highlight changes in condensate material properties brought about by condensate-membrane interactions, proposing how condensates-membrane interfaces could potentially affect interorganellar communication, development, and growth, but also adaptation in an evolutionary context. We would thus like to stimulate research in this area, which is much less understood in plants compared with the animal field.
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Affiliation(s)
- Ioannis H Hatzianestis
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | - Fanourios Mountourakis
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
| | | | - Panagiotis N Moschou
- Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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Li Y, Qin J, Chen M, Sun N, Tan F, Zhang H, Zou Y, Uversky VN, Liu Y. The Moonlighting Function of Soybean Disordered Methyl-CpG-Binding Domain 10c Protein. Int J Mol Sci 2023; 24:ijms24108677. [PMID: 37240035 DOI: 10.3390/ijms24108677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are multifunctional due to their ability to adopt different structures depending on the local conditions. The intrinsically disordered regions of methyl-CpG-binding domain (MBD) proteins play important roles in regulating growth and development by interpreting DNA methylation patterns. However, whether MBDs have a stress-protective function is far from clear. In this paper, soybean GmMBD10c protein, which contains an MBD and is conserved in Leguminosae, was predicted to be located in the nucleus. It was found to be partially disordered by bioinformatic prediction, circular dichroism and a nuclear magnetic resonance spectral analysis. The enzyme activity assay and SDS-PAGE results showed that GmMBD10c can protect lactate dehydrogenase and a broad range of other proteins from misfolding and aggregation induced by the freeze-thaw process and heat stress, respectively. Furthermore, overexpression of GmMBD10c enhanced the salt tolerance of Escherichia coli. These data validate that GmMBD10c is a moonlighting protein with multiple functions.
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Affiliation(s)
- Yanling Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jiawei Qin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Menglu Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Nan Sun
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Fangmei Tan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yongdong Zou
- The Instrumental Analysis Center of Shenzhen University, Shenzhen University, Shenzhen 518060, China
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Yun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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Hernández-Sánchez IE, Maruri-López I, Martinez-Martinez C, Janis B, Jiménez-Bremont JF, Covarrubias AA, Menze MA, Graether SP, Thalhammer A. LEAfing through literature: late embryogenesis abundant proteins coming of age-achievements and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6525-6546. [PMID: 35793147 DOI: 10.1093/jxb/erac293] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
To deal with increasingly severe periods of dehydration related to global climate change, it becomes increasingly important to understand the complex strategies many organisms have developed to cope with dehydration and desiccation. While it is undisputed that late embryogenesis abundant (LEA) proteins play a key role in the tolerance of plants and many anhydrobiotic organisms to water limitation, the molecular mechanisms are not well understood. In this review, we summarize current knowledge of the physiological roles of LEA proteins and discuss their potential molecular functions. As these are ultimately linked to conformational changes in the presence of binding partners, post-translational modifications, or water deprivation, we provide a detailed summary of current knowledge on the structure-function relationship of LEA proteins, including their disordered state in solution, coil to helix transitions, self-assembly, and their recently discovered ability to undergo liquid-liquid phase separation. We point out the promising potential of LEA proteins in biotechnological and agronomic applications, and summarize recent advances. We identify the most relevant open questions and discuss major challenges in establishing a solid understanding of how these intriguing molecules accomplish their tasks as cellular sentinels at the limits of surviving water scarcity.
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Affiliation(s)
- Itzell E Hernández-Sánchez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Israel Maruri-López
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Coral Martinez-Martinez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Brett Janis
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Juan Francisco Jiménez-Bremont
- Laboratorio de Biotecnología Molecular de Plantas, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, 78216, San Luis Potosí, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Michael A Menze
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Anja Thalhammer
- Department of Physical Biochemistry, University of Potsdam, D-14476 Potsdam, Germany
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Zamora-Briseño JA, Pereira-Santana A, Reyes-Hernández SJ, Cerqueda-García D, Castaño E, Rodríguez-Zapata LC. Towards an understanding of the role of intrinsic protein disorder on plant adaptation to environmental challenges. Cell Stress Chaperones 2021; 26:141-150. [PMID: 32902806 PMCID: PMC7736417 DOI: 10.1007/s12192-020-01162-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/31/2020] [Accepted: 08/27/2020] [Indexed: 02/05/2023] Open
Abstract
Intrinsic protein disorder is an interesting structural feature where fully functional proteins lack a three-dimensional structure in solution. In this work, we estimated the relative content of intrinsic protein disorder in 96 plant proteomes including monocots and eudicots. In this analysis, we found variation in the relative abundance of intrinsic protein disorder among these major clades; the relative level of disorder is higher in monocots than eudicots. In turn, there is an inverse relationship between the degree of intrinsic protein disorder and protein length, with smaller proteins being more disordered. The relative abundance of amino acids depends on intrinsic disorder and also varies among clades. Within the nucleus, intrinsically disordered proteins are more abundant than ordered proteins. Intrinsically disordered proteins are specialized in regulatory functions, nucleic acid binding, RNA processing, and in response to environmental stimuli. The implications of this on plants' responses to their environment are discussed.
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Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, México
| | - Alejandro Pereira-Santana
- División de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del estado de Jalisco, Camino Arenero 1227, El Bajio, C.P. 45019, Zapopan, Jalisco, México
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnologia, Av. Insurgentes Sur 1582, Alcaldía Benito Juárez, C.P. 03940, Ciudad de México, México
| | - Sandi Julissa Reyes-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, México
| | - Daniel Cerqueda-García
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional- Unidad Mérida, Carr. Mérida - Progreso, colonia Loma Bonita, C.P. 97205, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, México.
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Zamora-Briseño JA, Pereira-Santana A, Reyes-Hernández SJ, Castaño E, Rodríguez-Zapata LC. Global Dynamics in Protein Disorder during Maize Seed Development. Genes (Basel) 2019; 10:genes10070502. [PMID: 31262071 PMCID: PMC6678312 DOI: 10.3390/genes10070502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
Intrinsic protein disorder is a physicochemical attribute of some proteins lacking tridimensional structure and is collectively known as intrinsically disordered proteins (IDPs). Interestingly, several IDPs have been associated with protective functions in plants and with their response to external stimuli. To correlate the modulation of the IDPs content with the developmental progression in seed, we describe the expression of transcripts according to the disorder content of the proteins that they codify during seed development, from the early embryogenesis to the beginning of the desiccation tolerance acquisition stage. We found that the total expression profile of transcripts encoding for structured proteins is highly increased during middle phase. However, the relative content of protein disorder is increased as seed development progresses. We identified several intrinsically disordered transcription factors that seem to play important roles throughout seed development. On the other hand, we detected a gene cluster encoding for IDPs at the end of the late phase, which coincides with the beginning of the acquisition of desiccation tolerance. In conclusion, the expression pattern of IDPs is highly dependent on the developmental stage, and there is a general reduction in the expression of transcripts encoding for structured proteins as seed development progresses. We proposed maize seeds as a model to study the regulation of protein disorder in plant development and its involvement in the acquisition of desiccation tolerance in plants.
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Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del estado de Jalisco. División de Biotecnología Industrial. Camino Arenero 1227, El Bajío, Zapopan, Jalisco. C.P. 45019
| | - Sandi Julissa Reyes-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México.
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