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Gonzalez JP, Frandsen KEH, Kesten C. The role of intrinsic disorder in binding of plant microtubule-associated proteins to the cytoskeleton. Cytoskeleton (Hoboken) 2023; 80:404-436. [PMID: 37578201 DOI: 10.1002/cm.21773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/15/2023]
Abstract
Microtubules (MTs) represent one of the main components of the eukaryotic cytoskeleton and support numerous critical cellular functions. MTs are in principle tube-like structures that can grow and shrink in a highly dynamic manner; a process largely controlled by microtubule-associated proteins (MAPs). Plant MAPs are a phylogenetically diverse group of proteins that nonetheless share many common biophysical characteristics and often contain large stretches of intrinsic protein disorder. These intrinsically disordered regions are determinants of many MAP-MT interactions, in which structural flexibility enables low-affinity protein-protein interactions that enable a fine-tuned regulation of MT cytoskeleton dynamics. Notably, intrinsic disorder is one of the major obstacles in functional and structural studies of MAPs and represents the principal present-day challenge to decipher how MAPs interact with MTs. Here, we review plant MAPs from an intrinsic protein disorder perspective, by providing a complete and up-to-date summary of all currently known members, and address the current and future challenges in functional and structural characterization of MAPs.
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Affiliation(s)
- Jordy Perez Gonzalez
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kristian E H Frandsen
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Christopher Kesten
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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2
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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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3
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Tan F, Sun N, Zhang L, Wu J, Xiao S, Tan Q, Uversky VN, Liu Y. Functional characterization of an unknown soybean intrinsically disordered protein in vitro and in Escherichia coli. Int J Biol Macromol 2021; 166:538-549. [PMID: 33137381 DOI: 10.1016/j.ijbiomac.2020.10.211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/18/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess a wide range of biological function in all organisms, however the specific functions of most IDPs are still unknown. Soybean LOC protein, LOC for short, is a heat-stable protein, which is more abundant in the stress-resistant radicles. Sequence alignment and phylogenetic analysis showed that LOC is a functionally unknown protein and conserved in Fabaceae. LOC, being enriched in most disorder-promoting residues and depleted in most order-promoting residues, was predicted to contain high levels of intrinsic disorder by several commonly used computational tools. However, it was also predicted to contain two disorder-based protein-protein binding sites and two short α-helical segments. The circular dichroism spectroscopic analysis showed that this protein is mostly disordered in water, but can form more α-helical structure in the presence of SDS and TFE. Functional in vitro studies showed that the LOC protein is able to prevent lactate dehydrogenase inactivation by freeze-thaw at a molar ratio of 10:1. Furthermore, in vivo analyses revealed the survival rate of Escherichia coli over-expressing LOC protein under the conditions of osmotic stress was noticeably increased in comparison with the control. These observations suggest that the intrinsically disordered protein LOC might serve as a chaperone and/or cell protector.
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Affiliation(s)
- Fangmei Tan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR 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, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Linsong Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Jiahui Wu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Shifeng Xiao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Qiulong Tan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, Florida, USA; Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow, region, Russia.
| | - Yun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Nanhai Ave 3688, Shenzhen, Guangdong, 518060, PR China.
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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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Genomic Analysis of Intrinsically Disordered Proteins in the Genus Camelus. Int J Mol Sci 2020; 21:ijms21114010. [PMID: 32503351 PMCID: PMC7312968 DOI: 10.3390/ijms21114010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
Intrinsically disordered proteins/regions (IDPs/IDRs) fail to fold completely into 3D structures, but have major roles in determining protein function. While natively disordered proteins/regions have been found to fulfill a wide variety of primary cellular roles, the functions of many disordered proteins in numerous species remain to be uncovered. Here, we perform the first large-scale study of IDPs/IDRs in the genus Camelus, one of the most important mammalians in Asia and North Africa, in order to explore the biological roles of these proteins. The study includes the prediction of disordered proteins/regions in Camelus species and in humans using multiple state-of-the-art prediction tools. Additionally, we provide a comparative analysis of Camelus and Homo sapiens IDPs/IDRs for the sake of highlighting the distinctive use of disorder in each genus. Our findings indicate that the human proteome is more disordered than the Camelus proteome. Gene Ontology analysis also revealed that Camelus IDPs are enriched in glutathione catabolism and lactose biosynthesis.
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Choura M, Rebaï A, Hanin M. Proteome-wide analysis of protein disorder in Triticum aestivum and Hordeum vulgare. Comput Biol Chem 2019; 84:107138. [PMID: 31767506 DOI: 10.1016/j.compbiolchem.2019.107138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/10/2019] [Accepted: 10/01/2019] [Indexed: 11/15/2022]
Abstract
There has been an increasing interest in Intrinsically Disordered Proteins (IDPs) ever since it was proven that they are ubiquitous and involved in key cellular functions. Interestingly, they have shown a large abundance in complete proteomes. In the current study, we have investigated the first large-scale study of the repertoire of IDPs in Triticum aestivum and Hordeum vulgare proteomes, in order to get insight into the biological roles of IDPs in both species. Results show that proteins in T. aestivum are significantly more disordered than those of H. vulgare. Moreover, the data revealed that DNA/RNA binding domains, co-factors, heme, metal ions binding domains, ATP/GTP binding proteins, ligands, linker domains and repeats, other domains typical to transcription factors such as zinc finger, F-box domain, homeodomain-like, l-domain like and chaperones, are predominantly present and co-occur in disordered proteins in T.aestivum and H.vulgare. The Gene Ontology analysis revealed that IDPs in T. aestivum and H. vulgare are mainly involved in regulation of cellular and biological processes up on response to stress. In future, this study may provide valuable information while considering IDPs in understanding the organism complexity and environmental adaptation.
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Affiliation(s)
- Mouna Choura
- Biotechnology and Plant Improvement Laboratory, Center of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia.
| | - Ahmed Rebaï
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia.
| | - Moez Hanin
- Biotechnology and Plant Improvement Laboratory, Center of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia; Plant Physiology and Functional Genomics Research Unit, Institute of Biotechnology, University of Sfax, BP "1175" , 3038 Sfax, Tunisia; Institute of Biotechnology, University of Sfax. BP "1175", 3038, Sfax, Tunisia.
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