1
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Hibshman JD, Goldstein B. LEA motifs promote desiccation tolerance in vivo. BMC Biol 2021; 19:263. [PMID: 34903234 PMCID: PMC8670023 DOI: 10.1186/s12915-021-01176-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cells and organisms typically cannot survive in the absence of water. However, some animals including nematodes, tardigrades, rotifers, and some arthropods are able to survive near-complete desiccation. One class of proteins known to play a role in desiccation tolerance is the late embryogenesis abundant (LEA) proteins. These largely disordered proteins protect plants and animals from desiccation. A multitude of studies have characterized stress-protective capabilities of LEA proteins in vitro and in heterologous systems. However, the extent to which LEA proteins exhibit such functions in vivo, in their native contexts in animals, is unclear. Furthermore, little is known about the distribution of LEA proteins in multicellular organisms or tissue-specific requirements in conferring stress protection. Here, we used the nematode C. elegans as a model to study the endogenous function of an LEA protein in an animal. RESULTS We created a null mutant of C. elegans LEA-1, as well as endogenous fluorescent reporters of the protein. LEA-1 mutant animals formed defective dauer larvae at high temperature. We confirmed that C. elegans lacking LEA-1 are sensitive to desiccation. LEA-1 mutants were also sensitive to heat and osmotic stress and were prone to protein aggregation. During desiccation, LEA-1 expression increased and became more widespread throughout the body. LEA-1 was required at high levels in body wall muscle for animals to survive desiccation and osmotic stress, but expression in body wall muscle alone was not sufficient for stress resistance, indicating a likely requirement in multiple tissues. We identified minimal motifs within C. elegans LEA-1 that were sufficient to increase desiccation survival of E. coli. To test whether such motifs are central to LEA-1's in vivo functions, we then replaced the sequence of lea-1 with these minimal motifs and found that C. elegans dauer larvae formed normally and survived osmotic stress and mild desiccation at the same levels as worms with the full-length protein. CONCLUSIONS Our results provide insights into the endogenous functions and expression dynamics of an LEA protein in a multicellular animal. The results show that LEA-1 buffers animals from a broad range of stresses. Our identification of LEA motifs that can function in both bacteria and in a multicellular organism in vivo suggests the possibility of engineering LEA-1-derived peptides for optimized desiccation protection.
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Affiliation(s)
- Jonathan D Hibshman
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA.
| | - Bob Goldstein
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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2
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Maula T, Vahvelainen N, Tossavainen H, Koivunen T, T. Pöllänen M, Johansson A, Permi P, Ihalin R. Decreased temperature increases the expression of a disordered bacterial late embryogenesis abundant (LEA) protein that enhances natural transformation. Virulence 2021; 12:1239-1257. [PMID: 33939577 PMCID: PMC8096337 DOI: 10.1080/21505594.2021.1918497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/22/2021] [Accepted: 04/03/2021] [Indexed: 11/02/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins are important players in the management of responses to stressful conditions, such as drought, high salinity, and changes in temperature. Many LEA proteins do not have defined three-dimensional structures, so they are intrinsically disordered proteins (IDPs) and are often highly hydrophilic. Although LEA-like sequences have been identified in bacterial genomes, the functions of bacterial LEA proteins have been studied only recently. Sequence analysis of outer membrane interleukin receptor I (BilRI) from the oral pathogen Aggregatibacter actinomycetemcomitans indicated that it shared sequence similarity with group 3/3b/4 LEA proteins. Comprehensive nuclearcgq magnetic resonance (NMR) studies confirmed its IDP nature, and expression studies in A. actinomycetemcomitans harboring a red fluorescence reporter protein-encoding gene revealed that bilRI promoter expression was increased at decreased temperatures. The amino acid backbone of BilRI did not stimulate either the production of reactive oxygen species from human leukocytes or the production of interleukin-6 from human macrophages. Moreover, BilRI-specific IgG antibodies could not be detected in the sera of A. actinomycetemcomitans culture-positive periodontitis patients. Since the bilRI gene is located near genes involved in natural competence (i.e., genes associated with the uptake of extracellular (eDNA) and its incorporation into the genome), we also investigated the role of BilRI in these events. Compared to wild-type cells, the ΔbilRI mutants showed a lower transformation efficiency, which indicates either a direct or indirect role in natural competence. In conclusion, A. actinomycetemcomitans might express BilRI, especially outside the host, to survive under stressful conditions and improve its transmission potential.
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Affiliation(s)
- Terhi Maula
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Nelli Vahvelainen
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Tuuli Koivunen
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Anders Johansson
- Division of Molecular Periodontology, Department of Odontology, Umeå University, Umeå, Sweden
| | - Perttu Permi
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Riikka Ihalin
- Department of Life Technologies, University of Turku, Turku, Finland
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3
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LeBlanc BM, Hand SC. Target enzymes are stabilized by AfrLEA6 and a gain of α-helix coincides with protection by a group 3 LEA protein during incremental drying. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140642. [PMID: 33647452 DOI: 10.1016/j.bbapap.2021.140642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/24/2022]
Abstract
Anhydrobiotic organisms accumulate late embryogenesis abundant (LEA) proteins, a family of intrinsically disordered proteins (IDPs) reported to improve cellular tolerance to water stress. Here we show that AfrLEA6, a Group 6 LEA protein only recently discovered in animals, protects lactate dehydrogenase (LDH), citrate synthase (CS) and phosphofructokinase (PFK) against damage during desiccation. In some cases, protection is enhanced by trehalose, a naturally-occurring protective solute. An open question is whether gain of secondary structure by LEA proteins during drying is a prerequisite for this stabilizing function. We used incremental drying (equilibration to a series of relative humidities, RH) to test the ability of AfrLEA2, a Group 3 LEA protein, to protect desiccation-sensitive PFK. AfrLEA2 was chosen due to its exceptional ability to protect PFK. In parallel, circular dichroism (CD) spectra were obtained for AfrLEA2 across the identical range of relative water contents. Protection of PFK by AfrLEA2, above that observed with trehalose and BSA, coincides with simultaneous gain of α-helix in AfrLEA2. At 100% RH, the CD spectrum for AfrLEA2 is typical of random coil, while at decreasing RH, the spectrum shows higher ellipticity at 191 nm and minima at 208 and 220 nm, diagnostic of α-helix. This study provides experimental evidence linking the gain of α-helix with stabilization of a target protein across a graded series of hydration states. Mechanistically, it is intriguing that certain other functions of these IDPs, like preventing aggregation of target proteins, can occur in fully hydrated cells and apparently do not require gain of α-helix.
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Affiliation(s)
- Blase M LeBlanc
- Division of Cellular Developmental and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Steven C Hand
- Division of Cellular Developmental and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; Division of Biochemistry and Molecular Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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4
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Anderson JM, Hand SC. Transgenic expression of late embryogenesis abundant proteins improves tolerance to water stress in Drosophila melanogaster. J Exp Biol 2021; 224:jeb.238204. [PMID: 33431592 DOI: 10.1242/jeb.238204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/29/2020] [Indexed: 11/20/2022]
Abstract
Four lines of Drosophila melanogaster were created that expressed transgenes encoding selected late embryogenesis abundant (LEA) proteins originally identified in embryos of the anhydrobiote Artemia franciscana The overall aim was to extend our understanding of the protective properties of LEA proteins documented with isolated cells to a desiccation-sensitive organism during exposure to drying and hyperosmotic stress. Embryos of D. melanogaster were dried at 57% relative humidity to promote a loss of 80% tissue water and then rehydrated. Embryos that expressed AfrLEA2 or AfrLEA3m eclosed 2 days earlier than wild-type embryos or embryos expressing green fluorescent protein (Gal4GFP control). For the third instar larval stage, all Afrlea lines and Gal4GFP controls experienced substantial drops in survivorship as desiccation proceeded. When results for all Afrlea lines were combined, Kaplan-Meier survival curves indicated a significant improvement in survivorship in fly lines expressing AfrLEA proteins compared with Gal4GFP controls. The percent water lost at the LT50 (lethal time for 50% mortality) for the AfrLEA lines was 78% versus 52% for Gal4GFP controls. Finally, offspring of fly lines that expressed AfrLEA2, AfrLEA3m or AfrLEA6 exhibited significantly greater success in reaching pupation, compared with wild-type flies, when adults were challenged with hyperosmotic stress (NaCl-fortified medium) and progeny forced to develop under these conditions. In conclusion, the gain of function studies reported here show that LEA proteins can improve tolerance to water stress in a desiccation-sensitive species that normally lacks these proteins, and, simultaneously, underscore the complexity of desiccation tolerance across multiple life stages in multicellular organisms.
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Affiliation(s)
- John M Anderson
- Division of Cellular Developmental and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Steven C Hand
- Division of Cellular Developmental and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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5
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Weng L. Technologies and Applications Toward Preservation of Cells in a Dry State for Therapies. Biopreserv Biobank 2021; 19:332-341. [PMID: 33493407 DOI: 10.1089/bio.2020.0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cell-based therapeutics promise to transform the treatment of a wide range of diseases, many of which, up to this point, are incurable. During the past decade, an increasing number of cell therapies have been approved by government regulatory agencies in the United States, Europe, and Japan. Thousands of clinical trials based on live cell therapies are now taking place around the world. But most of these live cell therapies face temporal and/or spatial distances between manufacture and administration, posing a risk of degradation in potency. Cryopreservation has become the predominant biobanking approach to maintain the product's safety and efficacy during transportation and storage. However, the necessity of cryogenic shipment and storage could limit patient access to these emerging therapies and increase the costs of logistics. In the (bio)pharmaceutical industries, freeze-drying and desiccation are established preservation procedures for manufacturing small molecule drugs, liposomes, and monoclonal antibodies. Over the past two decades, there has been a growing body of research exploring the freeze-drying or drying of mammalian cells, with varying degrees of success. This article provides an overview of the technologies that were adopted or developed in these pioneering studies, paving the road toward the preservation of cell-based therapeutics in a dry state for biomanufacturing.
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Affiliation(s)
- Lindong Weng
- Sana Biotechnology, Inc., South San Francisco, California, USA
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6
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Hibshman JD, Clegg JS, Goldstein B. Mechanisms of Desiccation Tolerance: Themes and Variations in Brine Shrimp, Roundworms, and Tardigrades. Front Physiol 2020; 11:592016. [PMID: 33192606 PMCID: PMC7649794 DOI: 10.3389/fphys.2020.592016] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/25/2020] [Indexed: 01/05/2023] Open
Abstract
Water is critical for the survival of most cells and organisms. Remarkably, a small number of multicellular animals are able to survive nearly complete drying. The phenomenon of anhydrobiosis, or life without water, has been of interest to researchers for over 300 years. In this review we discuss advances in our understanding of protectants and mechanisms of desiccation tolerance that have emerged from research in three anhydrobiotic invertebrates: brine shrimp (Artemia), roundworms (nematodes), and tardigrades (water bears). Discovery of molecular protectants that allow each of these three animals to survive drying diversifies our understanding of desiccation tolerance, and convergent themes suggest mechanisms that may offer a general model for engineering desiccation tolerance in other contexts.
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Affiliation(s)
- Jonathan D. Hibshman
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - James S. Clegg
- Bodega Marine Laboratory, University of California, Davis, Davis, CA, United States
| | - Bob Goldstein
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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7
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Kijak H, Ratajczak E. What Do We Know About the Genetic Basis of Seed Desiccation Tolerance and Longevity? Int J Mol Sci 2020; 21:E3612. [PMID: 32443842 PMCID: PMC7279459 DOI: 10.3390/ijms21103612] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023] Open
Abstract
Long-term seed storage is important for protecting both economic interests and biodiversity. The extraordinary properties of seeds allow us to store them in the right conditions for years. However, not all types of seeds are resilient, and some do not tolerate extreme desiccation or low temperature. Seeds can be divided into three categories: (1) orthodox seeds, which tolerate water losses of up to 7% of their water content and can be stored at low temperature; (2) recalcitrant seeds, which require a humidity of 27%; and (3) intermediate seeds, which lose their viability relatively quickly compared to orthodox seeds. In this article, we discuss the genetic bases for desiccation tolerance and longevity in seeds and the differences in gene expression profiles between the mentioned types of seeds.
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Affiliation(s)
- Hanna Kijak
- Institute of Dendrology, Polish Academy of Sciences, 62-035 Kórnik, Poland;
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8
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Common Functions of Disordered Proteins across Evolutionary Distant Organisms. Int J Mol Sci 2020; 21:ijms21062105. [PMID: 32204351 PMCID: PMC7139818 DOI: 10.3390/ijms21062105] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence–structure–function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.
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9
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Léon D, Vermeuel MP, Gupta P, Bunagan MR. The effect of salt and temperature on the conformational changes of P1LEA-22, a repeat unit of plant Late Embryogenesis Abundant proteins. J Pept Sci 2020; 26:e3247. [PMID: 32162463 DOI: 10.1002/psc.3247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 11/11/2022]
Abstract
The effect of choline chloride on the conformational dynamics of the 11-mer repeat unit P1LEA-22 of group 3 Late Embryogenesis Abundant (G3LEA) proteins was studied. Circular dichroism data of aqueous solutions of P1LEA-22 revealed that the peptide favors a polyproline II (PPII) helix structure at low temperature, with increasing temperature promoting a gain of unstructured conformations. Furthermore, increases in sample FeCl3 or choline chloride concentrations causes a gain in PPII helical structure at low temperature. The potential role of PPII structure in intrinsically disordered and G3LEA proteins is discussed, including its ability to easily access other secondary structural conformations such as α-helix and β-sheet, which have been observed for dehydrated G3LEA proteins. The observed effect of FeCl3 and choline chloride salts on P1LEA-22 suggests favorable cation interactions with the PPII helix, supporting ion sequestration as a G3LEA protein function. As choline chloride is suggested to improve salt tolerance and protect cell membrane in plants at low temperature, our results support adoption of the PPII structure as a possible damage-preventing measure of Late Embryogenesis Abundant proteins.
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Affiliation(s)
- David Léon
- Department of Chemistry, The College of New Jersey, Ewing, NJ, USA
| | | | - Priya Gupta
- Department of Chemistry, The College of New Jersey, Ewing, NJ, USA
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10
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Nishimoto T, Takahashi Y, Miyama S, Furuta T, Sakurai M. Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins. Biophys Physicobiol 2019; 16:196-204. [PMID: 31984172 PMCID: PMC6975979 DOI: 10.2142/biophysico.16.0_196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/03/2019] [Indexed: 02/04/2023] Open
Abstract
Group 3 late embryogenesis abundant (G3LEA) proteins, which act as a well-characterized desiccation protectant in anhydrobiotic organisms, are structurally disordered in solution, but they acquire a predominantly α-helical structure during drying. Thus, G3LEA proteins are now accepted as intrinsically disordered proteins (IDPs). Their functional regions involve characteristic 11-mer repeating motifs. In the present study, to elucidate the origin of the IDP property of G3LEA proteins, we applied replica exchange molecular dynamics (REMD) simulation to a model peptide composed of two tandem repeats of an 11-mer motif and its counterpart peptide whose amino acid sequence was randomized with the same amino acid composition as that of the 11-mer motif. REMD simulations were performed for a single α-helical chain of each peptide and its double-bundled strand in a wide water content ranging from 5 to 78.3 wt%. In the latter case, we tested different types of arrangement: 1) the dipole moments of the two helices were parallel or anti-parallel and 2) due to the amphiphilic nature of the α-helix of the 11-mer motif, two types of the side-to-side contact were tested: hydrophilic-hydrophilic facing or hydrophobic-hydrophobic facing. Here, we revealed that the single chain alone exhibits no IDP-like properties, even if it involves the 11-mer motif, and the hydrophilic interaction of the two chains leads to the formation of a left-handed α-helical coiled coil in the dry state. These results support the cytoskeleton hypothesis that has been proposed as a mechanism by which G3LEA proteins work as a desiccation protectant.
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Affiliation(s)
- Tatsushi Nishimoto
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Yuta Takahashi
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Shohei Miyama
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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11
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Preferential adsorption to air-water interfaces: a novel cryoprotective mechanism for LEA proteins. Biochem J 2019; 476:1121-1135. [PMID: 30898848 PMCID: PMC6458962 DOI: 10.1042/bcj20180901] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 01/17/2023]
Abstract
Late embryogenesis abundant (LEA) proteins comprise a diverse family whose members play a key role in abiotic stress tolerance. As intrinsically disordered proteins, LEA proteins are highly hydrophilic and inherently stress tolerant. They have been shown to stabilise multiple client proteins under a variety of stresses, but current hypotheses do not fully explain how such broad range stabilisation is achieved. Here, using neutron reflection and surface tension experiments, we examine in detail the mechanism by which model LEA proteins, AavLEA1 and ERD10, protect the enzyme citrate synthase (CS) from aggregation during freeze–thaw. We find that a major contributing factor to CS aggregation is the formation of air bubbles during the freeze–thaw process. This greatly increases the air–water interfacial area, which is known to be detrimental to folded protein stability. Both model LEA proteins preferentially adsorb to this interface and compete with CS, thereby reducing surface-induced aggregation. This novel surface activity provides a general mechanism by which diverse members of the LEA protein family might function to provide aggregation protection that is not specific to the client protein.
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12
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Janis B, Belott C, Menze MA. Role of Intrinsic Disorder in Animal Desiccation Tolerance. Proteomics 2018; 18:e1800067. [DOI: 10.1002/pmic.201800067] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/10/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Brett Janis
- Department of Biology University of Louisville Louisville KY 40292 USA
| | - Clinton Belott
- Department of Biology University of Louisville Louisville KY 40292 USA
| | - Michael A. Menze
- Department of Biology University of Louisville Louisville KY 40292 USA
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13
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Navarro-Retamal C, Bremer A, Alzate-Morales J, Caballero J, Hincha DK, González W, Thalhammer A. Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana. Phys Chem Chem Phys 2016; 18:25806-16. [PMID: 27255148 DOI: 10.1039/c6cp02272c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain α-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40%) or prevented (100%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state.
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Affiliation(s)
- Carlos Navarro-Retamal
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile. (Wendy González, for correspondence relating to protein modelling)
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14
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Hand SC, Menze MA. Molecular approaches for improving desiccation tolerance: insights from the brine shrimp Artemia franciscana. PLANTA 2015; 242:379-88. [PMID: 25809151 PMCID: PMC4498972 DOI: 10.1007/s00425-015-2281-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/12/2015] [Indexed: 05/06/2023]
Abstract
We have evaluated the endogenous expression and molecular properties of selected Group 3 LEA proteins from Artemia franciscana , and the capacity of selected Groups 1 and 3 proteins transfected into various desiccation-sensitive cell lines to improve tolerance to drying. Organisms inhabiting both aquatic and terrestrial ecosystems frequently are confronted with the problem of water loss for multiple reasons--exposure to hypersalinity, evaporative water loss, and restriction of intracellular water due to freezing of extracellular fluids. Seasonal desiccation can become severe and lead to the production of tolerant propagules and entry into the state of anhydrobiosis at various stages of the life cycle. Such is the case for gastrula-stage embryos of the brine shrimp, Artemia franciscana. Physiological and biochemical responses to desiccation are central for survival and are multifaceted. This review will evaluate the impact of multiple late embryogenesis abundant proteins originating from A. franciscana, together with the non-reducing sugar trehalose, on prevention of desiccation damage at multiple levels of biological organization. Survivorship of desiccation-sensitive cells during water stress can be improved by use of the above protective agents, coupled to metabolic preconditioning and rapid cell drying. However, obtaining long-term stability of cells in the dried state at room temperature has not been accomplished and will require continued efforts on both the physicochemical and biological fronts.
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Affiliation(s)
- Steven C Hand
- Division of Cellular, Developmental and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA,
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15
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Jaspard E, Hunault G. Comparison of amino acids physico-chemical properties and usage of late embryogenesis abundant proteins, hydrophilins and WHy domain. PLoS One 2014; 9:e109570. [PMID: 25296175 PMCID: PMC4190154 DOI: 10.1371/journal.pone.0109570] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/07/2014] [Indexed: 11/19/2022] Open
Abstract
Late Embryogenesis Abundant proteins (LEAPs) comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide family of proteins called hydrophilins, while a domain called WHy (Water stress and Hypersensitive response) was found in LEAP class 8 (according to our previous classification). Since little is known about hydrophilins and WHy domain, the cross-analysis of their amino acids physico-chemical properties and amino acids usage together with those of LEAPs helps to describe some of their structural features and to make hypothesis about their function. Physico-chemical properties of hydrophilins and WHy domain strongly suggest their role in dehydration tolerance, probably by interacting with water and small polar molecules. The computational analysis reveals that LEAP class 8 and hydrophilins are distinct protein families and that not all LEAPs are a protein subset of hydrophilins family as proposed earlier. Hydrophilins seem related to LEAP class 2 (also called dehydrins) and to Heat Shock Proteins 12 (HSP12). Hydrophilins are likely unstructured proteins while WHy domain is structured. LEAP class 2, hydrophilins and WHy domain are thus proposed to share a common physiological role by interacting with water or other polar/charged small molecules, hence contributing to dehydration tolerance.
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Affiliation(s)
- Emmanuel Jaspard
- Université d'Angers, UMR 1345 IRHS, SFR 4207 QUASAV, Angers, France
- INRA, UMR 1345 IRHS, Beaucouzé, France
- Agrocampus-Ouest, UMR 1345 IRHS, Angers, France
| | - Gilles Hunault
- Université d'Angers, Laboratoire d'Hémodynamique, Interaction Fibrose et Invasivité tumorale hépatique, UPRES 3859, IFR 132, F-49045 Angers, France
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Boswell LC, Menze MA, Hand SC. Group 3 late embryogenesis abundant proteins from embryos of Artemia franciscana: structural properties and protective abilities during desiccation. Physiol Biochem Zool 2014; 87:640-51. [PMID: 25244376 DOI: 10.1086/676936] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Group 3 late embryogenesis abundant (LEA) proteins are highly hydrophilic, and their expression is associated with desiccation tolerance in both plants and animals. Here we show that two LEA proteins from embryos of Artemia franciscana, AfrLEA2 and AfrLEA3m, are intrinsically disordered in solution but upon desiccation gain secondary structure, as measured by circular dichroism. Trifluoroethanol and sodium dodecyl sulfate are both shown to induce α-helical structure in AfrLEA2 and AfrLEA3m. Bioinformatic predictions of secondary-structure content for both proteins correspond most closely to conformations measured in the dry state. Because some LEA proteins afford protection to desiccation-sensitive proteins during drying and subsequent rehydration, we tested for this capacity in AfrLEA2 and AfrLEA3m. The protective capacities vary, depending on the target enzyme. For the cytoplasmic enzyme lactate dehydrogenase, neither AfrLEA2 nor AfrLEA3m, with or without trehalose present, was able to afford protection better than that provided by bovine serum albumin (BSA) under the same conditions. However, for another cytoplasmic enzyme, phosphofructokinase, both AfrLEA2 and AfrLEA3m in the presence of trehalose were able to afford protection far greater than that provided by BSA with trehalose. Finally, for the mitochondrial enzyme citrate synthase, 400-μg/mL AfrLEA3m without trehalose provided significantly more protection than the same concentration of either AfrLEA2 or BSA.
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Affiliation(s)
- Leaf C Boswell
- Division of Cellular, Developmental, and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; 2Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois 61920
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Amara I, Zaidi I, Masmoudi K, Ludevid MD, Pagès M, Goday A, Brini F. Insights into Late Embryogenesis Abundant (LEA) Proteins in Plants: From Structure to the Functions. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.522360] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Erkut C, Vasilj A, Boland S, Habermann B, Shevchenko A, Kurzchalia TV. Molecular strategies of the Caenorhabditis elegans dauer larva to survive extreme desiccation. PLoS One 2013; 8:e82473. [PMID: 24324795 PMCID: PMC3853187 DOI: 10.1371/journal.pone.0082473] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/02/2013] [Indexed: 11/19/2022] Open
Abstract
Massive water loss is a serious challenge for terrestrial animals, which usually has fatal consequences. However, some organisms have developed means to survive this stress by entering an ametabolic state called anhydrobiosis. The molecular and cellular mechanisms underlying this phenomenon are poorly understood. We recently showed that Caenorhabditis elegans dauer larva, an arrested stage specialized for survival in adverse conditions, is resistant to severe desiccation. However, this requires a preconditioning step at a mild desiccative environment to prepare the organism for harsher desiccation conditions. A systems approach was used to identify factors that are activated during this preconditioning. Using microarray analysis, proteomics, and bioinformatics, genes, proteins, and biochemical pathways that are upregulated during this process were identified. These pathways were validated via reverse genetics by testing the desiccation tolerances of mutants. These data show that the desiccation response is activated by hygrosensation (sensing the desiccative environment) via head neurons. This leads to elimination of reactive oxygen species and xenobiotics, expression of heat shock and intrinsically disordered proteins, polyamine utilization, and induction of fatty acid desaturation pathway. Remarkably, this response is specific and involves a small number of functional pathways, which represent the generic toolkit for anhydrobiosis in plants and animals.
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Affiliation(s)
- Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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19
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Li D, Guo B, Liu B, Zhai Z, Zhang Y, Liu Y, Yu H, Liu L, Yang C. Investigation on bioactive protection of the amino acids derived from LEA protein on insulin by molecular simulation. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.769682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Li D, Liu B, Guo B, Xu F, Yang C, Chen C, Zhang Y, Zhai Z. Investigation on bioactive protection of LEA protein to insulin by molecular simulation. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.708871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Petersen J, Eriksson SK, Harryson P, Pierog S, Colby T, Bartels D, Röhrig H. The lysine-rich motif of intrinsically disordered stress protein CDeT11-24 from Craterostigma plantagineum is responsible for phosphatidic acid binding and protection of enzymes from damaging effects caused by desiccation. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4919-29. [PMID: 22791833 PMCID: PMC3428009 DOI: 10.1093/jxb/ers173] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The late embryogenesis abundant (LEA)-like protein CDeT11-24 is one of the major desiccation-related phosphoproteins of the resurrection plant Craterostigma plantagineum. In this study, it was shown that CDeT11-24 is mostly intrinsically disordered and protects two different enzymes, citrate synthase and lactate dehydrogenase, against damaging effects caused by desiccation. Lipid-binding assays revealed that CDeT11-24 is able to interact with phosphatidic acid, although electrostatic repulsion was expected due to the overall negative net charge of the protein under the tested physiological conditions. CDeT11-24 carries an N-terminal lysine-rich sequence, which is predicted to form an amphipathic α-helix. Analysis of the truncated CDeT11-24 protein identified this region to be responsible for both activities: enzyme protection and phosphatidic acid interaction. Possible functions of the CDeT11-24 protein are discussed in the context of desiccation tolerance.
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Affiliation(s)
- Jan Petersen
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of BonnKirschallee 1, 53115 Bonn, Germany
| | - Sylvia K. Eriksson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University10691 Stockholm, Sweden
| | - Pia Harryson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University10691 Stockholm, Sweden
| | - Steffen Pierog
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of BonnKirschallee 1, 53115 Bonn, Germany
| | - Thomas Colby
- Max Planck Institute for Plant Breeding ResearchCarl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of BonnKirschallee 1, 53115 Bonn, Germany
| | - Horst Röhrig
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of BonnKirschallee 1, 53115 Bonn, Germany
- *To whom correspondence should be addressed. E-mail:
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Jaspard E, Macherel D, Hunault G. Computational and statistical analyses of amino acid usage and physico-chemical properties of the twelve late embryogenesis abundant protein classes. PLoS One 2012; 7:e36968. [PMID: 22615859 PMCID: PMC3353982 DOI: 10.1371/journal.pone.0036968] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/10/2012] [Indexed: 11/19/2022] Open
Abstract
Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs.
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Affiliation(s)
- Emmanuel Jaspard
- Université d'Angers, Institut de Recherche en Horticulture et Semences, INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QUASAV, LUNAM Université, Angers, France.
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Amara I, Odena A, Oliveira E, Moreno A, Masmoudi K, Pagès M, Goday A. Insights into Maize LEA proteins: from proteomics to functional approaches. PLANT & CELL PHYSIOLOGY 2012; 53:312-29. [PMID: 22199372 DOI: 10.1093/pcp/pcr183] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
LEA (late embryogenesis abundant) proteins participate in plant stress tolerance responses, but the mechanisms by which protection occurs are not fully understood. In the present work the unfolded proteins from maize dry embryos were analyzed by mass spectrometry. Twenty embryo proteins were identified, and among them 13 corresponded to LEA-type proteins. We selected three major LEA proteins, Emb564, Rab17 and Mlg3, belonging to groups 1, 2 and 3, respectively, and we undertook a comparative study in order to highlight differences among them. The post-translational modifications of native proteins were analyzed and the anti-aggregation properties of recombinant Emb564, Rab17 and Mgl3 proteins were evaluated in vitro. In addition, the protective effects of the LEA proteins were assessed in living cells under stress in Escherichia coli cells and in Nicotiana bentamiana leaves agroinfiltrated with fluorescent LEA-green fluorescent protein (GFP) fusions. Protein visualization by confocal microscopy indicated that cells expressing Mg3-GFP showed reduced cell shrinkage effects during dehydration and that Rab17-GFP co-localized to leaf oil bodies after heat shock. Overall, the results highlight differences and suggest functional diversity among maize LEA groups.
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Affiliation(s)
- Imen Amara
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola Del Vallès), 08193 Barcelona, Spain
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Furuki T, Shimizu T, Kikawada T, Okuda T, Sakurai M. Salt Effects on the Structural and Thermodynamic Properties of a Group 3 LEA Protein Model Peptide. Biochemistry 2011; 50:7093-103. [DOI: 10.1021/bi200719s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takao Furuki
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-62, Nagatsuta-cho,
Midori-ku, Yokohama, 226-8501, Japan
| | - Tempei Shimizu
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-62, Nagatsuta-cho,
Midori-ku, Yokohama, 226-8501, Japan
| | - Takahiro Kikawada
- National Institute of Agrobiological Sciences (NIAS), 1-2, Ohwashi, Tsukuba, 305-8634, Japan
| | - Takashi Okuda
- National Institute of Agrobiological Sciences (NIAS), 1-2, Ohwashi, Tsukuba, 305-8634, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-62, Nagatsuta-cho,
Midori-ku, Yokohama, 226-8501, Japan
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Hand SC, Menze MA, Toner M, Boswell L, Moore D. LEA proteins during water stress: not just for plants anymore. Annu Rev Physiol 2011; 73:115-34. [PMID: 21034219 DOI: 10.1146/annurev-physiol-012110-142203] [Citation(s) in RCA: 251] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Late embryogenesis abundant (LEA) proteins are extremely hydrophilic proteins that were first identified in land plants. Intracellular accumulation is tightly correlated with acquisition of desiccation tolerance, and data support their capacity to stabilize other proteins and membranes during drying, especially in the presence of sugars like trehalose. Exciting reports now show that LEA proteins are not restricted to plants; multiple forms are expressed in desiccation-tolerant animals from at least four phyla. We evaluate here the expression, subcellular localization, biochemical properties, and potential functions of LEA proteins in animal species during water stress. LEA proteins are intrinsically unstructured in aqueous solution, but surprisingly, many assume their native conformation during drying. They are targeted to multiple cellular locations, including mitochondria, and evidence supports that LEA proteins stabilize vitrified sugar glasses thought to be important in the dried state. More in vivo experimentation will be necessary to fully unravel the multiple functional properties of these macromolecules during water stress.
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Affiliation(s)
- Steven C Hand
- Division of Cellular, Developmental and Integrative Biology, Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, USA.
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He X. Thermostability of biological systems: fundamentals, challenges, and quantification. Open Biomed Eng J 2011; 5:47-73. [PMID: 21769301 PMCID: PMC3137158 DOI: 10.2174/1874120701105010047] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 12/25/2022] Open
Abstract
This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems.
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Affiliation(s)
- Xiaoming He
- Multiscale Biothermostability Engineering Laboratory, Department of Mechanical Engineering and Biomedical Engineering Program, University of South Carolina, 300 Main Street, Columbia, SC 29208, USA
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27
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Thalhammer A, Hundertmark M, Popova AV, Seckler R, Hincha DK. Interaction of two intrinsically disordered plant stress proteins (COR15A and COR15B) with lipid membranes in the dry state. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1812-20. [PMID: 20510170 DOI: 10.1016/j.bbamem.2010.05.015] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 04/27/2010] [Accepted: 05/14/2010] [Indexed: 10/19/2022]
Abstract
COR15A and COR15B form a tandem repeat of highly homologous genes in Arabidopsis thaliana. Both genes are highly cold induced and the encoded proteins belong to the Pfam LEA_4 group (group 3) of the late embryogenesis abundant (LEA) proteins. Both proteins were predicted to be intrinsically disordered in solution. Only COR15A has previously been characterized and it was shown to be localized in the soluble stroma fraction of chloroplasts. Ectopic expression of COR15A in Arabidopsis resulted in increased freezing tolerance of both chloroplasts after freezing and thawing of intact leaves and of isolated protoplasts frozen and thawed in vitro. In the present study we have generated recombinant mature COR15A and COR15B for a comparative study of their structure and possible function as membrane protectants. CD spectroscopy showed that both proteins are predominantly unstructured in solution and mainly alpha-helical after drying. Both proteins showed similar effects on the thermotropic phase behavior of dry liposomes. A decrease in the gel to liquid-crystalline phase transition temperature depended on both the unsaturation of the fatty acyl chains and lipid headgroup structure. FTIR spectroscopy indicated no strong interactions between the proteins and the lipid phosphate and carbonyl groups, but significant interactions with the galactose headgroup of the chloroplast lipid monogalactosyldiacylglycerol. These findings were rationalized by modeling the secondary structure of COR15A and COR15B. Helical wheel projection indicated the presence of amphipathic alpha-helices in both proteins. The helices lacked a clear separation of positive and negative charges on the hydrophilic face, but contained several hydroxylated amino acids.
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Affiliation(s)
- Anja Thalhammer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
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Hunault G, Jaspard E. LEAPdb: a database for the late embryogenesis abundant proteins. BMC Genomics 2010; 11:221. [PMID: 20359361 PMCID: PMC2858754 DOI: 10.1186/1471-2164-11-221] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 04/01/2010] [Indexed: 11/10/2022] Open
Abstract
Background Late Embryogenesis Abundant Proteins database (LEAPdb) contains resource regarding LEAP from plants and other organisms. Although LEAP are grouped into several families, there is no general consensus on their definition and on their classification. They are associated with abiotic stress tolerance, but their actual function at the molecular level is still enigmatic. The scarcity of 3-D structures for LEAP remains a handicap for their structure-function relationships analysis. Finally, the growing body of published data about LEAP represents a great amount of information that needs to be compiled, organized and classified. Results LEAPdb gathers data about 8 LEAP sub-families defined by the PFAM, the Conserved Domain and the InterPro databases. Among its functionalities, LEAPdb provides a browse interface for retrieving information on the whole database. A search interface using various criteria such as sophisticated text expression, amino acids motifs and other useful parameters allows the retrieving of refined subset of entries. LEAPdb also offers sequence similarity search. Information is displayed in re-ordering tables facilitating the analysis of data. LEAP sequences can be downloaded in three formats. Finally, the user can submit his sequence(s). LEAPdb has been conceived as a user-friendly web-based database with multiple functions to search and describe the different LEAP families. It will likely be helpful for computational analyses of their structure - function relationships. Conclusions LEAPdb contains 769 non-redundant and curated entries, from 196 organisms. All LEAP sequences are full-length. LEAPdb is publicly available at http://forge.info.univ-angers.fr/~gh/Leadb/index.php.
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Affiliation(s)
- Gilles Hunault
- Université d'Angers, Laboratoire d'Hémodynamique, Interaction Fibrose et Invasivité tumorale hépatique, UPRES 3859, IFR 132, Université d'Angers, F- 49045 Angers, France
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Dure L, Greenway SC, Galau GA. Developmental biochemistry of cottonseed embryogenesis and germination: changing messenger ribonucleic acid populations as shown by in vitro and in vivo protein synthesis. Biochemistry 1981; 59:377-86. [PMID: 7284317 DOI: 10.1016/j.jinsphys.2013.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 05/08/2023]
Abstract
Changes in messenger ribonucleic acid (mRNA) populations during embryogenesis of cottonseed have been followed by cataloging (a) extant proteins, (b) proteins synthesized in vivo, and (c) proteins synthesized in vitro from extracted RNA, all at specific stages of embryogenesis. Evidence is presented for the existence of five mRNA subsets, all apparently under different regulatory regimes, that produce the abundant proteins of embryogenesis. One of these functions principally during the cell division phase of embryogenesis and encodes among its products the seed storage proteins whose mRNA is superabundant during this period. This subset has disappeared from the abundant group by the mature seed stage. Two other subsets appear in late embryogenesis, one of which may result from the removal of the embryo from the maternal environment, since it is inducible by excision of the young embryo from the seed. The other appears to be induced by the plant growth regulator abscisic acid, whose endogenous concentration increases at this stage. It can be induced by incubating excised young embryos in abscisic acid. The last two subsets exist throughout embryogenesis, but only one of them appears to function in germination.
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