scholarly journals Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses

Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1662
Author(s):  
Mughair Abdul Aziz ◽  
Miloofer Sabeem ◽  
Sangeeta Kutty Mullath ◽  
Faical Brini ◽  
Khaled Masmoudi
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Association Studies ◽  
Environmental Stresses ◽  
Disordered Proteins ◽  
Genome Wide Association Studies ◽  
Lea Proteins ◽  
Lea Genes ◽  
Intrinsically Disordered ◽  
Wide Range ◽  
Group Ii

In response to various environmental stresses, plants have evolved a wide range of defense mechanisms, resulting in the overexpression of a series of stress-responsive genes. Among them, there is certain set of genes that encode for intrinsically disordered proteins (IDPs) that repair and protect the plants from damage caused by environmental stresses. Group II LEA (late embryogenesis abundant) proteins compose the most abundant and characterized group of IDPs; they accumulate in the late stages of seed development and are expressed in response to dehydration, salinity, low temperature, or abscisic acid (ABA) treatment. The physiological and biochemical characterization of group II LEA proteins has been carried out in a number of investigations because of their vital roles in protecting the integrity of biomolecules by preventing the crystallization of cellular components prior to multiple stresses. This review describes the distribution, structural architecture, and genomic diversification of group II LEA proteins, with some recent investigations on their regulation and molecular expression under various abiotic stresses. Novel aspects of group II LEA proteins in Phoenix dactylifera and in orthodox seeds are also presented. Genome-wide association studies (GWAS) indicated a ubiquitous distribution and expression of group II LEA genes in different plant cells. In vitro experimental evidence from biochemical assays has suggested that group II LEA proteins perform heterogenous functions in response to extreme stresses. Various investigations have indicated the participation of group II LEA proteins in the plant stress tolerance mechanism, spotlighting the molecular aspects of group II LEA genes and their potential role in biotechnological strategies to increase plants’ survival in adverse environments.

scholarly journals Characterization of the Heat-Stable Proteome During Seed Germination in Arabidopsis with Special Focus on LEA Proteins

2021 ◽  
Vol 22 (15) ◽  
pp. 8172
Author(s):  
Orarat Ginsawaeng ◽  
Michal Gorka ◽  
Alexander Erban ◽  
Carolin Heise ◽  
Franziska Brueckner ◽  
...  
Keyword(s):  
Seed Germination ◽  
Seedling Establishment ◽  
Intrinsically Disordered Proteins ◽  
Late Embryogenesis Abundant ◽  
Disordered Proteins ◽  
Similar Proportion ◽  
Special Focus ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Heat Stable

During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.

scholarly journals Supramolecular Fuzziness of Intracellular Liquid Droplets: Liquid–Liquid Phase Transitions, Membrane-Less Organelles, and Intrinsic Disorder

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3265 ◽  
Author(s):  
Vladimir N. Uversky
Keyword(s):  
Phase Transitions ◽  
Liquid Phase ◽  
Intrinsically Disordered Proteins ◽  
Intrinsically Disordered Protein ◽  
Disordered Proteins ◽  
Bacterial Cells ◽  
Liquid Droplets ◽  
Intrinsically Disordered ◽  
Wide Range ◽  
Characteristic Features

Cells are inhomogeneously crowded, possessing a wide range of intracellular liquid droplets abundantly present in the cytoplasm of eukaryotic and bacterial cells, in the mitochondrial matrix and nucleoplasm of eukaryotes, and in the chloroplast’s stroma of plant cells. These proteinaceous membrane-less organelles (PMLOs) not only represent a natural method of intracellular compartmentalization, which is crucial for successful execution of various biological functions, but also serve as important means for the processing of local information and rapid response to the fluctuations in environmental conditions. Since PMLOs, being complex macromolecular assemblages, possess many characteristic features of liquids, they represent highly dynamic (or fuzzy) protein–protein and/or protein–nucleic acid complexes. The biogenesis of PMLOs is controlled by specific intrinsically disordered proteins (IDPs) and hybrid proteins with ordered domains and intrinsically disordered protein regions (IDPRs), which, due to their highly dynamic structures and ability to facilitate multivalent interactions, serve as indispensable drivers of the biological liquid–liquid phase transitions (LLPTs) giving rise to PMLOs. In this article, the importance of the disorder-based supramolecular fuzziness for LLPTs and PMLO biogenesis is discussed.

scholarly journals Chasing coevolutionary signals in intrinsically disordered proteins complexes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Javier A. Iserte ◽  
Tamas Lazar ◽  
Silvio C. E. Tosatto ◽  
Peter Tompa ◽  
Cristina Marino-Buslje
Keyword(s):  
Protein Interactions ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Protein Protein Interactions ◽  
Contact Prediction ◽  
Intrinsically Disordered ◽  
Regulatory Processes ◽  
Wide Range ◽  
Predict Protein Structure ◽  
Biological Interpretation

Abstract Intrinsically disordered proteins/regions (IDPs/IDRs) are crucial components of the cell, they are highly abundant and participate ubiquitously in a wide range of biological functions, such as regulatory processes and cell signaling. Many of their important functions rely on protein interactions, by which they trigger or modulate different pathways. Sequence covariation, a powerful tool for protein contact prediction, has been applied successfully to predict protein structure and to identify protein–protein interactions mostly of globular proteins. IDPs/IDRs also mediate a plethora of protein–protein interactions, highlighting the importance of addressing sequence covariation-based inter-protein contact prediction of this class of proteins. Despite their importance, a systematic approach to analyze the covariation phenomena of intrinsically disordered proteins and their complexes is still missing. Here we carry out a comprehensive critical assessment of coevolution-based contact prediction in IDP/IDR complexes and detail the challenges and possible limitations that emerge from their analysis. We found that the coevolutionary signal is faint in most of the complexes of disordered proteins but positively correlates with the interface size and binding affinity between partners. In addition, we discuss the state-of-art methodology by biological interpretation of the results, formulate evaluation guidelines and suggest future directions of development to the field.

scholarly journals A Family of Small Intrinsically Disordered Proteins Involved in Flagellum-Dependent Motility inSalmonella enterica

2018 ◽  
Vol 201 (2) ◽  
Author(s):  
Tamiko Oguri ◽  
Youjeong Kwon ◽  
Jerry K. K. Woo ◽  
Gerd Prehna ◽  
Hyun Lee ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Disordered Proteins ◽  
Wild Type ◽  
Content Type ◽  
Cellular Pathway ◽  
Intrinsically Disordered ◽  
Small Proteins ◽  
Wide Range

ABSTRACTBy screening a collection ofSalmonellamutants deleted for genes encoding small proteins of ≤60 amino acids, we identified three paralogous small genes (ymdF,STM14_1829, andyciG) required for wild-type flagellum-dependent swimming and swarming motility. TheymdF,STM14_1829, andyciGgenes encode small proteins of 55, 60, and 60 amino acid residues, respectively. A bioinformatics analysis predicted that these small proteins are intrinsically disordered proteins, and circular dichroism analysis of purified recombinant proteins confirmed that all three proteins are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a key protein required for wild-type motility. We determined that relative to the wild type, the expression of the flagellin protein FliC is lower in the ΔSTM14_1829mutant due to the downregulation of theflhDCoperon encoding the FlhDC master regulator. By comparing the gene expression profiles between the wild-type and ΔSTM14_1829strains via RNA sequencing, we found that the gene encoding the response regulator PhoP is upregulated in the ΔSTM14_1829mutant, suggesting the indirect repression of theflhDCoperon by the activated PhoP. Homologs of STM14_1829 are conserved in a wide range of bacteria, includingEscherichia coliandPseudomonas aeruginosa. We showed that the inactivation of STM14_1829 homologs inE. coliandP. aeruginosaalso alters motility, suggesting that this family of small intrinsically disordered proteins may play a role in the cellular pathway(s) that affects motility.IMPORTANCEThis study reports the identification of a novel family of small intrinsically disordered proteins that are conserved in a wide range of flagellated and nonflagellated bacteria. Although this study identifies the role of these small proteins in the scope of flagellum-dependent motility inSalmonella, they likely play larger roles in a more conserved cellular pathway(s) that indirectly affects flagellum expression in the case of motile bacteria. Small intrinsically disordered proteins have not been well characterized in prokaryotes, and the results of our study provide a basis for their detailed functional characterization.

scholarly journals Preferential adsorption to air–water interfaces: a novel cryoprotective mechanism for LEA proteins

2019 ◽  
Vol 476 (7) ◽  
pp. 1121-1135 ◽  
Author(s):  
Fanny Yuen ◽  
Matthew Watson ◽  
Robert Barker ◽  
Isabelle Grillo ◽  
Richard K. Heenan ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Citrate Synthase ◽  
Abiotic Stress Tolerance ◽  
Interfacial Area ◽  
Disordered Proteins ◽  
General Mechanism ◽  
Lea Proteins ◽  
Freeze Thaw ◽  
Intrinsically Disordered ◽  
Induced Aggregation

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.

scholarly journals On the roles of intrinsically disordered proteins and regions in cell communication and signaling

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Sarah E. Bondos ◽  
A. Keith Dunker ◽  
Vladimir N. Uversky
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Cell Communication ◽  
Disordered Proteins ◽  
Sequence Structure ◽  
Intrinsically Disordered ◽  
Wide Range ◽  
Micro Organisms ◽  
Signaling Domains ◽  
Structured Proteins ◽  
Water Bears

AbstractFor proteins, the sequence → structure → function paradigm applies primarily to enzymes, transmembrane proteins, and signaling domains. This paradigm is not universal, but rather, in addition to structured proteins, intrinsically disordered proteins and regions (IDPs and IDRs) also carry out crucial biological functions. For these proteins, the sequence → IDP/IDR ensemble → function paradigm applies primarily to signaling and regulatory proteins and regions. Often, in order to carry out function, IDPs or IDRs cooperatively interact, either intra- or inter-molecularly, with structured proteins or other IDPs or intermolecularly with nucleic acids. In this IDP/IDR thematic collection published in Cell Communication and Signaling, thirteen articles are presented that describe IDP/IDR signaling molecules from a variety of organisms from humans to fruit flies and tardigrades (“water bears”) and that describe how these proteins and regions contribute to the function and regulation of cell signaling. Collectively, these papers exhibit the diverse roles of disorder in responding to a wide range of signals as to orchestrate an array of organismal processes. They also show that disorder contributes to signaling in a broad spectrum of species, ranging from micro-organisms to plants and animals.

Intrinsically disordered chaperones in plants and animalsThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 167-174 ◽  
Author(s):  
Peter Tompa ◽  
Denes Kovacs
Keyword(s):  
Stress Proteins ◽  
Intrinsically Disordered Proteins ◽  
Peer Review Process ◽  
Plant Stress ◽  
Late Embryogenesis Abundant ◽  
Disordered Proteins ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
And Function

Intrinsically disordered proteins (IDPs) are widespread in eukaryotes and fulfill important functions associated with signaling and regulation. Recent evidence points to a special and thus largely disrespected functional capacity of IDPs—that they can assist the folding of other proteins and prevent their aggregation, i.e., that they can act as chaperones. In this paper, we survey current information available on this phenomenon, with particular focus on (i) the structure and function of IDPs in general, (ii) disordered chaperones in plants, (iii) disordered chaperones in other organisms spanning from insects to mammals, (iv) the possible mechanisms of action of disordered chaperones, and (v) the possibility of two-faced (Janus) chaperone activity of disordered chaperones, which can assist the folding of both RNA and protein substrates. The evidence is most conclusive in the case of plant stress proteins, such as late embryogenesis abundant (LEA) proteins or dehydrins. We will show that the cellular function of LEA proteins in mitigating the damage caused by stress is clear; nevertheless, experiments carried out in vivo must be extended and the molecular mechanism of the action of IDP chaperones also requires clarification. Using these details, we chart out how far the field has progressed only to emphasize the long road ahead before chaperone function can be firmly established as part of the physiological mechanistic arsenal of the emerging group of IDPs.

scholarly journals The dynein light chain 8 (LC8) binds predominantly “in-register” to a multivalent intrinsically disordered partner

2020 ◽  
Vol 295 (15) ◽  
pp. 4912-4922 ◽  
Author(s):  
Patrick N. Reardon ◽  
Kayla A. Jara ◽  
Amber D. Rolland ◽  
Delaney A. Smith ◽  
Hanh T. M. Hoang ◽  
...  
Keyword(s):  
Light Chain ◽  
Intrinsically Disordered Proteins ◽  
Analytical Ultracentrifugation ◽  
Complex Dynamics ◽  
Regulatory Protein ◽  
Disordered Proteins ◽  
Dynein Light Chain ◽  
Linker Length ◽  
Intrinsically Disordered ◽  
Wide Range

Dynein light chain 8 (LC8) interacts with intrinsically disordered proteins (IDPs) and influences a wide range of biological processes. It is becoming apparent that among the numerous IDPs that interact with LC8, many contain multiple LC8-binding sites. Although it is established that LC8 forms parallel IDP duplexes with some partners, such as nucleoporin Nup159 and dynein intermediate chain, the molecular details of these interactions and LC8's interactions with other diverse partners remain largely uncharacterized. LC8 dimers could bind in either a paired “in-register” or a heterogeneous off-register manner to any of the available sites on a multivalent partner. Here, using NMR chemical shift perturbation, analytical ultracentrifugation, and native electrospray ionization MS, we show that LC8 forms a predominantly in-register complex when bound to an IDP domain of the multivalent regulatory protein ASCIZ. Using saturation transfer difference NMR, we demonstrate that at substoichiometric LC8 concentrations, the IDP domain preferentially binds to one of the three LC8 recognition motifs. Further, the differential dynamic behavior for the three sites and the size of the fully bound complex confirmed an in-register complex. Dynamics measurements also revealed that coupling between sites depends on the linker length separating these sites. These results identify linker length and motif specificity as drivers of in-register binding in the multivalent LC8–IDP complex assembly and the degree of compositional and conformational heterogeneity as a promising emerging mechanism for tuning of binding and regulation.

scholarly journals The Prediction of Intrinsically Disordered Proteins Based on Feature Selection

Algorithms ◽  
2019 ◽  
Vol 12 (2) ◽  
pp. 46 ◽  
Author(s):  
Hao He ◽  
Jiaxiang Zhao ◽  
Guiling Sun
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Back Propagation ◽  
Disordered Proteins ◽  
Evolutionary Information ◽  
Multi Layer Perceptron ◽  
Biological Functions ◽  
Training Process ◽  
Intrinsically Disordered ◽  
Wide Range ◽  
Simulation Results

Intrinsically disordered proteins perform a variety of important biological functions, which makes their accurate prediction useful for a wide range of applications. We develop a scheme for predicting intrinsically disordered proteins by employing 35 features including eight structural properties, seven physicochemical properties and 20 pieces of evolutionary information. In particular, the scheme includes a preprocessing procedure which greatly reduces the input features. Using two different windows, the preprocessed data containing not only the properties of the surroundings of the target residue but also the properties related to the specific target residue are fed into a multi-layer perceptron neural network as its inputs. The Adam algorithm for the back propagation together with the dropout algorithm to avoid overfitting are introduced during the training process. The training as well as testing our procedure is performed on the dataset DIS803 from a DisProt database. The simulation results show that the performance of our scheme is competitive in comparison with ESpritz and IsUnstruct.

scholarly journals Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1

2020 ◽  
Vol 48 (10) ◽  
pp. 5318-5331 ◽  
Author(s):  
Akshay Sridhar ◽  
Modesto Orozco ◽  
Rosana Collepardo-Guevara
Keyword(s):  
Binding Affinity ◽  
Binding Proteins ◽  
Intrinsically Disordered Proteins ◽  
Order Transition ◽  
Disordered Proteins ◽  
Chromatin Binding ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Wide Range ◽  
Nucleosome Binding

Abstract Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous binding to a wide range of different molecular targets, consistent with structural heterogeneity. Among the partially disordered chromatin-binding proteins, the H1 linker histone influences a myriad of chromatin characteristics including compaction, nucleosome spacing, transcription regulation, and the recruitment of other chromatin regulating proteins. Although it is now established that the long C-terminal domain (CTD) of H1 remains disordered upon nucleosome binding and that such disorder favours chromatin fluidity, the structural behaviour and thereby the role/function of the N-terminal domain (NTD) within chromatin is yet unresolved. On the basis of microsecond-long parallel-tempering metadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subtypes, we demonstrate that the NTD is completely unstructured in solution but undergoes an important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its DNA binding ability. Further, we show that the helical propensity of the H1 NTD is subtype-dependent and correlates with the experimentally observed binding affinity of H1 subtypes, suggesting an important functional implication of this disorder-to-order transition.

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