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Protein Intrinsic Disorder in Plant Biology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 May 2020) | Viewed by 23401

Special Issue Editors

Department of Biology, Kobenhavns Universitet, Copenhagen, Denmark
Interests: abiotic stress; gene regulatory networks; hormone responses; plant-specific transcription factors; protein intrinsic disorder
Special Issues, Collections and Topics in MDPI journals
Københavns Universitet, Copenhagen, Denmark
Interests: Structural biology, function from structural disorder, transmembrane signaling, transcriptional regulation, protein science, cellular hubs
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Topical Collection aims to collect high-quality review and original papers in the research field of plant protein intrinsic disorder. That intrinsically disordered proteins and regions, which lack a stable tertiary structure, participate in biological complexes, challenges our current perceptions of molecular interactions. Intrinsic disorder (ID) is especially prevalent in proteins involved in transcriptional regulation and cellular signaling but it also plays significant roles in other functional systems involving, e.g., chaperones and receptors and in physical phenomena such as the formation of membraneless organelles through phase separation. The flexibility and conformational plasticity of ID regions represent obvious functional advantages, making them readily accessible for various interactions and post-translational modifications. ID is challenging to investigate, but the recent rapid development of methods and strategies that can be specifically applied in studies of ID has dramatically increased the understanding of ID. Within recent years, ID has also emerged as important to plant biology, as documented by an increasing number of publications focusing on plant protein ID. Therefore, a topical collection on plant protein disorder is timely and highly relevant, broadly, to all fields within plant biology.

Prof. Dr. Karen Skriver
Prof. Dr. Birthe Kragelund
Guest Editors

Manuscript Submission Information

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Keywords

  • Plant sciences
  • Protein intrinsic disorder
  • Plant protein interactions
  • Chaperones
  • Phase separation
  • Transcriptional regulation
  • Cellular signaling

Published Papers (6 papers)

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Research

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18 pages, 5717 KiB  
Article
Evolution of A bHLH Interaction Motif
by Peter S. Millard, Birthe B. Kragelund and Meike Burow
Int. J. Mol. Sci. 2021, 22(1), 447; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22010447 - 05 Jan 2021
Cited by 5 | Viewed by 3577
Abstract
Intrinsically disordered proteins and regions with their associated short linear motifs play key roles in transcriptional regulation. The disordered MYC-interaction motif (MIM) mediates interactions between MYC and MYB transcription factors in Arabidopsis thaliana that are critical for constitutive and induced glucosinolate (GLS) biosynthesis. [...] Read more.
Intrinsically disordered proteins and regions with their associated short linear motifs play key roles in transcriptional regulation. The disordered MYC-interaction motif (MIM) mediates interactions between MYC and MYB transcription factors in Arabidopsis thaliana that are critical for constitutive and induced glucosinolate (GLS) biosynthesis. GLSs comprise a class of plant defense compounds that evolved in the ancestor of the Brassicales order. We used a diverse set of search strategies to discover additional occurrences of the MIM in other proteins and in other organisms and evaluate the findings by means of structural predictions, interaction assays, and biophysical experiments. Our search revealed numerous MIM instances spread throughout the angiosperm lineage. Experiments verify that several of the newly discovered MIM-containing proteins interact with MYC TFs. Only hits found within the same transcription factor family and having similar characteristics could be validated, indicating that structural predictions and sequence similarity are good indicators of whether the presence of a MIM mediates interaction. The experimentally validated MIMs are found in organisms outside the Brassicales order, showing that MIM function is broader than regulating GLS biosynthesis. Full article
(This article belongs to the Special Issue Protein Intrinsic Disorder in Plant Biology)
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25 pages, 5284 KiB  
Article
Similar Yet Different–Structural and Functional Diversity among Arabidopsis thaliana LEA_4 Proteins
by Patrick Knox-Brown, Tobias Rindfleisch, Anne Günther, Kim Balow, Anne Bremer, Dirk Walther, Markus S. Miettinen, Dirk K. Hincha and Anja Thalhammer
Int. J. Mol. Sci. 2020, 21(8), 2794; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21082794 - 17 Apr 2020
Cited by 12 | Viewed by 3434
Abstract
The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been [...] Read more.
The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics. Full article
(This article belongs to the Special Issue Protein Intrinsic Disorder in Plant Biology)
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24 pages, 40850 KiB  
Article
Computational Disorder Analysis in Ethylene Response Factors Uncovers Binding Motifs Critical to Their Diverse Functions
by Xiaolin Sun, Nawar Malhis, Bi Zhao, Bin Xue, Joerg Gsponer and Erik H. A. Rikkerink
Int. J. Mol. Sci. 2020, 21(1), 74; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010074 - 20 Dec 2019
Cited by 7 | Viewed by 3309
Abstract
APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERFs) play crucial roles in adaptation to stresses such as those caused by pathogens, wounding and cold. Although their name suggests a specific role in ethylene signalling, some ERF members also co-ordinate signals regulated by other key plant [...] Read more.
APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERFs) play crucial roles in adaptation to stresses such as those caused by pathogens, wounding and cold. Although their name suggests a specific role in ethylene signalling, some ERF members also co-ordinate signals regulated by other key plant stress hormones such as jasmonate, abscisic acid and salicylate. We analysed a set of ERF proteins from three divergent plant species for intrinsically disorder regions containing conserved segments involved in protein–protein interaction known as Molecular Recognition Features (MoRFs). Then we correlated the MoRFs identified with a number of known functional features where these could be identified. Our analyses suggest that MoRFs, with plasticity in their disordered surroundings, are highly functional and may have been shuffled between related protein families driven by selection. A particularly important role may be played by the alpha helical component of the structured DNA binding domain to permit specificity. We also present examples of computationally identified MoRFs that have no known function and provide a valuable conceptual framework to link both disordered and ordered structural features within this family to diverse function. Full article
(This article belongs to the Special Issue Protein Intrinsic Disorder in Plant Biology)
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20 pages, 2538 KiB  
Article
Soyuretox, an Intrinsically Disordered Polypeptide Derived from Soybean (Glycine Max) Ubiquitous Urease with Potential Use as a Biopesticide
by Karine Kappaun, Anne H. S. Martinelli, Valquiria Broll, Barbara Zambelli, Fernanda C. Lopes, Rodrigo Ligabue-Braun, Leonardo L. Fruttero, Natalia R. Moyetta, Carla D. Bonan, Celia R. Carlini and Stefano Ciurli
Int. J. Mol. Sci. 2019, 20(21), 5401; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20215401 - 30 Oct 2019
Cited by 5 | Viewed by 3029
Abstract
Ureases from different biological sources display non-ureolytic properties that contribute to plant defense, in addition to their classical enzymatic urea hydrolysis. Antifungal and entomotoxic effects were demonstrated for Jaburetox, an intrinsically disordered polypeptide derived from jack bean (Canavalia ensiformis) urease. Here [...] Read more.
Ureases from different biological sources display non-ureolytic properties that contribute to plant defense, in addition to their classical enzymatic urea hydrolysis. Antifungal and entomotoxic effects were demonstrated for Jaburetox, an intrinsically disordered polypeptide derived from jack bean (Canavalia ensiformis) urease. Here we describe the properties of Soyuretox, a polypeptide derived from soybean (Glycine max) ubiquitous urease. Soyuretox was fungitoxic to Candida albicans, leading to the production of reactive oxygen species. Soyuretox further induced aggregation of Rhodnius prolixus hemocytes, indicating an interference on the insect immune response. No relevant toxicity of Soyuretox to zebrafish larvae was observed. These data suggest the presence of antifungal and entomotoxic portions of the amino acid sequences encompassing both Soyuretox and Jaburetox, despite their small sequence identity. Nuclear Magnetic Resonance (NMR) and circular dichroism (CD) spectroscopic data revealed that Soyuretox, in analogy with Jaburetox, possesses an intrinsic and largely disordered nature. Some folding is observed upon interaction of Soyuretox with sodium dodecyl sulfate (SDS) micelles, taken here as models for membranes. This observation suggests the possibility for this protein to modify its secondary structure upon interaction with the cells of the affected organisms, leading to alterations of membrane integrity. Altogether, Soyuretox can be considered a promising biopesticide for use in plant protection. Full article
(This article belongs to the Special Issue Protein Intrinsic Disorder in Plant Biology)
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Review

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35 pages, 2662 KiB  
Review
Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications
by Edoardo Salladini, Maria L. M. Jørgensen, Frederik F. Theisen and Karen Skriver
Int. J. Mol. Sci. 2020, 21(24), 9755; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21249755 - 21 Dec 2020
Cited by 11 | Viewed by 4667
Abstract
Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors [...] Read more.
Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering. Full article
(This article belongs to the Special Issue Protein Intrinsic Disorder in Plant Biology)
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26 pages, 2047 KiB  
Review
Common Functions of Disordered Proteins across Evolutionary Distant Organisms
by Arndt Wallmann and Christopher Kesten
Int. J. Mol. Sci. 2020, 21(6), 2105; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21062105 - 19 Mar 2020
Cited by 27 | Viewed by 4809
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Protein Intrinsic Disorder in Plant Biology)
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