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Structural/Functional Characterization of Plant Proteins

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 (30 September 2020) | Viewed by 31723

Special Issue Editors


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Guest Editor
Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20122 Milan, Italy
Interests: food recycling; plant enzyme inhibitors; protein structure and function; recombinant proteins; seed germination; seed storage proteins
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Co-Guest Editor
Department of Food, Environmental and Nutritional Sciences, University of Milan, DISMA, Via G Celoria 2, I-20133 Milan, Italy
Interests: food allergens; structural investigation methodologies

Special Issue Information

Dear Colleagues,

Disentangling the relationship between protein structure and function continues to be a priority not only in several fields of structural biology, including molecular biology, biochemistry, and protein engineering, but also in plant physiology and food sciences, including new industrial applications.

It is a well-established fact that even minor structural variations of a protein may dramatically affect its function and its capacity to interact with other molecules, no matter which structural level is involved. Moreover, protein conformation is influenced, and can be modified, by its environmental surrounding. This is especially true for plant proteins that find applications in several complex systems.

Today, there is an increasing interest in plant proteins. Plants are able to accumulate—in specialized reserve tissues—huge amounts of proteins with unique and interesting structural features.

Apart from their natural biology, their nutritional impact, and their relevance to the food industry, plant proteins find applications in a variety of non-food systems. These are usually complex systems, where the interactions between different components are key factors that determine and influence some typical features of the final product.

This Special Issue aims to collect, from the broadest context, the current status about plant proteins and to contribute to their exploitation and valorization. Research papers and reviews that expand knowledge about the molecular determinants driving their structure–function relationships, including in vivo and in vitro interactions with other proteins and other macromolecules, as well as their potential for innovative applications in all fields, taking into account bioactivities implicated in human nutrition and health, are welcome.

Prof. Alessio Scarafoni
Prof. Stefania Iametti
Guest Editors

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Keywords

  • protein–protein interactions
  • protein structure
  • complex systems
  • food systems
  • plant biochemistry
  • plant seeds.

Published Papers (10 papers)

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Research

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9 pages, 2061 KiB  
Communication
The Nuclear Localization of the DnaJ-Like Zinc Finger Domain-Containing Protein EDA3 Affects Seed Development in Arabidopsis thaliana
by Meng-Juan Kong, Na Huang, Si-Ming Chen, Han-Yu Liang, Xin-Ya Liu, Zhong Zhuang and Shan Lu
Int. J. Mol. Sci. 2020, 21(21), 7979; https://doi.org/10.3390/ijms21217979 - 27 Oct 2020
Cited by 4 | Viewed by 2005
Abstract
The DnaJ-like zinc finger domain-containing proteins are involved in different aspects of plastid function and development. Some of these proteins were recently reported to have dual subcellular localization in the nucleus and plastids. One member of this family, PSA2 (AT2G34860), was found to [...] Read more.
The DnaJ-like zinc finger domain-containing proteins are involved in different aspects of plastid function and development. Some of these proteins were recently reported to have dual subcellular localization in the nucleus and plastids. One member of this family, PSA2 (AT2G34860), was found to localize to the thylakoid lumen and regulate the assembly of photosystem I (PSI). However, PSA2 was also annotated as Embryo sac Development Arrest 3 (EDA3) from the observation that its embryo sac development was arrested at the two-nuclear stage. In this study, we characterized the eda3 mutant, and demonstrated that, as compared with the wild-type (WT) plants, the mutant has shorter siliques, fewer siliques per plant, and fewer seeds per silique. Both aborted and undeveloped ovules were observed in siliques of the mutant. By immunoblot analysis, we found that, different from the chloroplast localization in mature leaves, EDA3 localizes in the nucleus in seeds. A nuclear localization signal was identified from the deduced amino acid sequence of EDA3, and also proved to be sufficient for directing its fusion peptide into the nucleus. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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26 pages, 9421 KiB  
Article
Hevein-Like Antimicrobial Peptides Wamps: Structure–Function Relationship in Antifungal Activity and Sensitization of Plant Pathogenic Fungi to Tebuconazole by WAMP-2-Derived Peptides
by Tatyana Odintsova, Larisa Shcherbakova, Marina Slezina, Tatyana Pasechnik, Bakhyt Kartabaeva, Ekaterina Istomina and Vitaly Dzhavakhiya
Int. J. Mol. Sci. 2020, 21(21), 7912; https://doi.org/10.3390/ijms21217912 - 24 Oct 2020
Cited by 18 | Viewed by 2660
Abstract
Hevein-like antimicrobial peptides (AMPs) comprise a family of plant AMPs with antifungal activity, which harbor a chitin-binding site involved in interactions with chitin of fungal cell walls. However, the mode of action of hevein-like AMPs remains poorly understood. This work reports the structure–function [...] Read more.
Hevein-like antimicrobial peptides (AMPs) comprise a family of plant AMPs with antifungal activity, which harbor a chitin-binding site involved in interactions with chitin of fungal cell walls. However, the mode of action of hevein-like AMPs remains poorly understood. This work reports the structure–function relationship in WAMPs—hevein-like AMPs found in wheat (Triticum kiharae Dorof. et Migush.) and later in other Poaceae species. The effect of WAMP homologues differing at position 34 and the antifungal activity of peptide fragments derived from the central, N- and C-terminal regions of one of the WAMPs, namely WAMP-2, on spore germination of different plant pathogenic fungi were studied. Additionally, the ability of WAMP-2-derived peptides to potentiate the fungicidal effect of tebuconazole, one of the triazole fungicides, towards five cereal-damaging fungi was explored in vitro by co-application of WAMP-2 fragments with Folicur® EC 250 (25% tebuconazole). The antifungal activity of WAMP homologues and WAMP-2-derived peptides varied depending on the fungus, suggesting multiple modes of action for WAMPs against diverse pathogens. Folicur® combined with the WAMP-2 fragments inhibited the spore germination at a much greater level than the fungicide alone, and the type of interactions was either synergistic or additive, depending on the target fungus and concentration combinations of the compounds. The combinations, which resulted in synergism and drastically enhanced the sensitivity to tebuconazole, were revealed for all five fungi by a checkerboard assay. The ability to synergistically interact with a fungicide and exacerbate the sensitivity of plant pathogenic fungi to a commercial antifungal agent is a novel and previously uninvestigated property of hevein-like AMPs. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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15 pages, 2853 KiB  
Article
High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtii—An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle
by Théo Le Moigne, Pierre Crozet, Stéphane D. Lemaire and Julien Henri
Int. J. Mol. Sci. 2020, 21(20), 7787; https://doi.org/10.3390/ijms21207787 - 21 Oct 2020
Cited by 6 | Viewed by 3118
Abstract
The Calvin–Benson cycle is the key metabolic pathway of photosynthesis responsible for carbon fixation and relies on eleven conserved enzymes. Ribose-5-phosphate isomerase (RPI) isomerizes ribose-5-phosphate into ribulose-5-phosphate and contributes to the regeneration of the Rubisco substrate. Plant RPI is the target of diverse [...] Read more.
The Calvin–Benson cycle is the key metabolic pathway of photosynthesis responsible for carbon fixation and relies on eleven conserved enzymes. Ribose-5-phosphate isomerase (RPI) isomerizes ribose-5-phosphate into ribulose-5-phosphate and contributes to the regeneration of the Rubisco substrate. Plant RPI is the target of diverse post-translational modifications including phosphorylation and thiol-based modifications to presumably adjust its activity to the photosynthetic electron flow. Here, we describe the first experimental structure of a photosynthetic RPI at 1.4 Å resolution. Our structure confirms the composition of the catalytic pocket of the enzyme. We describe the homo-dimeric state of the protein that we observed in the crystal and in solution. We also map the positions of previously reported post-translational modifications and propose mechanisms by which they may impact the catalytic parameters. The structural data will inform the biochemical modeling of photosynthesis. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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15 pages, 2956 KiB  
Article
Lupinus albus γ-Conglutin, a Protein Structurally Related to GH12 Xyloglucan-Specific Endo-Glucanase Inhibitor Proteins (XEGIPs), Shows Inhibitory Activity against GH2 β-Mannosidase
by Stefano De Benedetti, Elisabetta Galanti, Jessica Capraro, Chiara Magni and Alessio Scarafoni
Int. J. Mol. Sci. 2020, 21(19), 7305; https://doi.org/10.3390/ijms21197305 - 3 Oct 2020
Cited by 8 | Viewed by 2403
Abstract
γ-conglutin (γC) is a major protein of Lupinus albus seeds, but its function is still unknown. It shares high structural similarity with xyloglucan-specific endo-glucanase inhibitor proteins (XEGIPs) and, to a lesser extent, with Triticum aestivum endoxylanase inhibitors (TAXI-I), active against fungal glycoside hydrolases [...] Read more.
γ-conglutin (γC) is a major protein of Lupinus albus seeds, but its function is still unknown. It shares high structural similarity with xyloglucan-specific endo-glucanase inhibitor proteins (XEGIPs) and, to a lesser extent, with Triticum aestivum endoxylanase inhibitors (TAXI-I), active against fungal glycoside hydrolases GH12 and GH11, respectively. However, γC lacks both these inhibitory activities. Since β-galactomannans are major components of the cell walls of endosperm in several legume plants, we tested the inhibitory activity of γC against a GH2 β-mannosidase (EC 3.2.1.25). γC was actually able to inhibit the enzyme, and this effect was enhanced by the presence of zinc ions. The stoichiometry of the γC/enzyme interaction was 1:1, and the calculated Ki was 1.55 μM. To obtain further insights into the interaction between γC and β-mannosidase, an in silico structural bioinformatic approach was followed, including some docking analyses. By and large, this work describes experimental findings that highlight new scenarios for understanding the natural role of γC. Although structural predictions can leave space for speculative interpretations, the full complexity of the data reported in this work allows one to hypothesize mechanisms of action for the basis of inhibition. At least two mechanisms seem plausible, both involving lupin-γC-peculiar structures. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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15 pages, 3218 KiB  
Article
Characterization of FcXTH2, a Novel Xyloglucan Endotransglycosylase/Hydrolase Enzyme of Chilean Strawberry with Hydrolase Activity
by Luis Morales-Quintana, Dina Beltrán, Ángela Mendez-Yañez, Felipe Valenzuela-Riffo, Raúl Herrera and María Alejandra Moya-León
Int. J. Mol. Sci. 2020, 21(9), 3380; https://doi.org/10.3390/ijms21093380 - 11 May 2020
Cited by 9 | Viewed by 3208
Abstract
Xyloglucan endotransglycosylase/hydrolases (XTHs) are cell wall enzymes with hydrolase (XEH) and/or endotransglycosylase (XET) activities. As they are involved in the modification of the xyloglucans, a type of hemicellulose present in the cell wall, they are believed to be very important in different processes, [...] Read more.
Xyloglucan endotransglycosylase/hydrolases (XTHs) are cell wall enzymes with hydrolase (XEH) and/or endotransglycosylase (XET) activities. As they are involved in the modification of the xyloglucans, a type of hemicellulose present in the cell wall, they are believed to be very important in different processes, including growth, development, and fruit ripening. Previous studies suggest that XTHs might play a key role in development and ripening of Fragaria chiloensis fruit, and its characterization is pending. Therefore, in order to provide a biochemical characterization of the FcXTH2 enzyme to explain its possible role in strawberry development, the molecular cloning and the heterologous expression of FcXTH2 were performed. The recombinant FcXTH2 was active and displayed mainly XEH activity. The optimal pH and temperature are 5.5 and 37 °C, respectively. A KM value of 0.029 mg mL−1 was determined. Additionally, its protein structural model was built through comparative modeling methodology. The model showed a typically β-jelly-roll type folding in which the catalytic motif was oriented towards the FcXTH2 central cavity. Using molecular docking, protein-ligand interactions were explored, finding better interaction with xyloglucan than with cellulose. The data provided groundwork for understanding, at a molecular level, the enzymatic mechanism of FcXTH2, an important enzyme acting during the development of the Chilean strawberry. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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16 pages, 7268 KiB  
Article
Engineering Herbicide-Tolerance Rice Expressing an Acetohydroxyacid Synthase with a Single Amino Acid Deletion
by Jun Fang,, Changzhao Wan, Wei Wang, Liuyin Ma, Xinqi Wang, Can Cheng, Jihua Zhou, Yongjin Qiao and Xiao Wang
Int. J. Mol. Sci. 2020, 21(4), 1265; https://doi.org/10.3390/ijms21041265 - 13 Feb 2020
Cited by 2 | Viewed by 3055
Abstract
The acetohydroxyacid synthase (AHAS) is an essential enzyme involved in branched amino acids. Several herbicides wither weeds via inhibiting AHAS activity, and the AHAS mutants show tolerance to these herbicides. However, most AHAS mutations are residue substitutions but not residue deletion. Here, residue [...] Read more.
The acetohydroxyacid synthase (AHAS) is an essential enzyme involved in branched amino acids. Several herbicides wither weeds via inhibiting AHAS activity, and the AHAS mutants show tolerance to these herbicides. However, most AHAS mutations are residue substitutions but not residue deletion. Here, residue deletion was used to engineering the AHAS gene and herbicide-tolerant rice. Molecular docking analysis predicted that the W548 of the AHAS was a residue deletion to generate herbicide tolerance. The AHAS-ΔW548 protein was generated in vitro to remove the W548 residue. Interestingly, the deletion led to the tetramer dissociation of the AHAS, while this dissociation did not reduce the activity of the AHAS. Moreover, the W548 deletion contributed to multi-family herbicides tolerance. Specially, it conferred more tolerance to sulfometuron-methyl and bispyribac-sodium than the W548L substitution. Further analysis revealed that AHAS-ΔW548 had the best performance on the sulfometuron-methyl tolerance compared to the wild-type control. Over-expression of the AHAS-ΔW548 gene into rice led to the tolerance of multiple herbicides in the transgenic line. The T-DNA insertion and the herbicide treatment did not affect the agronomic traits and yields, while more branched-chain amino acids were detected in transgenic rice seeds. Residue deletion of W548 in the AHAS could be a useful strategy for engineering herbicide tolerant rice. The increase of branched-chain amino acids might improve the umami tastes of the rice. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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19 pages, 4807 KiB  
Article
New Insights into the Structure-Function Relationship of the Endosomal-Type Na+, K+/H+ Antiporter NHX6 from Mulberry (Morus notabilis)
by Boning Cao, Zhongqiang Xia, Changying Liu, Wei Fan, Shuai Zhang, Qiao Liu, Zhonghuai Xiang and Aichun Zhao
Int. J. Mol. Sci. 2020, 21(2), 428; https://doi.org/10.3390/ijms21020428 - 9 Jan 2020
Cited by 8 | Viewed by 2760
Abstract
The endosomal-type Na+, K+/H+ antiporters (NHXs) play important roles in K+, vesicle pH homeostasis, and protein trafficking in plant. However, the structure governing ion transport mechanism and the key residues related to the structure–function of the [...] Read more.
The endosomal-type Na+, K+/H+ antiporters (NHXs) play important roles in K+, vesicle pH homeostasis, and protein trafficking in plant. However, the structure governing ion transport mechanism and the key residues related to the structure–function of the endosomal-type NHXs remain unclear. Here, the structure-function relationship of the only endosomal-type NHX from mulberry, MnNHX6, was investigated by homology modeling, mutagenesis, and localization analyses in yeast. The ectopic expression of MnNHX6 in arabidopsis and Nhx1 mutant yeast can enhance their salt tolerance. MnNHX6’s three-dimensional structure, established by homology modeling, was supported by empirical, phylogenetic, and experimental data. Structure analysis showed that MnNHX6 contains unusual 13 transmembrane helices, but the structural core formed by TM5-TM12 assembly is conserved. Localization analysis showed that MnNHX6 has the same endosomal localization as yeast Nhx1/VPS44, and Arg402 is important for protein stability of MnNHX6. Mutagenesis analysis demonstrated MnNHX6 contains a conserved cation binding mechanism and a similar charge-compensated pattern as NHE1, but shares a different role in ion selectivity than the vacuolar-type NHXs. These results improve our understanding of the role played by the structure–function related key residues of the plant endosomal-type NHXs, and provide a basis for the ion transport mechanism study of endosomal-type NHXs. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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17 pages, 2557 KiB  
Article
Comparative Analysis of the PIN Auxin Transporter Gene Family in Different Plant Species: A Focus on Structural and Expression Profiling of PINs in Solanum tuberosum
by Chenghui Yang, Dongdong Wang, Chao Zhang, Nana Kong, Haoli Ma and Qin Chen
Int. J. Mol. Sci. 2019, 20(13), 3270; https://doi.org/10.3390/ijms20133270 - 3 Jul 2019
Cited by 15 | Viewed by 3776
Abstract
Plant growth and morphogenesis largely benefit from cell elongation and expansion and are normally regulated by environmental stimuli and endogenous hormones. Auxin, as one of the most significant plant growth regulators, controls various phases of plant growth and development. The PIN-FORMED (PIN) gene [...] Read more.
Plant growth and morphogenesis largely benefit from cell elongation and expansion and are normally regulated by environmental stimuli and endogenous hormones. Auxin, as one of the most significant plant growth regulators, controls various phases of plant growth and development. The PIN-FORMED (PIN) gene family of trans-membrane proteins considered as auxin efflux carriers plays a pivotal role in polar auxin transport and then mediates the growth of different plant tissues. In this study, the phylogenetic relationship and structural compositions of the PIN gene family in 19 plant species covering plant major lineages from algae to angiosperms were identified and analyzed by employing multiple bioinformatics methods. A total of 155 PIN genes were identified in these species and found that representative of the PIN gene family in algae came into existence and rapidly expanded in angiosperms (seed plants). The phylogenetic analysis indicated that the PIN proteins could be divided into 14 distinct clades, and the origin of PIN proteins could be traced back to the common ancestor of green algae. The structural analysis revealed that two putative types (canonical and noncanonical PINs) existed among the PIN proteins according to the length and the composition of the hydrophilic domain of the protein. The expression analysis of the PIN genes exhibited inordinate responsiveness to auxin (IAA) and ABA both in shoots and roots of Solanum tuberosum. While the majority of the StPINs were up-regulated in shoot and down-regulated in root by the two hormones. The majority of PIN genes had one or more putative auxin responses and ABA-inducible response elements in their promoter regions, respectively, implying that these phytohormones regulated the expression of StPIN genes. Our study emphasized the origin and expansion of the PIN gene family and aimed at providing useful insights for further structural and functional exploration of the PIN gene family in the future. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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Review

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17 pages, 2409 KiB  
Review
Roles of Organellar RNA-Binding Proteins in Plant Growth, Development, and Abiotic Stress Responses
by Kwanuk Lee and Hunseung Kang
Int. J. Mol. Sci. 2020, 21(12), 4548; https://doi.org/10.3390/ijms21124548 - 26 Jun 2020
Cited by 29 | Viewed by 4138
Abstract
Organellar gene expression (OGE) in chloroplasts and mitochondria is primarily modulated at post-transcriptional levels, including RNA processing, intron splicing, RNA stability, editing, and translational control. Nucleus-encoded Chloroplast or Mitochondrial RNA-Binding Proteins (nCMRBPs) are key regulatory factors that are crucial for the fine-tuned regulation [...] Read more.
Organellar gene expression (OGE) in chloroplasts and mitochondria is primarily modulated at post-transcriptional levels, including RNA processing, intron splicing, RNA stability, editing, and translational control. Nucleus-encoded Chloroplast or Mitochondrial RNA-Binding Proteins (nCMRBPs) are key regulatory factors that are crucial for the fine-tuned regulation of post-transcriptional RNA metabolism in organelles. Although the functional roles of nCMRBPs have been studied in plants, their cellular and physiological functions remain largely unknown. Nevertheless, existing studies that have characterized the functions of nCMRBP families, such as chloroplast ribosome maturation and splicing domain (CRM) proteins, pentatricopeptide repeat (PPR) proteins, DEAD-Box RNA helicase (DBRH) proteins, and S1-domain containing proteins (SDPs), have begun to shed light on the role of nCMRBPs in plant growth, development, and stress responses. Here, we review the latest research developments regarding the functional roles of organellar RBPs in RNA metabolism during growth, development, and abiotic stress responses in plants. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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25 pages, 2950 KiB  
Review
Molecular Functionality of Plant Proteins from Low- to High-Solid Systems with Ligand and Co-Solute
by Vilia Darma Paramita, Naksit Panyoyai and Stefan Kasapis
Int. J. Mol. Sci. 2020, 21(7), 2550; https://doi.org/10.3390/ijms21072550 - 6 Apr 2020
Cited by 11 | Viewed by 3667
Abstract
In the food industry, proteins are regarded as multifunctional systems whose bioactive hetero-polymeric properties are affected by physicochemical interactions with the surrounding components in formulations. Due to their nutritional value, plant proteins are increasingly considered by the new product developer to provide three-dimensional [...] Read more.
In the food industry, proteins are regarded as multifunctional systems whose bioactive hetero-polymeric properties are affected by physicochemical interactions with the surrounding components in formulations. Due to their nutritional value, plant proteins are increasingly considered by the new product developer to provide three-dimensional assemblies of required structure, texture, solubility and interfacial/bulk stability with physical, chemical or enzymatic treatment. This molecular flexibility allows them to form systems for the preservation of fresh food, retention of good nutrition and interaction with a range of microconstituents. While, animal- and milk-based proteins have been widely discussed in the literature, the role of plant proteins in the development of functional foods with enhanced nutritional profile and targeted physiological effects can be further explored. This review aims to look into the molecular functionality of plant proteins in relation to the transport of bioactive ingredients and interaction with other ligands and proteins. In doing so, it will consider preparations from low- to high-solids and the effect of structural transformation via gelation, phase separation and vitrification on protein functionality as a delivery vehicle or heterologous complex. Applications for the design of novel functional foods and nutraceuticals will also be discussed. Full article
(This article belongs to the Special Issue Structural/Functional Characterization of Plant Proteins)
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