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Peirats-Llobet M, Yi C, Liew L, Berkowitz O, Narsai R, Lewsey M, Whelan J. Spatially resolved transcriptomic analysis of the germinating barley grain. Nucleic Acids Res 2023; 51:7798-7819. [PMID: 37351575 PMCID: PMC10450182 DOI: 10.1093/nar/gkad521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 06/24/2023] Open
Abstract
Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.
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Affiliation(s)
- Marta Peirats-Llobet
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Changyu Yi
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Lim Chee Liew
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
- Research Centre for Engineering Biology, College of Life Science, Zhejiang University, 718 East Haizhou Road, Haining, Jiaxing, Zhejiang 314400, China
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Li J, Hu S, Jian W, Xie C, Yang X. Plant antimicrobial peptides: structures, functions, and applications. BOTANICAL STUDIES 2021; 62:5. [PMID: 33914180 PMCID: PMC8085091 DOI: 10.1186/s40529-021-00312-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/13/2021] [Indexed: 05/20/2023]
Abstract
Antimicrobial peptides (AMPs) are a class of short, usually positively charged polypeptides that exist in humans, animals, and plants. Considering the increasing number of drug-resistant pathogens, the antimicrobial activity of AMPs has attracted much attention. AMPs with broad-spectrum antimicrobial activity against many gram-positive bacteria, gram-negative bacteria, and fungi are an important defensive barrier against pathogens for many organisms. With continuing research, many other physiological functions of plant AMPs have been found in addition to their antimicrobial roles, such as regulating plant growth and development and treating many diseases with high efficacy. The potential applicability of plant AMPs in agricultural production, as food additives and disease treatments, has garnered much interest. This review focuses on the types of plant AMPs, their mechanisms of action, the parameters affecting the antimicrobial activities of AMPs, and their potential applications in agricultural production, the food industry, breeding industry, and medical field.
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Affiliation(s)
- Junpeng Li
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China
| | - Shuping Hu
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China
| | - Wei Jian
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China
| | - Chengjian Xie
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China.
| | - Xingyong Yang
- College of Life Science, Chongqing Normal University, Chongqing, 401331, China.
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3
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Dib HX, de Oliveira DGL, de Oliveira CFR, Taveira GB, de Oliveira Mello E, Verbisk NV, Chang MR, Corrêa Junior D, Gomes VM, Macedo MLR. Biochemical characterization of a Kunitz inhibitor from Inga edulis seeds with antifungal activity against Candida spp. Arch Microbiol 2018; 201:223-233. [DOI: 10.1007/s00203-018-1598-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/03/2018] [Accepted: 11/19/2018] [Indexed: 11/25/2022]
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Das S, Pal U, Chandra Maiti N. Metal ions provide structural stability and compactness to tetrameric purothionin. RSC Adv 2016. [DOI: 10.1039/c6ra16576a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metal ions impart structural stability to the purothionin tetramer.
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Affiliation(s)
- Swagata Das
- Structural Biology & Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Uttam Pal
- Structural Biology & Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Nakul Chandra Maiti
- Structural Biology & Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
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5
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Vriens K, Cammue BPA, Thevissen K. Antifungal plant defensins: mechanisms of action and production. Molecules 2014; 19:12280-303. [PMID: 25153857 PMCID: PMC6271847 DOI: 10.3390/molecules190812280] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 07/29/2014] [Accepted: 08/04/2014] [Indexed: 12/18/2022] Open
Abstract
Plant defensins are small, cysteine-rich peptides that possess biological activity towards a broad range of organisms. Their activity is primarily directed against fungi, but bactericidal and insecticidal actions have also been reported. The mode of action of various antifungal plant defensins has been studied extensively during the last decades and several of their fungal targets have been identified to date. This review summarizes the mechanism of action of well-characterized antifungal plant defensins, including RsAFP2, MsDef1, MtDef4, NaD1 and Psd1, and points out the variety by which antifungal plant defensins affect microbial cell viability. Furthermore, this review summarizes production routes for plant defensins, either via heterologous expression or chemical synthesis. As plant defensins are generally considered non-toxic for plant and mammalian cells, they are regarded as attractive candidates for further development into novel antimicrobial agents.
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Affiliation(s)
- Kim Vriens
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, Heverlee 3001, Belgium
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, Heverlee 3001, Belgium.
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, Heverlee 3001, Belgium
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Oard SV. Deciphering a mechanism of membrane permeabilization by α-hordothionin peptide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1737-45. [PMID: 21315063 DOI: 10.1016/j.bbamem.2011.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Revised: 01/19/2011] [Accepted: 02/01/2011] [Indexed: 11/19/2022]
Abstract
α-Hordothionin (αHTH) belongs to thionins, the plant antimicrobial peptides with membrane-permeabilizing activity which is associated with broad-range antimicrobial activity. Experimental data have revealed a phospholipid-binding site and indicated formation of ion channels as well as membrane disruption activity of thionin. However, the mechanism of membrane permeabilization by thionin remained unknown. Here it is shown that thionin is a small water-selective channel. Unbiased high-precision molecular modeling revealed formation of a water-selective pore running through the αHTH double α-helix core when the peptide interacted with anions. Anion-induced unfolding of the C-end of the α2-helix opened a pore mouth. The pore started at the α2 C-end between the hydrophilic and the hydrophobic regions of the peptide surface and ended in the middle of the unique hydrophobic region at the C-end of the α1-helix. Highly conserved residues including cysteines and tyrosine lined the pore walls. A large positive electrostatic potential accumulated inside the pore. The narrow pore was, nonetheless, sufficient to accommodate at least one water molecule along the channel except for two constriction sites. Both constriction sites were formed by residues participating in the phospholipid-binding site. The channel properties resembled that of aquaporins with two selectivity filters, one at the entrance, inside the α2 C-end cavity, and a second in the middle of the channel. It is proposed that the αHTH water channel delivers water molecules to the bilayer center that leads to local membrane disruption. The proposed mechanism of membrane permeabilization by thionins explains seemingly controversial experimental data.
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Affiliation(s)
- Svetlana V Oard
- School of Plant, Environmental, and Soil Sciences, Louisiana State Agricultural Center, Louisiana State University, Baton Rouge, LA 70803, USA.
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Structural changes induced in thionins by chloride anions as determined by molecular dynamics simulations. Biophys Chem 2010; 147:42-52. [DOI: 10.1016/j.bpc.2009.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 12/21/2009] [Accepted: 12/23/2009] [Indexed: 11/23/2022]
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8
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Chen HF. Molecular dynamics simulation of phosphorylated KID post-translational modification. PLoS One 2009; 4:e6516. [PMID: 19654879 PMCID: PMC2717803 DOI: 10.1371/journal.pone.0006516] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 06/23/2009] [Indexed: 12/13/2022] Open
Abstract
Background Kinase-inducible domain (KID) as transcriptional activator can stimulate target gene expression in signal transduction by associating with KID interacting domain (KIX). NMR spectra suggest that apo-KID is an unstructured protein. After post-translational modification by phosphorylation, KID undergoes a transition from disordered to well folded protein upon binding to KIX. However, the mechanism of folding coupled to binding is poorly understood. Methodology To get an insight into the mechanism, we have performed ten trajectories of explicit-solvent molecular dynamics (MD) for both bound and apo phosphorylated KID (pKID). Ten MD simulations are sufficient to capture the average properties in the protein folding and unfolding. Conclusions Room-temperature MD simulations suggest that pKID becomes more rigid and stable upon the KIX-binding. Kinetic analysis of high-temperature MD simulations shows that bound pKID and apo-pKID unfold via a three-state and a two-state process, respectively. Both kinetics and free energy landscape analyses indicate that bound pKID folds in the order of KIX access, initiation of pKID tertiary folding, folding of helix αB, folding of helix αA, completion of pKID tertiary folding, and finalization of pKID-KIX binding. Our data show that the folding pathways of apo-pKID are different from the bound state: the foldings of helices αA and αB are swapped. Here we also show that Asn139, Asp140 and Leu141 with large Φ-values are key residues in the folding of bound pKID. Our results are in good agreement with NMR experimental observations and provide significant insight into the general mechanisms of binding induced protein folding and other conformational adjustment in post-translational modification.
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Affiliation(s)
- Hai-Feng Chen
- College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China.
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Carvalho ADO, Gomes VM. Plant defensins--prospects for the biological functions and biotechnological properties. Peptides 2009; 30:1007-20. [PMID: 19428780 DOI: 10.1016/j.peptides.2009.01.018] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 01/22/2009] [Accepted: 01/26/2009] [Indexed: 01/07/2023]
Abstract
Plant defensins are a prominent family of cationic peptides in the plant kingdom. They are structurally and functionally related to defensins that have been previously characterized in mammals and insects. They present molecular masses between 5 and 7kDa and possess a pattern of eight conserved Cys residues. The three-dimensional structure of plant defensins is small and globular. It has three anti-parallel beta-sheets and one alpha-helix that is stabilized by a structural motif composed of disulfide bridges. This motif is found in other peptides with biological activity and is called the Cys stabilized alphabeta motif (CSalphabeta). Based on the growing knowledge on defensin structure, gene expression and regulation, and also their in vitro biological activity, it has become clear that plant defensins are complex and sophisticated peptides whose function extends beyond their role in defense of plants against microbial infection. This review discusses recent data and will present comprehensive information regarding the study of defensins.
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Affiliation(s)
- André de Oliveira Carvalho
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense-Darcy Ribeiro, Campos dos Goytacazes-RJ, Brazil.
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10
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Chen HF. Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex. J Chem Theory Comput 2008; 4:1360-8. [DOI: 10.1021/ct800030s] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hai-Feng Chen
- College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
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11
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Oard S, Karki B, Enright F. Is there a difference in metal ion-based inhibition between members of thionin family: Molecular dynamics simulation study. Biophys Chem 2007; 130:65-75. [PMID: 17703869 DOI: 10.1016/j.bpc.2007.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 07/18/2007] [Accepted: 07/19/2007] [Indexed: 10/23/2022]
Abstract
Thionins have a considerable potential as antimicrobial compounds although their application may be restricted by metal ion-based inhibition of membrane permeabilizing activity. We previously reported the properties associated with the proposed mechanism of metal ion-based inhibition of beta-purothionin. In this study, we investigated the effects of metal ions on alpha-hordothionin which differs from beta-purothionin by eight out of 45 residues. Three of the differing residues are thought to be involved in the mechanism of metal ion-based inhibition in beta-purothionin. The structure and dynamics of alpha-hordothionin were explored using unconstrained molecular dynamics (MD) simulations in explicit water as a function of metal ions. Although the global fold is almost identical to that of beta-purothionin, alpha-hordothionin displays reduced fluctuating motions. Moreover, alpha-hordothionin is more resistant to the presence of metal ions than beta-purothionin. Mg(+2) ions do not affect alpha-hordothionin, whereas K(+) ions induce perturbations in the alpha2 helix, modify dynamics and electrostatic properties. Nevertheless, these changes are considerably smaller than those in beta-purothionin. The proposed mechanism of metal ion-based inhibition involves the hydrogen bonding network of Arg5-Arg30-Gly27, which regulates dynamic unfolding of the alpha2 C-end which is similar to beta-purothionin response. The key residues responsible for the increased resistance for alpha-hordothionin are Gly27 and Gly42 which replace Asn27 and Asp42 involved into the mechanism of metal ion-based inhibition in beta-purothionin. Comparison of MD simulations of alpha-hordothionin with beta-purothionin reveals dynamic properties which we believe are intrinsic properties of thionins with four disulphide bonds.
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Affiliation(s)
- Svetlana Oard
- LSU AgCenter Biotechnology Laboratory, Louisiana State University, 115 Wilson Bldg., LSU, Baton Rouge, LA 70803, USA.
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Soltani S, Keymanesh K, Sardari S. In silicoanalysis of antifungal peptides. Expert Opin Drug Discov 2007; 2:837-47. [DOI: 10.1517/17460441.2.6.837] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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