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Long Q, Qiu S, Man J, Ren D, Xu N, Luo R. OsAAI1 Increases Rice Yield and Drought Tolerance Dependent on ABA-Mediated Regulatory and ROS Scavenging Pathway. RICE (NEW YORK, N.Y.) 2023; 16:35. [PMID: 37535208 PMCID: PMC10400514 DOI: 10.1186/s12284-023-00650-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023]
Abstract
In this study, we investigated the function of OsAAI1 in yield and drought tolerance by constructing overexpression line OE-OsAAI1 and mutant line osaai1. Bioinformatics analysis showed that the AAI gene-OsAAI1- belongs to the HPS_like subfamily of the AAI_LTSS superfamily, and OsAAI1 was localized in the nucleus. The expression of OsAAI1 was significantly induced by ABA and drought stress. OsAAI1 overexpression (OE19) significantly increased, and gene mutant (osaai1-1) repressed plant height, primary root length, lateral root number, grain size and yield in rice. Moreover, physiological and biochemical analyses showed that osaai1 was sensitive to drought stress, while OE19 enhanced the drought tolerance in rice. DAB and NBT staining revealed that under drought treatment, osaai1 accumulated a large amount of ROS compared with the wild type, while OE19 accumulated the least, and CAT, APX, GPX, GR activities were higher in OE19 and lower in osaai1, suggesting that OE19 improves rice tolerance to drought stress by enhancing ROS scavenging ability. OE19 also induce the expression of ABA-mediated regulatory pathway genes and enhance accumulation of ABA content in rice seedling. Predictably, OE19 displayed enhanced sensitivity to ABA, and ROS accumulation was significantly higher than in wild type and osaai1 under 3 µM ABA treatment. Thus, these results suggest that OsAAI1 is a positive regulator of rice yield and drought tolerance dependent on the ABA-mediated regulatory and ROS scavenging pathway.
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Affiliation(s)
- Qing Long
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Shichun Qiu
- Chongqing Three Gorges Academy of Agricultural Sciences, Wanzhou, Chongqing City, 404155, China
| | - Jianmin Man
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Denghong Ren
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Ning Xu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Rui Luo
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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Dos Santos C, Franco OL. Pathogenesis-Related Proteins (PRs) with Enzyme Activity Activating Plant Defense Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112226. [PMID: 37299204 DOI: 10.3390/plants12112226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 06/12/2023]
Abstract
Throughout evolution, plants have developed a highly complex defense system against different threats, including phytopathogens. Plant defense depends on constitutive and induced factors combined as defense mechanisms. These mechanisms involve a complex signaling network linking structural and biochemical defense. Antimicrobial and pathogenesis-related (PR) proteins are examples of this mechanism, which can accumulate extra- and intracellular space after infection. However, despite their name, some PR proteins are present at low levels even in healthy plant tissues. When they face a pathogen, these PRs can increase in abundance, acting as the first line of plant defense. Thus, PRs play a key role in early defense events, which can reduce the damage and mortality caused by pathogens. In this context, the present review will discuss defense response proteins, which have been identified as PRs, with enzymatic action, including constitutive enzymes, β-1,3 glucanase, chitinase, peroxidase and ribonucleases. From the technological perspective, we discuss the advances of the last decade applied to the study of these enzymes, which are important in the early events of higher plant defense against phytopathogens.
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Affiliation(s)
- Cristiane Dos Santos
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
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3
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Barashkova AS, Smirnov AN, Zorina ES, Rogozhin EA. Diversity of Cationic Antimicrobial Peptides in Black Cumin ( Nigella sativa L.) Seeds. Int J Mol Sci 2023; 24:ijms24098066. [PMID: 37175769 PMCID: PMC10179141 DOI: 10.3390/ijms24098066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Black cumin (Nigella sativa L.) is known to possess a wide variety of antimicrobial peptides belonging to different structural families. Three novel antimicrobial peptides have been isolated from black cumin seeds. Two of them were attributed as members of the non-specific lipid transfer proteins family, and one as a defensin. We have made an attempt of using the proteomic approach for novel antimicrobial peptides search in N. sativa seeds as well. The use of a well-established approach that includes extraction and fractionation stages remains relevant even in the case of novel peptides search because of the lacking N. sativa genome data. Novel peptides demonstrate a spectrum of antimicrobial activity against plant pathogenic organisms that may cause economically important crop diseases. These results obtained allow considering these molecules as candidates to be applied in "next-generation" biopesticides development for agricultural use.
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Affiliation(s)
- Anna S Barashkova
- Laboratory of Neuroreceptors and Neuroregulators, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117437 Moscow, Russia
- Laboratory of Biochemistry and Ecology of Microorganisms, All-Russian Institute for Plant Protection, 196608 Pushkin, Russia
| | - Alexey N Smirnov
- Department of Plant Protection, Timiryazev Russian State Agrarian University, 127434 Moscow, Russia
| | - Elena S Zorina
- Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Eugene A Rogozhin
- Laboratory of Neuroreceptors and Neuroregulators, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117437 Moscow, Russia
- Laboratory of Biochemistry and Ecology of Microorganisms, All-Russian Institute for Plant Protection, 196608 Pushkin, Russia
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, 152742 Borok, Russia
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Li Q, Zhai W, Wei J, Jia Y. Rice lipid transfer protein, OsLTPL23, controls seed germination by regulating starch-sugar conversion and ABA homeostasis. Front Genet 2023; 14:1111318. [PMID: 36726806 PMCID: PMC9885049 DOI: 10.3389/fgene.2023.1111318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Abstract
Seed germination is vital for ensuring the continuity of life in spermatophyte. High-quality seed germination usually represents good seedling establishment and plant production. Here, we identified OsLTPL23, a putative rice non-specific lipid transport protein, as an important regulator responsible for seed germination. Subcellular localization analysis confirmed that OsLTPL23 is present in the plasma membrane and nucleus. The knockout mutants of OsLTPL23 were generated by CRISPR/Cas9-mediated genome editing, and osltpl23 lines significantly germinated slower and lower than the Nipponbare (NIP). Starch and soluble sugar contents measurement showed that OsLTPL23 may have alpha-amylase inhibitor activity, and high soluble sugar content may be a causal agent for the delayed seed germination of osltpl23 mutants. Transcript profiles in the germinating seeds exhibited that the abscisic acid (ABA)-responsive genes, OsABI3 and OsABI5, and biosynthesis genes, OsNCED1, OsNCED2, OsNCED3 and OsNCED4, are obviously upregulated in the osltpl23 mutants compared to NIP plants, conversely, ABA metabolism genes OsABA8ox1, OsABA8ox2 and OsABA8ox3 are stepwise decreased. Further investigations found that osltpl23 mutants displays weakened early seedling growth, with elevated gene expresssion of ABA catabolism genes and repressive transcription response of defence-related genes OsWRKY45, OsEiN3, OsPR1a, OsPR1b and OsNPR1. Integrated analysis indicated that OsLTPL23 may exert an favorable effect on rice seed germination and early seedling growth via modulating endogenous ABA homeostasis. Collectively, our study provides important insights into the roles of OsLTPL23-mediated carbohydrate conversion and endogenous ABA pathway on seed germination and early seedling growth, which contributes to high-vigor seed production in rice breeding.
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Affiliation(s)
- Quanlin Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiaping Wei
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Yanfeng Jia
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China,*Correspondence: Yanfeng Jia,
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Huang MD, Wu CW, Chou HY, Cheng SY, Chang HY. The revealing of a novel lipid transfer protein lineage in green algae. BMC PLANT BIOLOGY 2023; 23:21. [PMID: 36627558 PMCID: PMC9832785 DOI: 10.1186/s12870-023-04040-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Non-specific lipid transfer proteins (nsLTPs) are a group of small and basic proteins that can bind and transfer various lipid molecules to the apoplastic space. A typical nsLTP carries a conserved architecture termed eight-cysteine motif (8CM), a scaffold of loop-linked helices folding into a hydrophobic cavity for lipids binding. Encoded by a multigene family, nsLTPs are widely distributed in terrestrial plants from bryophytes to angiosperms with dozens of gene members in a single species. Although the nsLTPs in the most primitive plants such as Marchantia already reach 14 members and are divergent enough to form separate groups, so far none have been identified in any species of green algae. RESULTS By using a refined searching strategy, we identified putative nsLTP genes in more than ten species of green algae as one or two genes per haploid genome but not in red and brown algae. The analyses show that the algal nsLTPs carry unique characteristics, including the extended 8CM spacing, larger molecular mass, lower pI value and multiple introns in a gene, which suggests that they could be a novel nsLTP lineage. Moreover, the results of further investigation on the two Chlamydomonas nsLTPs using transcript and protein assays demonstrated their late zygotic stage expression patterns and the canonical nsLTP properties were also verified, such as the fatty acids binding and proteinase resistance activities. CONCLUSIONS In conclusion, a novel nsLTP lineage is identified in green algae, which carries some unique sequences and molecular features that are distinguishable from those in land plants. Combined with the results of further examinations of the Chlamydomonas nsLTPs in vitro, possible roles of the algal nsLTPs are also suggested. This study not only reveals the existence of the nsLTPs in green algae but also contributes to facilitating future studies on this enigmatic protein family.
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Affiliation(s)
- Ming-Der Huang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424.
| | - Chin-Wei Wu
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424
| | - Hong-Yun Chou
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424
| | - Sou-Yu Cheng
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424
| | - Hsin-Yang Chang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan, 80424.
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan, 11221.
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6
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Missaoui K, Gonzalez-Klein Z, Pazos-Castro D, Hernandez-Ramirez G, Garrido-Arandia M, Brini F, Diaz-Perales A, Tome-Amat J. Plant non-specific lipid transfer proteins: An overview. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:115-127. [PMID: 34992048 DOI: 10.1016/j.plaphy.2021.12.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 05/26/2023]
Abstract
Plant non-specific lipid transfer proteins (nsLTPs) are usually defined as small, basic proteins, with a wide distribution in all orders of higher plants. Structurally, nsLTPs contain a conserved motif of eight cysteines, linked by four disulphide bonds, and a hydrophobic cavity in which the ligand is housed. This structure confers stability and enhances the ability to bind and transport a variety of hydrophobic molecules. Their highly conserved structural resemblance but low sequence identity reflects the wide variety of ligands they can carry, as well as the broad biological functions to which they are linked to, such as membrane stabilization, cell wall organization and signal transduction. In addition, they have also been described as essential in resistance to biotic and abiotic stresses, plant growth and development, seed development, and germination. Hence, there is growing interest in this family of proteins for their critical roles in plant development and for the many unresolved questions that need to be clarified, regarding their subcellular localization, transfer capacity, expression profile, biological function, and evolution.
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Affiliation(s)
- Khawla Missaoui
- Laboratory of Biotechnology and Plant Improvement, Centre of Biotechnology of Sfax (CBS), University of Sfax, Tunisia
| | - Zulema Gonzalez-Klein
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Spain
| | - Diego Pazos-Castro
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Spain
| | - Guadalupe Hernandez-Ramirez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Spain
| | - Maria Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Spain
| | - Faical Brini
- Laboratory of Biotechnology and Plant Improvement, Centre of Biotechnology of Sfax (CBS), University of Sfax, Tunisia
| | - Araceli Diaz-Perales
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Spain
| | - Jaime Tome-Amat
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Spain.
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7
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Amador VC, dos Santos-Silva CA, Vilela LMB, Oliveira-Lima M, de Santana Rêgo M, Roldan-Filho RS, de Oliveira-Silva RL, Lemos AB, de Oliveira WD, Ferreira-Neto JRC, Crovella S, Benko-Iseppon AM. Lipid Transfer Proteins (LTPs)-Structure, Diversity and Roles beyond Antimicrobial Activity. Antibiotics (Basel) 2021; 10:1281. [PMID: 34827219 PMCID: PMC8615156 DOI: 10.3390/antibiotics10111281] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 01/21/2023] Open
Abstract
Lipid transfer proteins (LTPs) are among the most promising plant-exclusive antimicrobial peptides (AMPs). They figure among the most challenging AMPs from the point of view of their structural diversity, functions and biotechnological applications. This review presents a current picture of the LTP research, addressing not only their structural, evolutionary and further predicted functional aspects. Traditionally, LTPs have been identified by their direct isolation by biochemical techniques, whereas omics data and bioinformatics deserve special attention for their potential to bring new insights. In this context, new possible functions have been identified revealing that LTPs are actually multipurpose, with many additional predicted roles. Despite some challenges due to the toxicity and allergenicity of LTPs, a systematic review and search in patent databases, indicate promising perspectives for the biotechnological use of LTPs in human health and also plant defense.
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Affiliation(s)
- Vinícius Costa Amador
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Carlos André dos Santos-Silva
- Department of Advanced Diagnostics, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, 34100 Trieste, Italy;
| | - Lívia Maria Batista Vilela
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Marx Oliveira-Lima
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Mireli de Santana Rêgo
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Ricardo Salas Roldan-Filho
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Roberta Lane de Oliveira-Silva
- General Microbiology Laboratory, Agricultural Science Campus, Universidade Federal do Vale do São Francisco, Petrolina 56300-990, Brazil;
| | - Ayug Bezerra Lemos
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Wilson Dias de Oliveira
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - José Ribamar Costa Ferreira-Neto
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Sérgio Crovella
- Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha 1883, Qatar;
| | - Ana Maria Benko-Iseppon
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
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Dufayard JF, Bocs S, Guignon V, Larivière D, Louis A, Oubda N, Rouard M, Ruiz M, de Lamotte F. RapGreen, an interactive software and web package to explore and analyze phylogenetic trees. NAR Genom Bioinform 2021; 3:lqab088. [PMID: 34568824 PMCID: PMC8459725 DOI: 10.1093/nargab/lqab088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
RapGreen is a modular software package targeted at scientists handling large datasets for phylogenetic analysis. Its primary function is the graphical visualization and exploration of large trees. In addition, RapGreen offers a tree pattern search function to seek evolutionary scenarios among large collections of phylogenetic trees. Other functionalities include tree reconciliation with a given species tree: the detection of duplication or loss events during evolution and tree rooting. Last but not least, RapGreen features the ability to integrate heterogeneous data while visualizing and otherwise analyzing phylogenetic trees.
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Affiliation(s)
- Jean-François Dufayard
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Valentin Guignon
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Delphine Larivière
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Alexandra Louis
- IBENS, Institut de Biologie de l’ENS, Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Nicolas Oubda
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Mathieu Rouard
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Manuel Ruiz
- CIRAD, UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Frédéric de Lamotte
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
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9
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Martín-Pedraza L, Mayorga C, Gomez F, Bueno-Díaz C, Blanca-Lopez N, González M, Martínez-Blanco M, Cuesta-Herranz J, Molina E, Villalba M, Benedé S. IgE-Reactivity Pattern of Tomato Seed and Peel Nonspecific Lipid-Transfer Proteins after in Vitro Gastrointestinal Digestion. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3511-3518. [PMID: 33719421 PMCID: PMC9134490 DOI: 10.1021/acs.jafc.0c06949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/29/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
The influence of gastrointestinal digestion on the immunological properties of three different nonspecific lipid-transfer proteins (nsLTPs) described in tomato fruit has been assessed using an in vitro system mimicking the stomach and intestine digestion conditions. Tomato peel/pulp nsLTP, Sola l 3, was degraded after digestion, although the immunoglobulin E (IgE) recognition of intact protein and a 10 kDa band were still observed after 30 min of duodenal digestion in the presence of phosphatidylcholine. The tomato seed nsLTP, Sola l 7, showed a higher stability than the other seed allergen, Sola l 6, during digestion. Sola l 7 showed an IgE immunoreactive 6.5 kDa band in immunoblotting analysis, retaining up to 7% of its IgE-binding capacity in inhibition ELISA test after 60 min of duodenal digestion and keeping intact its ability to activate basophils after digestion. These results suggest that the tomato seed allergen Sola l 7 might be considered as an important allergen in the induction of allergic responses to tomato due to its high stability against gastrointestinal digestion.
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Affiliation(s)
- Laura Martín-Pedraza
- Department
of Biochemistry and Molecular Biology, Universidad
Complutense de Madrid, 28040 Madrid, Spain
| | - Cristobalina Mayorga
- Allergy
Research Laboratory, IBIMA, Regional University
Hospital of Málaga, UMA, 29009 Málaga, Spain
| | - Francisca Gomez
- Allergy
Research Laboratory, IBIMA, Regional University
Hospital of Málaga, UMA, 29009 Málaga, Spain
| | - Cristina Bueno-Díaz
- Department
of Biochemistry and Molecular Biology, Universidad
Complutense de Madrid, 28040 Madrid, Spain
| | | | - Miguel González
- Allergy
Research Laboratory, IBIMA, Regional University
Hospital of Málaga, UMA, 29009 Málaga, Spain
| | - Mónica Martínez-Blanco
- Instituto
de Investigación en Ciencias de la Alimentación (CIAL,
CSIC-UAM), Nicolás Cabrera 9, 28049 Madrid, Spain
| | | | - Elena Molina
- Instituto
de Investigación en Ciencias de la Alimentación (CIAL,
CSIC-UAM), Nicolás Cabrera 9, 28049 Madrid, Spain
| | - Mayte Villalba
- Department
of Biochemistry and Molecular Biology, Universidad
Complutense de Madrid, 28040 Madrid, Spain
| | - Sara Benedé
- Instituto
de Investigación en Ciencias de la Alimentación (CIAL,
CSIC-UAM), Nicolás Cabrera 9, 28049 Madrid, Spain
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10
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Yang Y, Bocs S, Fan H, Armero A, Baudouin L, Xu P, Xu J, This D, Hamelin C, Iqbal A, Qadri R, Zhou L, Li J, Wu Y, Ma Z, Issali AE, Rivallan R, Liu N, Xia W, Peng M, Xiao Y. Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance. Commun Biol 2021; 4:105. [PMID: 33483627 PMCID: PMC7822834 DOI: 10.1038/s42003-020-01593-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 12/09/2020] [Indexed: 01/30/2023] Open
Abstract
Coconut (Cocos nucifera) is the emblematic palm of tropical coastal areas all around the globe. It provides vital resources to millions of farmers. In an effort to better understand its evolutionary history and to develop genomic tools for its improvement, a sequence draft was recently released. Here, we present a dense linkage map (8402 SNPs) aiming to assemble the large genome of coconut (2.42 Gbp, 2n = 32) into 16 pseudomolecules. As a result, 47% of the sequences (representing 77% of the genes) were assigned to 16 linkage groups and ordered. We observed segregation distortion in chromosome Cn15, which is a signature of strong selection among pollen grains, favouring the maternal allele. Comparing our results with the genome of the oil palm Elaeis guineensis allowed us to identify major events in the evolutionary history of palms. We find that coconut underwent a massive transposable element invasion in the last million years, which could be related to the fluctuations of sea level during the glaciations at Pleistocene that would have triggered a population bottleneck. Finally, to better understand the facultative halophyte trait of coconut, we conducted an RNA-seq experiment on leaves to identify key players of signaling pathways involved in salt stress response. Altogether, our findings represent a valuable resource for the coconut breeding community.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398, Montpellier, France
| | - Haikuo Fan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Alix Armero
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Luc Baudouin
- CIRAD, UMR AGAP, F-34398, Montpellier, France.
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France.
| | - Pengwei Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Junyang Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Dominique This
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Chantal Hamelin
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398, Montpellier, France
| | - Amjad Iqbal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Rashad Qadri
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Lixia Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China
| | - Zilong Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, P. R. China
| | - Auguste Emmanuel Issali
- Station Cocotier Marc Delorme, Centre National De Recherche Agronomique (CNRA)07 B.P. 13, Port Bouet, Côte d'Ivoire
| | - Ronan Rivallan
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Na Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, P. R. China
| | - Wei Xia
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, P. R. China.
| | - Yong Xiao
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, Hainan, P. R. China.
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11
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Melnikova D, Bogdanov I, Ovchinnikova T, Finkina E. Interaction between the Lentil Lipid Transfer Protein Lc-LTP2 and Its Novel Signal Ligand PI(4,5)P2. MEMBRANES 2020; 10:membranes10110357. [PMID: 33233540 PMCID: PMC7699592 DOI: 10.3390/membranes10110357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022]
Abstract
It is known that plant lipid transfer proteins (LTPs) bind a broad spectrum of ligands including fatty acids (FAs), phospho- and glycolipids, acyl-coenzyme A and secondary metabolites. In this work, we used protein−lipid overlay assays to identify new putative LTP ligands. In our experiments, the lentil lipid transfer protein Lc-LTP2 as well as LTPs from other plants were shown to bind phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2). Molecular modeling, 2-p-toluidinonaphthalene-6-sulphonate (TNS) displacement and liposome leakage experiments with Lc-LTP2 and its mutant analogs (R45A, Y80A, R45A/Y80A) were performed to investigate interactions between the protein and PI(4,5)P2. It was shown that PI(4,5)P2 initially interacted with the “bottom” entrance of the protein cavity and after complex formation the large polar head of this ligand was also oriented towards the same entrance. We also found that two highly conserved residues in plant LTPs, Arg45 and Tyr80, played an important role in protein-ligand interactions. Apparently, Arg45 is a key residue for interaction with PI(4,5)P2 during both initial contacting and holding in the protein cavity, while Tyr80 is probably a key amino acid playing an essential role in Lc-LTP2 docking to the membrane. Thus, we assumed that the ability of Lc-LTP2 to bind PI(4,5)P2 suggests the involvement of this protein in plant signal transduction.
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Affiliation(s)
- Daria Melnikova
- Science-Educational Center, M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.M.); (I.B.); (T.O.)
- Department of Physicochemical Biology and Biotechnology, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Ivan Bogdanov
- Science-Educational Center, M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.M.); (I.B.); (T.O.)
| | - Tatiana Ovchinnikova
- Science-Educational Center, M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.M.); (I.B.); (T.O.)
- Department of Physicochemical Biology and Biotechnology, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Department of Bioorganic Chemistry, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ekaterina Finkina
- Science-Educational Center, M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (D.M.); (I.B.); (T.O.)
- Correspondence: ; Tel.: +7-495-335-42-00
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