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Sui J, Chen J, Chen Y, Iwamori N, Sun J. Identification of plant vacuole proteins by using graph neural network and contact maps. BMC Bioinformatics 2023; 24:357. [PMID: 37740195 PMCID: PMC10517492 DOI: 10.1186/s12859-023-05475-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Plant vacuoles are essential organelles in the growth and development of plants, and accurate identification of their proteins is crucial for understanding their biological properties. In this study, we developed a novel model called GraphIdn for the identification of plant vacuole proteins. The model uses SeqVec, a deep representation learning model, to initialize the amino acid sequence. We utilized the AlphaFold2 algorithm to obtain the structural information of corresponding plant vacuole proteins, and then fed the calculated contact maps into a graph convolutional neural network. GraphIdn achieved accuracy values of 88.51% and 89.93% in independent testing and fivefold cross-validation, respectively, outperforming previous state-of-the-art predictors. As far as we know, this is the first model to use predicted protein topology structure graphs to identify plant vacuole proteins. Furthermore, we assessed the effectiveness and generalization capability of our GraphIdn model by applying it to identify and locate peroxisomal proteins, which yielded promising outcomes. The source code and datasets can be accessed at https://github.com/SJNNNN/GraphIdn .
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Affiliation(s)
- Jianan Sui
- School of Information Science and Engineering, University of Jinan, Jinan, China
| | - Jiazi Chen
- Laboratory of Zoology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka-Shi, Fukuoka, Japan
| | - Yuehui Chen
- School of Artificial Intelligence Institute and Information Science and Engineering, University of Jinan, Jinan, China.
| | - Naoki Iwamori
- Laboratory of Zoology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka-Shi, Fukuoka, Japan
| | - Jin Sun
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
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2
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Yuan P, Borrego E, Park YS, Gorman Z, Huang PC, Tolley J, Christensen SA, Blanford J, Kilaru A, Meeley R, Koiwa H, Vidal S, Huffaker A, Schmelz E, Kolomiets MV. 9,10-KODA, an α-ketol produced by the tonoplast-localized 9-lipoxygenase ZmLOX5, plays a signaling role in maize defense against insect herbivory. MOLECULAR PLANT 2023; 16:1283-1303. [PMID: 37434355 DOI: 10.1016/j.molp.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/10/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
13-Lipoxygenases (LOXs) initiate the synthesis of jasmonic acid (JA), the best-understood oxylipin hormone in herbivory defense. However, the roles of 9-LOX-derived oxylipins in insect resistance remain unclear. Here, we report a novel anti-herbivory mechanism mediated by a tonoplast-localized 9-LOX, ZmLOX5, and its linolenic acid-derived product, 9-hydroxy-10-oxo-12(Z),15(Z)-octadecadienoic acid (9,10-KODA). Transposon-insertional disruption of ZmLOX5 resulted in the loss of resistance to insect herbivory. lox5 knockout mutants displayed greatly reduced wound-induced accumulation of multiple oxylipins and defense metabolites, including benzoxazinoids, abscisic acid (ABA), and JA-isoleucine (JA-Ile). However, exogenous JA-Ile failed to rescue insect defense in lox5 mutants, while applications of 1 μM 9,10-KODA or the JA precursor, 12-oxo-phytodienoic acid (12-OPDA), restored wild-type resistance levels. Metabolite profiling revealed that exogenous 9,10-KODA primed the plants for increased production of ABA and 12-OPDA, but not JA-Ile. While none of the 9-oxylipins were able to rescue JA-Ile induction, the lox5 mutant accumulated lower wound-induced levels of Ca2+, suggesting this as a potential explanation for lower wound-induced JA. Seedlings pretreated with 9,10-KODA exhibited rapid or more robust wound-induced defense gene expression. In addition, an artificial diet supplemented with 9,10-KODA arrested fall armyworm larvae growth. Finally, analysis of single and double lox5 and lox10 mutants showed that ZmLOX5 also contributed to insect defense by modulating ZmLOX10-mediated green leaf volatile signaling. Collectively, our study uncovered a previously unknown anti-herbivore defense and hormone-like signaling activity for a major 9-oxylipin α-ketol.
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Affiliation(s)
- Peiguo Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA
| | - Eli Borrego
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA; Currently at Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Yong-Soon Park
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA; Department of Plant Resources, Agriculture and Fisheries Life Science Research Institute, Kongju National University, Yesan, Chungnam 32439, South Korea
| | - Zachary Gorman
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA
| | - Pei-Cheng Huang
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA
| | - Jordan Tolley
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Shawn A Christensen
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA; College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Jantana Blanford
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37659, USA
| | - Robert Meeley
- Formerly at Corteva Agriscience, Johnston, IA 50131, USA
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Stefan Vidal
- Department of Crop Sciences, Agricultural Entomology, Georg-August-Universität, 37077 Göttingen, Germany
| | - Alisa Huffaker
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Eric Schmelz
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Michael V Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840-2132, USA.
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3
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Modulation of Anionic Lipid Bilayers by Specific Interplay of Protons and Calcium Ions. Biomolecules 2022; 12:biom12121894. [PMID: 36551322 PMCID: PMC9775051 DOI: 10.3390/biom12121894] [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: 10/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Biomembranes, important building blocks of living organisms, are often exposed to large local fluctuations of pH and ionic strength. To capture changes in the membrane organization under such harsh conditions, we investigated the mobility and hydration of zwitterionic and anionic lipid bilayers upon elevated H3O+ and Ca2+ content by the time-dependent fluorescence shift (TDFS) technique. While the zwitterionic bilayers remain inert to lower pH and increased calcium concentrations, anionic membranes are responsive. Specifically, both bilayers enriched in phosphatidylserine (PS) and phosphatidylglycerol (PG) become dehydrated and rigidified at pH 4.0 compared to at pH 7.0. However, their reaction to the gradual Ca2+ increase in the acidic environment differs. While the PG bilayers exhibit strong rehydration and mild loosening of the carbonyl region, restoring membrane properties to those observed at pH 7.0, the PS bilayers remain dehydrated with minor bilayer stiffening. Molecular dynamics (MD) simulations support the strong binding of H3O+ to both PS and PG. Compared to PS, PG exhibits a weaker binding of Ca2+ also at a low pH.
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Aniento F, Sánchez de Medina Hernández V, Dagdas Y, Rojas-Pierce M, Russinova E. Molecular mechanisms of endomembrane trafficking in plants. THE PLANT CELL 2022; 34:146-173. [PMID: 34550393 PMCID: PMC8773984 DOI: 10.1093/plcell/koab235] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/12/2021] [Indexed: 05/10/2023]
Abstract
Endomembrane trafficking is essential for all eukaryotic cells. The best-characterized membrane trafficking organelles include the endoplasmic reticulum (ER), Golgi apparatus, early and recycling endosomes, multivesicular body, or late endosome, lysosome/vacuole, and plasma membrane. Although historically plants have given rise to cell biology, our understanding of membrane trafficking has mainly been shaped by the much more studied mammalian and yeast models. Whereas organelles and major protein families that regulate endomembrane trafficking are largely conserved across all eukaryotes, exciting variations are emerging from advances in plant cell biology research. In this review, we summarize the current state of knowledge on plant endomembrane trafficking, with a focus on four distinct trafficking pathways: ER-to-Golgi transport, endocytosis, trans-Golgi network-to-vacuole transport, and autophagy. We acknowledge the conservation and commonalities in the trafficking machinery across species, with emphasis on diversity and plant-specific features. Understanding the function of organelles and the trafficking machinery currently nonexistent in well-known model organisms will provide great opportunities to acquire new insights into the fundamental cellular process of membrane trafficking.
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Affiliation(s)
| | - Víctor Sánchez de Medina Hernández
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria
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Denne NL, Hiles RR, Kyrysyuk O, Iyer-Pascuzzi AS, Mitra RM. Ralstonia solanacearum Effectors Localize to Diverse Organelles in Solanum Hosts. PHYTOPATHOLOGY 2021; 111:2213-2226. [PMID: 33720750 DOI: 10.1094/phyto-10-20-0483-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytopathogenic bacteria secrete type III effector (T3E) proteins directly into host plant cells. T3Es can interact with plant proteins and frequently manipulate plant host physiological or developmental processes. The proper subcellular localization of T3Es is critical for their ability to interact with plant targets, and knowledge of T3E localization can be informative for studies of effector function. Here we investigated the subcellular localization of 19 T3Es from the phytopathogenic bacteria Ralstonia pseudosolanacearum and Ralstonia solanacearum. Approximately 45% of effectors in our library localize to both the plant cell periphery and the nucleus, 15% exclusively to the cell periphery, 15% exclusively to the nucleus, and 25% to other organelles, including tonoplasts and peroxisomes. Using tomato hairy roots, we show that T3E localization is similar in both leaves and roots and is not impacted by Solanum species. We find that in silico prediction programs are frequently inaccurate, highlighting the value of in planta localization experiments. Our data suggest that Ralstonia targets a wide diversity of cellular organelles and provides a foundation for developing testable hypotheses about Ralstonia effector function.
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Affiliation(s)
- Nina L Denne
- Department of Biology, Carleton College, Northfield, MN 55057
| | - Rachel R Hiles
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, IN 47907
| | | | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, IN 47907
| | - Raka M Mitra
- Department of Biology, Carleton College, Northfield, MN 55057
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6
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Weigle AT, Carr M, Shukla D. Impact of Increased Membrane Realism on Conformational Sampling of Proteins. J Chem Theory Comput 2021; 17:5342-5357. [PMID: 34339605 DOI: 10.1021/acs.jctc.1c00276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The realism and accuracy of lipid bilayer simulations through molecular dynamics (MD) are heavily dependent on the lipid composition. While the field is pushing toward implementing more heterogeneous and realistic membrane compositions, a lack of high-resolution lipidomic data prevents some membrane protein systems from being modeled with the highest level of realism. Given the additional diversity of real-world cellular membranes and protein-lipid interactions, it is still not fully understood how altering membrane complexity affects modeled membrane protein functions or if it matters over long-timescale simulations. This is especially true for organisms whose membrane environments have little to no computational study, such as the plant plasma membrane. Tackling these issues in tandem, a generalized, realistic, and asymmetric plant plasma membrane with more than 10 different lipid species is constructed herein. Classical MD simulations of pure membrane constructs were performed to evaluate how altering the compositional complexity of the membrane impacted the plant membrane properties. The apo form of a plant sugar transporter, OsSWEET2b, was inserted into membrane models where lipid diversity was calculated in either a size-dependent or size-independent manner. An adaptive sampling simulation regime validated by Markov-state models was performed to capture the gating dynamics of OsSWEET2b in each of these membrane constructs. In comparison to previous OsSWEET2b simulations performed in a pure POPC bilayer, we confirm that simulations performed within a native-like membrane composition alter the stabilization of apo OsSWEET2b conformational states by ∼1 kcal/mol. The free-energy barriers of intermediate conformational states decrease when realistic membrane complexity is simplified, albeit roughly within sampling error, suggesting that protein-specific responses to membranes differ due to altered packing caused by compositional fluctuations. This work serves as a case study where a more realistic bilayer composition makes unbiased conformational sampling easier to achieve than with simplified bilayers.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Matthew Carr
- Independent Software Development Provider310 East Marlette Avenue, Phoenix, Arizona 85012, United States
| | - Diwakar Shukla
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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Carmona-Salazar L, Cahoon RE, Gasca-Pineda J, González-Solís A, Vera-Estrella R, Treviño V, Cahoon EB, Gavilanes-Ruiz M. Plasma and vacuolar membrane sphingolipidomes: composition and insights on the role of main molecular species. PLANT PHYSIOLOGY 2021; 186:624-639. [PMID: 33570616 PMCID: PMC8154057 DOI: 10.1093/plphys/kiab064] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/24/2021] [Indexed: 05/04/2023]
Abstract
Lipid structures affect membrane biophysical properties such as thickness, stability, permeability, curvature, fluidity, asymmetry, and interdigitation, contributing to membrane function. Sphingolipids are abundant in plant endomembranes and plasma membranes (PMs) and comprise four classes: ceramides, hydroxyceramides, glucosylceramides, and glycosylinositolphosphoceramides (GIPCs). They constitute an array of chemical structures whose distribution in plant membranes is unknown. With the aim of describing the hydrophobic portion of sphingolipids, 18 preparations from microsomal (MIC), vacuolar (VM), PM, and detergent-resistant membranes (DRM) were isolated from Arabidopsis (Arabidopsis thaliana) leaves. Sphingolipid species, encompassing pairing of long-chain bases and fatty acids, were identified and quantified in these membranes. Sphingolipid concentrations were compared using univariate and multivariate analysis to assess sphingolipid diversity, abundance, and predominance across membranes. The four sphingolipid classes were present at different levels in each membrane: VM was enriched in glucosylceramides, hydroxyceramides, and GIPCs; PM in GIPCs, in agreement with their key role in signal recognition and sensing; and DRM in GIPCs, as reported by their function in nanodomain formation. While a total of 84 sphingolipid species was identified in MIC, VM, PM, and DRM, only 34 were selectively distributed in the four membrane types. Conversely, every membrane contained a different number of predominant species (11 in VM, 6 in PM, and 17 in DRM). This study reveals that MIC, VM, PM, and DRM contain the same set of sphingolipid species but every membrane source contains its own specific assortment based on the proportion of sphingolipid classes and on the predominance of individual species.
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Affiliation(s)
- Laura Carmona-Salazar
- Dpto. de Bioquímica, Facultad de Química, Conj. E. Universidad Nacional Autónoma de México, UNAM. Cd. Universitaria, Coyoacán. 04510, Cd. de México, México
| | - Rebecca E Cahoon
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, NE 68588–0665, USA
| | - Jaime Gasca-Pineda
- UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, UNAM, 54090, Estado de México, México
| | - Ariadna González-Solís
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, NE 68588–0665, USA
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM. Cuernavaca, Morelos, México
| | - Victor Treviño
- Tecnológico de Monterrey, Escuela de Medicina, 64710 Monterrey, Nuevo León, México
| | - Edgar B Cahoon
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, NE 68588–0665, USA
| | - Marina Gavilanes-Ruiz
- Dpto. de Bioquímica, Facultad de Química, Conj. E. Universidad Nacional Autónoma de México, UNAM. Cd. Universitaria, Coyoacán. 04510, Cd. de México, México
- Author for communication:
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8
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Sweetman C, Khassanova G, Miller TK, Booth NJ, Kurishbayev A, Jatayev S, Gupta NK, Langridge P, Jenkins CLD, Soole KL, Day DA, Shavrukov Y. Salt-induced expression of intracellular vesicle trafficking genes, CaRab-GTP, and their association with Na + accumulation in leaves of chickpea (Cicer arietinum L.). BMC PLANT BIOLOGY 2020; 20:183. [PMID: 33050887 PMCID: PMC7557026 DOI: 10.1186/s12870-020-02331-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/06/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Chickpea is an important legume and is moderately tolerant to salinity stress during the growing season. However, the level and mechanisms for salinity tolerance can vary among accessions and cultivars. A large family of CaRab-GTP genes, previously identified in chickpea, is homologous to intracellular vesicle trafficking superfamily genes that play essential roles in response to salinity stress in plants. RESULTS To determine which of the gene family members are involved in the chickpea salt response, plants from six selected chickpea accessions (Genesis 836, Hattrick, ICC12726, Rupali, Slasher and Yubileiny) were exposed to salinity stress and expression profiles resolved for the major CaRab-GTP gene clades after 5, 9 and 15 days of salt exposure. Gene clade expression profiles (using degenerate primers targeting all members of each clade) were tested for their relationship to salinity tolerance measures, namely plant biomass and Na+ accumulation. Transcripts representing 11 out of the 13 CaRab clades could be detected by RT-PCR, but only six (CaRabA2, -B, -C, -D, -E and -H) could be quantified using qRT-PCR due to low expression levels or poor amplification efficiency of the degenerate primers for clades containing several gene members. Expression profiles of three gene clades, CaRabB, -D and -E, were very similar across all six chickpea accessions, showing a strongly coordinated network. Salt-induced enhancement of CaRabA2 expression at 15 days showed a very strong positive correlation (R2 = 0.905) with Na+ accumulation in leaves. However, salinity tolerance estimated as relative plant biomass production compared to controls, did not correlate with Na+ accumulation in leaves, nor with expression profiles of any of the investigated CaRab-GTP genes. CONCLUSION A coordinated network of CaRab-GTP genes, which are likely involved in intracellular trafficking, are important for the salinity stress response of chickpea plants.
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Affiliation(s)
- Crystal Sweetman
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Troy K Miller
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia
| | - Nicholas J Booth
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan.
| | - Narendra K Gupta
- College of Agriculture, SKN Agriculture University, Jobner, Rajasthan, India
| | | | - Colin L D Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia
| | - Kathleen L Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia
| | - David A Day
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia
- School of Life Science, AgriBio, LaTrobe University, Melbourne, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, Australia.
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Yadav AK, Singla D. VacPred: Sequence-based prediction of plant vacuole proteins using machine-learning techniques. J Biosci 2020. [DOI: 10.1007/s12038-020-00076-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Brahem M, Bornard I, Renard CMGC, Le Bourvellec C. Multiscale Localization of Procyanidins in Ripe and Overripe Perry Pears by Light and Transmission Electron Microscopy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8900-8906. [PMID: 32706965 DOI: 10.1021/acs.jafc.0c02036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Histochemical staining with 4-dimethylaminocinnamaldehyde (DMACA), light microscopy, and transmission electron microscopy (TEM) were applied to characterize procyanidin localization at ripe and overripe stages in perry pear flesh (cv. 'De Cloche'). Pear flesh contained stone cell clusters surrounded by very large parenchyma cells. DMACA staining showed procyanidins mainly located in parenchyma cells from the fruit mesocarp. Under light microscopy and TEM, procyanidins appeared in the vacuole of parenchyma cells as uniformly stained granules, probably tannosomes. They were differently dispersed in ripe and overripe perry pears, as the granules remained free inside the vacuole in ripe pears and mostly attached to the tonoplast in overripe pears.
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Affiliation(s)
- Marwa Brahem
- UMR408 SQPOV, INRAE, Avignon Université, F-84000 Avignon, France
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11
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Effect of Auxin (IAA) on the Fast Vacuolar (FV) Channels in Red Beet ( Beta vulgaris L.) Taproot Vacuoles. Int J Mol Sci 2020; 21:ijms21144876. [PMID: 32664260 PMCID: PMC7402332 DOI: 10.3390/ijms21144876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/18/2022] Open
Abstract
In contrast to the well-studied effect of auxin on the plasma membrane K+ channel activity, little is known about the role of this hormone in regulating the vacuolar K+ channels. Here, the patch-clamp technique was used to investigate the effect of auxin (IAA) on the fast-activating vacuolar (FV) channels. It was found that the macroscopic currents displayed instantaneous currents, which at the positive potentials were about three-fold greater compared to the one at the negative potentials. When auxin was added to the bath solution at a final concentration of 1 µM, it increased the outward currents by about 60%, but did not change the inward currents. The imposition of a ten-fold vacuole-to-cytosol KCl gradient stimulated the efflux of K+ from the vacuole into the cytosol and reduced the K+ current in the opposite direction. The addition of IAA to the bath solution with the 10/100 KCl gradient decreased the outward current and increased the inward current. Luminal auxin reduced both the outward and inward current by approximately 25% compared to the control. The single channel recordings demonstrated that cytosolic auxin changed the open probability of the FV channels at the positive voltages to a moderate extent, while it significantly increased the amplitudes of the single channel outward currents and the number of open channels. At the positive voltages, auxin did not change the unitary conductance of the single channels. We suggest that auxin regulates the activity of the fast-activating vacuolar (FV) channels, thereby causing changes of the K+ fluxes across the vacuolar membrane. This mechanism might serve to tightly adjust the volume of the vacuole during plant cell expansion.
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12
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Ozolina NV, Gurina VV, Nesterkina IS, Nurminsky VN. Variations in the content of tonoplast lipids under abiotic stress. PLANTA 2020; 251:107. [PMID: 32440739 DOI: 10.1007/s00425-020-03399-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
The vacuolar membrane is an essential component in protecting the plant cell from stress factors. Different variations in the tonoplast lipid content, which depend on the type of stress, have been reviewed. The lipid content of vacuolar membranes of beet roots (Beta vulgaris L.) under hypoosmotic, hyperosmotic and oxidative types of stress has been studied. These types of stress induce variations in the content of almost all the classes of studied lipids (phospholipids, glycoglycerolipids, sterols and fatty acids). The variations, which are characteristic of a single stress, include the variations (i) in the content of individual glycoglycerolipids and in their total content, (ii) in the total content of sterols, and (iii) in the ratio of content of phosphatidylcholine/phosphatidylethanolamine in the scope of tonoplast phospholipids. Variations observed under all of the types of stress under scrutiny include (i) variations in the content of fatty acids of tonoplast lipids, (ii) some decrease in the content of phosphatidic acid and phosphatidylethanolamine, and (iii) variations in the content of individual sterols. Stigmasterol, campesterol, as well as the stigmasterol/sitosterol ratio increased in varying degrees under all of the types of stress. The most substantial variations have been observed in the content of sterols under abiotic stress. This is probably due to role of sterols in regulation of such membrane characteristics as permeability and microviscosity. In our opinion, sterols may represent one of the main components of tonoplast adaptive mechanisms.
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Affiliation(s)
- Natalia V Ozolina
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, 132, Lermontov St., Irkutsk, 664033, Russia
| | - Veronika V Gurina
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, 132, Lermontov St., Irkutsk, 664033, Russia.
| | - Irina S Nesterkina
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, 132, Lermontov St., Irkutsk, 664033, Russia
| | - Vadim N Nurminsky
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, 132, Lermontov St., Irkutsk, 664033, Russia
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13
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Cheng KJ, Selvam B, Chen LQ, Shukla D. Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters. J Phys Chem B 2019; 123:8411-8418. [DOI: 10.1021/acs.jpcb.9b08257] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kevin J. Cheng
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Champaign, Illinois 61801, United States
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Champaign, Illinois 61801, United States
| | - Li-Qing Chen
- Department of Plant Biology, University of Illinois at Urbana−Champaign, Champaign, Illinois 61801, United States
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Champaign, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Champaign, Illinois 61801, United States
- Department of Plant Biology, University of Illinois at Urbana−Champaign, Champaign, Illinois 61801, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana−Champaign, Champaign, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Champaign, Illinois 61801, United States
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14
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Höhner R, Galvis VC, Strand DD, Völkner C, Krämer M, Messer M, Dinc F, Sjuts I, Bölter B, Kramer DM, Armbruster U, Kunz HH. Photosynthesis in Arabidopsis Is Unaffected by the Function of the Vacuolar K + Channel TPK3. PLANT PHYSIOLOGY 2019; 180:1322-1335. [PMID: 31053658 PMCID: PMC6752931 DOI: 10.1104/pp.19.00255] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/25/2019] [Indexed: 05/21/2023]
Abstract
Photosynthesis is limited by the slow relaxation of nonphotochemical quenching, which primarily dissipates excess absorbed light energy as heat. Because the heat dissipation process is proportional to light-driven thylakoid lumen acidification, manipulating thylakoid ion and proton flux via transport proteins could improve photosynthesis. However, an important aspect of the current understanding of the thylakoid ion transportome is inaccurate. Using fluorescent protein fusions, we show that the Arabidopsis (Arabidopsis thaliana) two-pore K+ channel TPK3, which had been reported to mediate thylakoid K+ flux, localizes to the tonoplast, not the thylakoid. The localization of TPK3 outside of the thylakoids is further supported by the absence of TPK3 in isolated thylakoids as well as the inability of isolated chloroplasts to import TPK3 protein. In line with the subcellular localization of TPK3 in the vacuole, we observed that photosynthesis in the Arabidopsis null mutant tpk3-1, which carries a transfer DNA insertion in the first exon, remains unaffected. To gain a comprehensive understanding of how thylakoid ion flux impacts photosynthetic efficiency under dynamic growth light regimes, we performed long-term photosynthesis imaging of established and newly isolated transthylakoid K+- and Cl--flux mutants. Our results underpin the importance of the thylakoid ion transport proteins potassium cation efflux antiporter KEA3 and voltage-dependent chloride channel VCCN1 and suggest that the activity of yet unknown K+ channel(s), but not TPK3, is critical for optimal photosynthesis in dynamic light environments.
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Affiliation(s)
- Ricarda Höhner
- Plant Physiology, School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236
| | - Viviana Correa Galvis
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476 Potsdam, Germany
| | - Deserah D Strand
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476 Potsdam, Germany
| | - Carsten Völkner
- Plant Physiology, School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236
| | - Moritz Krämer
- Plant Physiology, School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236
| | - Michaela Messer
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476 Potsdam, Germany
| | - Firdevs Dinc
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476 Potsdam, Germany
| | - Inga Sjuts
- Ludwig Maximilian University Munich, Department I, Plant Biochemistry, 82152 Planegg-Martinsried, Germany
| | - Bettina Bölter
- Ludwig Maximilian University Munich, Department I, Plant Biochemistry, 82152 Planegg-Martinsried, Germany
| | - David M Kramer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Ute Armbruster
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, 14476 Potsdam, Germany
| | - Hans-Henning Kunz
- Plant Physiology, School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236
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15
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Selvam B, Yu YC, Chen LQ, Shukla D. Molecular Basis of the Glucose Transport Mechanism in Plants. ACS CENTRAL SCIENCE 2019; 5:1085-1096. [PMID: 31263768 PMCID: PMC6598156 DOI: 10.1021/acscentsci.9b00252] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 05/04/2023]
Abstract
The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane (SWEET, Sugars Will Eventually Be Exported Transporter). However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in the OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as for the glucose transport mechanism. SWEETs undergo a structural transition to outward-facing (OF), occluded (OC), and inward-facing (IF) and strongly support an alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly the same for OF, OC, and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and acts as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass-like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.
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Affiliation(s)
- Balaji Selvam
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ya-Chi Yu
- Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Li-Qing Chen
- Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Diwakar Shukla
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Plant Biology, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- NIH
Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- E-mail:
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16
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Regulatory Aspects of the Vacuolar CAT2 Arginine Transporter of S. lycopersicum: Role of Osmotic Pressure and Cations. Int J Mol Sci 2019; 20:ijms20040906. [PMID: 30791488 PMCID: PMC6413183 DOI: 10.3390/ijms20040906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/11/2019] [Accepted: 02/15/2019] [Indexed: 12/22/2022] Open
Abstract
Many proteins are localized at the vacuolar membrane, but most of them are still poorly described, due to the inaccessibility of this membrane from the extracellular environment. This work focused on the characterization of the CAT2 transporter from S. lycopersicum (SlCAT2) that was previously overexpressed in E. coli and reconstituted in proteoliposomes for transport assay as [3H]Arg uptake. The orientation of the reconstituted transporter has been attempted and current data support the hypothesis that the protein is inserted in the liposome in the same orientation as in the vacuole. SlCAT2 activity was dependent on the pH, with an optimum at pH 7.5. SlCAT2 transport activity was stimulated by the increase of internal osmolality from 0 to 175 mOsmol while the activity was inhibited by the increase of external osmolality. K+, Na+, and Mg2+ present on the external side of proteoliposomes at physiological concentrations, inhibited the transport activity; differently, the cations had no effect when included in the internal proteoliposome compartment. This data highlighted an asymmetric regulation of SlCAT2. Cholesteryl hemisuccinate, included in the proteoliposomal membrane, stimulated the SlCAT2 transport activity. The homology model of the protein was built using, as a template, the 3D structure of the amino acid transporter GkApcT. Putative substrate binding residues and cholesterol binding domains were proposed. Altogether, the described results open new perspectives for studying the response of SlCAT2 and, in general, of plant vacuolar transporters to metabolic and environmental changes.
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17
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Rodrigues JMP, Pereira CS, Fontes N, Gerós H, Côrte-Real M. Flow Cytometry and Fluorescence Microscopy as Tools for Structural and Functional Analysis of Vacuoles Isolated from Yeast and Plant Cells. Methods Mol Biol 2018; 1789:101-115. [PMID: 29916074 DOI: 10.1007/978-1-4939-7856-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A series of optimized protocols to isolate vacuoles from both yeast and plant cells, and to characterize the purified organelles at a functional and structural level, are described. For this purpose, we took advantage of the combined use of cell fractionation techniques with different fluorescence-based approaches namely flow cytometry, fluorescence microscopy and spectrofluorimetry. These protocols altogether constitute valuable tools for the study of vacuole structure and function, as well as for the high-throughput screening of drug libraries to identify new molecules that target the vacuole.
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Affiliation(s)
- Jorge M P Rodrigues
- Centre of Molecular and Environmental Biology, CBMA, University of Minho, Braga, Portugal
| | - Cátia S Pereira
- Centre of Molecular and Environmental Biology, CBMA, University of Minho, Braga, Portugal
- Centre of Biological Engineering, CEB, University of Minho, Braga, Portugal
| | - Natacha Fontes
- Sogrape Vinhos, S.A., Research and Development Department, Aldeia Nova, Avintes, Portugal
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology, CBMA, University of Minho, Braga, Portugal.
- Centre of Biological Engineering, CEB, University of Minho, Braga, Portugal.
- Centre for the Research and Technology of Agro-environmental and Biological Sciences, CITAB-UMinho Pole, University of Minho, Braga, Portugal.
| | - Manuela Côrte-Real
- Centre of Molecular and Environmental Biology, CBMA, University of Minho, Braga, Portugal
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18
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Brillada C, Rojas-Pierce M. Vacuolar trafficking and biogenesis: a maturation in the field. CURRENT OPINION IN PLANT BIOLOGY 2017; 40:77-81. [PMID: 28865974 DOI: 10.1016/j.pbi.2017.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/20/2017] [Accepted: 08/15/2017] [Indexed: 05/24/2023]
Abstract
The vacuole is a prominent organelle that is essential for plant viability. The vacuole size, and its role in ion homeostasis, protein degradation and storage, place significant demands for trafficking of vacuolar cargo along the endomembrane system. Recent studies indicate that sorting of vacuolar cargo initiates at the ER and Golgi, but not the trans-Golgi network/early endosome, as previously thought. Furthermore, maturation of the trans-Golgi network into pre-vacuolar compartments seems to contribute to a major route for plant vacuolar traffic that works by bulk flow and ends with membrane fusion between the pre-vacuolar compartment and the tonoplast. Here we summarize recent evidence that indicates conserved and plant-specific mechanisms involved in sorting and trafficking of proteins to this major organelle.
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Affiliation(s)
- Carla Brillada
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Marcela Rojas-Pierce
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States.
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19
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McCarthy JK, Smith SR, McCrow JP, Tan M, Zheng H, Beeri K, Roth R, Lichtle C, Goodenough U, Bowler CP, Dupont CL, Allen AE. Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom. THE PLANT CELL 2017; 29:2047-2070. [PMID: 28765511 PMCID: PMC5590495 DOI: 10.1105/tpc.16.00910] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/06/2017] [Accepted: 07/29/2017] [Indexed: 05/03/2023]
Abstract
The ecological prominence of diatoms in the ocean environment largely results from their superior competitive ability for dissolved nitrate (NO3-). To investigate the cellular and genetic basis of diatom NO3- assimilation, we generated a knockout in the nitrate reductase gene (NR-KO) of the model pennate diatom Phaeodactylum tricornutum In NR-KO cells, N-assimilation was abolished although NO3- transport remained intact. Unassimilated NO3- accumulated in NR-KO cells, resulting in swelling and associated changes in biochemical composition and physiology. Elevated expression of genes encoding putative vacuolar NO3- chloride channel transporters plus electron micrographs indicating enlarged vacuoles suggested vacuolar storage of NO3- Triacylglycerol concentrations in the NR-KO cells increased immediately following the addition of NO3-, and these increases coincided with elevated gene expression of key triacylglycerol biosynthesis components. Simultaneously, induction of transcripts encoding proteins involved in thylakoid membrane lipid recycling suggested more abrupt repartitioning of carbon resources in NR-KO cells compared with the wild type. Conversely, ribosomal structure and photosystem genes were immediately deactivated in NR-KO cells following NO3- addition, followed within hours by deactivation of genes encoding enzymes for chlorophyll biosynthesis and carbon fixation and metabolism. N-assimilation pathway genes respond uniquely, apparently induced simultaneously by both NO3- replete and deplete conditions.
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Affiliation(s)
- James K McCarthy
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Sarah R Smith
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California 92037
| | - John P McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Maxine Tan
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Hong Zheng
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Karen Beeri
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Robyn Roth
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Christian Lichtle
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR8197 INSERM U1024, 75005 Paris, France
| | - Ursula Goodenough
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Chris P Bowler
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR8197 INSERM U1024, 75005 Paris, France
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California 92037
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California 92037
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20
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Kumar P, Kesari P, Dhindwal S, Choudhary AK, Katiki M, Neetu, Verma A, Ambatipudi K, Tomar S, Sharma AK, Mishra G, Kumar P. A novel function for globulin in sequestering plant hormone: Crystal structure of Wrightia tinctoria 11S globulin in complex with auxin. Sci Rep 2017; 7:4705. [PMID: 28680092 PMCID: PMC5498579 DOI: 10.1038/s41598-017-04518-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/17/2017] [Indexed: 11/20/2022] Open
Abstract
Auxin levels are tightly regulated within the plant cell, and its storage in the isolated cavity of proteins is a measure adopted by cells to maintain the availability of auxin. We report the first crystal structure of Wrightia tinctoria 11S globulin (WTG) in complex with Indole-3-acetic acid (IAA), an auxin, at 1.7 Å resolution. WTG hexamers assemble as a result of the stacking interaction between the hydrophobic surfaces of two trimers, leaving space for the binding of charged ligands. The bound auxin is stabilized by non-covalent interactions, contributed by four chains in each cavity. The presence of bound ligand was confirmed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and high-resolution mass spectrometry (HRMS). Here, we hypothesize that the cleavage of globulins by endopeptidases leads to the movement of the hydrophilic loop region from the surface to the periphery, leaving space for the binding of auxin, and promotes hexamer formation. As the process of germination proceeds, there is a change in the pH, which induces the dissociation of the hexamer and the release of auxin. The compact hexameric assembly ensures the long-term, stable storage of the hormone. This suggests a role for globulin as a novel player in auxin homeostasis.
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Affiliation(s)
- Pramod Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pooja Kesari
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Sonali Dhindwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | | | - Madhusudhanarao Katiki
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Neetu
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Aparna Verma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Kiran Ambatipudi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Girish Mishra
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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21
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Pérez Koldenkova V, Hatsugai N. Vacuolar convolution: possible mechanisms and role of phosphatidylinositol 3,5-bisphosphate. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:751-760. [PMID: 32480604 DOI: 10.1071/fp16443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 05/19/2017] [Indexed: 06/11/2023]
Abstract
The central or lytic vacuole is the largest intracellular organelle in plant cells, but we know unacceptably little about the mechanisms regulating its function in vivo. The underlying reasons are related to difficulties in accessing this organelle without disrupting the cellular integrity and to the dynamic morphology of the vacuole, which lacks a defined structure. Among such morphological changes, vacuolar convolution is probably the most commonly observed event, reflected in the (reversible) transformation of a large central vacuole into a structure consisting of interconnected bubbles of a smaller size. Such behaviour is observed in plant cells subjected to hyperosmotic stress but also takes place in physiological conditions (e.g. during stomatal closure). Although vacuolar convolution is a relatively common phenomenon in plants, studies aimed at elucidating its execution mechanisms are rather scarce. In the present review, we analyse the available evidence on the participation of the cellular cytoskeleton and ion transporters in vacuolar morphology dynamics, putting special emphasis on the available evidence of the role played by phosphatidylinositol 3,5-bisphosphate in this process.
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Affiliation(s)
- Vadim Pérez Koldenkova
- Laboratorio Nacional de Microscopía Avanzada, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc, 330, Col. Doctores, Del. Cuauhtémoc. 06720, México D.F., Mexico
| | - Noriyuki Hatsugai
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota St Paul, MN 55108, USA
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22
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Cedeño C, Pauwels K, Tompa P. Protein Delivery into Plant Cells: Toward In vivo Structural Biology. FRONTIERS IN PLANT SCIENCE 2017; 8:519. [PMID: 28469623 PMCID: PMC5395622 DOI: 10.3389/fpls.2017.00519] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/23/2017] [Indexed: 05/22/2023]
Abstract
Understanding the biologically relevant structural and functional behavior of proteins inside living plant cells is only possible through the combination of structural biology and cell biology. The state-of-the-art structural biology techniques are typically applied to molecules that are isolated from their native context. Although most experimental conditions can be easily controlled while dealing with an isolated, purified protein, a serious shortcoming of such in vitro work is that we cannot mimic the extremely complex intracellular environment in which the protein exists and functions. Therefore, it is highly desirable to investigate proteins in their natural habitat, i.e., within live cells. This is the major ambition of in-cell NMR, which aims to approach structure-function relationship under true in vivo conditions following delivery of labeled proteins into cells under physiological conditions. With a multidisciplinary approach that includes recombinant protein production, confocal fluorescence microscopy, nuclear magnetic resonance (NMR) spectroscopy and different intracellular protein delivery strategies, we explore the possibility to develop in-cell NMR studies in living plant cells. While we provide a comprehensive framework to set-up in-cell NMR, we identified the efficient intracellular introduction of isotope-labeled proteins as the major bottleneck. Based on experiments with the paradigmatic intrinsically disordered proteins (IDPs) Early Response to Dehydration protein 10 and 14, we also established the subcellular localization of ERD14 under abiotic stress.
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Affiliation(s)
- Cesyen Cedeño
- VIB Structural Biology Research Center, Vlaams Instituut voor BiotechnologieBrussels, Belgium
- Structural Biology Brussels, Vrije Universiteit BrusselBrussels, Belgium
| | - Kris Pauwels
- VIB Structural Biology Research Center, Vlaams Instituut voor BiotechnologieBrussels, Belgium
- Structural Biology Brussels, Vrije Universiteit BrusselBrussels, Belgium
| | - Peter Tompa
- VIB Structural Biology Research Center, Vlaams Instituut voor BiotechnologieBrussels, Belgium
- Structural Biology Brussels, Vrije Universiteit BrusselBrussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of SciencesBudapest, Hungary
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23
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Liu R, Wang Y, Qin G, Tian S. iTRAQ-based quantitative proteomic analysis reveals the role of the tonoplast in fruit senescence. J Proteomics 2016; 146:80-9. [DOI: 10.1016/j.jprot.2016.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 01/09/2023]
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