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Schlößer M, Moseler A, Bodnar Y, Homagk M, Wagner S, Pedroletti L, Gellert M, Ugalde JM, Lillig CH, Meyer AJ. Localization of four class I glutaredoxins in the cytosol and the secretory pathway and characterization of their biochemical diversification. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1455-1474. [PMID: 38394181 DOI: 10.1111/tpj.16687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
Class I glutaredoxins (GRXs) are catalytically active oxidoreductases and considered key proteins mediating reversible glutathionylation and deglutathionylation of protein thiols during development and stress responses. To narrow in on putative target proteins, it is mandatory to know the subcellular localization of the respective GRXs and to understand their catalytic activities and putative redundancy between isoforms in the same compartment. We show that in Arabidopsis thaliana, GRXC1 and GRXC2 are cytosolic proteins with GRXC1 being attached to membranes through myristoylation. GRXC3 and GRXC4 are identified as type II membrane proteins along the early secretory pathway with their enzymatic function on the luminal side. Unexpectedly, neither single nor double mutants lacking both GRXs isoforms in the cytosol or the ER show phenotypes that differ from wild-type controls. Analysis of electrostatic surface potentials and clustering of GRXs based on their electrostatic interaction with roGFP2 mirrors the phylogenetic classification of class I GRXs, which clearly separates the cytosolic GRXC1 and GRXC2 from the luminal GRXC3 and GRXC4. Comparison of all four studied GRXs for their oxidoreductase function highlights biochemical diversification with GRXC3 and GRXC4 being better catalysts than GRXC1 and GRXC2 for the reduction of bis(2-hydroxyethyl) disulfide. With oxidized roGFP2 as an alternative substrate, GRXC1 and GRXC2 catalyze the reduction faster than GRXC3 and GRXC4, which suggests that catalytic efficiency of GRXs in reductive reactions depends on the respective substrate. Vice versa, GRXC3 and GRXC4 are faster than GRXC1 and GRXC2 in catalyzing the oxidation of pre-reduced roGFP2 in the reverse reaction.
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Affiliation(s)
- Michelle Schlößer
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Anna Moseler
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Yana Bodnar
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, Ferdinand-Sauerbruch-Straße, D-17475, Greifswald, Germany
| | - Maria Homagk
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Stephan Wagner
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Luca Pedroletti
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Manuela Gellert
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, Ferdinand-Sauerbruch-Straße, D-17475, Greifswald, Germany
| | - José M Ugalde
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
| | - Christopher H Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine, University of Greifswald, Ferdinand-Sauerbruch-Straße, D-17475, Greifswald, Germany
| | - Andreas J Meyer
- INRES-Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, D-53113, Bonn, Germany
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Salazar OR, Chen K, Melino VJ, Reddy MP, Hřibová E, Čížková J, Beránková D, Arciniegas Vega JP, Cáceres Leal LM, Aranda M, Jaremko L, Jaremko M, Fedoroff NV, Tester M, Schmöckel SM. SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii. Nat Commun 2024; 15:4279. [PMID: 38769297 PMCID: PMC11106269 DOI: 10.1038/s41467-024-48595-5] [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: 05/01/2023] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
The identification of genes involved in salinity tolerance has primarily focused on model plants and crops. However, plants naturally adapted to highly saline environments offer valuable insights into tolerance to extreme salinity. Salicornia plants grow in coastal salt marshes, stimulated by NaCl. To understand this tolerance, we generated genome sequences of two Salicornia species and analyzed the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Subcellular membrane proteomes reveal that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, consistent with subcellular localization assays in tobacco. This neo-localized protein can pump Na+ into the vacuole, preventing toxicity in the cytosol. We further identify 11 proteins of interest, of which SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR identified it as an intrinsically disordered protein, localizing to the endoplasmic reticulum in planta, where it can interact with ribosomes and RNA, stabilizing or protecting them during salt stress.
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Affiliation(s)
- Octavio R Salazar
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ke Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Vanessa J Melino
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Muppala P Reddy
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Denisa Beránková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Juan Pablo Arciniegas Vega
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lina María Cáceres Leal
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Manuel Aranda
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Nina V Fedoroff
- Department of Biology, Penn State University, University Park, PA, 16801, US
| | - Mark Tester
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Sandra M Schmöckel
- Department Physiology of Yield Stability, Institute of Crop Science, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
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Lathe RS, McFarlane HE, Kesten C, Wang L, Khan GA, Ebert B, Ramírez-Rodríguez EA, Zheng S, Noord N, Frandsen K, Bhalerao RP, Persson S. NKS1/ELMO4 is an integral protein of a pectin synthesis protein complex and maintains Golgi morphology and cell adhesion in Arabidopsis. Proc Natl Acad Sci U S A 2024; 121:e2321759121. [PMID: 38579009 PMCID: PMC11009649 DOI: 10.1073/pnas.2321759121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.
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Affiliation(s)
- Rahul S. Lathe
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- Max-Planck Institute for Molecular Plant Physiology, Potsdam14476, Germany
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Heather E. McFarlane
- Department of Cell & Systems Biology, University of Toronto, Toronto, ONM5S 3G5, Canada
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
| | - Christopher Kesten
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Liu Wang
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
| | - Ghazanfar Abbas Khan
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC3086, Australia
| | - Berit Ebert
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Department of Biology and Biotechnology, Ruhr University Bochum, Bochum44780, Germany
| | | | - Shuai Zheng
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Niels Noord
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Kristian Frandsen
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
| | - Rishikesh P. Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, UmeåSE-90187, Sweden
| | - Staffan Persson
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C1871, Denmark
- Max-Planck Institute for Molecular Plant Physiology, Potsdam14476, Germany
- School of Biosciences, University of Melbourne, Parkville, VIC3010, Australia
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, University of AdelaideJoint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
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4
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Cho Y, Kim Y, Lee H, Kim S, Kang J, Kadam US, Ju Park S, Sik Chung W, Chan Hong J. Cellular and physiological functions of SGR family in gravitropic response in higher plants. J Adv Res 2024:S2090-1232(24)00039-0. [PMID: 38295878 DOI: 10.1016/j.jare.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/29/2023] [Accepted: 01/24/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND In plants, gravity directs bidirectional growth; it specifies upward growth of shoots and downward growth of roots. Due to gravity, roots establish robust anchorage and shoot, which enables to photosynthesize. It sets optimum posture and develops plant architecture to efficiently use resources like water, nutrients, CO2, and gaseous exchange. Hence, gravitropism is crucial for crop productivity as well as for the growth of plants in challenging climate. Some SGR members are known to affect tiller and shoot angle, organ size, and inflorescence stem in plants. AIM OF REVIEW Although the SHOOT GRAVITROPISM (SGR) family plays a key role in regulating the fate of shoot gravitropism, little is known about its function compared to other proteins involved in gravity response in plant cells and tissues. Moreover, less information on the SGR family's physiological activities and biochemical responses in shoot gravitropism is available. This review scrutinizes and highlights the recent developments in shoot gravitropism and provides an outlook for future crop development, multi-application scenarios, and translational research to improve agricultural productivity. KEY SCIENTIFIC CONCEPTS OF REVIEW Plants have evolved multiple gene families specialized in gravitropic responses, of which the SGR family is highly significant. The SGR family regulates the plant's gravity response by regulating specific physiological and biochemical processes such as transcription, cell division, amyloplast sedimentation, endodermis development, and vacuole formation. Here, we analyze the latest discoveries in shoot gravitropism with particular attention to SGR proteins in plant cell biology, cellular physiology, and homeostasis. Plant cells detect gravity signals by sedimentation of amyloplast (starch granules) in the direction of gravity, and the signaling cascade begins. Gravity sensing, signaling, and auxin redistribution (organ curvature) are the three components of plant gravitropism. Eventually, we focus on the role of multiple SGR genes in shoot and present a complete update on the participation of SGR family members in gravity.
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Affiliation(s)
- Yuhan Cho
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Yujeong Kim
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Hyebi Lee
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Sundong Kim
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Jaehee Kang
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Ulhas S Kadam
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea.
| | - Soon Ju Park
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Woo Sik Chung
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Jong Chan Hong
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea.
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5
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Fuchs P, Feixes-Prats E, Arruda P, Feitosa-Araújo E, Fernie AR, Grefen C, Lichtenauer S, Linka N, de Godoy Maia I, Meyer AJ, Schilasky S, Sweetlove LJ, Wege S, Weber APM, Millar AH, Keech O, Florez-Sarasa I, Barreto P, Schwarzländer M. PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 2 localizes to the Golgi. PLANT PHYSIOLOGY 2024; 194:623-628. [PMID: 37820040 DOI: 10.1093/plphys/kiad540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 10/13/2023]
Abstract
In contrast to its close homolog PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 1 (UCP1), which is an abundant carrier protein in the mitochondria, UCP2 localizes to the Golgi.
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Affiliation(s)
- Philippe Fuchs
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Elisenda Feixes-Prats
- Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Paulo Arruda
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas, 13083-875 Campinas, Brazil
| | - Elias Feitosa-Araújo
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, D-14476 Postdam-Golm, Germany
| | - Christopher Grefen
- Institute of Molecular and Cellular Botany, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Sophie Lichtenauer
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Nicole Linka
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Ivan de Godoy Maia
- Institute of Biosciences, São Paulo State University (UNESP), 18618-970 Botucatu, Brazil
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Sören Schilasky
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Lee J Sweetlove
- Department of Biology, South Parks Road, University of Oxford, OX1 3RB Oxford, UK
| | - Stefanie Wege
- Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, D-53113 Bonn, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 6009 Perth, Western Australia, Australia
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umea, Sweden
| | - Igor Florez-Sarasa
- Centre for Research in Agricultural Genomics (CRAG), Campus UAB Bellaterra, 08193 Barcelona, Spain
- Institut de Recerca i Tecnología Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Pedro Barreto
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology (IBBP), Universität Münster, D-48143 Münster, Germany
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6
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Lindberg S, Premkumar A. Ion Changes and Signaling under Salt Stress in Wheat and Other Important Crops. PLANTS (BASEL, SWITZERLAND) 2023; 13:46. [PMID: 38202354 PMCID: PMC10780558 DOI: 10.3390/plants13010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024]
Abstract
High concentrations of sodium (Na+), chloride (Cl-), calcium (Ca2+), and sulphate (SO42-) are frequently found in saline soils. Crop plants cannot successfully develop and produce because salt stress impairs the uptake of Ca2+, potassium (K+), and water into plant cells. Different intracellular and extracellular ionic concentrations change with salinity, including those of Ca2+, K+, and protons. These cations serve as stress signaling molecules in addition to being essential for ionic homeostasis and nutrition. Maintaining an appropriate K+:Na+ ratio is one crucial plant mechanism for salt tolerance, which is a complicated trait. Another important mechanism is the ability for fast extrusion of Na+ from the cytosol. Ca2+ is established as a ubiquitous secondary messenger, which transmits various stress signals into metabolic alterations that cause adaptive responses. When plants are under stress, the cytosolic-free Ca2+ concentration can rise to 10 times or more from its resting level of 50-100 nanomolar. Reactive oxygen species (ROS) are linked to the Ca2+ alterations and are produced by stress. Depending on the type, frequency, and intensity of the stress, the cytosolic Ca2+ signals oscillate, are transient, or persist for a longer period and exhibit specific "signatures". Both the influx and efflux of Ca2+ affect the length and amplitude of the signal. According to several reports, under stress Ca2+ alterations can occur not only in the cytoplasm of the cell but also in the cell walls, nucleus, and other cell organelles and the Ca2+ waves propagate through the whole plant. Here, we will focus on how wheat and other important crops absorb Na+, K+, and Cl- when plants are under salt stress, as well as how Ca2+, K+, and pH cause intracellular signaling and homeostasis. Similar mechanisms in the model plant Arabidopsis will also be considered. Knowledge of these processes is important for understanding how plants react to salinity stress and for the development of tolerant crops.
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Affiliation(s)
- Sylvia Lindberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-114 18 Stockholm, Sweden
| | - Albert Premkumar
- Bharathiyar Group of Institutes, Guduvanchery 603202, Tamilnadu, India;
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7
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Zhang L, Liang X, Takáč T, Komis G, Li X, Zhang Y, Ovečka M, Chen Y, Šamaj J. Spatial proteomics of vesicular trafficking: coupling mass spectrometry and imaging approaches in membrane biology. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:250-269. [PMID: 36204821 PMCID: PMC9884029 DOI: 10.1111/pbi.13929] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
In plants, membrane compartmentalization requires vesicle trafficking for communication among distinct organelles. Membrane proteins involved in vesicle trafficking are highly dynamic and can respond rapidly to changes in the environment and to cellular signals. Capturing their localization and dynamics is thus essential for understanding the mechanisms underlying vesicular trafficking pathways. Quantitative mass spectrometry and imaging approaches allow a system-wide dissection of the vesicular proteome, the characterization of ligand-receptor pairs and the determination of secretory, endocytic, recycling and vacuolar trafficking pathways. In this review, we highlight major proteomics and imaging methods employed to determine the location, distribution and abundance of proteins within given trafficking routes. We focus in particular on methodologies for the elucidation of vesicle protein dynamics and interactions and their connections to downstream signalling outputs. Finally, we assess their biological applications in exploring different cellular and subcellular processes.
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Affiliation(s)
- Liang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
- College of Life ScienceHenan Normal UniversityXinxiangChina
| | - Xinlin Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Tomáš Takáč
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Xiaojuan Li
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuan Zhang
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
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8
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Pollen Coat Proteomes of Arabidopsis thaliana, Arabidopsis lyrata, and Brassica oleracea Reveal Remarkable Diversity of Small Cysteine-Rich Proteins at the Pollen-Stigma Interface. Biomolecules 2023; 13:biom13010157. [PMID: 36671543 PMCID: PMC9856046 DOI: 10.3390/biom13010157] [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: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
The pollen coat is the outermost domain of the pollen grain and is largely derived from the anther tapetum, which is a secretory tissue that degenerates late in pollen development. By being localised at the interface of the pollen-stigma interaction, the pollen coat plays a central role in mediating early pollination events, including molecular recognition. Amongst species of the Brassicaceae, a growing body of data has revealed that the pollen coat carries a range of proteins, with a number of small cysteine-rich proteins (CRPs) being identified as important regulators of the pollen-stigma interaction. By utilising a state-of-the-art liquid chromatography/tandem mass spectrometry (LC-MS/MS) approach, rich pollen coat proteomic profiles were obtained for Arabidopsis thaliana, Arabidopsis lyrata, and Brassica oleracea, which greatly extended previous datasets. All three proteomes revealed a strikingly large number of small CRPs that were not previously reported as pollen coat components. The profiling also uncovered a wide range of other protein families, many of which were enriched in the pollen coat proteomes and had functions associated with signal transduction, cell walls, lipid metabolism and defence. These proteomes provide an excellent source of molecular targets for future investigations into the pollen-stigma interaction and its potential evolutionary links to plant-pathogen interactions.
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9
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Mou M, Pan Z, Lu M, Sun H, Wang Y, Luo Y, Zhu F. Application of Machine Learning in Spatial Proteomics. J Chem Inf Model 2022; 62:5875-5895. [PMID: 36378082 DOI: 10.1021/acs.jcim.2c01161] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics of proteins, and it has gained extensive attention in recent years, especially the subcellular proteomics. Numerous evidence indicate that the subcellular localization of proteins is associated with various cellular processes and disease progression. Mass spectrometry (MS)-based and imaging-based experimental approaches have been developed to acquire large-scale spatial proteomic data. To allow the reliable analysis of increasingly complex spatial proteomics data, machine learning (ML) methods have been widely used in both MS-based and imaging-based spatial proteomic data analysis pipelines. Here, we comprehensively survey the applications of ML in spatial proteomics from following aspects: (1) data resources for spatial proteome are comprehensively introduced; (2) the roles of different ML algorithms in data analysis pipelines are elaborated; (3) successful applications of spatial proteomics and several analytical tools integrating ML methods are presented; (4) challenges existing in modern ML-based spatial proteomics studies are discussed. This review provides guidelines for researchers seeking to apply ML methods to analyze spatial proteomic data and can facilitate insightful understanding of cell biology as well as the future research in medical and drug discovery communities.
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Affiliation(s)
- Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huaicheng Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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10
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Crook OM, Lilley KS, Gatto L, Kirk PD. Semi-Supervised Non-Parametric Bayesian Modelling of Spatial Proteomics. Ann Appl Stat 2022; 16:22-aoas1603. [PMID: 36507469 PMCID: PMC7613899 DOI: 10.1214/22-aoas1603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding sub-cellular protein localisation is an essential component in the analysis of context specific protein function. Recent advances in quantitative mass-spectrometry (MS) have led to high resolution mapping of thousands of proteins to sub-cellular locations within the cell. Novel modelling considerations to capture the complex nature of these data are thus necessary. We approach analysis of spatial proteomics data in a non-parametric Bayesian framework, using K-component mixtures of Gaussian process regression models. The Gaussian process regression model accounts for correlation structure within a sub-cellular niche, with each mixture component capturing the distinct correlation structure observed within each niche. The availability of marker proteins (i.e. proteins with a priori known labelled locations) motivates a semi-supervised learning approach to inform the Gaussian process hyperparameters. We moreover provide an efficient Hamiltonian-within-Gibbs sampler for our model. Furthermore, we reduce the computational burden associated with inversion of covariance matrices by exploiting the structure in the covariance matrix. A tensor decomposition of our covariance matrices allows extended Trench and Durbin algorithms to be applied to reduce the computational complexity of inversion and hence accelerate computation. We provide detailed case-studies on Drosophila embryos and mouse pluripotent embryonic stem cells to illustrate the benefit of semi-supervised functional Bayesian modelling of the data.
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11
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Amos RA, Atmodjo MA, Huang C, Gao Z, Venkat A, Taujale R, Kannan N, Moremen KW, Mohnen D. Polymerization of the backbone of the pectic polysaccharide rhamnogalacturonan I. NATURE PLANTS 2022; 8:1289-1303. [PMID: 36357524 PMCID: PMC10115348 DOI: 10.1038/s41477-022-01270-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/05/2022] [Indexed: 06/10/2023]
Abstract
Rhamnogalacturonan I (RG-I) is a major plant cell wall pectic polysaccharide defined by its repeating disaccharide backbone structure of [4)-α-D-GalA-(1,2)-α-L-Rha-(1,]. A family of RG-I:Rhamnosyltransferases (RRT) has previously been identified, but synthesis of the RG-I backbone has not been demonstrated in vitro because the identity of Rhamnogalacturonan I:Galaturonosyltransferase (RG-I:GalAT) was unknown. Here a putative glycosyltransferase, At1g28240/MUCI70, is shown to be an RG-I:GalAT. The name RGGAT1 is proposed to reflect the catalytic activity of this enzyme. When incubated together with the rhamnosyltransferase RRT4, the combined activities of RGGAT1 and RRT4 result in elongation of RG-I acceptors in vitro into a polymeric product. RGGAT1 is a member of a new GT family categorized as GT116, which does not group into existing GT-A clades and is phylogenetically distinct from the GALACTURONOSYLTRANSFERASE (GAUT) family of GalA transferases that synthesize the backbone of the pectin homogalacturonan. RGGAT1 has a predicted GT-A fold structure but employs a metal-independent catalytic mechanism that is rare among glycosyltransferases with this fold type. The identification of RGGAT1 and the 8-member Arabidopsis GT116 family provides a new avenue for studying the mechanism of RG-I synthesis and the function of RG-I in plants.
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Affiliation(s)
- Robert A Amos
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Melani A Atmodjo
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Chin Huang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Zhongwei Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Debra Mohnen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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12
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Yu L, Yoshimi Y, Cresswell R, Wightman R, Lyczakowski JJ, Wilson LFL, Ishida K, Stott K, Yu X, Charalambous S, Wurman-Rodrich J, Terrett OM, Brown SP, Dupree R, Temple H, Krogh KBRM, Dupree P. Eudicot primary cell wall glucomannan is related in synthesis, structure, and function to xyloglucan. THE PLANT CELL 2022; 34:4600-4622. [PMID: 35929080 PMCID: PMC9614514 DOI: 10.1093/plcell/koac238] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Hemicellulose polysaccharides influence assembly and properties of the plant primary cell wall (PCW), perhaps by interacting with cellulose to affect the deposition and bundling of cellulose fibrils. However, the functional differences between plant cell wall hemicelluloses such as glucomannan, xylan, and xyloglucan (XyG) remain unclear. As the most abundant hemicellulose, XyG is considered important in eudicot PCWs, but plants devoid of XyG show relatively mild phenotypes. We report here that a patterned β-galactoglucomannan (β-GGM) is widespread in eudicot PCWs and shows remarkable similarities to XyG. The sugar linkages forming the backbone and side chains of β-GGM are analogous to those that make up XyG, and moreover, these linkages are formed by glycosyltransferases from the same CAZy families. Solid-state nuclear magnetic resonance indicated that β-GGM shows low mobility in the cell wall, consistent with interaction with cellulose. Although Arabidopsis β-GGM synthesis mutants show no obvious growth defects, genetic crosses between β-GGM and XyG mutants produce exacerbated phenotypes compared with XyG mutants. These findings demonstrate a related role of these two similar but distinct classes of hemicelluloses in PCWs. This work opens avenues to study the roles of β-GGM and XyG in PCWs.
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Affiliation(s)
- Li Yu
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Yoshihisa Yoshimi
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | | | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | | | | | - Konan Ishida
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Xiaolan Yu
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Stephan Charalambous
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | | | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Henry Temple
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge CB2 1QW, UK
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13
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Temple H, Phyo P, Yang W, Lyczakowski JJ, Echevarría-Poza A, Yakunin I, Parra-Rojas JP, Terrett OM, Saez-Aguayo S, Dupree R, Orellana A, Hong M, Dupree P. Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation. NATURE PLANTS 2022; 8:656-669. [PMID: 35681018 DOI: 10.1038/s41477-022-01156-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, so far, no Golgi SAM transporter has been identified in plants. Here we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knockout of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesized polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, NMR revealed the existence of pectin 'egg-box' structures in intact cell walls and showed that their formation is enhanced by reduced methyl esterification. These changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters involved in import of SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.
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Affiliation(s)
- Henry Temple
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pyae Phyo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Weibing Yang
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS) and CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Shanghai, China
| | - Jan J Lyczakowski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Yakunin
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juan Pablo Parra-Rojas
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Susana Saez-Aguayo
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry, UK
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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14
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Hooper CM, Castleden IR, Tanz SK, Grasso SV, Millar AH. Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1346:67-89. [PMID: 35113396 DOI: 10.1007/978-3-030-80352-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?
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Affiliation(s)
- Cornelia M Hooper
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Ian R Castleden
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sandra K Tanz
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sally V Grasso
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - A Harvey Millar
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
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15
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Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Mol Cell Proteomics 2022; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics.
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Affiliation(s)
- Josie A Christopher
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Aikaterini Geladaki
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - Charlotte S Dawson
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Owen L Vennard
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
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16
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Chen Y, Wang Y, Yang J, Zhou W, Dai S. Exploring the diversity of plant proteome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1197-1210. [PMID: 33650765 DOI: 10.1111/jipb.13087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/25/2021] [Indexed: 05/10/2023]
Abstract
The tremendous functional, spatial, and temporal diversity of the plant proteome is regulated by multiple factors that continuously modify protein abundance, modifications, interactions, localization, and activity to meet the dynamic needs of plants. Dissecting the proteome complexity and its underlying genetic variation is attracting increasing research attention. Mass spectrometry (MS)-based proteomics has become a powerful approach in the global study of protein functions and their relationships on a systems level. Here, we review recent breakthroughs and strategies adopted to unravel the diversity of the proteome, with a specific focus on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. We also consider PTM crosstalk and multiple PTMs temporally regulating the life cycle of proteins. Finally, we discuss recent quantitative studies using MS to measure protein turnover rates and examine future directions in the study of the plant proteome.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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17
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Jiang M, Wang P, Xu L, Ye X, Fan H, Cheng J, Chen J. In silico analysis of glycosyltransferase 2 family genes in duckweed ( Spirodela polyrhiza) and its role in salt stress tolerance. Open Life Sci 2021; 16:583-593. [PMID: 34179502 PMCID: PMC8216227 DOI: 10.1515/biol-2021-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/27/2021] [Accepted: 05/22/2021] [Indexed: 11/15/2022] Open
Abstract
Plant glycosyltransferase 2 (GT2) family genes are involved in plant abiotic stress tolerance. However, the roles of GT2 genes in the abiotic resistance in freshwater plants are largely unknown. We identified seven GT2 genes in duckweed, remarkably more than those in the genomes of Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Nymphaea tetragona, Persea americana, Zostera marina, and Ginkgo biloba, suggesting a significant expansion of this family in the duckweed genome. Phylogeny resolved the GT2 family into two major clades. Six duckweed genes formed an independent subclade in Clade I, and the other was clustered in Clade II. Gene structure and protein domain analysis showed that the lengths of the seven duckweed GT2 genes were varied, and the majority of GT2 genes harbored two conserved domains, PF04722.12 and PF00535.25. The expression of all Clade I duckweed GT2 genes was elevated at 0 h after salt treatment, suggesting a common role of these genes in rapid response to salt stress. The gene Sp01g00794 was highly expressed at 12 and 24 h after salt treatment, indicating its association with salt stress resilience. Overall, these results are essential for studies on the molecular mechanisms in stress response and resistance in aquatic plants.
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Affiliation(s)
- Mingliang Jiang
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
| | - Ligang Xu
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
| | - Hongxiang Fan
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Junxiang Cheng
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jinting Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, No. 4 Xueyuan Road, Haikou 571100, Hainan, China
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18
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Mehta D, Krahmer J, Uhrig RG. Closing the protein gap in plant chronobiology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1509-1522. [PMID: 33783885 DOI: 10.1111/tpj.15254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Our modern understanding of diel cell regulation in plants stems from foundational work in the late 1990s that analysed the dynamics of selected genes and mutants in Arabidopsis thaliana. The subsequent rise of transcriptomics technologies such as microarrays and RNA sequencing has substantially increased our understanding of anticipatory (circadian) and reactive (light- or dark-triggered) diel events in plants. However, it is also becoming clear that gene expression data fail to capture critical events in diel regulation that can only be explained by studying protein-level dynamics. Over the past decade, mass spectrometry technologies and quantitative proteomic workflows have significantly advanced, finally allowing scientists to characterise diel protein regulation at high throughput. Initial proteomic investigations suggest that the diel transcriptome and proteome generally lack synchrony and that the timing of daily regulatory events in plants is impacted by multiple levels of protein regulation (e.g., post-translational modifications [PTMs] and protein-protein interactions [PPIs]). Here, we highlight and summarise how the use of quantitative proteomics to elucidate diel plant cell regulation has advanced our understanding of these processes. We argue that this new understanding, coupled with the extraordinary developments in mass spectrometry technologies, demands greater focus on protein-level regulation of, and by, the circadian clock. This includes hitherto unexplored diel dynamics of protein turnover, PTMs, protein subcellular localisation and PPIs that can be masked by simple transcript- and protein-level changes. Finally, we propose new directions for how the latest advancements in quantitative proteomics can be utilised to answer outstanding questions in plant chronobiology.
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Affiliation(s)
- Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Johanna Krahmer
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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19
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Pacheco JM, Canal MV, Pereyra CM, Welchen E, Martínez-Noël GMA, Estevez JM. The tip of the iceberg: emerging roles of TORC1, and its regulatory functions in plant cells. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4085-4101. [PMID: 33462577 DOI: 10.1093/jxb/eraa603] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that plays a central role in coordinating cell growth with light availability, the diurnal cycle, energy availability, and hormonal pathways. TOR Complex 1 (TORC1) controls cell proliferation, growth, metabolism, and defense in plants. Sugar availability is the main signal for activation of TOR in plants, as it also is in mammals and yeast. Specific regulators of the TOR kinase pathway in plants are inorganic compounds in the form of major nutrients in the soils, and light inputs via their impact on autotrophic metabolism. The lack of TOR is embryo-lethal in plants, whilst dysregulation of TOR signaling causes major alterations in growth and development. TOR exerts control as a regulator of protein translation via the action of proteins such as S6K, RPS6, and TAP46. Phytohormones are central players in the downstream systemic physiological TOR effects. TOR has recently been attributed to have roles in the control of DNA methylation, in the abundance of mRNA splicing variants, and in the variety of regulatory lncRNAs and miRNAs. In this review, we summarize recent discoveries in the plant TOR signaling pathway in the context of our current knowledge of mammalian and yeast cells, and highlight the most important gaps in our understanding of plants that need to be addressed in the future.
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Affiliation(s)
| | - María Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas,, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Cintia M Pereyra
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes, Mar Del Plata, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas,, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes, Mar Del Plata, Argentina
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires CP, Argentina
- Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida (FCsV), Universidad Andres Bello, Santiago, Chile and Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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20
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Hiroguchi A, Sakamoto S, Mitsuda N, Miwa K. Golgi-localized membrane protein AtTMN1/EMP12 functions in the deposition of rhamnogalacturonan II and I for cell growth in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3611-3629. [PMID: 33587102 PMCID: PMC8096605 DOI: 10.1093/jxb/erab065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/10/2021] [Indexed: 05/20/2023]
Abstract
Appropriate pectin deposition in cell walls is important for cell growth in plants. Rhamnogalacturonan II (RG-II) is a portion of pectic polysaccharides; its borate crosslinking is essential for maintenance of pectic networks. However, the overall process of RG-II synthesis is not fully understood. To identify a novel factor for RG-II deposition or dimerization in cell walls, we screened Arabidopsis mutants with altered boron (B)-dependent growth. The mutants exhibited alleviated disorders of primary root and stem elongation, and fertility under low B, but reduced primary root lengths under sufficient B conditions. Altered primary root elongation was associated with cell elongation changes caused by loss of function in AtTMN1 (Transmembrane Nine 1)/EMP12, which encodes a Golgi-localized membrane protein of unknown function that is conserved among eukaryotes. Mutant leaf and root dry weights were lower than those of wild-type plants, regardless of B conditions. In cell walls, AtTMN1 mutations reduced concentrations of B, RG-II specific 2-keto-3-deoxy monosaccharides, and rhamnose largely derived from rhamnogalacturonan I (RG-I), suggesting reduced RG-II and RG-I. Together, our findings demonstrate that AtTMN1 is required for the deposition of RG-II and RG-I for cell growth and suggest that pectin modulates plant growth under low B conditions.
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Affiliation(s)
- Akihiko Hiroguchi
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305–8566, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305–8566, Japan
| | - Kyoko Miwa
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
- Correspondence:
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21
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Christopher JA, Stadler C, Martin CE, Morgenstern M, Pan Y, Betsinger CN, Rattray DG, Mahdessian D, Gingras AC, Warscheid B, Lehtiö J, Cristea IM, Foster LJ, Emili A, Lilley KS. Subcellular proteomics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:32. [PMID: 34549195 PMCID: PMC8451152 DOI: 10.1038/s43586-021-00029-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 12/11/2022]
Abstract
The eukaryotic cell is compartmentalized into subcellular niches, including membrane-bound and membrane-less organelles. Proteins localize to these niches to fulfil their function, enabling discreet biological processes to occur in synchrony. Dynamic movement of proteins between niches is essential for cellular processes such as signalling, growth, proliferation, motility and programmed cell death, and mutations causing aberrant protein localization are associated with a wide range of diseases. Determining the location of proteins in different cell states and cell types and how proteins relocalize following perturbation is important for understanding their functions, related cellular processes and pathologies associated with their mislocalization. In this Primer, we cover the major spatial proteomics methods for determining the location, distribution and abundance of proteins within subcellular structures. These technologies include fluorescent imaging, protein proximity labelling, organelle purification and cell-wide biochemical fractionation. We describe their workflows, data outputs and applications in exploring different cell biological scenarios, and discuss their main limitations. Finally, we describe emerging technologies and identify areas that require technological innovation to allow better characterization of the spatial proteome.
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Affiliation(s)
- Josie A. Christopher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Charlotte Stadler
- Department of Protein Sciences, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Claire E. Martin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marcel Morgenstern
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Yanbo Pan
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Cora N. Betsinger
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David G. Rattray
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Diana Mahdessian
- Department of Protein Sciences, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS and CIBSS Signaling Research Centers, University of Freiburg, Freiburg, Germany
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Kathryn S. Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
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22
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Jasieniecka-Gazarkiewicz K, Demski K, Gidda SK, Klińska S, Niedojadło J, Lager I, Carlsson AS, Minina EA, Mullen RT, Bozhkov PV, Stymne S, Banaś A. Subcellular Localization of Acyl-CoA: Lysophosphatidylethanolamine Acyltransferases (LPEATs) and the Effects of Knocking-Out and Overexpression of Their Genes on Autophagy Markers Level and Life Span of A. thaliana. Int J Mol Sci 2021; 22:ijms22063006. [PMID: 33809440 PMCID: PMC8000221 DOI: 10.3390/ijms22063006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
Arabidopsis thaliana possesses two acyl-CoA:lysophosphatidylethanolamine acyltransferases, LPEAT1 and LPEAT2, which are encoded by At1g80950 and At2g45670 genes, respectively. Both single lpeat2 mutant and double lpeat1 lpeat2 mutant plants exhibit a variety of conspicuous phenotypes, including dwarfed growth. Confocal microscopic analysis of tobacco suspension-cultured cells transiently transformed with green fluorescent protein-tagged versions of LPEAT1 or LPEAT2 revealed that LPEAT1 is localized to the endoplasmic reticulum (ER), whereas LPEAT2 is localized to both Golgi and late endosomes. Considering that the primary product of the reaction catalyzed by LPEATs is phosphatidylethanolamine, which is known to be covalently conjugated with autophagy-related protein ATG8 during a key step of the formation of autophagosomes, we investigated the requirements for LPEATs to engage in autophagic activity in Arabidopsis. Knocking out of either or both LPEAT genes led to enhanced accumulation of the autophagic adaptor protein NBR1 and decreased levels of both ATG8a mRNA and total ATG8 protein. Moreover, we detected significantly fewer membrane objects in the vacuoles of lpeat1 lpeat2 double mutant mesophyll cells than in vacuoles of control plants. However, contrary to what has been reported on autophagy deficient plants, the lpeat mutants displayed a prolonged life span compared to wild type, including delayed senescence.
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Affiliation(s)
- Katarzyna Jasieniecka-Gazarkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland; (K.D.); (S.K.); (A.B.)
- Correspondence:
| | - Kamil Demski
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland; (K.D.); (S.K.); (A.B.)
| | - Satinder K. Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.K.G.); (R.T.M.)
| | - Sylwia Klińska
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland; (K.D.); (S.K.); (A.B.)
| | - Janusz Niedojadło
- Department of Cell Biology, Department of Cellular and Molecular Biology, Nicolaus Copernicus University, 87-100 Torun, Poland;
| | - Ida Lager
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230-53 Alnarp, Sweden; (I.L.); (A.S.C.); (S.S.)
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230-53 Alnarp, Sweden; (I.L.); (A.S.C.); (S.S.)
| | - Elena A. Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (E.A.M.); (P.V.B.)
| | - Robert T. Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.K.G.); (R.T.M.)
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (E.A.M.); (P.V.B.)
| | - Sten Stymne
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230-53 Alnarp, Sweden; (I.L.); (A.S.C.); (S.S.)
| | - Antoni Banaś
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland; (K.D.); (S.K.); (A.B.)
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23
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A Pipeline towards the Biochemical Characterization of the Arabidopsis GT14 Family. Int J Mol Sci 2021; 22:ijms22031360. [PMID: 33572987 PMCID: PMC7866395 DOI: 10.3390/ijms22031360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Glycosyltransferases (GTs) catalyze the synthesis of glycosidic linkages and are essential in the biosynthesis of glycans, glycoconjugates (glycolipids and glycoproteins), and glycosides. Plant genomes generally encode many more GTs than animal genomes due to the synthesis of a cell wall and a wide variety of glycosylated secondary metabolites. The Arabidopsis thaliana genome is predicted to encode over 573 GTs that are currently classified into 42 diverse families. The biochemical functions of most of these GTs are still unknown. In this study, we updated the JBEI Arabidopsis GT clone collection by cloning an additional 105 GT cDNAs, 508 in total (89%), into Gateway-compatible vectors for downstream characterization. We further established a functional analysis pipeline using transient expression in tobacco (Nicotiana benthamiana) followed by enzymatic assays, fractionation of enzymatic products by reversed-phase HPLC (RP-HPLC) and characterization by mass spectrometry (MS). Using the GT14 family as an exemplar, we outline a strategy for identifying effective substrates of GT enzymes. By addition of UDP-GlcA as donor and the synthetic acceptors galactose-nitrobenzodiazole (Gal-NBD), β-1,6-galactotetraose (β-1,6-Gal4) and β-1,3-galactopentose (β-1,3-Gal5) to microsomes expressing individual GT14 enzymes, we verified the β-glucuronosyltransferase (GlcAT) activity of three members of this family (AtGlcAT14A, B, and E). In addition, a new family member (AT4G27480, 248) was shown to possess significantly higher activity than other GT14 enzymes. Our data indicate a likely role in arabinogalactan-protein (AGP) biosynthesis for these GT14 members. Together, the updated Arabidopsis GT clone collection and the biochemical analysis pipeline present an efficient means to identify and characterize novel GT catalytic activities.
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24
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Silva J, Ferraz R, Dupree P, Showalter AM, Coimbra S. Three Decades of Advances in Arabinogalactan-Protein Biosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:610377. [PMID: 33384708 PMCID: PMC7769824 DOI: 10.3389/fpls.2020.610377] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/23/2020] [Indexed: 05/18/2023]
Abstract
Arabinogalactan-proteins (AGPs) are a large, complex, and highly diverse class of heavily glycosylated proteins that belong to the family of cell wall hydroxyproline-rich glycoproteins. Approximately 90% of the molecules consist of arabinogalactan polysaccharides, which are composed of arabinose and galactose as major sugars and minor sugars such as glucuronic acid, fucose, and rhamnose. About half of the AGP family members contain a glycosylphosphatidylinositol (GPI) lipid anchor, which allows for an association with the outer leaflet of the plasma membrane. The mysterious AGP family has captivated the attention of plant biologists for several decades. This diverse family of glycoproteins is widely distributed in the plant kingdom, including many algae, where they play fundamental roles in growth and development processes. The journey of AGP biosynthesis begins with the assembly of amino acids into peptide chains of proteins. An N-terminal signal peptide directs AGPs toward the endoplasmic reticulum, where proline hydroxylation occurs and a GPI anchor may be added. GPI-anchored AGPs, as well as unanchored AGPs, are then transferred to the Golgi apparatus, where extensive glycosylation occurs by the action of a variety glycosyltransferase enzymes. Following glycosylation, AGPs are transported by secretory vesicles to the cell wall or to the extracellular face of the plasma membrane (in the case of GPI-anchored AGPs). GPI-anchored proteins can be released from the plasma membrane into the cell wall by phospholipases. In this review, we present an overview of the accumulated knowledge on AGP biosynthesis over the past three decades. Particular emphasis is placed on the glycosylation of AGPs as the sugar moiety is essential to their function. Recent genetics and genomics approaches have significantly contributed to a broader knowledge of AGP biosynthesis. However, many questions remain to be elucidated in the decades ahead.
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Affiliation(s)
- Jessy Silva
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Ricardo Ferraz
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Allan M. Showalter
- Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
| | - Sílvia Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
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25
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Pothion H, Jehan C, Tostivint H, Cartier D, Bucharles C, Falluel-Morel A, Boukhzar L, Anouar Y, Lihrmann I. Selenoprotein T: An Essential Oxidoreductase Serving as a Guardian of Endoplasmic Reticulum Homeostasis. Antioxid Redox Signal 2020; 33:1257-1275. [PMID: 32524825 DOI: 10.1089/ars.2019.7931] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Selenoproteins incorporate the essential nutrient selenium into their polypeptide chain. Seven members of this family reside in the endoplasmic reticulum (ER), the exact function of most of which is poorly understood. Especially, how ER-resident selenoproteins control the ER redox and ionic environment is largely unknown. Since alteration of ER function is observed in many diseases, the elucidation of the role of selenoproteins could enhance our understanding of the mechanisms involved in ER homeostasis. Recent Advances: Among selenoproteins, selenoprotein T (SELENOT) is remarkable as the most evolutionarily conserved and the only ER-resident selenoprotein whose gene knockout in mouse is lethal. Recent data indicate that SELENOT contributes to ER homeostasis: reduced expression of SELENOT in transgenic cell and animal models promotes accumulation of reactive oxygen and nitrogen species, depletion of calcium stores, activation of the unfolded protein response and impaired hormone secretion. Critical Issues: SELENOT is anchored to the ER membrane and associated with the oligosaccharyltransferase complex, suggesting that it regulates the early steps of N-glycosylation. Furthermore, it exerts a selenosulfide oxidoreductase activity carried by its thioredoxin-like domain. However, the physiological role of the redox activity of SELENOT is not fully understood. Likewise, the nature of its redox partners needs to be further characterized. Future Directions: Given the impact of ER stress in pathologies such as neurodegenerative, cardiovascular, metabolic and immune diseases, understanding the role of SELENOT and developing derived therapeutic tools such as selenopeptides to improve ER proteostasis and prevent ER stress could contribute to a better management of these diseases.
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Affiliation(s)
- Hugo Pothion
- Rouen-Normandie University, UNIROUEN, Inserm, U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Mont-Saint-Aignan Cedex, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Cédric Jehan
- Rouen-Normandie University, UNIROUEN, Inserm, U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Mont-Saint-Aignan Cedex, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Hervé Tostivint
- Physiologie moléculaire et Adaptation, UMR 7221 CNRS and Muséum National d'Histoire Naturelle, Paris, France
| | - Dorthe Cartier
- Rouen-Normandie University, UNIROUEN, Inserm, U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Mont-Saint-Aignan Cedex, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Christine Bucharles
- Rouen-Normandie University, UNIROUEN, Inserm, U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Mont-Saint-Aignan Cedex, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Anthony Falluel-Morel
- Rouen-Normandie University, UNIROUEN, Inserm, U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Mont-Saint-Aignan Cedex, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Loubna Boukhzar
- Rouen-Normandie University, UNIROUEN, Inserm, U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Mont-Saint-Aignan Cedex, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Youssef Anouar
- Rouen-Normandie University, UNIROUEN, Inserm, U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Mont-Saint-Aignan Cedex, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Isabelle Lihrmann
- Rouen-Normandie University, UNIROUEN, Inserm, U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Mont-Saint-Aignan Cedex, France.,Institute for Research and Innovation in Biomedicine, Rouen, France
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26
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Meyer AJ, Dreyer A, Ugalde JM, Feitosa-Araujo E, Dietz KJ, Schwarzländer M. Shifting paradigms and novel players in Cys-based redox regulation and ROS signaling in plants - and where to go next. Biol Chem 2020; 402:399-423. [PMID: 33544501 DOI: 10.1515/hsz-2020-0291] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Cys-based redox regulation was long regarded a major adjustment mechanism of photosynthesis and metabolism in plants, but in the recent years, its scope has broadened to most fundamental processes of plant life. Drivers of the recent surge in new insights into plant redox regulation have been the availability of the genome-scale information combined with technological advances such as quantitative redox proteomics and in vivo biosensing. Several unexpected findings have started to shift paradigms of redox regulation. Here, we elaborate on a selection of recent advancements, and pinpoint emerging areas and questions of redox biology in plants. We highlight the significance of (1) proactive H2O2 generation, (2) the chloroplast as a unique redox site, (3) specificity in thioredoxin complexity, (4) how to oxidize redox switches, (5) governance principles of the redox network, (6) glutathione peroxidase-like proteins, (7) ferroptosis, (8) oxidative protein folding in the ER for phytohormonal regulation, (9) the apoplast as an unchartered redox frontier, (10) redox regulation of respiration, (11) redox transitions in seed germination and (12) the mitochondria as potential new players in reductive stress safeguarding. Our emerging understanding in plants may serve as a blueprint to scrutinize principles of reactive oxygen and Cys-based redox regulation across organisms.
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Affiliation(s)
- Andreas J Meyer
- Chemical Signalling, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, D-53113Bonn, Germany
| | - Anna Dreyer
- Biochemistry and Physiology of Plants, Faculty of Biology, W5-134, Bielefeld University, University Street 25, D-33501Bielefeld, Germany
| | - José M Ugalde
- Chemical Signalling, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, D-53113Bonn, Germany
| | - Elias Feitosa-Araujo
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, D-48143Münster, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology, W5-134, Bielefeld University, University Street 25, D-33501Bielefeld, Germany
| | - Markus Schwarzländer
- Plant Energy Biology, Institute of Plant Biology and Biotechnology (IBBP), University of Münster, Schlossplatz 8, D-48143Münster, Germany
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27
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Characterization of In Vivo Function(s) of Members of the Plant Mitochondrial Carrier Family. Biomolecules 2020; 10:biom10091226. [PMID: 32846873 PMCID: PMC7565455 DOI: 10.3390/biom10091226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
Although structurally related, mitochondrial carrier family (MCF) proteins catalyze the specific transport of a range of diverse substrates including nucleotides, amino acids, dicarboxylates, tricarboxylates, cofactors, vitamins, phosphate and H+. Despite their name, they do not, however, always localize to the mitochondria, with plasma membrane, peroxisomal, chloroplast and thylakoid and endoplasmic reticulum localizations also being reported. The existence of plastid-specific MCF proteins is suggestive that the evolution of these proteins occurred after the separation of the green lineage. That said, plant-specific MCF proteins are not all plastid-localized, with members also situated at the endoplasmic reticulum and plasma membrane. While by no means yet comprehensive, the in vivo function of a wide range of these transporters is carried out here, and we discuss the employment of genetic variants of the MCF as a means to provide insight into their in vivo function complementary to that obtained from studies following their reconstitution into liposomes.
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28
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Fernie AR, Cavalcanti JHF, Nunes-Nesi A. Metabolic Roles of Plant Mitochondrial Carriers. Biomolecules 2020; 10:E1013. [PMID: 32650612 PMCID: PMC7408384 DOI: 10.3390/biom10071013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial carriers (MC) are a large family (MCF) of inner membrane transporters displaying diverse, yet often redundant, substrate specificities, as well as differing spatio-temporal patterns of expression; there are even increasing examples of non-mitochondrial subcellular localization. The number of these six trans-membrane domain proteins in sequenced plant genomes ranges from 39 to 141, rendering the size of plant families larger than that found in Saccharomyces cerevisiae and comparable with Homo sapiens. Indeed, comparison of plant MCs with those from these better characterized species has been highly informative. Here, we review the most recent comprehensive studies of plant MCFs, incorporating the torrent of genomic data emanating from next-generation sequencing techniques. As such we present a more current prediction of the substrate specificities of these carriers as well as review the continuing quest to biochemically characterize this feature of the carriers. Taken together, these data provide an important resource to guide direct genetic studies aimed at addressing the relevance of these vital carrier proteins.
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Affiliation(s)
- Alisdair R. Fernie
- Max-Planck-Instiute of Molecular Plant Physiology, 14476 Postdam-Golm, Germany
| | - João Henrique F. Cavalcanti
- Instituto de Educação, Agricultura e Ambiente, Universidade Federal do Amazonas, Humaitá 69800-000, Amazonas, Brazil;
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, Minas Gerais, Brazil
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29
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Kennedy MA, Hofstadter WA, Cristea IM. TRANSPIRE: A Computational Pipeline to Elucidate Intracellular Protein Movements from Spatial Proteomics Data Sets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1422-1439. [PMID: 32401031 PMCID: PMC7737664 DOI: 10.1021/jasms.0c00033] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein localization is paramount to protein function, and the intracellular movement of proteins underlies the regulation of numerous cellular processes. Given advances in spatial proteomics, the investigation of protein localization at a global scale has become attainable. Also becoming apparent is the need for dedicated analytical frameworks that allow the discovery of global intracellular protein movement events. Here, we describe TRANSPIRE, a computational pipeline that facilitates TRanslocation ANalysis of SPatIal pRotEomics data sets. TRANSPIRE leverages synthetic translocation profiles generated from organelle marker proteins to train a probabilistic Gaussian process classifier that predicts changes in protein distribution. This output is then integrated with information regarding co-translocating proteins and complexes and enriched gene ontology associations to discern the putative regulation and function of movement. We validate TRANSPIRE performance for predicting nuclear-cytoplasmic shuttling events. Analyzing an existing data set of nuclear and cytoplasmic proteomes during Kaposi Sarcoma-associated herpesvirus (KSHV)-induced cellular mRNA decay, we confirm that TRANSPIRE readily discerns expected translocations of RNA binding proteins. We next investigate protein translocations during infection with human cytomegalovirus (HCMV), a β-herpesvirus known to induce global organelle remodeling. We find that HCMV infection induces broad changes in protein localization, with over 800 proteins predicted to translocate during virus replication. Evident are protein movements related to HCMV modulation of host defense, metabolism, cellular trafficking, and Wnt signaling. For example, the low-density lipoprotein receptor (LDLR) translocates to the lysosome early in infection in conjunction with its degradation, which we validate by targeted mass spectrometry. Using microscopy, we also validate the translocation of the multifunctional kinase DAPK3, a movement that may contribute to HCMV activation of Wnt signaling.
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Affiliation(s)
- Michelle A Kennedy
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - William A Hofstadter
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
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30
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Gigli-Bisceglia N, Engelsdorf T, Hamann T. Plant cell wall integrity maintenance in model plants and crop species-relevant cell wall components and underlying guiding principles. Cell Mol Life Sci 2020; 77:2049-2077. [PMID: 31781810 PMCID: PMC7256069 DOI: 10.1007/s00018-019-03388-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/28/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
Abstract
The walls surrounding the cells of all land-based plants provide mechanical support essential for growth and development as well as protection from adverse environmental conditions like biotic and abiotic stress. Composition and structure of plant cell walls can differ markedly between cell types, developmental stages and species. This implies that wall composition and structure are actively modified during biological processes and in response to specific functional requirements. Despite extensive research in the area, our understanding of the regulatory processes controlling active and adaptive modifications of cell wall composition and structure is still limited. One of these regulatory processes is the cell wall integrity maintenance mechanism, which monitors and maintains the functional integrity of the plant cell wall during development and interaction with environment. It is an important element in plant pathogen interaction and cell wall plasticity, which seems at least partially responsible for the limited success that targeted manipulation of cell wall metabolism has achieved so far. Here, we provide an overview of the cell wall polysaccharides forming the bulk of plant cell walls in both monocotyledonous and dicotyledonous plants and the effects their impairment can have. We summarize our current knowledge regarding the cell wall integrity maintenance mechanism and discuss that it could be responsible for several of the mutant phenotypes observed.
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Affiliation(s)
- Nora Gigli-Bisceglia
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands
| | - Timo Engelsdorf
- Division of Plant Physiology, Department of Biology, Philipps University of Marburg, 35043, Marburg, Germany
| | - Thorsten Hamann
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, 7491, Trondheim, Norway.
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31
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Sánchez-Caballero L, Elurbe DM, Baertling F, Guerrero-Castillo S, van den Brand M, van Strien J, van Dam TJP, Rodenburg R, Brandt U, Huynen MA, Nijtmans LGJ. TMEM70 functions in the assembly of complexes I and V. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148202. [PMID: 32275929 DOI: 10.1016/j.bbabio.2020.148202] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/19/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
Abstract
Protein complexes from the oxidative phosphorylation (OXPHOS) system are assembled with the help of proteins called assembly factors. We here delineate the function of the inner mitochondrial membrane protein TMEM70, in which mutations have been linked to OXPHOS deficiencies, using a combination of BioID, complexome profiling and coevolution analyses. TMEM70 interacts with complex I and V and for both complexes the loss of TMEM70 results in the accumulation of an assembly intermediate followed by a reduction of the next assembly intermediate in the pathway. This indicates that TMEM70 has a role in the stability of membrane-bound subassemblies or in the membrane recruitment of subunits into the forming complex. Independent evidence for a role of TMEM70 in OXPHOS assembly comes from evolutionary analyses. The TMEM70/TMEM186/TMEM223 protein family, of which we show that TMEM186 and TMEM223 are mitochondrial in human as well, only occurs in species with OXPHOS complexes. Our results validate the use of combining complexome profiling with BioID and evolutionary analyses in elucidating congenital defects in protein complex assembly.
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Affiliation(s)
- Laura Sánchez-Caballero
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Dei M Elurbe
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Fabian Baertling
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands; Department of General Paediatrics, Neonatology and Paediatric Cardiology, University Children's Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Sergio Guerrero-Castillo
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Mariel van den Brand
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Joeri van Strien
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Teunis J P van Dam
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Richard Rodenburg
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Ulrich Brandt
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands.
| | - Leo G J Nijtmans
- Department of Paediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
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32
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Jung H, Jo SH, Park HJ, Lee A, Kim HS, Lee HJ, Cho HS. Golgi-localized cyclophilin 21 proteins negatively regulate ABA signalling via the peptidyl prolyl isomerase activity during early seedling development. PLANT MOLECULAR BIOLOGY 2020; 102:19-38. [PMID: 31786704 DOI: 10.1007/s11103-019-00928-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/24/2019] [Indexed: 05/20/2023]
Abstract
Plant possesses particular Golgi-resident cyclophilin 21 proteins (CYP21s) and the catalytic isomerase activities have a negative effect on ABA signalling gene expression during early seedling development. Cyclophilins (CYPs) are essential for diverse cellular process, as these catalyse a rate-limiting step in protein folding. Although Golgi proteomics in Arabidopsis thaliana suggests the existence of several CYPs in the Golgi apparatus, only one putative Golgi-resident CYP protein has been reported in rice (Oryza sativa L.; OsCYP21-4). Here, we identified the Golgi-resident CYP21 family genes and analysed their molecular characteristics in Arabidopsis and rice. The CYP family genes (CYP21-1, CYP21-2, CYP21-3, and CYP21-4) are plant-specific, and their appearance and copy numbers differ among plant species. CYP21-1 and CYP21-4 are common to all angiosperms, whereas CYP21-2 and CYP21-3 evolved in the Malvidae subclass. Furthermore, all CYP21 proteins localize to cis-Golgi, trans-Golgi or both cis- and trans-Golgi membranes in plant cells. Additionally, based on the structure, enzymatic function, and topological orientation in Golgi membranes, CYP21 proteins are divided into two groups. Genetic analysis revealed that Group I proteins (CYP21-1 and CYP21-2) exhibit peptidyl prolyl cis-trans isomerase (PPIase) activity and regulate seed germination and seedling growth and development by affecting the expression levels of abscisic acid signalling genes. Thus, we identified the Golgi-resident CYPs and demonstrated that their PPIase activities are required for early seedling growth and development in higher plants.
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Affiliation(s)
- Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea.
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33
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Navazio L, Formentin E, Cendron L, Szabò I. Chloroplast Calcium Signaling in the Spotlight. FRONTIERS IN PLANT SCIENCE 2020; 11:186. [PMID: 32226434 PMCID: PMC7081724 DOI: 10.3389/fpls.2020.00186] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/07/2020] [Indexed: 05/22/2023]
Abstract
Calcium has long been known to regulate the metabolism of chloroplasts, concerning both light and carbon reactions of photosynthesis, as well as additional non photosynthesis-related processes. In addition to undergo Ca2+ regulation, chloroplasts can also influence the overall Ca2+ signaling pathways of the plant cell. Compelling evidence indicate that chloroplasts can generate specific stromal Ca2+ signals and contribute to the fine tuning of cytoplasmic Ca2+ signaling in response to different environmental stimuli. The recent set up of a toolkit of genetically encoded Ca2+ indicators, targeted to different chloroplast subcompartments (envelope, stroma, thylakoids) has helped to unravel the participation of chloroplasts in intracellular Ca2+ handling in resting conditions and during signal transduction. Intra-chloroplast Ca2+ signals have been demonstrated to occur in response to specific environmental stimuli, suggesting a role for these plant-unique organelles in transducing Ca2+-mediated stress signals. In this mini-review we present current knowledge of stimulus-specific intra-chloroplast Ca2+ transients, as well as recent advances in the identification and characterization of Ca2+-permeable channels/transporters localized at chloroplast membranes. In particular, the potential role played by cMCU, a chloroplast-localized member of the mitochondrial calcium uniporter (MCU) family, as component of plant environmental sensing is discussed in detail, taking into account some specific structural features of cMCU. In summary, the recent molecular identification of some players of chloroplast Ca2+ signaling has opened new avenues in this rapidly developing field and will hopefully allow a deeper understanding of the role of chloroplasts in shaping physiological responses in plants.
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Affiliation(s)
- Lorella Navazio
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
| | - Elide Formentin
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Ildikò Szabò
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
- *Correspondence: Ildikò Szabò,
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34
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Sialoglycans and genetically engineered plants. SIALIC ACIDS AND SIALOGLYCOCONJUGATES IN THE BIOLOGY OF LIFE, HEALTH AND DISEASE 2020. [PMCID: PMC7153322 DOI: 10.1016/b978-0-12-816126-5.00002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Plants express N-glycosylation pathways and produce N-glycosylated proteins but differ from the mammalian-type proteins. Therefore attempts are made to design and engineer plant glycosylation pathways that can produce mammalian-type glycosylated moieties so that large quantities of biopharmaceuticals compatible to the human body can be produced. Most of the studies of plant expression systems for molecular farming have been conducted on Nicotiana sp. and genetic engineering and molecular biology tools have enabled the generation of glycoengineered plant for human use in the production of therapeutic recombinant proteins. We have discussed in this chapter the advances of glycoengineering in plants with special reference to the reconstruction of silaylation pathways in plants and the latest application in the production of antibody and therapeutics in plants.
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35
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Lande NV, Barua P, Gayen D, Kumar S, Chakraborty S, Chakraborty N. Proteomic dissection of the chloroplast: Moving beyond photosynthesis. J Proteomics 2019; 212:103542. [PMID: 31704367 DOI: 10.1016/j.jprot.2019.103542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/15/2019] [Accepted: 10/03/2019] [Indexed: 01/28/2023]
Abstract
Chloroplast, the photosynthetic machinery, converts photoenergy to ATP and NADPH, which powers the production of carbohydrates from atmospheric CO2 and H2O. It also serves as a major production site of multivariate pro-defense molecules, and coordinate with other organelles for cell defense. Chloroplast harbors 30-50% of total cellular proteins, out of which 80% are membrane residents and are difficult to solubilize. While proteome profiling has illuminated vast areas of biological protein space, a great deal of effort must be invested to understand the proteomic landscape of the chloroplast, which plays central role in photosynthesis, energy metabolism and stress-adaptation. Therefore, characterization of chloroplast proteome would not only provide the foundation for future investigation of expression and function of chloroplast proteins, but would open up new avenues for modulation of plant productivity through synchronizing chloroplastic key components. In this review, we summarize the progress that has been made to build new understanding of the chloroplast proteome and implications of chloroplast dynamicsing generate metabolic energy and modulating stress adaptation.
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Affiliation(s)
- Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dipak Gayen
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India.
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36
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Parsons HT, Stevens TJ, McFarlane HE, Vidal-Melgosa S, Griss J, Lawrence N, Butler R, Sousa MML, Salemi M, Willats WGT, Petzold CJ, Heazlewood JL, Lilley KS. Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization. THE PLANT CELL 2019; 31:2010-2034. [PMID: 31266899 PMCID: PMC6751122 DOI: 10.1105/tpc.19.00081] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/03/2019] [Accepted: 06/29/2019] [Indexed: 05/15/2023]
Abstract
The order of enzymatic activity across Golgi cisternae is essential for complex molecule biosynthesis. However, an inability to separate Golgi cisternae has meant that the cisternal distribution of most resident proteins, and their underlying localization mechanisms, are unknown. Here, we exploit differences in surface charge of intact cisternae to perform separation of early to late Golgi subcompartments. We determine protein and glycan abundance profiles across the Golgi; over 390 resident proteins are identified, including 136 new additions, with over 180 cisternal assignments. These assignments provide a means to better understand the functional roles of Golgi proteins and how they operate sequentially. Protein and glycan distributions are validated in vivo using high-resolution microscopy. Results reveal distinct functional compartmentalization among resident Golgi proteins. Analysis of transmembrane proteins shows several sequence-based characteristics relating to pI, hydrophobicity, Ser abundance, and Phe bilayer asymmetry that change across the Golgi. Overall, our results suggest that a continuum of transmembrane features, rather than discrete rules, guide proteins to earlier or later locations within the Golgi stack.
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Affiliation(s)
- Harriet T Parsons
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, United Kingdom
- Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark
| | - Tim J Stevens
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom
| | - Heather E McFarlane
- School of Biosciences, University of Melbourne, Parkville VIC 3052, , Australia
| | - Silvia Vidal-Melgosa
- Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark
| | - Johannes Griss
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
| | - Nicola Lawrence
- The Wellcome Trust and Cancer Research UK Gurdon Institute, Cambridge University, Cambridge CB2 1QN, United Kingdom
| | - Richard Butler
- The Wellcome Trust and Cancer Research UK Gurdon Institute, Cambridge University, Cambridge CB2 1QN, United Kingdom
| | - Mirta M L Sousa
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, California 95616
| | - William G T Willats
- Department of Plant and Environmental Sciences, Copenhagen University, 1871 Frederiksberg C, Denmark
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Joshua L Heazlewood
- School of Biosciences, University of Melbourne, Parkville VIC 3052, , Australia
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge University, Cambridge, CB2 1QW, United Kingdom
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37
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A signal motif retains Arabidopsis ER-α-mannosidase I in the cis-Golgi and prevents enhanced glycoprotein ERAD. Nat Commun 2019; 10:3701. [PMID: 31420549 PMCID: PMC6697737 DOI: 10.1038/s41467-019-11686-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/01/2019] [Indexed: 11/09/2022] Open
Abstract
The Arabidopsis ER-α-mannosidase I (MNS3) generates an oligomannosidic N-glycan structure that is characteristically found on ER-resident glycoproteins. The enzyme itself has so far not been detected in the ER. Here, we provide evidence that in plants MNS3 exclusively resides in the Golgi apparatus at steady-state. Notably, MNS3 remains on dispersed punctate structures when subjected to different approaches that commonly result in the relocation of Golgi enzymes to the ER. Responsible for this rare behavior is an amino acid signal motif (LPYS) within the cytoplasmic tail of MNS3 that acts as a specific Golgi retention signal. This retention is a means to spatially separate MNS3 from ER-localized mannose trimming steps that generate the glycan signal required for flagging terminally misfolded glycoproteins for ERAD. The physiological importance of the very specific MNS3 localization is demonstrated here by means of a structurally impaired variant of the brassinosteroid receptor BRASSINOSTEROID INSENSITIVE 1. The Arabidopsis ER-α-mannosidase I MNS3 generates N-glycan structures typical of ER-resident glycoproteins. Here Schoberer et al. identify a novel motif that anchors MNS3 to the cis-Golgi, spatially separating MNS3 from ER-localized mannose trimming associated with the ER-associated degradation pathway.
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38
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Welch LG, Munro S. A tale of short tails, through thick and thin: investigating the sorting mechanisms of Golgi enzymes. FEBS Lett 2019; 593:2452-2465. [DOI: 10.1002/1873-3468.13553] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Lawrence G. Welch
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge UK
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39
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Brault ML, Petit JD, Immel F, Nicolas WJ, Glavier M, Brocard L, Gaston A, Fouché M, Hawkins TJ, Crowet J, Grison MS, Germain V, Rocher M, Kraner M, Alva V, Claverol S, Paterlini A, Helariutta Y, Deleu M, Lins L, Tilsner J, Bayer EM. Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata. EMBO Rep 2019; 20:e47182. [PMID: 31286648 PMCID: PMC6680132 DOI: 10.15252/embr.201847182] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/28/2019] [Accepted: 06/06/2019] [Indexed: 12/20/2022] Open
Abstract
In eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved a unique type of MCS, inside intercellular pores, the plasmodesmata, where endoplasmic reticulum (ER)-plasma membrane (PM) contacts coincide with regulation of cell-to-cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remain unknown. Here, we show that the multiple C2 domains and transmembrane region protein (MCTP) family, key regulators of cell-to-cell signalling in plants, act as ER-PM tethers specifically at plasmodesmata. We report that MCTPs are plasmodesmata proteins that insert into the ER via their transmembrane region while their C2 domains dock to the PM through interaction with anionic phospholipids. A Atmctp3/Atmctp4 loss of function mutant induces plant developmental defects, impaired plasmodesmata function and composition, while MCTP4 expression in a yeast Δtether mutant partially restores ER-PM tethering. Our data suggest that MCTPs are unique membrane tethers controlling both ER-PM contacts and cell-to-cell signalling.
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Affiliation(s)
- Marie L Brault
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Jules D Petit
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
- Laboratoire de Biophysique Moléculaire aux InterfacesTERRA Research Centre, GX ABTUniversité de LiègeGemblouxBelgium
| | - Françoise Immel
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - William J Nicolas
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
- Present address:
Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Marie Glavier
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Lysiane Brocard
- Bordeaux Imaging CentrePlant Imaging PlatformUMS 3420, INRA‐CNRS‐INSERM‐University of BordeauxVillenave‐d'OrnonFrance
| | - Amèlia Gaston
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
- Present address:
UMR 1332 BFPINRAUniversity of BordeauxBordeauxFrance
| | - Mathieu Fouché
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
- Present address:
UMR 1332 BFPINRAUniversity of BordeauxBordeauxFrance
| | | | - Jean‐Marc Crowet
- Laboratoire de Biophysique Moléculaire aux InterfacesTERRA Research Centre, GX ABTUniversité de LiègeGemblouxBelgium
- Present address:
Matrice Extracellulaire et Dynamique Cellulaire MEDyCUMR7369, CNRSUniversité de Reims‐Champagne‐ArdenneReimsFrance
| | - Magali S Grison
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Véronique Germain
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Marion Rocher
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
| | - Max Kraner
- Division of BiochemistryDepartment of BiologyFriedrich‐Alexander University Erlangen‐NurembergErlangenGermany
| | - Vikram Alva
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Stéphane Claverol
- Proteome PlatformFunctional Genomic Center of BordeauxUniversity of BordeauxBordeaux CedexFrance
| | | | - Ykä Helariutta
- The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux InterfacesTERRA Research Centre, GX ABTUniversité de LiègeGemblouxBelgium
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux InterfacesTERRA Research Centre, GX ABTUniversité de LiègeGemblouxBelgium
| | - Jens Tilsner
- Biomedical Sciences Research ComplexUniversity of St AndrewsFifeUK
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse MembranaireUMR5200, CNRSUniversité de BordeauxVillenave d'OrnonFrance
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40
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Plant cell-surface GIPC sphingolipids sense salt to trigger Ca 2+ influx. Nature 2019; 572:341-346. [PMID: 31367039 DOI: 10.1038/s41586-019-1449-z] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/03/2019] [Indexed: 12/12/2022]
Abstract
Salinity is detrimental to plant growth, crop production and food security worldwide. Excess salt triggers increases in cytosolic Ca2+ concentration, which activate Ca2+-binding proteins and upregulate the Na+/H+ antiporter in order to remove Na+. Salt-induced increases in Ca2+ have long been thought to be involved in the detection of salt stress, but the molecular components of the sensing machinery remain unknown. Here, using Ca2+-imaging-based forward genetic screens, we isolated the Arabidopsis thaliana mutant monocation-induced [Ca2+]i increases 1 (moca1), and identified MOCA1 as a glucuronosyltransferase for glycosyl inositol phosphorylceramide (GIPC) sphingolipids in the plasma membrane. MOCA1 is required for salt-induced depolarization of the cell-surface potential, Ca2+ spikes and waves, Na+/H+ antiporter activation, and regulation of growth. Na+ binds to GIPCs to gate Ca2+ influx channels. This salt-sensing mechanism might imply that plasma-membrane lipids are involved in adaption to various environmental salt levels, and could be used to improve salt resistance in crops.
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Nightingale DJH, Lilley KS, Oliver SG. A Protocol to Map the Spatial Proteome Using HyperLOPIT in Saccharomyces cerevisiae. Bio Protoc 2019; 9:e3303. [PMID: 33654815 PMCID: PMC7854154 DOI: 10.21769/bioprotoc.3303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/12/2019] [Accepted: 06/25/2019] [Indexed: 11/02/2022] Open
Abstract
The correct subcellular localization of proteins is vital for cellular function and the study of this process at the systems level will therefore enrich our understanding of the roles of proteins within the cell. Multiple methods are available for the study of protein subcellular localization, including fluorescence microscopy, organelle cataloging, proximity labeling methods, and whole-cell protein correlation profiling methods. We provide here a protocol for the systems-level study of the subcellular localization of the yeast proteome, using a version of hyperplexed Localization of Organelle Proteins by Isotope Tagging (hyperLOPIT) that has been optimized for use with Saccharomyces cerevisiae. The entire protocol encompasses cell culture, cell lysis by nitrogen cavitation, subcellular fractionation, monitoring of the fractionation using Western blotting, labeling of samples with TMT isobaric tags and mass spectrometric analysis. Also included is a brief explanation of downstream processing of the mass spectrometry data to produce a map of the spatial proteome. If required, the nitrogen cavitation lysis and Western blotting portions of the protocol may be performed independently of the mass spectrometry analysis. The protocol in its entirety, however, enables the unbiased, systems-level and high-resolution analysis of the localizations of thousands of proteins in parallel within a single experiment.
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Affiliation(s)
- Daniel J. H. Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, United Kingdom
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, United Kingdom
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, United Kingdom
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Okekeogbu IO, Pattathil S, González Fernández-Niño SM, Aryal UK, Penning BW, Lao J, Heazlewood JL, Hahn MG, McCann MC, Carpita NC. Glycome and Proteome Components of Golgi Membranes Are Common between Two Angiosperms with Distinct Cell-Wall Structures. THE PLANT CELL 2019; 31:1094-1112. [PMID: 30914498 PMCID: PMC6533026 DOI: 10.1105/tpc.18.00755] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/28/2019] [Accepted: 03/24/2019] [Indexed: 05/20/2023]
Abstract
The plant endoplasmic reticulum-Golgi apparatus is the site of synthesis, assembly, and trafficking of all noncellulosic polysaccharides, proteoglycans, and proteins destined for the cell wall. As grass species make cell walls distinct from those of dicots and noncommelinid monocots, it has been assumed that the differences in cell-wall composition stem from differences in biosynthetic capacities of their respective Golgi. However, immunosorbence-based screens and carbohydrate linkage analysis of polysaccharides in Golgi membranes, enriched by flotation centrifugation from etiolated coleoptiles of maize (Zea mays) and leaves of Arabidopsis (Arabidopsis thaliana), showed that arabinogalactan-proteins and arabinans represent substantial portions of the Golgi-resident polysaccharides not typically found in high abundance in cell walls of either species. Further, hemicelluloses accumulated in Golgi at levels that contrasted with those found in their respective cell walls, with xyloglucans enriched in maize Golgi, and xylans enriched in Arabidopsis. Consistent with this finding, maize Golgi membranes isolated by flotation centrifugation and enriched further by free-flow electrophoresis, yielded >200 proteins known to function in the biosynthesis and metabolism of cell-wall polysaccharides common to all angiosperms, and not just those specific to cell-wall type. We propose that the distinctive compositions of grass primary cell walls compared with other angiosperms result from differential gating or metabolism of secreted polysaccharides post-Golgi by an as-yet unknown mechanism, and not necessarily by differential expression of genes encoding specific synthase complexes.
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Affiliation(s)
- Ikenna O Okekeogbu
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | | | | | - Bryan W Penning
- U.S. Department of Agriculture, Agricultural Research Service, Corn, Soybean and Wheat Quality Research, Wooster, Ohio 44691
| | - Jeemeng Lao
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Joshua L Heazlewood
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Nicholas C Carpita
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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43
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Wilkop T, Pattathil S, Ren G, Davis DJ, Bao W, Duan D, Peralta AG, Domozych DS, Hahn MG, Drakakaki G. A Hybrid Approach Enabling Large-Scale Glycomic Analysis of Post-Golgi Vesicles Reveals a Transport Route for Polysaccharides. THE PLANT CELL 2019; 31:627-644. [PMID: 30760563 PMCID: PMC6482635 DOI: 10.1105/tpc.18.00854] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/22/2019] [Accepted: 02/12/2019] [Indexed: 05/10/2023]
Abstract
The plant endomembrane system facilitates the transport of polysaccharides, associated enzymes, and glycoproteins through its dynamic pathways. Although enzymes involved in cell wall biosynthesis have been identified, little is known about the endomembrane-based transport of glycan components. This is partially attributed to technical challenges in biochemically determining polysaccharide cargo in specific vesicles. Here, we introduce a hybrid approach addressing this limitation. By combining vesicle isolation with a large-scale carbohydrate antibody arraying technique, we charted an initial large-scale map describing the glycome profile of the SYNTAXIN OF PLANTS61 (SYP61) trans-Golgi network compartment in Arabidopsis (Arabidopsis thaliana). A library of antibodies recognizing specific noncellulosic carbohydrate epitopes allowed us to identify a range of diverse glycans, including pectins, xyloglucans (XyGs), and arabinogalactan proteins in isolated vesicles. Changes in XyG- and pectin-specific epitopes in the cell wall of an Arabidopsis SYP61 mutant corroborate our findings. Our data provide evidence that SYP61 vesicles are involved in the transport and deposition of structural polysaccharides and glycoproteins. Adaptation of our methodology can enable studies characterizing the glycome profiles of various vesicle populations in plant and animal systems and their respective roles in glycan transport defined by subcellular markers, developmental stages, or environmental stimuli.
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Affiliation(s)
- Thomas Wilkop
- Department of Plant Sciences, University of California, Davis, California 95616
- Light Microscopy Core, University of Kentucky, Lexington, Kentucky 40536
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
| | - Guangxi Ren
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Destiny J Davis
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Wenlong Bao
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Dechao Duan
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Angelo G Peralta
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
| | - David S Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602-7271
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California, Davis, California 95616
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44
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Gatto L, Breckels LM, Lilley KS. Assessing sub-cellular resolution in spatial proteomics experiments. Curr Opin Chem Biol 2019; 48:123-149. [PMID: 30711721 PMCID: PMC6391913 DOI: 10.1016/j.cbpa.2018.11.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 12/04/2022]
Abstract
The sub-cellular localisation of a protein is vital in defining its function, and a protein's mis-localisation is known to lead to adverse effect. As a result, numerous experimental techniques and datasets have been published, with the aim of deciphering the localisation of proteins at various scales and resolutions, including high profile mass spectrometry-based efforts. Here, we present a meta-analysis assessing and comparing the sub-cellular resolution of 29 such mass spectrometry-based spatial proteomics experiments using a newly developed tool termed QSep. Our goal is to provide a simple quantitative report of how well spatial proteomics resolve the sub-cellular niches they describe to inform and guide developers and users of such methods.
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Affiliation(s)
- Laurent Gatto
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK; Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK; de Duve Institute, UCLouvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
| | - Lisa M Breckels
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK; Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
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45
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Temple H, Mortimer JC, Tryfona T, Yu X, Lopez‐Hernandez F, Sorieul M, Anders N, Dupree P. Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. PLANT DIRECT 2019; 3:e00117. [PMID: 31245760 PMCID: PMC6508755 DOI: 10.1002/pld3.117] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/21/2018] [Accepted: 01/06/2019] [Indexed: 05/07/2023]
Abstract
All members of the DUF579 family characterized so far have been described to affect the integrity of the hemicellulosic cell wall component xylan: GXMs are glucuronoxylan methyltransferases catalyzing 4-O-methylation of glucuronic acid on xylan; IRX15 and IRX15L, although their enzymatic activity is unknown, are required for xylan biosynthesis and/or xylan deposition. Here we show that the DUF579 family members, AGM1 and AGM2, are required for 4-O-methylation of glucuronic acid of a different plant cell wall component, the highly glycosylated arabinogalactan proteins (AGPs).
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Affiliation(s)
- Henry Temple
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Xiaolan Yu
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Mathias Sorieul
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Nadine Anders
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Paul Dupree
- Department of BiochemistryUniversity of CambridgeCambridgeUK
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46
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Meyer AJ, Riemer J, Rouhier N. Oxidative protein folding: state-of-the-art and current avenues of research in plants. THE NEW PHYTOLOGIST 2019; 221:1230-1246. [PMID: 30230547 DOI: 10.1111/nph.15436] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/01/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 1230 I. Introduction 1230 II. Formation and isomerization of disulfides in the ER and the Golgi apparatus 1231 III. The disulfide relay in the mitochondrial intermembrane space: why are plants different? 1236 IV. Disulfide bond formation on luminal proteins in thylakoids 1240 V. Conclusion 1242 Acknowledgements 1242 References 1242 SUMMARY: Disulfide bonds are post-translational modifications crucial for the structure and function of thousands of proteins. Their formation and isomerization, referred to as oxidative folding, require specific protein machineries found in oxidizing subcellular compartments, namely the endoplasmic reticulum and the associated endomembrane system, the intermembrane space of mitochondria and the thylakoid lumen of chloroplasts. At least one protein component is required for transferring electrons from substrate proteins to an acceptor that is usually molecular oxygen. For oxidation reactions, incoming reduced substrates are oxidized by thiol-oxidoreductase proteins (or domains in case of chimeric proteins), which are usually themselves oxidized by a single thiol oxidase, the enzyme generating disulfide bonds de novo. By contrast, the description of the molecular actors and pathways involved in proofreading and isomerization of misfolded proteins, which require a tightly controlled redox balance, lags behind. Herein we provide a general overview of the knowledge acquired on the systems responsible for oxidative protein folding in photosynthetic organisms, highlighting their particularities compared to other eukaryotes. Current research challenges are discussed including the importance and specificity of these oxidation systems in the context of the existence of reducing systems in the same compartments.
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Affiliation(s)
- Andreas J Meyer
- INRES-Chemical Signalling, University of Bonn, 53113, Bonn, Germany
| | - Jan Riemer
- Institute of Biochemistry, University of Cologne, 50674, Cologne, Germany
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47
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Geladaki A, Kočevar Britovšek N, Breckels LM, Smith TS, Vennard OL, Mulvey CM, Crook OM, Gatto L, Lilley KS. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat Commun 2019; 10:331. [PMID: 30659192 PMCID: PMC6338729 DOI: 10.1038/s41467-018-08191-w] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/18/2018] [Indexed: 01/09/2023] Open
Abstract
The study of protein localisation has greatly benefited from high-throughput methods utilising cellular fractionation and proteomic profiling. Hyperplexed Localisation of Organelle Proteins by Isotope Tagging (hyperLOPIT) is a well-established method in this area. It achieves high-resolution separation of organelles and subcellular compartments but is relatively time- and resource-intensive. As a simpler alternative, we here develop Localisation of Organelle Proteins by Isotope Tagging after Differential ultraCentrifugation (LOPIT-DC) and compare this method to the density gradient-based hyperLOPIT approach. We confirm that high-resolution maps can be obtained using differential centrifugation down to the suborganellar and protein complex level. HyperLOPIT and LOPIT-DC yield highly similar results, facilitating the identification of isoform-specific localisations and high-confidence localisation assignment for proteins in suborganellar structures, protein complexes and signalling pathways. By combining both approaches, we present a comprehensive high-resolution dataset of human protein localisations and deliver a flexible set of protocols for subcellular proteomics.
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Affiliation(s)
- Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, 20 Downing Place, Cambridge, CB2 3EJ, UK
| | - Nina Kočevar Britovšek
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Tom S Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Owen L Vennard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Claire M Mulvey
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- de Duve Institute, UC Louvain, Avenue Hippocrate 75, Brussels, 1200, Belgium
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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48
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Panzade G, Gangwar I, Awasthi S, Sharma N, Shankar R. Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5650983. [PMID: 31796964 PMCID: PMC6891001 DOI: 10.1093/database/baz130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022]
Abstract
Gene regulation is a highly complex and networked phenomenon where multiple tiers of control determine the cell state in a spatio-temporal manner. Among these, the transcription factors, DNA and histone modifications, and post-transcriptional control by small RNAs like miRNAs serve as major regulators. An understanding of the integrative and spatio-temporal impact of these regulatory factors can provide better insights into the state of a ‘cell system’. Yet, there are limited resources available to this effect. Therefore, we hereby report an integrative information portal (Plant Regulomics Portal; PRP) for plants for the first time. The portal has been developed by integrating a huge amount of curated data from published sources, RNA-, methylome- and sRNA/miRNA sequencing, histone modifications and repeats, gene ontology, digital gene expression and characterized pathways. The key features of the portal include a regulatory search engine for fetching numerous analytical outputs and tracks of the abovementioned regulators and also a genome browser for integrated visualization of the search results. It also has numerous analytical features for analyses of transcription factors (TFs) and sRNA/miRNA, spot-specific methylation, gene expression and interactions and details of pathways for any given genomic element. It can also provide information on potential RdDM regulation, while facilitating enrichment analysis, generation of visually rich plots and downloading of data in a selective manner. Visualization of intricate biological networks is an important feature which utilizes the Neo4j Graph database making analysis of relationships and long-range system viewing possible. Till date, PRP hosts 571-GB processed data for four plant species namely Arabidopsis thaliana, Oryza sativa subsp. japonica, Zea mays and Glycine max. Database URL: https://scbb.ihbt.res.in/PRP
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Affiliation(s)
- Ganesh Panzade
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India.,Division of Biology, Kansas State University, Zinovyeva Lab, 28 Ackert Hall, Manhattan, KS, USA, 66506
| | - Indu Gangwar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Supriya Awasthi
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India
| | - Nitesh Sharma
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Kangra, Himachal Pradesh 176061, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-HRDC Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
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49
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Liu S, Zheng L, Jia J, Guo J, Zheng M, Zhao J, Shao J, Liu X, An L, Yu F, Qi Y. Chloroplast Translation Elongation Factor EF-Tu/SVR11 Is Involved in var2-Mediated Leaf Variegation and Leaf Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:295. [PMID: 30915096 PMCID: PMC6423176 DOI: 10.3389/fpls.2019.00295] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/22/2019] [Indexed: 05/02/2023]
Abstract
Chloroplasts are semiautonomous organelles, retaining their own genomes and gene expression apparatuses but controlled by nucleus genome encoded protein factors during evolution. To analyze the genetic regulatory network of FtsH-mediated chloroplast development in Arabidopsis, a set of suppressor mutants of yellow variegated (var2) have been identified. In this research, we reported the identification of another new var2 suppressor locus, SUPPRESSOR OF VARIEGATION11 (SVR11), which encodes a putative chloroplast-localized prokaryotic type translation elongation factor EF-Tu. SVR11 is likely essential to chloroplast development and plant survival. GUS activity reveals that SVR11 is abundant in the juvenile leaf tissue, lateral roots, and root tips. Interestingly, we found that SVR11 and SVR9 together regulate leaf development, including leaf margin development and cotyledon venation patterns. These findings reinforce the notion that chloroplast translation state triggers retrograde signals regulate not only chloroplast development but also leaf development.
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50
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Wahyudi A, Ariyani D, Ma G, Inaba R, Fukasawa C, Nakano R, Motohashi R. Functional analyses of lipocalin proteins in tomato. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:303-312. [PMID: 31892817 PMCID: PMC6905218 DOI: 10.5511/plantbiotechnology.18.0620a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/20/2018] [Indexed: 05/30/2023]
Abstract
In this study, two temperature-induced lipocalin genes SlTIL1 and SlTIL2, and a chloroplastic lipocalin gene SlCHL were isolated from 'Micro-Tom' tomato. The coding sequences of SlTIL1, SlTIL2 and SlCHL were 558, 558, and 1002 bp, respectively. By TargetP analysis, no characteristic transit peptides were predicted in the proteins of SlTIL1 and SlTIL2, while a chloroplastic transit peptide was predicted in the protein of SlCHL. The subcellular localization results indicated that SlTIL1 and SlTIL2 proteins were major localized in the plasma membrane, while SlCHL was localized in chloroplast. To understand the function of lipocalins, transgenic tomato over-expressed SlTIL1, SlTIL2 and SlCHL and their virus-induced gene silencing (VIGS) plants were generated. The phenotypes were significantly affected when the SlTIL1, SlTIL2 and SlCHL were over-expressed or silenced by VIGS, which suggested that the three lipocalins played important roles in regulating the growth and development of tomato. In addition, the level of ROS (O2 - and H2O2) was low in SlTIL1, SlTIL2 and SlCHL over-expressed plants, while it was high in their silenced plants. The changes in the expression of SODs were consistent with the accumulations of ROS, which indicated that lipocalins might have an important role in abiotic oxidative stress tolerance in tomato plants. Especially SlTIL1 and SlTIL2 are localized around their membranes and protect them from ROS. The results will contribute to elucidating the functions of lipocalin in plants, and provide new strategies to improve the tolerance to abiotic stress in tomato plants.
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Affiliation(s)
- Anung Wahyudi
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
- Politeknik Negeri Lampung-Indonesia, Jl. Soekarno-Hatta no.10 Rajabasa, Bandar Lampung-Indonesia
| | - Dinni Ariyani
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Gang Ma
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Ryosuke Inaba
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Chikako Fukasawa
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Ryohei Nakano
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama, Okayama 700-8530, Japan
| | - Reiko Motohashi
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
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