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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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Tyagi S, Sharma Y, Sharma A, Pandey A, Singh K, Upadhyay SK. Expression of TaNCL2-A ameliorates cadmium toxicity by increasing calcium and enzymatic antioxidants activities in arabidopsis. CHEMOSPHERE 2023; 329:138636. [PMID: 37040835 DOI: 10.1016/j.chemosphere.2023.138636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Cadmium (Cd) is a heavy metal that occurs naturally in the environment and is toxic to both animals and plants. The impact of Cd toxicity is shown to be reduced by the exogenous application of calcium (Ca) in crop plants. The sodium/calcium exchanger-like (NCL) protein is involved in Ca enrichment in the cytoplasm by transporting it from the vacuole in the exchange of cytosolic sodium (Na). However, it has not been utilized to ameliorate the Cd toxicity, to date. An elevated expression of TaNCL2-A gene in the root and shoot tissues of bread wheat seedlings, and a higher growth rate of recombinant yeast cells, suggested its role in Cd stress response. The TaNCL2-A expressing transgenic Arabidopsis lines exhibited significant Cd tolerance with increased Ca (∼10-fold) accumulation. The proline content and antioxidant enzymes activities were increased while oxidative stress-related molecules such as H2O2 and MDA were reduced in the transgenic lines. In addition, the growth and yield parameters of transgenic lines such as seed germination rate, root length, leaf biomass, leaf area index, rosette diameter, leaf length and width, and silique count, along with various physiological indicators like chlorophyll, carotenoid, and relative water contents were also improved in comparison to the control plants. Further, the transgenic lines exhibited significant salinity and osmotic stress tolerance, as well. Taken together, these results suggested that the TaNCL2-A could mitigate Cd toxicity along with salinity and osmotic stress. This gene may also be utilized for phytoremediation and Cd sequestration in future studies.
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Affiliation(s)
- Shivi Tyagi
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Yashraaj Sharma
- Department of Botany, Panjab University, Chandigarh, 160014, India; Department of Biotechnology, Panjab University, Chandigarh, 160014, India
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, New Delhi, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, 160014, India
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Cold Tolerance of ScCBL6 Is Associated with Tonoplast Transporters and Photosynthesis in Arabidopsis. Curr Issues Mol Biol 2022; 44:5579-5592. [DOI: 10.3390/cimb44110378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Plants that are adapted to harsh environments offer enormous opportunity to understand stress responses in ecological systems. Stipa capillacea is widely distributed in the frigid and arid region of the Tibetan Plateau, but its signal transduction system under cold stress has not been characterized. In this study, we isolated a cDNA encoding the signal transduction protein, ScCBL6, from S. capillacea, and evaluated its role in cold tolerance by ectopically expressing it in Arabidopsis. Full-length ScCBL6 encode 227 amino acids, and are clustered with CBL6 in Stipa purpurea and Oryza sativa in a phylogenetic analysis. Compared with tolerance in wild-type (WT) plants, ScCBL6-overexpressing plants (ScCBL6-OXP) were more tolerant to cold stress but not to drought stress, as confirmed by their high photosynthetic capacity (Fv/Fm) and survival rate under cold stress. We further compared their cold-responsive transcriptome profiles by RNA sequencing. In total, 3931 genes were differentially expressed by the introduction of ScCBL6. These gene products were involved in multiple processes such as the immune system, lipid catabolism, and secondary metabolism. A KEGG pathway analysis revealed that they were mainly enriched in plant hormone signal transduction and biomacromolecule metabolism. Proteins encoded by differentially expressed genes were predicted to be localized in chloroplasts, mitochondria, and vacuoles, suggesting that ScCBL6 exerts a wide range of functions. Based on its tonoplast subcellular location combined with integrated transcriptome and physiological analyses of ScCBL6-OXP, we inferred that ScCBL6 improves plant cold stress tolerance in Arabidopsis via the regulation of photosynthesis, redox status, and tonoplast metabolite transporters.
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Detoxification and Excretion of Trichothecenes in Transgenic Arabidopsisthaliana Expressing Fusarium graminearum Trichothecene 3- O-acetyltransferase. Toxins (Basel) 2021; 13:toxins13050320. [PMID: 33946742 PMCID: PMC8145220 DOI: 10.3390/toxins13050320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
Fusarium graminearum, the causal agent of Fusarium head blight (FHB), produces trichothecenes including deoxynivalenol (DON), nivalenol (NIV), and 3,7,15-trihydroxy-12,13-epoxytrichothec-9-ene (NX-3). These toxins contaminate grains and cause profound health problems in humans and animals. To explore exploiting a fungal self-protection mechanism in plants, we examined the ability of F. graminearum trichothecene 3-O-acetyltransferase (FgTri101) to detoxify several key trichothecenes produced by F. graminearum: DON, 15-ADON, NX-3, and NIV. FgTri101 was cloned from F. graminearum and expressed in Arabidopsis plants. We compared the phytotoxic effects of purified DON, NIV, and NX-3 on the root growth of transgenic Arabidopsis expressing FgTri101. Compared to wild type and GUS controls, FgTri101 transgenic Arabidopsis plants displayed significantly longer root length on media containing DON and NX-3. Furthermore, we confirmed that the FgTri101 transgenic plants acetylated DON to 3-ADON, 15-ADON to 3,15-diADON, and NX-3 to NX-2, but did not acetylate NIV. Approximately 90% of the converted toxins were excreted into the media. Our study indicates that transgenic Arabidopsis expressing FgTri101 can provide plant protection by detoxifying trichothecenes and excreting the acetylated toxins out of plant cells. Characterization of plant transporters involved in trichothecene efflux will provide novel targets to reduce FHB and mycotoxin contamination in economically important plant crops.
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Gu X, Brennan A, Wei W, Guo G, Lindsey K. Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins. Evol Bioinform Online 2020; 16:1176934320956575. [PMID: 33116351 PMCID: PMC7573729 DOI: 10.1177/1176934320956575] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
Communication systems within and between plant cells involve the transfer of ions and molecules between compartments, and are essential for development and responses to biotic and abiotic stresses. This in turn requires the regulated movement and fusion of membrane systems with their associated cargo. Recent advances in genomics has provided new resources with which to investigate the evolutionary relationships between membrane proteins across plant species. Members of the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are known to play important roles in vesicle trafficking across plant, animal and microbial species. Using recent public expression and transcriptomic data from 9 representative green plants, we investigated the evolution of the SNARE classes and linked protein changes to functional specialization (expression patterns). We identified an additional 3 putative SNARE genes in the model plant Arabidopsis. We found that all SNARE classes have expanded in number to a greater or lesser degree alongside the evolution of multicellularity, and that within-species expansions are also common. These gene expansions appear to be associated with the accumulation of amino acid changes and with sub-functionalization of SNARE family members to different tissues. These results provide an insight into SNARE protein evolution and functional specialization. The work provides a platform for hypothesis-building and future research into the precise functions of these proteins in plant development and responses to the environment.
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Affiliation(s)
- Xiaoyan Gu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Department of Biosciences, Durham University, Durham, UK
| | - Adrian Brennan
- Department of Biosciences, Durham University, Durham, UK
| | - Wenbin Wei
- Department of Biosciences, Durham University, Durham, UK
| | - Guangqin Guo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
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Liu R, Wang Y, Qin G, Tian S. iTRAQ-based quantitative proteomic analysis reveals the role of the tonoplast in fruit senescence. J Proteomics 2016; 146:80-9. [DOI: 10.1016/j.jprot.2016.06.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 01/09/2023]
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Sugano S, Hayashi N, Kawagoe Y, Mochizuki S, Inoue H, Mori M, Nishizawa Y, Jiang CJ, Matsui M, Takatsuji H. Rice OsVAMP714, a membrane-trafficking protein localized to the chloroplast and vacuolar membrane, is involved in resistance to rice blast disease. PLANT MOLECULAR BIOLOGY 2016; 91:81-95. [PMID: 26879413 DOI: 10.1007/s11103-016-0444-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 01/26/2016] [Indexed: 06/05/2023]
Abstract
Membrane trafficking plays pivotal roles in many cellular processes including plant immunity. Here, we report the characterization of OsVAMP714, an intracellular SNARE protein, focusing on its role in resistance to rice blast disease caused by the fungal pathogen Magnaporthe oryzae. Disease resistance tests using OsVAMP714 knockdown and overexpressing rice plants demonstrated the involvement of OsVAMP714 in blast resistance. The overexpression of OsVAMP7111, whose product is highly homologous to OsVAMP714, did not enhance blast resistance to rice, implying a potential specificity of OsVAMP714 to blast resistance. OsVAMP714 was localized to the chloroplast in mesophyll cells and to the cellular periphery in epidermal cells of transgenic rice plant leaves. We showed that chloroplast localization is critical for the normal OsVAMP714 functioning in blast resistance by analyzing the rice plants overexpressing OsVAMP714 mutants whose products did not localize in the chloroplast. We also found that OsVAMP714 was located in the vacuolar membrane surrounding the invasive hyphae of M. oryzae. Furthermore, we showed that OsVAMP714 overexpression promotes leaf sheath elongation and that the first 19 amino acids, which are highly conserved between animal and plant VAMP7 proteins, are crucial for normal rice plant growths. Our studies imply that the OsVAMP714-mediated trafficking pathway plays an important role in rice blast resistance as well as in the vegetative growth of rice.
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Affiliation(s)
- Shoji Sugano
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Nagao Hayashi
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yasushi Kawagoe
- Functional Plant Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Susumu Mochizuki
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School and Faculty of Agriculture, Kagawa University, Miki, Kagawa, 761-0795, Japan
| | - Haruhiko Inoue
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Masaki Mori
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yoko Nishizawa
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Chang-Jie Jiang
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
| | - Minami Matsui
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiroshi Takatsuji
- Disease Resistant Crops Research Unit, GMO Center, National Institute of Agrobiological Sciences (NIAS), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
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Pedrazzini E, Caprera A, Fojadelli I, Stella A, Rocchetti A, Bassin B, Martinoia E, Vitale A. The Arabidopsis tonoplast is almost devoid of glycoproteins with complex N-glycans, unlike the rat lysosomal membrane. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1769-81. [PMID: 26748395 PMCID: PMC4783361 DOI: 10.1093/jxb/erv567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The distribution of the N-glycoproteome in integral membrane proteins of the vacuolar membrane (tonoplast) or the plasma membrane of Arabidopsis thaliana and, for further comparison, of the Rattus norvegicus lysosomal and plasma membranes, was analyzed. In silico analysis showed that potential N-glycosylation sites are much less frequent in tonoplast proteins. Biochemical analysis of Arabidopsis subcellular fractions with the lectin concanavalin A, which recognizes mainly unmodified N-glycans, or with antiserum against Golgi-modified N-glycans confirmed the in silico results and showed that, unlike the plant plasma membrane, the tonoplast is almost or totally devoid of N-glycoproteins with Golgi-modified glycans. Lysosomes share with vacuoles the hydrolytic functions and the position along the secretory pathway; however, our results indicate that their membranes had a divergent evolution. We propose that protection against the luminal hydrolases that are abundant in inner hydrolytic compartments, which seems to have been achieved in many lysosomal membrane proteins by extensive N-glycosylation of the luminal domains, has instead been obtained in the vast majority of tonoplast proteins by limiting the length of such domains.
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Affiliation(s)
| | | | | | | | | | - Barbara Bassin
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Enrico Martinoia
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
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Li P, Zhang G, Gonzales N, Guo Y, Hu H, Park S, Zhao J. Ca(2+) -regulated and diurnal rhythm-regulated Na(+) /Ca(2+) exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:377-92. [PMID: 26296956 DOI: 10.1111/pce.12620] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/09/2015] [Accepted: 07/30/2015] [Indexed: 05/21/2023]
Abstract
Calcium (Ca(2+) ) is vital for plant growth, development, hormone response and adaptation to environmental stresses, yet the mechanisms regulating plant cytosolic Ca(2+) homeostasis are not fully understood. Here, we characterize an Arabidopsis Ca(2+) -regulated Na(+) /Ca(2+) exchanger AtNCL that regulates Ca(2+) and multiple physiological processes. AtNCL was localized to the tonoplast in yeast and plant cells. AtNCL appeared to mediate sodium (Na(+) ) vacuolar sequestration and meanwhile Ca(2+) release. The EF-hand domains within AtNCL regulated Ca(2+) binding and transport of Ca(2+) and Na(+) . Plants with diminished AtNCL expression were more tolerant to high CaCl2 but more sensitive to both NaCl and auxin; heightened expression of AtNCL rendered plants more sensitive to CaCl2 but tolerant to NaCl. AtNCL expression appeared to be regulated by the diurnal rhythm and suppressed by auxin. DR5::GUS expression and root responses to auxin were altered in AtNCL mutants. The auxin-induced suppression of AtNCL was attenuated in SLR/IAA14 and ARF6/8 mutants. The mutants with altered AtNCL expression also altered flowering time and FT and CO expression; FT may mediate AtNCL-regulated flowering time change. Therefore, AtNCL is a vacuolar Ca(2+) -regulated Na(+) /Ca(2+) exchanger that regulates auxin responses and flowering time.
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Affiliation(s)
- Penghui Li
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Gaoyang Zhang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Naomi Gonzales
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yingqing Guo
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Honghong Hu
- College of Life Science and technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Sunghun Park
- Department of Horticulture, Forestry and Recreation Resources, Kansas State University, Manhattan, KS, 66506, USA
| | - Jian Zhao
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
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Kanazawa T, Era A, Minamino N, Shikano Y, Fujimoto M, Uemura T, Nishihama R, Yamato KT, Ishizaki K, Nishiyama T, Kohchi T, Nakano A, Ueda T. SNARE Molecules in Marchantia polymorpha: Unique and Conserved Features of the Membrane Fusion Machinery. PLANT & CELL PHYSIOLOGY 2016; 57:307-24. [PMID: 26019268 DOI: 10.1093/pcp/pcv076] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/22/2015] [Indexed: 05/18/2023]
Abstract
The membrane trafficking pathway has been diversified in a specific way for each eukaryotic lineage, probably to fulfill specific functions in the organisms. In green plants, comparative genomics has supported the possibility that terrestrialization and/or multicellularization could be associated with the elaboration and diversification of membrane trafficking pathways, which have been accomplished by an expansion of the numbers of genes required for machinery components of membrane trafficking, including soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. However, information regarding membrane trafficking pathways in basal land plant lineages remains limited. In the present study, we conducted extensive analyses of SNARE molecules, which mediate membrane fusion between target membranes and transport vesicles or donor organelles, in the liverwort, Marchantia polymorpha. The M. polymorpha genome contained at least 34 genes for 36 SNARE proteins, comprising fundamental sets of SNARE proteins that are shared among land plant lineages with low degrees of redundancy. We examined the subcellular distribution of a major portion of these SNARE proteins by expressing Citrine-tagged SNARE proteins in M. polymorpha, and the results showed that some of the SNARE proteins were targeted to different compartments from their orthologous products in Arabidopsis thaliana. For example, MpSYP12B was localized to the surface of the oil body, which is a unique organelle in liverworts. Furthermore, we identified three VAMP72 members with distinctive structural characteristics, whose N-terminal extensions contain consensus sequences for N-myristoylation. These results suggest that M. polymorpha has acquired unique membrane trafficking pathways associated with newly acquired machinery components during evolution.
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Affiliation(s)
- Takehiko Kanazawa
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Atsuko Era
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan Department of Cell Genetics, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan
| | - Naoki Minamino
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yu Shikano
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masaru Fujimoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Tomohiro Uemura
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kinki University, Nishimitani, Kinokawa, Wakayama, 649-6493 Japan
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-0934 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Akihiko Nakano
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Takashi Ueda
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
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Feldman MJ, Poirier BC, Lange BM. Misexpression of the Niemann-Pick disease type C1 (NPC1)-like protein in Arabidopsis causes sphingolipid accumulation and reproductive defects. PLANTA 2015; 242:921-33. [PMID: 26007685 DOI: 10.1007/s00425-015-2322-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/04/2015] [Indexed: 05/25/2023]
Abstract
Misexpression of the AtNPC1 - 1 and AtNPC1 - 2 genes leads to altered sphingolipid metabolism, growth impairment, and male reproductive defects in a hemizygous Arabidopsis thaliana (L.) double-mutant population. Abolishing the expression of both gene copies has lethal effects. Niemann-Pick disease type C1 is a lysosomal storage disorder caused by mutations in the NPC1 gene. At the cellular level, the disorder is characterized by the accumulation of storage lipids and lipid trafficking defects. The Arabidopsis thaliana genome contains two genes (At1g42470 and At4g38350) with weak homology to mammalian NPC1. The corresponding proteins have 11 predicted membrane-spanning regions and contain a putative sterol-sensing domain. The At1g42470 protein is localized to the plasma membrane, while At4g38350 protein has a dual localization in the plasma and tonoplast membranes. A phenotypic analysis of T-DNA insertion mutants indicated that At1g42470 and At4g38350 (designated AtNPC1-1 and AtNPC1-2, respectively) have partially redundant functions and are essential for plant reproductive viability and development. Homozygous plants impaired in the expression of both genes were not recoverable. Plants of a hemizygous AtNPC1-1/atnpc1-1/atnpc1-2/atnpc1-2 population were severely dwarfed and exhibited male gametophytic defects. These gene disruptions did not have an effect on sterol concentrations; however, hemizygous AtNPC1-1/atnpc1-1/atnpc1-2/atnpc1-2 mutants had increased fatty acid amounts. Among these, fatty acid α-hydroxytetracosanoic acid (h24:0) occurs in plant sphingolipids. Follow-up analyses confirmed the accumulation of significantly increased levels of sphingolipids (assayed as hydrolyzed sphingoid base component) in the hemizygous double-mutant population. Certain effects of NPC1 misexpression may be common across divergent lineages of eukaryotes (sphingolipid accumulation), while other defects (sterol accumulation) may occur only in certain groups of eukaryotic organisms.
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Affiliation(s)
- Maximilian J Feldman
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
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12
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Zhang C, Hicks GR, Raikhel NV. Molecular Composition of Plant Vacuoles: Important but Less Understood Regulations and Roles of Tonoplast Lipids. PLANTS 2015; 4:320-33. [PMID: 27135331 PMCID: PMC4844321 DOI: 10.3390/plants4020320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/21/2015] [Accepted: 06/03/2015] [Indexed: 11/16/2022]
Abstract
The vacuole is an essential organelle for plant growth and development. It is the location for the storage of nutrients; such as sugars and proteins; and other metabolic products. Understanding the mechanisms of vacuolar trafficking and molecule transport across the vacuolar membrane is of great importance in understanding basic plant development and cell biology and for crop quality improvement. Proteins play important roles in vacuolar trafficking; such proteins include Rab GTPase signaling proteins; cargo recognition receptors; and SNAREs (Soluble NSF Attachment Protein Receptors) that are involved in membrane fusion. Some vacuole membrane proteins also serve as the transporters or channels for transport across the tonoplast. Less understood but critical are the roles of lipids in vacuolar trafficking. In this review, we will first summarize molecular composition of plant vacuoles and we will then discuss our latest understanding on the role of lipids in plant vacuolar trafficking and a surprising connection to ribosome function through the study of ribosomal mutants.
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Affiliation(s)
- Chunhua Zhang
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
| | - Glenn R Hicks
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
| | - Natasha V Raikhel
- Center for Plant Cell Biology & Department of Botany and Plant Sciences, University of California, 900 University Ave., Riverside, CA 92521, USA.
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13
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Jung B, Ludewig F, Schulz A, Meißner G, Wöstefeld N, Flügge UI, Pommerrenig B, Wirsching P, Sauer N, Koch W, Sommer F, Mühlhaus T, Schroda M, Cuin TA, Graus D, Marten I, Hedrich R, Neuhaus HE. Identification of the transporter responsible for sucrose accumulation in sugar beet taproots. NATURE PLANTS 2015; 1:14001. [PMID: 27246048 DOI: 10.1038/nplants.2014.1] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/24/2014] [Indexed: 05/21/2023]
Abstract
Sugar beet provides around one third of the sugar consumed worldwide and serves as a significant source of bioenergy in the form of ethanol. Sucrose accounts for up to 18% of plant fresh weight in sugar beet. Most of the sucrose is concentrated in the taproot, where it accumulates in the vacuoles. Despite 30 years of intensive research, the transporter that facilitates taproot sucrose accumulation has escaped identification. Here, we combine proteomic analyses of the taproot vacuolar membrane, the tonoplast, with electrophysiological analyses to show that the transporter BvTST2.1 is responsible for vacuolar sucrose uptake in sugar beet taproots. We show that BvTST2.1 is a sucrose-specific transporter, and present evidence to suggest that it operates as a proton antiporter, coupling the import of sucrose into the vacuole to the export of protons. BvTST2.1 exhibits a high amino acid sequence similarity to members of the tonoplast monosaccharide transporter family in Arabidopsis, prompting us to rename this group of proteins 'tonoplast sugar transporters'. The identification of BvTST2.1 could help to increase sugar yields from sugar beet and other sugar-storing plants in future breeding programs.
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Affiliation(s)
- Benjamin Jung
- Pflanzenphysiologie, University Kaiserslautern, Erwin Schrödinger Straße, D-67653 Kaiserslautern, Germany
| | - Frank Ludewig
- Biocenter Cologne, Botanical Institute II and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, D-50674, Germany
| | - Alexander Schulz
- Biophysics and Molecular Plant Physiology, University Würzburg, Julius von Sachs Platz 2, D-97082 Würzburg, Germany
| | - Garvin Meißner
- Pflanzenphysiologie, University Kaiserslautern, Erwin Schrödinger Straße, D-67653 Kaiserslautern, Germany
| | - Nicole Wöstefeld
- Biocenter Cologne, Botanical Institute II and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, D-50674, Germany
| | - Ulf-Ingo Flügge
- Biocenter Cologne, Botanical Institute II and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, D-50674, Germany
| | - Benjamin Pommerrenig
- Molecular Plant Physiology, University Erlangen-Nuremberg, Staudtstraße 5, D-91058 Erlangen, Germany
| | - Petra Wirsching
- Molecular Plant Physiology, University Erlangen-Nuremberg, Staudtstraße 5, D-91058 Erlangen, Germany
| | - Norbert Sauer
- Molecular Plant Physiology, University Erlangen-Nuremberg, Staudtstraße 5, D-91058 Erlangen, Germany
| | - Wolfgang Koch
- KWS Saat AG, Grimsehlstr.31, D37555 Einbeck, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University Kaiserslautern, Paul-Ehrlich-Straße, D-67653 Kaiserslautern Germany
| | - Timo Mühlhaus
- Molecular Biotechnology and Systems Biology, University Kaiserslautern, Paul-Ehrlich-Straße, D-67653 Kaiserslautern Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University Kaiserslautern, Paul-Ehrlich-Straße, D-67653 Kaiserslautern Germany
| | - Tracey Ann Cuin
- Biophysics and Molecular Plant Physiology, University Würzburg, Julius von Sachs Platz 2, D-97082 Würzburg, Germany
| | - Dorothea Graus
- Biophysics and Molecular Plant Physiology, University Würzburg, Julius von Sachs Platz 2, D-97082 Würzburg, Germany
| | - Irene Marten
- Biophysics and Molecular Plant Physiology, University Würzburg, Julius von Sachs Platz 2, D-97082 Würzburg, Germany
| | - Rainer Hedrich
- Biophysics and Molecular Plant Physiology, University Würzburg, Julius von Sachs Platz 2, D-97082 Würzburg, Germany
| | - H Ekkehard Neuhaus
- Pflanzenphysiologie, University Kaiserslautern, Erwin Schrödinger Straße, D-67653 Kaiserslautern, Germany
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Neuhaus HE, Trentmann O. Regulation of transport processes across the tonoplast. FRONTIERS IN PLANT SCIENCE 2014; 5:460. [PMID: 25309559 PMCID: PMC4160088 DOI: 10.3389/fpls.2014.00460] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 08/26/2014] [Indexed: 05/24/2023]
Abstract
In plants, the vacuole builds up the cellular turgor and represents an important component in cellular responses to diverse stress stimuli. Rapid volume changes of cells, particularly of motor cells, like guard cells, are caused by variation of osmolytes and consequently of the water contents in the vacuole. Moreover, directed solute uptake into or release out of the large central vacuole allows adaptation of cytosolic metabolite levels according to the current physiological requirements and specific cellular demands. Therefore, solute passage across the vacuolar membrane, the tonoplast, has to be tightly regulated. Important principles in vacuolar transport regulation are changes of tonoplast transport protein abundances by differential expression of genes or changes of their activities, e.g., due to post-translational modification or by interacting proteins. Because vacuolar transport is in most cases driven by an electro-chemical gradient altered activities of tonoplast proton pumps significantly influence vacuolar transport capacities. Intense studies on individual tonoplast proteins but also unbiased system biological approaches have provided important insights into the regulation of vacuolar transport. This short review refers to selected examples of tonoplast proteins and their regulation, with special focus on protein phosphorylation.
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Affiliation(s)
| | - Oliver Trentmann
- *Correspondence: Oliver Trentmann, Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Postfach 3049, Kaiserslautern D-67653, Germany e-mail:
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15
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Pan S, Carter CJ, Raikhel NV. Understanding protein trafficking in plant cells through proteomics. Expert Rev Proteomics 2014; 2:781-92. [PMID: 16209656 DOI: 10.1586/14789450.2.5.781] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The functions of approximately one-third of the proteins encoded by the Arabidopsis thaliana genome are completely unknown. Moreover, many annotations of the remainder of the genome supply tentative functions, at best. Knowing the ultimate localization of these proteins, as well as the pathways used for getting there, may provide clues as to their functions. The putative localization of most proteins currently relies on in silico-based bioinformatics approaches, which, unfortunately, often result in erroneous predictions. Emerging proteomics techniques coupled with other systems biology approaches now provide researchers with a plethora of methods for elucidating the final location of these proteins on a large scale, as well as the ability to dissect protein-sorting pathways in plants.
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Affiliation(s)
- Songqin Pan
- WM Keck Proteomics Laboratory, Center for Plant Cell Biology, Botany & Plant Sciences, University of California, Riverside, CA 92521, USA.
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16
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Cabello S, Lorenz C, Crespo S, Cabrera J, Ludwig R, Escobar C, Hofmann J. Altered sucrose synthase and invertase expression affects the local and systemic sugar metabolism of nematode-infected Arabidopsis thaliana plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:201-12. [PMID: 24187419 PMCID: PMC3883288 DOI: 10.1093/jxb/ert359] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Sedentary endoparasitic nematodes of plants induce highly specific feeding cells in the root central cylinder. From these, the obligate parasites withdraw all required nutrients. The feeding cells were described as sink tissues in the plant's circulation system that are supplied with phloem-derived solutes such as sugars. Currently, there are several publications describing mechanisms of sugar import into the feeding cells. However, sugar processing has not been studied so far. Thus, in the present work, the roles of the sucrose-cleaving enzymes sucrose synthases (SUS) and invertases (INV) in the development of Heterodera schachtii were studied. Gene expression analyses indicate that both enzymes are regulated transcriptionally. Nematode development was enhanced on multiple INV and SUS mutants. Syncytia of these mutants were characterized by altered enzyme activity and changing sugar pool sizes. Further, the analyses revealed systemically affected sugar levels and enzyme activities in the shoots of the tested mutants, suggesting changes in the source-sink relationship. Finally, the development of the root-knot nematode Meloidogyne javanica was studied in different INV and SUS mutants and wild-type Arabidopsis plants. Similar effects on the development of both sedentary endoparasitic nematode species (root-knot and cyst nematode) were observed, suggesting a more general role of sucrose-degrading enzymes during plant-nematode interactions.
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Affiliation(s)
- Susana Cabello
- University of Natural Resources and Applied Life Sciences, Department of Crop Sciences, Konrad Lorenz Str. 24, Tulln a. d. Donau A-3430, Austria
| | - Cindy Lorenz
- University of Natural Resources and Applied Life Sciences, Department of Food Sciences and Technology, Vienna, Austria
| | - Sara Crespo
- University of Natural Resources and Applied Life Sciences, Department of Crop Sciences, Konrad Lorenz Str. 24, Tulln a. d. Donau A-3430, Austria
| | - Javier Cabrera
- Universidad de Castilla-La Mancha, Facultad de Ciencias del Medio Ambiente, Avenida de Carlos III s/n, 45071 Toledo, Spain
| | - Roland Ludwig
- University of Natural Resources and Applied Life Sciences, Department of Food Sciences and Technology, Vienna, Austria
| | - Carolina Escobar
- Universidad de Castilla-La Mancha, Facultad de Ciencias del Medio Ambiente, Avenida de Carlos III s/n, 45071 Toledo, Spain
| | - Julia Hofmann
- University of Natural Resources and Applied Life Sciences, Department of Crop Sciences, Konrad Lorenz Str. 24, Tulln a. d. Donau A-3430, Austria
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17
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Dadacz-Narloch B, Kimura S, Kurusu T, Farmer EE, Becker D, Kuchitsu K, Hedrich R. On the cellular site of two-pore channel TPC1 action in the Poaceae. THE NEW PHYTOLOGIST 2013; 200:663-674. [PMID: 23845012 DOI: 10.1111/nph.12402] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/02/2013] [Indexed: 06/02/2023]
Abstract
The slow vacuolar (SV) channel has been characterized in different dicots by patch-clamp recordings. This channel represents the major cation conductance of the largest organelle in most plant cells. Studies with the tpc1-2 mutant of the model dicot plant Arabidopsis thaliana identified the SV channel as the product of the TPC1 gene. By contrast, research on rice and wheat TPC1 suggested that the monocot gene encodes a plasma membrane calcium-permeable channel. To explore the site of action of grass TPC1 channels, we expressed OsTPC1 from rice (Oryza sativa) and TaTPC1 from wheat (Triticum aestivum) in the background of the Arabidopsis tpc1-2 mutant. Cross-species tpc1 complementation and patch-clamping of vacuoles using Arabidopsis and rice tpc1 null mutants documented that both monocot TPC1 genes were capable of rescuing the SV channel deficit. Vacuoles from wild-type rice but not the tpc1 loss-of-function mutant harbor SV channels exhibiting the hallmark properties of dicot TPC1/SV channels. When expressed in human embryonic kidney (HEK293) cells OsTPC1 was targeted to Lysotracker-Red-positive organelles. The finding that the rice TPC1, just like those from the model plant Arabidopsis and even animal cells, is localized and active in lyso-vacuolar membranes associates this cation channel species with endomembrane function.
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Affiliation(s)
- Beata Dadacz-Narloch
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
| | - Sachie Kimura
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
| | - Takamitsu Kurusu
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
- School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo, 192-0982, Japan
| | - Edward E Farmer
- Department of Plant Molecular Biology, University of Lausanne, Biophore, 1015, Lausanne, Switzerland
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Wuerzburg, D-97082, Wuerzburg, Germany
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18
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Mattei B, Sabatini S, Schininà ME. Proteomics in deciphering the auxin commitment in the Arabidopsis thaliana root growth. J Proteome Res 2013; 12:4685-701. [PMID: 24032454 DOI: 10.1021/pr400697s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The development of plant root systems is characterized by a high plasticity, made possible by the continual propagation of new meristems. Root architecture is fundamental for overall plant growth, abiotic stress resistance, nutrient uptake, and response to environmental changes. Understanding the function of genes and proteins that control root architecture and stress resistance will contribute to the development of more sustainable systems of intensified crop production. To meet these challenges, proteomics provide the genome-wide scale characterization of protein expression pattern, subcellular localization, post-translational modifications, activity regulation, and molecular interactions. In this review, we describe a variety of proteomic strategies that have been applied to study the proteome of the whole organ and of specific cell types during root development. Each has advantages and limitations, but collectively they are providing important insights into the mechanisms by which auxin structures and patterns the root system and into the interplay between signaling networks, auxin transport and growth. The acquisition of proteomic, transcriptomic, and metabolomic data sets of the root apex on the cell scale has revealed the high spatial complexity of regulatory networks and fosters the use of new powerful proteomic tools for a full understanding of the control of root developmental processes and environmental responses.
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Affiliation(s)
- Benedetta Mattei
- Department Biology and Biotechnology, Sapienza University of Rome , Via dei Sardi 70, 00185 Rome, Italy
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19
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Colcombet J, Lopez-Obando M, Heurtevin L, Bernard C, Martin K, Berthomé R, Lurin C. Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles. RNA Biol 2013; 10:1557-75. [PMID: 24037373 PMCID: PMC3858439 DOI: 10.4161/rna.26128] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Four hundred and fifty-eight genes coding for PentatricoPeptide Repeat (PPR) proteins are annotated in the Arabidopsis thaliana genome. Over the past 10 years, numerous reports have shown that many of these proteins function in organelles to target specific transcripts and are involved in post-transcriptional regulation. Therefore, they are thought to be important players in the coordination between nuclear and organelle genome expression. Only four of these proteins have been described to be addressed outside organelles, indicating that some PPRs could function in post-transcriptional regulations of nuclear genes. In this work, we updated and improved our current knowledge on the localization of PPR proteins of Arabidopsis within the plant cell. We particularly investigated the subcellular localization of 166 PPR proteins whose targeting predictions were ambiguous, using a combination of high-throughput cloning and microscopy. Through systematic localization experiments and data integration, we confirmed that PPR proteins are largely targeted to organelles and showed that dual targeting to both the mitochondria and plastid occurs more frequently than expected. These results allow us to speculate that dual-targeted PPR proteins could be important for the fine coordination of gene expressions in both organelles.
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Affiliation(s)
- Jean Colcombet
- Unité de Recherche en Génomique Végétale (URGV); UMR INRA/UEVE - ERL CNRS 91057; CP 5708; 91057 EVRY CEDEX, France
| | - Mauricio Lopez-Obando
- Unité de Recherche en Génomique Végétale (URGV); UMR INRA/UEVE - ERL CNRS 91057; CP 5708; 91057 EVRY CEDEX, France
| | - Laure Heurtevin
- Unité de Recherche en Génomique Végétale (URGV); UMR INRA/UEVE - ERL CNRS 91057; CP 5708; 91057 EVRY CEDEX, France
| | - Clément Bernard
- Unité de Recherche en Génomique Végétale (URGV); UMR INRA/UEVE - ERL CNRS 91057; CP 5708; 91057 EVRY CEDEX, France
| | - Karine Martin
- Unité de Recherche en Génomique Végétale (URGV); UMR INRA/UEVE - ERL CNRS 91057; CP 5708; 91057 EVRY CEDEX, France
| | - Richard Berthomé
- Unité de Recherche en Génomique Végétale (URGV); UMR INRA/UEVE - ERL CNRS 91057; CP 5708; 91057 EVRY CEDEX, France
| | - Claire Lurin
- Unité de Recherche en Génomique Végétale (URGV); UMR INRA/UEVE - ERL CNRS 91057; CP 5708; 91057 EVRY CEDEX, France
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20
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Trentmann O, Haferkamp I. Current progress in tonoplast proteomics reveals insights into the function of the large central vacuole. FRONTIERS IN PLANT SCIENCE 2013; 4:34. [PMID: 23459586 PMCID: PMC3584717 DOI: 10.3389/fpls.2013.00034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 02/11/2013] [Indexed: 05/20/2023]
Abstract
Vacuoles of plants fulfill various biologically important functions, like turgor generation and maintenance, detoxification, solute sequestration, or protein storage. Different types of plant vacuoles (lytic versus protein storage) are characterized by different functional properties apparently caused by a different composition/abundance and regulation of transport proteins in the surrounding membrane, the tonoplast. Proteome analyses allow the identification of vacuolar proteins and provide an informative basis for assigning observed transport processes to specific carriers or channels. This review summarizes techniques required for vacuolar proteome analyses, like e.g., isolation of the large central vacuole or tonoplast membrane purification. Moreover, an overview about diverse published vacuolar proteome studies is provided. It becomes evident that qualitative proteomes from different plant species represent just the tip of the iceberg. During the past few years, mass spectrometry achieved immense improvement concerning its accuracy, sensitivity, and application. As a consequence, modern tonoplast proteome approaches are suited for detecting alterations in membrane protein abundance in response to changing environmental/physiological conditions and help to clarify the regulation of tonoplast transport processes.
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Affiliation(s)
- Oliver Trentmann
- Pflanzenphysiologie, Technische Universität KaiserslauternKaiserslautern, Germany
- *Correspondence: Oliver Trentmann, Pflanzenphysiologie, Technische Universität Kaiserslautern, Postfach 3049, D-67653 Kaiserslautern, Germany. e-mail:
| | - Ilka Haferkamp
- Pflanzenphysiologie, Technische Universität KaiserslauternKaiserslautern, Germany
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21
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Wang P, Li Z, Wei J, Zhao Z, Sun D, Cui S. A Na+/Ca2+ exchanger-like protein (AtNCL) involved in salt stress in Arabidopsis. J Biol Chem 2012; 287:44062-70. [PMID: 23148213 DOI: 10.1074/jbc.m112.351643] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Calcium ions (Ca(2+)) play a crucial role in many key physiological processes; thus, the maintenance of Ca(2+) homeostasis is of primary importance. Na(+)/Ca(2+) exchangers (NCXs) play an important role in Ca(2+) homeostasis in animal excitable cells. Bioinformatic analysis of the Arabidopsis genome suggested the existence of a putative NCX gene, Arabidopsis NCX-like (AtNCL), encoding a protein with an NCX-like structure and different from Ca(2+)/H(+) exchangers and Na(+)/H(+) exchangers previously identified in plant. AtNCL was identified to localize in the Arabidopsis cell membrane fraction, have the ability of binding Ca(2+), and possess NCX-like activity in a heterologous expression system of cultured mammalian CHO-K1 cells. AtNCL is broadly expressed in Arabidopsis, and abiotic stresses stimulated its transcript expression. Loss-of-function atncl mutants were less sensitive to salt stress than wild-type or AtNCL transgenic overexpression lines. In addition, the total calcium content in whole atncl mutant seedlings was higher than that in wild type by atomic absorption spectroscopy. The level of free Ca(2+) in the cytosol and Ca(2+) flux at the root tips of atncl mutant plants, as detected using transgenic aequorin and a scanning ion-selective electrode, required a longer recovery time following NaCl stress compared with that in wild type. All of these data suggest that AtNCL encodes a Na(+)/Ca(2+) exchanger-like protein that participates in the maintenance of Ca(2+) homeostasis in Arabidopsis. AtNCL may represent a new type of Ca(2+) transporter in higher plants.
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Affiliation(s)
- Peng Wang
- Hebei Key Laboratory of Molecular Cell Biology, College of Life Science, Hebei Normal University, Shijiazhuang 050024, China
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22
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Tan YF, Millar AH, Taylor NL. Components of mitochondrial oxidative phosphorylation vary in abundance following exposure to cold and chemical stresses. J Proteome Res 2012; 11:3860-79. [PMID: 22574745 DOI: 10.1021/pr3003535] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plant mitochondria are highly responsive organelles that vary their metabolism in response to a wide range of chemical and environmental conditions. Quantitative proteomics studies have begun to allow the analysis of these large-scale protein changes in mitochondria. However studies of the integral membrane proteome of plant mitochondria, arguably the site responsible for the most fundamental mitochondrial processes of oxidative phosphorylation, protein import and metabolite transport, remain a technical challenge. Here we have investigated the changes in protein abundance in response to a number of chemical stresses and cold. In addition to refining the subcellular localization of 66 proteins, we have been able to characterize 596 protein × treatment combinations following a range of stresses. To date it has been assumed that the main mitochondrial response to stress involved the induction of alternative respiratory proteins such as AOX, UCPs, and alternative NAD(P)H dehydrogenases; we now provide evidence for a number of very specific protein abundance changes that have not been highlighted previously by transcript studies. This includes both previously characterized stress responsive proteins as well as major components of oxidative phosphorylation, protein import/export, and metabolite transport.
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Affiliation(s)
- Yew-Foon Tan
- ARC Centre of Excellence in Plant Energy Biology, MCS Building M316, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Western Australia, Australia
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23
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Schulze WX, Schneider T, Starck S, Martinoia E, Trentmann O. Cold acclimation induces changes in Arabidopsis tonoplast protein abundance and activity and alters phosphorylation of tonoplast monosaccharide transporters. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:529-41. [PMID: 21988472 DOI: 10.1111/j.1365-313x.2011.04812.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Because they are immotile organisms, higher plants have developed efficient strategies for adaptation to temperature changes. During cold acclimation, plants accumulate specific types of solutes to enhance freezing tolerance. The vacuole is a major solute storage organelle, but until now the role of tonoplast proteins in cold acclimation has not been investigated. In a comparative tonoplast proteome analysis, we identified several membrane proteins with altered abundance upon cold acclimation. We found an increased protein abundance of the tonoplast pyrophosphatase and subunits of the vacuolar V-ATPase and a significantly increased V-ATPase activity. This was accompanied by increased vacuolar concentrations of dicarbonic acids and soluble sugars. Consistently, the abundance of the tonoplast dicarbonic acid transporter was also higher in cold-acclimatized plants. However, no change in the protein abundance of tonoplast monosaccharide transporters was detectable. However, a generally higher cold-induced phosphorylation of members of this sugar transporter sub-group was observed. Our results indicate that cold-induced solute accumulation in the vacuole is mediated by increased acidification of this organelle. Thus solute transport activity is either modulated by increased protein amounts or by modification of proteins via phosphorylation.
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Affiliation(s)
- Waltraud X Schulze
- Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Golm, Germany
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24
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Jørgensen M, Stensballe A, Welinder KG. Extensive post-translational processing of potato tuber storage proteins and vacuolar targeting. FEBS J 2011; 278:4070-87. [PMID: 21851554 DOI: 10.1111/j.1742-4658.2011.08311.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Potato tuber storage proteins were obtained from vacuoles isolated from field-grown starch potato tubers cv. Kuras. Vacuole sap proteins fractionated by gel filtration were studied by mass spectrometric analyses of trypsin and chymotrypsin digestions. The tuber vacuole appears to be a typical protein storage vacuole absent of proteolytic and glycolytic enzymes. The major soluble storage proteins included 28 Kunitz protease inhibitors, nine protease inhibitors 1, eight protease inhibitors 2, two carboxypeptidase inhibitors, eight patatins and five lipoxygenases (lox), which all showed cultivar-specific sequence variations. These proteins, except for lox, have typical endoplasmic reticulum (ER) signal peptides and putative vacuolar sorting determinants of either the sequence or structure specific type or the C-terminal type, or both. Unexpectedly, sap protein variants imported via the ER showed multiple molecular forms because of extensive and unspecific proteolytic cleavage of exposed N- and C-terminal propeptides and surface loops, in spite of the abundance of protease inhibitors. Some propeptides are potential novel vacuolar targeting peptides. In the insoluble vacuole fraction two variants of phytepsin (aspartate protease) were identified. These are most probably the processing enzymes of potato tuber vacuolar proteins. Database Proteome data have been submitted to the PRIDE database under accession number 17707.
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Affiliation(s)
- Malene Jørgensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
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25
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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26
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Kota U, Goshe MB. Advances in qualitative and quantitative plant membrane proteomics. PHYTOCHEMISTRY 2011; 72:1040-60. [PMID: 21367437 DOI: 10.1016/j.phytochem.2011.01.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/13/2011] [Accepted: 01/19/2011] [Indexed: 05/08/2023]
Abstract
The membrane proteome consists of integral and membrane-associated proteins that are involved in various physiological and biochemical functions critical for cellular function. It is also dynamic in nature, where many proteins are only expressed during certain developmental stages or in response to environmental stress. These proteins can undergo post-translational modifications in response to these different conditions, allowing them to transiently associate with the membrane or other membrane proteins. Along with their increased size, hydrophobicity, and the additional organelle and cellular features of plant cells relative to mammalian systems, the characterization of the plant membrane proteome presents unique challenges for effective qualitative and quantitative analysis using mass spectrometry (MS) analysis. Here, we present the latest advancements developed for the isolation and fractionation of plant organelles and their membrane components amenable to MS analysis. Separations of membrane proteins from these enriched preparations that have proven effective are discussed for both gel- and liquid chromatography-based MS analysis. In this context, quantitative membrane proteomic analyses using both isotope-coded and label-free approaches are presented and reveal the potential to establish a wider-biological interpretation of the function of plant membrane proteins that will ultimately lead to a more comprehensive understanding of plant physiology and their response mechanisms.
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Affiliation(s)
- Uma Kota
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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Lubkowitz M. The oligopeptide transporters: a small gene family with a diverse group of substrates and functions? MOLECULAR PLANT 2011; 4:407-15. [PMID: 21310763 DOI: 10.1093/mp/ssr004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genes in the Oligopeptide Transport family encode integral membrane proteins that are believed to translocate their substrates from either the extracellular environment or an organelle into the cytosol. Phylogenetic analyses of plant transporters have revealed two distant clades: the Yellow Stripe-Like (YSL) proteins and the so-called Oligopeptide Transporters (OPTs), for which the family was named. Three categories of substrates have been identified for this family: small peptides, secondary amino acids bound to metals, and glutathione. Notably, the YSL transporters are involved in metal homeostasis through the translocation of metal-chelates, indicating a level of conservation both in biological function as well as substrates. In contrast, the functions of OPT proteins seem to be less defined and, in this review, I will examine the supporting and contradictory evidence for the proposed roles of OPTs in such diverse functions as long-distance sulfur distribution, nitrogen mobilization, metal homeostasis, and heavy metal sequestration through the transport of glutathione, metal-chelates, and peptides.
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Affiliation(s)
- Mark Lubkowitz
- Department of Biology, Saint Michael's College, 1 Winooski Park, Colchester, VT 05439, USA.
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28
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Villiers F, Ducruix C, Hugouvieux V, Jarno N, Ezan E, Garin J, Junot C, Bourguignon J. Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches. Proteomics 2011; 11:1650-63. [PMID: 21462346 DOI: 10.1002/pmic.201000645] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/25/2011] [Accepted: 02/01/2011] [Indexed: 11/10/2022]
Abstract
Monitoring molecular dynamics of an organism upon stress is probably the best approach to decipher physiological mechanisms involved in the stress response. Quantitative analysis of proteins and metabolites is able to provide accurate information about molecular changes allowing the establishment of a range of more or less specific mechanisms, leading to the identification of major players in the considered pathways. Such tools have been successfully used to analyze the plant response to cadmium (Cd), a major pollutant capable of causing severe health issues as it accumulates in the food chain. We present a summary of proteomics and metabolomics works that contributed to a better understanding of the molecular aspects involved in the plant response to Cd. This work allowed us to provide a finer picture of general signaling, regulatory and metabolic pathways that appeared to be affected upon Cd stress. In particular, we conclude on the advantage of employing different approaches of global proteome- and metabolome-wide techniques, combined with more targeted analysis to answer molecular questions and unravel biological networks. Finally, we propose possible directions and methodologies for future prospectives in this field, as many aspects of the plant-Cd interaction remain to be discovered.
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Affiliation(s)
- Florent Villiers
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Physiologie Cellulaire Végétale, Grenoble, France
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29
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Peiter E. The plant vacuole: emitter and receiver of calcium signals. Cell Calcium 2011; 50:120-8. [PMID: 21376393 DOI: 10.1016/j.ceca.2011.02.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Revised: 02/04/2011] [Accepted: 02/05/2011] [Indexed: 12/20/2022]
Abstract
This review portrays the plant vacuole as both a source and a target of Ca(2+) signals. In plants, the vacuole represents a Ca(2+) store of enormous size and capacity. Total and free Ca(2+) concentrations in the vacuole vary with plant species, cell type, and environment, which is likely to have an impact on vacuolar function and the release of vacuolar Ca(2+). It is known that cytosolic Ca(2+) signals are often generated by release of the ion from internal stores, but in very few cases has a role of the vacuole been directly demonstrated. Biochemical and electrophysical studies have provided evidence for the operation of ligand- and voltage-gated Ca(2+)-permeable channels in the vacuolar membrane. The underlying molecular mechanisms are largely unknown with one exception: the slow vacuolar channel, encoded by TPC1, is the only vacuolar Ca(2+)-permeable channel cloned to date. However, due to its complex regulation and its low selectivity amongst cations, the role of this channel in Ca(2+) signalling is still debated. Many transport proteins at the vacuolar membrane are also targets of Ca(2+) signals, both by direct binding of Ca(2+) and by Ca(2+)-dependent phosphorylation. This enables the operation of feedback mechanisms and integrates vacuolar transport systems in the wider signalling network of the plant cell.
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Affiliation(s)
- Edgar Peiter
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences (IAEW), Faculty of Natural Sciences III, Martin-Luther-University of Halle-Wittenberg, 06099 Halle (Saale), Germany.
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30
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Vertommen A, Panis B, Swennen R, Carpentier SC. Challenges and solutions for the identification of membrane proteins in non-model plants. J Proteomics 2011; 74:1165-81. [PMID: 21354347 DOI: 10.1016/j.jprot.2011.02.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/04/2011] [Accepted: 02/16/2011] [Indexed: 01/27/2023]
Abstract
The workhorse for proteomics in non-model plants is classical two-dimensional electrophoresis, a combination of iso-electric focusing and SDS-PAGE. However, membrane proteins with multiple membrane spanning domains are hardly detected on classical 2-DE gels because of their low abundance and poor solubility in aqueous media. In the current review, solutions that have been proposed to handle these two problems in non-model plants are discussed. An overview of alternative techniques developed for membrane proteomics is provided together with a comparison of their strong and weak points. Subsequently, strengths and weaknesses of the different techniques and methods to evaluate the identification of membrane proteins are discussed. Finally, an overview of recent plant membrane proteome studies is provided with the used separation technique and the number of identified membrane proteins listed.
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Affiliation(s)
- A Vertommen
- Laboratory of Tropical Crop Improvement, Department of Biosystems, K.U. Leuven, Kasteelpark Arenberg 13, B-3001 Heverlee, Belgium
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31
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Joyard J, Ferro M, Masselon C, Seigneurin-Berny D, Salvi D, Garin J, Rolland N. Chloroplast proteomics highlights the subcellular compartmentation of lipid metabolism. Prog Lipid Res 2010; 49:128-58. [DOI: 10.1016/j.plipres.2009.10.003] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 10/22/2009] [Accepted: 10/23/2009] [Indexed: 01/14/2023]
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32
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Yagisawa F, Nishida K, Yoshida M, Ohnuma M, Shimada T, Fujiwara T, Yoshida Y, Misumi O, Kuroiwa H, Kuroiwa T. Identification of novel proteins in isolated polyphosphate vacuoles in the primitive red alga Cyanidioschyzon merolae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:882-93. [PMID: 19709388 DOI: 10.1111/j.1365-313x.2009.04008.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant vacuoles are organelles bound by a single membrane, and involved in various functions such as intracellular digestion, metabolite storage, and secretion. To understand their evolution and fundamental mechanisms, characterization of vacuoles in primitive plants would be invaluable. Algal cells often contain polyphosphate-rich compartments, which are thought to be the counterparts of seed plant vacuoles. Here, we developed a method for isolating these vacuoles from Cyanidioschyzon merolae, and identified their proteins by MALDI TOF-MS. The vacuoles were of unexpectedly high density, and were highly enriched at the boundary between 62 and 80% w/v iodixanol by density-gradient ultracentrifugation. The vacuole-containing fraction was subjected to SDS-PAGE, and a total of 46 proteins were identified, including six lytic enzymes, 13 transporters, six proteins for membrane fusion or vesicle trafficking, five non-lytic enzymes, 13 proteins of unknown function, and three miscellaneous proteins. Fourteen proteins were homologous to known vacuolar or lysosomal proteins from seed plants, yeasts or mammals, suggesting functional and evolutionary relationships between C. merolae vacuoles and these compartments. The vacuolar localization of four novel proteins, namely CMP249C (metallopeptidase), CMJ260C (prenylated Rab receptor), CMS401C (ABC transporter) and CMT369C (o-methyltransferase), was confirmed by labeling with specific antibodies or transient expression of hemagglutinin-tagged proteins. The results presented here provide insights into the proteome of C. merolae vacuoles and shed light on their functions, as well as indicating new features.
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Affiliation(s)
- Fumi Yagisawa
- Research Information Center for Extremophiles, Rikkyo (St Paul's) University, Nishi-Ikebukuro, Tokyo 171-8501, Japan.
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33
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Tan DJL, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS. Mapping organelle proteins and protein complexes in Drosophila melanogaster. J Proteome Res 2009; 8:2667-78. [PMID: 19317464 DOI: 10.1021/pr800866n] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Many proteins within eukaryotic cells are organized spatially and functionally into membrane bound organelles and complexes. A protein's location thus provides information about its function. Here, we apply LOPIT, a mass-spectrometry based technique that simultaneously maps proteins to specific subcellular compartments, to Drosophila embryos. We determine the subcellular distribution of hundreds of proteins, and protein complexes. Our results reveal the potential of LOPIT to provide average snapshots of cells.
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Affiliation(s)
- Denise J L Tan
- Cambridge Systems Biology Centre, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
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34
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Rabilloud T, Vaezzadeh AR, Potier N, Lelong C, Leize-Wagner E, Chevallet M. Power and limitations of electrophoretic separations in proteomics strategies. MASS SPECTROMETRY REVIEWS 2009; 28:816-843. [PMID: 19072760 DOI: 10.1002/mas.20204] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.
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35
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Komatsu S, Ahsan N. Soybean proteomics and its application to functional analysis. J Proteomics 2009; 72:325-36. [PMID: 19022415 DOI: 10.1016/j.jprot.2008.10.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/07/2008] [Accepted: 10/21/2008] [Indexed: 12/16/2022]
Abstract
Complete genome sequences, which are available for rice and Arabidopsis, provide insights into many fundamental aspects of plant biology; they do not, however, address some important aspects of legume biology. Legumes are important for maintenance of human health and as crops for sustainable agriculture. Two model species of legume, Lotus japonicus and Medicago truncatula, have been the focus of projects on genome sequencing and functional genomics. A project aimed at sequencing the genome of the agricultural legume soybean recently began, but functional genomics studies of this plant are in their infancy, and therefore proteomics approaches could be a powerful tool for functional analysis. In this review, we discuss the strengths and weaknesses of proteomics technologies in soybean biology and we examine the limitations of current techniques.
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36
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Zhang Y, Lv Z, Chen J, Chen Q, Quan Y, Kong L, Zhang H, Li S, Zheng Q, Chen J, Nie Z, Wang J, Jin Y, Wu X. A novel method for isolation of membrane proteins: a baculovirus surface display system. Proteomics 2009; 8:4178-85. [PMID: 18814327 DOI: 10.1002/pmic.200800133] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have developed a novel baculovirus surface display (BVSD) system for the isolation of membrane proteins. We expressed a reporter gene that encoded hemagglutinin gene fused in frame with the signal peptide and transmembrane domain of the baculovirus gp64 protein, which is displayed on the surface of BmNPV virions. The expression of this fusion protein on the virion envelope allowed us to develop two methods for isolating membrane proteins. In the first method, we isolated proteins directly from the envelope of budding BmNPV virions. In the second method, we isolated proteins from cellular membranes that had disintegrated due to viral egress. We isolated 6756 proteins. Of these, 1883 have sequence similarities to membrane proteins and 1550 proteins are homologous to known membrane proteins. This study indicates that membrane proteins can be effectively isolated using our BVSD system. Using an analogous method, membrane proteins can be isolated from other eukaryotic organisms, including human beings, by employing a host cell-specific budding virus.
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Affiliation(s)
- Yaozhou Zhang
- The Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Province; Institute of Biochemistry, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.
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37
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Endler A, Reiland S, Gerrits B, Schmidt UG, Baginsky S, Martinoia E. In vivo phosphorylation sites of barley tonoplast proteins identified by a phosphoproteomic approach. Proteomics 2009; 9:310-21. [DOI: 10.1002/pmic.200800323] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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38
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Whiteman SA, Serazetdinova L, Jones AME, Sanders D, Rathjen J, Peck SC, Maathuis FJM. Identification of novel proteins and phosphorylation sites in a tonoplast enriched membrane fraction of Arabidopsis thaliana. Proteomics 2008; 8:3536-47. [PMID: 18686298 DOI: 10.1002/pmic.200701104] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plant vacuoles play essential roles in many physiological processes, particularly in mineral nutrition, turgor provision and cellular signalling. The vacuolar membrane, the tonoplast, contains many membrane transporters that are critical in the execution of these processes. However, although increasing knowledge is available about the identity of proteins involved in these processes very little is known about the regulation of tonoplast transporters. By studying the phosphoproteome of tonoplast-enriched membranes, we identified 66 phosphorylation sites on 58 membrane proteins. Amongst these, 31 sites were identified in 28 membrane transporters of various families including tonoplast anion transporters of the CLC family, potassium transporters of the KUP family, tonoplast sugar transporters and ABC transporters. In a number of cases, the detected sites were well conserved across isoforms of one family pointing to common mechanisms of regulation. In other cases, isoform-unique sites were present, suggesting regulatory mechanisms tailored to the function of individual proteins. These results provide the basis for future studies to elucidate the mechanistic regulation of tonoplast membrane transporters.
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Schneider S, Beyhl D, Hedrich R, Sauer N. Functional and physiological characterization of Arabidopsis INOSITOL TRANSPORTER1, a novel tonoplast-localized transporter for myo-inositol. THE PLANT CELL 2008; 20:1073-87. [PMID: 18441213 PMCID: PMC2390729 DOI: 10.1105/tpc.107.055632] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana INOSITOL TRANSPORTER1 (INT1) is a member of a small gene family with only three more genes (INT2 to INT4). INT2 and INT4 were shown to encode plasma membrane-localized transporters for different inositol epimers, and INT3 was characterized as a pseudogene. Here, we present the functional and physiological characterization of the INT1 protein, analyses of the tissue-specific expression of the INT1 gene, and analyses of phenotypic differences observed between wild-type plants and mutant lines carrying the int1.1 and int1.2 alleles. INT1 is a ubiquitously expressed gene, and Arabidopsis lines with T-DNA insertions in INT1 showed increased intracellular myo-inositol concentrations and reduced root growth. In Arabidopsis, tobacco (Nicotiana tabacum), and Saccharomyces cerevisiae, fusions of the green fluorescent protein to the C terminus of INT1 were targeted to the tonoplast membranes. Finally, patch-clamp analyses were performed on vacuoles from wild-type plants and from both int1 mutant lines to study the transport properties of INT1 at the tonoplast. In summary, the presented molecular, physiological, and functional studies demonstrate that INT1 is a tonoplast-localized H(+)/inositol symporter that mediates the efflux of inositol that is generated during the degradation of inositol-containing compounds in the vacuolar lumen.
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Affiliation(s)
- Sabine Schneider
- Molekulare Pflanzenphysiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
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40
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Yamaryo Y, Dubots E, Albrieux C, Baldan B, Block MA. Phosphate availability affects the tonoplast localization of PLDzeta2, an Arabidopsis thaliana phospholipase D. FEBS Lett 2008; 582:685-90. [PMID: 18242181 DOI: 10.1016/j.febslet.2008.01.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 01/16/2008] [Accepted: 01/24/2008] [Indexed: 11/24/2022]
Abstract
Under phosphate deprivation, higher plants change their lipid composition and recycle phosphate from phospholipids. A phospholipase D, PLDzeta2, is involved in this recycling and in other cellular functions related to plant development. We investigated the localization of Arabidopsis PLDzeta2 by cell fractionation and in vivo GFP confocal imaging. AtPLDzeta2 localizes to the tonoplast and the Nter regulatory domain is sufficient for its sorting. Under phosphate deprivation, AtPLDzeta2 remains located in the tonoplast but its distribution is uneven. We observed PLDzeta2-enriched tonoplast domains preferentially positioned close to mitochondria and beside chloroplasts. In absence of PLDzeta2, membrane developments were visualized inside vacuoles.
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Affiliation(s)
- Yoshiki Yamaryo
- Laboratoire de Physiologie Cellulaire Végétale, CNRS, CEA, INRA, Université J. Fourier, CEA-Grenoble, iRTSV/LPCV, 17 Rue des Martyrs, Grenoble, France
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41
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Lilley KS, Dupree P. Plant organelle proteomics. CURRENT OPINION IN PLANT BIOLOGY 2007; 10:594-9. [PMID: 17913569 DOI: 10.1016/j.pbi.2007.08.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 08/13/2007] [Accepted: 08/16/2007] [Indexed: 05/09/2023]
Abstract
It is important for cell biologists to know the subcellular localization of proteins to understand fully the functions of organelles and the compartmentation of plant metabolism. The accurate description of an organelle proteome requires the ability to identify genuine protein residents. Such accurate assignment is difficult in situations where a pure homogeneous preparation of the organelle cannot be achieved. Practical limitations in both organelle isolation and also analysis of low abundance proteins have resulted in limited datasets from high throughput proteomics approaches. Here, we discuss some examples of quantitative proteomic methods and their use to study plant organelle proteomes, with particular reference to methods designed to give unequivocal assignments to organelles.
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Affiliation(s)
- Kathryn S Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QR, United Kingdom.
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42
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Strasser R, Bondili JS, Schoberer J, Svoboda B, Liebminger E, Glössl J, Altmann F, Steinkellner H, Mach L. Enzymatic properties and subcellular localization of Arabidopsis beta-N-acetylhexosaminidases. PLANT PHYSIOLOGY 2007; 145:5-16. [PMID: 17644627 PMCID: PMC1976588 DOI: 10.1104/pp.107.101162] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Plant glycoproteins contain substantial amounts of paucimannosidic N-glycans lacking terminal GlcNAc residues at their nonreducing ends. It has been proposed that this is due to the action of beta-hexosaminidases during late stages of N-glycan processing or in the course of N-glycan turnover. We have now cloned the three putative beta-hexosaminidase sequences present in the Arabidopsis (Arabidopsis thaliana) genome. When heterologously expressed as soluble forms in Spodoptera frugiperda cells, the enzymes (termed HEXO1-3) could all hydrolyze the synthetic substrates p-nitrophenyl-2-acetamido-2-deoxy-beta-d-glucopyranoside, p-nitrophenyl-2-acetamido-2-deoxy-beta-d-galactopyranoside, 4-methylumbelliferyl-2-acetamido-2-deoxy-beta-d-glucopyranoside, and 4-methylumbelliferyl-6-sulfo-2-acetamido-2-deoxy-beta-d-glucopyranoside, albeit to a varying extent. HEXO1 to HEXO3 were further able to degrade pyridylaminated chitotriose, whereas pyridylaminated chitobiose was only cleaved by HEXO1. With N-glycan substrates, HEXO1 displayed a much higher specific activity than HEXO2 and HEXO3. Nevertheless, all three enzymes were capable of removing terminal GlcNAc residues from the alpha1,3- and alpha1,6-mannosyl branches of biantennary N-glycans without any strict branch preference. Subcellular localization studies with HEXO-fluorescent protein fusions transiently expressed in Nicotiana benthamiana plants showed that HEXO1 is a vacuolar protein. In contrast, HEXO2 and HEXO3 are mainly located at the plasma membrane. These results indicate that HEXO1 participates in N-glycan trimming in the vacuole, whereas HEXO2 and/or HEXO3 could be responsible for the processing of N-glycans present on secretory glycoproteins.
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Affiliation(s)
- Richard Strasser
- Institute of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Applied Life Sciences, A-1190 Vienna, Austria.
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Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, Garin J, Bourguignon J. A Proteomics Approach Highlights a Myriad of Transporters in the Arabidopsis thaliana Vacuolar Membrane. PLANT SIGNALING & BEHAVIOR 2007; 2:413-5. [PMID: 19704618 PMCID: PMC2634231 DOI: 10.4161/psb.2.5.4415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 05/10/2007] [Indexed: 05/09/2023]
Abstract
To better understand plant vacuolar functions and identify new transporters present on the tonoplast, a proteomic work was initiated on Arabidopsis thaliana. A procedure was developed to prepare highly purified vacuoles from protoplasts isolated from Arabidopsis cell cultures, and a proteomics approach was designed to identify the protein components present in both the membrane and soluble fractions of the vacuoles. This procedure allowed the identification of 650 proteins, 2/3 of which copurify with the hydrophobic membrane fraction and 1/3 with the soluble fraction. With regard to function, only 20% of the proteins identified were previously known to be associated with vacuolar activities.
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Affiliation(s)
- Michel Jaquinod
- Laboratoire d'Etude de la Dynamique des Protéomes Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Florent Villiers
- Laboratoire de Physiologie Cellulaire Végétale; Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Sylvie Kieffer-Jaquinod
- Laboratoire d'Etude de la Dynamique des Protéomes Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire Végétale; Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Christophe Bruley
- Laboratoire d'Etude de la Dynamique des Protéomes Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Jérôme Garin
- Laboratoire d'Etude de la Dynamique des Protéomes Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
| | - Jacques Bourguignon
- Laboratoire de Physiologie Cellulaire Végétale; Institut de Recherches en Technologies et Sciences pour le Vivant; Commissariat à l'Energie Atomique; Université Joseph Fourier, Grenoble France
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Schmidt UG, Endler A, Schelbert S, Brunner A, Schnell M, Neuhaus HE, Marty-Mazars D, Marty F, Baginsky S, Martinoia E. Novel tonoplast transporters identified using a proteomic approach with vacuoles isolated from cauliflower buds. PLANT PHYSIOLOGY 2007; 145:216-29. [PMID: 17660356 PMCID: PMC1976570 DOI: 10.1104/pp.107.096917] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Young meristematic plant cells contain a large number of small vacuoles, while the largest part of the vacuome in mature cells is composed by a large central vacuole, occupying 80% to 90% of the cell volume. Thus far, only a limited number of vacuolar membrane proteins have been identified and characterized. The proteomic approach is a powerful tool to identify new vacuolar membrane proteins. To analyze vacuoles from growing tissues we isolated vacuoles from cauliflower (Brassica oleracea) buds, which are constituted by a large amount of small cells but also contain cells in expansion as well as fully expanded cells. Here we show that using purified cauliflower vacuoles and different extraction procedures such as saline, NaOH, acetone, and chloroform/methanol and analyzing the data against the Arabidopsis (Arabidopsis thaliana) database 102 cauliflower integral proteins and 214 peripheral proteins could be identified. The vacuolar pyrophosphatase was the most prominent protein. From the 102 identified proteins 45 proteins were already described. Nine of these, corresponding to 46% of peptides detected, are known vacuolar proteins. We identified 57 proteins (55.9%) containing at least one membrane spanning domain with unknown subcellular localization. A comparison of the newly identified proteins with expression profiles from in silico data revealed that most of them are highly expressed in young, developing tissues. To verify whether the newly identified proteins were indeed localized in the vacuole we constructed and expressed green fluorescence protein fusion proteins for five putative vacuolar membrane proteins exhibiting three to 11 transmembrane domains. Four of them, a putative organic cation transporter, a nodulin N21 family protein, a membrane protein of unknown function, and a senescence related membrane protein were localized in the vacuolar membrane, while a white-brown ATP-binding cassette transporter homolog was shown to reside in the plasma membrane. These results demonstrate that proteomic analysis of highly purified vacuoles from specific tissues allows the identification of new vacuolar proteins and provides an additional view of tonoplastic proteins.
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Affiliation(s)
- Ulrike G Schmidt
- University of Zürich, Institute of Plant Biology, CH-8008 Zurich, Switzerland
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45
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Sarry JE, Chen S, Collum RP, Liang S, Peng M, Lang A, Naumann B, Dzierszinski F, Yuan CX, Hippler M, Rea PA. Analysis of the vacuolar luminal proteome of Saccharomyces cerevisiae. FEBS J 2007; 274:4287-305. [PMID: 17651441 DOI: 10.1111/j.1742-4658.2007.05959.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Despite its large size and the numerous processes in which it is implicated, neither the identity nor the functions of the proteins targeted to the yeast vacuole have been defined comprehensively. In order to establish a methodological platform and protein inventory to address this shortfall, we refined techniques for the purification of 'proteomics-grade' intact vacuoles. As confirmed by retention of the preloaded fluorescent conjugate glutathione-bimane throughout the fractionation procedure, the resistance of soluble proteins that copurify with this fraction to digestion by exogenous extravacuolar proteinase K, and the results of flow cytometric, western and marker enzyme activity analyses, vacuoles prepared in this way retain most of their protein content and are of high purity and integrity. Using this material, 360 polypeptides species associated with the soluble fraction of the vacuolar isolates were resolved reproducibly by 2D gel electrophoresis. Of these, 260 were identified by peptide mass fingerprinting and peptide sequencing by MALDI-MS and liquid chromatography coupled to ion trap or quadrupole TOF tandem MS, respectively. The polypeptides identified in this way, many of which correspond to alternate size and charge states of the same parent translation product, can be assigned to 117 unique ORFs. Most of the proteins identified are canonical vacuolar proteases, glycosidases, phosphohydrolases, lipid-binding proteins or established vacuolar proteins of unknown function, or other proteases, glycosidases, lipid-binding proteins, regulatory proteins or proteins involved in intermediary metabolism, protein synthesis, folding or targeting, or the alleviation of oxidative stress. On the basis of the high purity of the vacuolar preparations, the electrophoretic properties of the proteins identified and the results of quantitative proteinase K protection measurements, many of the noncanonical vacuolar proteins identified are concluded to have entered this compartment for breakdown, processing and/or salvage purposes.
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Affiliation(s)
- Jean-Emmanuel Sarry
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Barkla BJ, Vera-Estrella R, Pantoja O. Enhanced separation of membranes during free flow zonal electrophoresis in plants. Anal Chem 2007; 79:5181-7. [PMID: 17566980 DOI: 10.1021/ac070159v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Free flow zonal electrophoresis (FFZE) is a versatile technique that allows for the separation of cells, organelles, membranes, and proteins based on net surface charge during laminar flow through a thin aqueous layer. We have been optimizing the FFZE technique to enhance separation of plant vacuolar membranes (tonoplast) from other endomembranes to pursue a directed proteomics approach to identify novel tonoplast transporters. Addition of ATP to a mixture of endomembranes selectively enhanced electrophoretic mobility of acidic vesicular compartments during FFZE toward the positive electrode. This has been attributed to activation of the V-ATPase generating a more negative membrane potential outside the vesicles, resulting in enhanced migration of acidic vesicles, including tonoplast, to the anode (Morré, D. J.; Lawrence, J.; Safranski, K.; Hammond, T.; Morré, D. M. J. Chromatogr., A 1994, 668, 201-213). We confirm that ATP does induce a redistribution of membranes during FFZE of microsomal membranes isolated from several plant species, including Arabidopsis thaliana, Thellungiella halophila, Mesembryanthemum crystallinum, and Ananas comosus. However, we demonstrate, using V-ATPase-specific inhibitors, nonhydrolyzable ATP analogs, and ionophores to dissipate membrane potential, that the ATP-dependent migrational shift of membranes under FFZE is not due to activation of the V-ATPase. Addition of EDTA to chelate Mg2+, leading to the production of the tetravalent anionic form of ATP, resulted in a further enhancement of membrane migration toward the anode, and manipulation of cell surface charge by addition of polycations also influenced the ATP-dependent migration of membranes. We propose that ATP enhances the mobility of endomembranes by screening positive surface charges on the membrane surface.
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Affiliation(s)
- Bronwyn J Barkla
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Colonia Miraval, Cuernavaca, Morelos, México.
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Lasseur B, Lothier J, Morvan-Bertrand A, Escobar-Guttiérez A, Humphreys MO, Prud'homme MP. Impact of defoliation frequency on regrowth and carbohydrate metabolism in contrasting varieties of Lolium perenne. FUNCTIONAL PLANT BIOLOGY : FPB 2007; 34:418-430. [PMID: 32689369 DOI: 10.1071/fp06286] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 03/01/2007] [Indexed: 06/11/2023]
Abstract
The aims of the study were to gain a better understanding of fructan metabolism regulation during regrowth of Lolium perenne, and to evaluate the role of fructans of remaining tissues as well as carbon assimilation of new leaf tissues in refoliation. Two varieties that contrast for carbohydrate metabolism, Aurora and Perma, were subject to severe and frequent or infrequent defoliations before regrowth. Aurora, which had a greater content of fructans in leaf sheaths than Perma before defoliation, produced more leaf biomass within the 4 days following the first cut. At the end of the regrowth period, Aurora produced more leaf biomass than Perma. Photosynthetic parameters, which were barely affected by defoliation frequency, could not explain these differences. Fructan synthesising activities [sucrose:sucrose 1-fructosyltransferase (1-SST) and fructan:fructan 6G-fructosyltransferase (6G-FFT)], declined after defoliation. In elongating leaf bases, corresponding transcript levels did not decline concomitantly, suggesting a post-transcriptional regulation of expression, while in leaf sheaths the gene expression pattern mostly followed the time-course of the enzyme activities. Regulation of Lp1-SST and Lp6G-FFT gene expression depends, therefore, on the sink-source status of the tissue after defoliation. During the phase of reserve accumulation, fructosyltransferase activities together with corresponding transcripts increased more in frequently defoliated plants than in infrequently defoliated plants.
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Affiliation(s)
- Bertrand Lasseur
- UMR INRA-UCN 950 EVA Ecophysiologie Végétale, Agronomie & Nutritions NCS, Université de Caen, Esplanade de la Paix, F-14032 Caen cedex, France
| | - Jérémy Lothier
- UMR INRA-UCN 950 EVA Ecophysiologie Végétale, Agronomie & Nutritions NCS, Université de Caen, Esplanade de la Paix, F-14032 Caen cedex, France
| | - Annette Morvan-Bertrand
- UMR INRA-UCN 950 EVA Ecophysiologie Végétale, Agronomie & Nutritions NCS, Université de Caen, Esplanade de la Paix, F-14032 Caen cedex, France
| | | | - Mervyn O Humphreys
- Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth SY23 3EB, UK
| | - Marie-Pascale Prud'homme
- UMR INRA-UCN 950 EVA Ecophysiologie Végétale, Agronomie & Nutritions NCS, Université de Caen, Esplanade de la Paix, F-14032 Caen cedex, France
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Murcha MW, Elhafez D, Lister R, Tonti-Filippini J, Baumgartner M, Philippar K, Carrie C, Mokranjac D, Soll J, Whelan J. Characterization of the preprotein and amino acid transporter gene family in Arabidopsis. PLANT PHYSIOLOGY 2007; 143:199-212. [PMID: 17098851 PMCID: PMC1761978 DOI: 10.1104/pp.106.090688] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Seventeen loci encode proteins of the preprotein and amino acid transporter family in Arabidopsis (Arabidopsis thaliana). Some of these genes have arisen from recent duplications and are not in annotated duplicated regions of the Arabidopsis genome. In comparison to a number of other eukaryotic organisms, this family of proteins has greatly expanded in plants, with 24 loci in rice (Oryza sativa). Most of the Arabidopsis and rice genes are orthologous, indicating expansion of this family before monocot and dicot divergence. In vitro protein uptake assays, in vivo green fluorescent protein tagging, and immunological analyses of selected proteins determined either mitochondrial or plastidic localization for 10 and six proteins, respectively. The protein encoded by At5g24650 is targeted to both mitochondria and chloroplasts and, to our knowledge, is the first membrane protein reported to be targeted to mitochondria and chloroplasts. Three genes encoded translocase of the inner mitochondrial membrane (TIM)17-like proteins, three TIM23-like proteins, and three outer envelope protein16-like proteins in Arabidopsis. The identity of Arabidopsis TIM22-like proteins is most likely a protein encoded by At3g10110/At1g18320, based on phylogenetic analysis, subcellular localization, and complementation of a yeast (Saccharomyces cerevisiae) mutant and coexpression analysis. The lack of a preprotein and amino acid transporter domain in some proteins, localization in mitochondria, plastids, or both, variation in gene structure, and the differences in expression profiles indicate that the function of this family has diverged in plants beyond roles in protein translocation.
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Affiliation(s)
- Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
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Becker B. Function and evolution of the vacuolar compartment in green algae and land plants (Viridiplantae). INTERNATIONAL REVIEW OF CYTOLOGY 2007; 264:1-24. [PMID: 17964920 DOI: 10.1016/s0074-7696(07)64001-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Plant vacuoles perform several different functions and are essential for the plant cell. The large central vacuoles of mature plant cells provide structural support, and they serve other functions, such as protein degradation and turnover, waste disposal, storage of metabolites, and cell growth. A unique feature of the plant vacuolar system is the presence of different types of vacuoles within the same cell. The current knowledge about the vacuolar compartments in plants and green algae is summarized and a hypothesis is presented to explain the origin of multiple types of vacuoles in plants.
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Affiliation(s)
- Burkhard Becker
- Botanical Institute, University of Cologne, 50931 Köln, Germany
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