Citation: | Wei Li, Liu Jian-Li. Overview of research on protein subcellular localization in plants[J]. Plant Science Journal, 2021, 39(1): 93-101. DOI: 10.11913/PSJ.2095-0837.2021.10093 |
[1] |
Lunn JE. Compartmentation in plant metabolism[J]. J Exp Bot, 2007, 58(1):35-47.
|
[2] |
Tanz SK, Castleden I, Small ID, Millar AH. Fluorescent protein tagging as a tool to define the subcellular distribution of proteins in plant[J]. Front Plant Sci, 2013, 24(4):214.
|
[3] |
Dangol S, Singh R, Chen Y, Jwa N. Visualization of multicolored in vivo organelle markers for co-localization studies in Oryza sativa[J]. Mol Cells, 2017, 40(11):828-836.
|
[4] |
Naohiro K, Dominique P, Eric L. Spectral profiling for the simultaneous observation of four distinct fluorescent proteins and detection of protein-protein interaction via fluorescence resonance energy transfer in tobacco leaf nuclei[J]. Plant Physiol, 2002, 129(3):931-942.
|
[5] |
Kohler RH, Zipfer WR, Webb WW, Hanson MR. The green fluorescent protein as a marker to visualize plant mitochondria in vivo[J]. Plant J, 1997, 11(3):613-621.
|
[6] |
Mankin SL, Thompson WF. New green fluorescent protein genes for plant transformation:intron-containing, ER loca-lized, and soluble-modified[J]. Plant Mol Biol Rep, 2001, 19:13-26.
|
[7] |
Sedbrook JC, Carroll KL, Hung KF, Masson PH, Somerville CR. The ArabidopsisSKU5 gene encodes an extracellular glycosyl phosphatidylinositol-anchored glycoprotein involved in directional root growth[J]. Plant Cell, 2002, 14(7):1635-1648.
|
[8] |
Gardiner JC, Taylor NG, Turner SR. Control of cellulose synthase complex localization in developing xylem[J]. Plant Cell, 2003, 15(8):1740-1748.
|
[9] |
Tian G, Mohanty A, Chary SN, Li S, Paap B, Drakakaki G, et al. High-throughput fluorescent tagging of full-length Arabidopsisgene products in planta[J]. Plant Physiol, 2004, 135(1):25-38.
|
[10] |
Thomas CL, Maule AJ. Limitations on the use of fused green fluorescent protein to investigate structure-function relationships for the cauliflower mosaic virus movement protein[J]. J Gen Virol, 2000, 81(Pt7):1851-1855.
|
[11] |
DeBlasio SL, Sylvester AW, Jackson D. Illuminating plant biology:using fluorescent proteins for high-throughput analysis of protein localization and function in plants[J]. Brief Funct Genomics, 2010, 9(2):129-138.
|
[12] |
Griesen D, Su D, Bérczi A, Asard H. Localization of an ascorbate-reducible cytochrome b561 in the plant tonoplast[J]. Plant Physiol, 2004, 134(2):726-734.
|
[13] |
Hao H, Chen T, Fan L, Li R, Wang X. 2, 6-dichlorobenzonitrile causes multiple effects on pollen tube growth beyond altering cellulose synthesis in Pinus bungeanaZucc.[J]. PLoS One, 2013, 8(10):e76660.
|
[14] |
Astruc T, Marinova P, Labas R, Gatellier P, Santé-Lhoutellier V. Detection and localization of oxidized proteins in muscle cells by fluorescence microscopy[J]. J Agric Food Chem, 2007, 55(23):9554-9558.
|
[15] |
Bauer M, Dietrich C, Nowak K, Sierralta WD, Papenbrock J. Intracellular localization of Arabidopsis sulfurtransferases[J]. Plant Physiol, 2004, 135(2):916-926.
|
[16] |
Ueki S, Citovsky V. Identification of an interactor of cadmium ion-induced glycine-rich protein involved in regulation of callose levels in plant vasculature[J]. Proc Natl Acad Sci USA, 2005, 102(34):12089-12094.
|
[17] |
Hou Z, Huang WD. Immunohistochemical localization of IAA and ABP1 in strawberry shoot apexes during floral induction[J]. Planta, 2005, 222(4):678-687.
|
[18] |
Xu RY, Niimi Y, Kojima K. Exogenous GA3 overcomes bud deterioration in tulip (Tulipa gesneriana L.) bulbs du-ring dry storage by promoting endogenous IAA activity in the internodes[J]. Plant Growth Regul, 2007, 52:1-8.
|
[19] |
Peng YB, Zou C, Wang DH, Gong HQ, Xu ZH, Bai SN. Preferential localization of abscisic acid in primordial and nursing cells of reproductive organs of Arabidopsis and cucumber[J]. New Phytol, 2006, 170(3):459-466.
|
[20] |
Gao W, Nan T, Tan G, Zhao H, Tan W, et al. Cellular and subcellular immunohistochemical localization and quantification of cadmium ions in wheat(Triticum aestivum)[J]. PLoS One, 2015, 10(5):e0123779.
|
[21] |
Douchiche O, Driouich A, Morvan C. Spatial regulation of cell-wall structure in response to heavy metal stress:cadmium-induced alteration of the methyl-esterification pattern of homogalacturonans[J]. Ann Bot, 2010, 105:481-491.
|
[22] |
Tanaka N, Fujita M, Handa H, Murayama S, Uemura M, et al. Proteomics of the rice cell:systematic identification of the protein populations in subcellular compartment[J]. Mol Genet Genomics, 2004, 271(5):566-576.
|
[23] |
Titus DE, Hondred D, Becker WM. Purification and cha-racterization of hydroxypyruvate reductase from cucumber cotyledons[J]. Plant Physiol, 1983, 72(2):402-408.
|
[24] |
Fürtauer L, Küstner L, Weckwerth W, Heyer AG, Nägele T. Resolving subcellular plant metabolism[J]. Plant J, 2019, 100(3):438-455.
|
[25] |
Aidemark M, Andersson C, Rasmusson AG, Widell S. Regulation of callose synthase activity in situ in alamethicin-permeabilized Arabidopsis and tobacco suspension cells[J]. BMC Plant Biol, 2009, 9(27):1186-1471.
|
[26] |
Maeshima M. Vacuolar H+-pyrophophatase[J]. Biochim Biophys Acta, 2000, 1465:37-51.
|
[27] |
Vance JE. Phospholipid synthesis in a membrane fraction associated with mitochondria[J]. J Biol Chem, 1990, 265(13):7248-7256.
|
[28] |
Kong FJ, Oyanagi A, Komatsu S. Cell wall proteome of wheat roots under flooding stress using gel-based and LC MS/MS-based proteomics approaches[J]. Biochim Biophys Acta, 2010, 1804(1):124-136.
|
[29] |
Francin-Allami M, Merah K, Albenne C, Rogniaux H, Pavlovic M, et al. Cell wall proteomic of Brachypodium distachyon grains:a focus on cell wall remodeling proteins[J]. Proteomics, 2015, 15(13):2296-2306.
|
[30] |
Bernfur K, Larsson O, Larsson C, Gustavsson N. Relative abundance of integral plasma membrane proteins in Arabidopsis leaf and root tissue determined by metabolic labeling and mass spectrometry[J]. PLoS One, 2013, 8(8):e71206.
|
[31] |
张丽军,谢锦云,李选文,梁宋平. 真核细胞质膜蛋白质组研究进展[J]. 生命科学,2005, 17(5):398-403.
Zhang LJ, Xie JY, Li XW, Liang SP. Progress in proteomic research of eukaryotic cell plasma membrane[J]. Chinese Bulletin of Life Sciences, 2005, 17(5):398-403.
|
[32] |
Taylor NL, Heazlewood JL, Millar AH. The Arabidopsis thaliana 2-D gel mitochondrial proteome:refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications[J]. Proteomics, 2011, 11(9):1720-1733.
|
[33] |
Lundquist PK, Poliakov A, Bhuiyan NH, Zybailov B, Sun Q, Wijk KJV. The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis[J]. Plant Phy-siol, 2012, 158(3):1172-1192.
|
[34] |
Jaquinod M, Villiers F, Kieffer-Jaquinod S, Hugouvieux V, Bruley C, et al. A proteomics dissection of Arabidopsis thalianavacuoles isolated from cell culture[J]. Mol Cell Proteomics, 2007, 6(3):394-412.
|
[35] |
Reumann S, Babujee L, Ma C, Wienkoop S, Siemsen T, et al. Proteome analysis of Arabidopsisleaf peroxisomes reveals novel targeting peptides, metabolic pathways, and defense mechanisms[J]. Plant Cell, 2007, 19(10):3170-3193.
|
[36] |
Reumann S, Quan S, Aung K, Yang P, Manandhar-Shrestha K, et al. In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes[J]. Plant Physiol, 2009, 150(1):125-143.
|
[37] |
Barba-Espín G, Dedvisitsakul P, Hägglund P, Svensson B, Finnie C. Gibberellic acid-induced aleurone layers responding to heat shock or tunicamycin provide insight into the N-glycoproteome, protein secretion, and endoplasmic reticulum stress[J]. Plant Physiol, 2014, 164(2):951-965.
|
[38] |
Behrens C, Blume C, Senkler M, Eubel H, Peterhänsel C, Braun HP. The ‘protein complex proteome’ of chloroplasts in Arabidopsis thaliana[J]. J Proteomics, 2013, 91:73-83.
|
[39] |
Wang X, Komatsu S. Plant subcellular proteomics:application for exploring optimal cell function in soybean[J]. J Proteomics, 2016, 143:45-56.
|
[40] |
Pierleoni A, Martelli PL, Fariselli P, Casadio R. BaCelLo:a balanced subcellular localization predictor[J]. Bioinformatics, 2006, 22(14):e408-e416.
|
[41] |
Dobson L, Reményi I, Tusnády GE. CCTOP:a consensus constrained TOPology prediction web server[J]. Nucleic Acids Res, 2015, 43(W1):W408-W412.
|
[42] |
Emanuelsson O, Nielsen H, Heijine GV. ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites[J]. Protein Sci, 1999, 8(5):978-984.
|
[43] |
Almagro Armenteros JJ, Sønderby C, Sønderby SK, Nielsen H, Winther O. DeepLoc:prediction of protein subcellular localization using deep learning[J]. Bioinforma-tics, 2017, 33(21):3387-3395.
|
[44] |
Savojardo C, Martelli PL, Fariselli P, Casadio R. DeepSig:deep learning improves signal peptide detection in protein[J]. Bioinformatics, 2018, 34(10):1690-1696.
|
[45] |
Pierleoni A, Martelli PL, Fariselli P, Casadio R. eSLDB:eukaryotic subcellular localization database[J]. Nucleic Acids Res, 2007, 35(Database issue):D208-D212.
|
[46] |
Sperschneider J, Catanzariti AM, DeBoer K, Petre B, Gardiner DM, et al. LOCALIZER:subcellular localization prediction of both plant and effector proteins in the plant cell[J]. Sci Rep, 2017, 16(7):44598.
|
[47] |
Nair R, Rost B. LOCnet and LOCtarget:sub-cellular loca-lization for structural genomics targets[J]. Nucleic Acids Res, 2004, 32:W517-W521.
|
[48] |
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, et al. LocTree3 prediction of localization[J]. Nucleic Acids Res, 2014, 42:W350-W355.
|
[49] |
Nugent T, Jones DT. Transmembrane protein topology prediction using support vector machines[J]. BMC Bioinformatics, 2009, 10:159.
|
[50] |
Wan S, Mak MW, Kung SY. mGOASVM:multi-label protein subcellular localization based on gene ontology and support vector machines[J]. BMC Bioinformatics, 2012, 13:290.
|
[51] |
Bernhofer M, Goldberg T, Wolf S, Ahmed M, Zaugg J, et al. NLSdb-major update for database of nuclear localization signals and nuclear export signals[J]. Nucleic Acids Res, 2018, 46(1):503-508.
|
[52] |
Viklund H, Elofsson A, Notes A. OCTOPUS:improving topology prediction by two-track ANN-based preference scores and an extended topological grammar[J]. Bioinformatics, 2008, 24(15):1662-1668.
|
[53] |
Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, et al. Predicting subcellular localization of protein using machine-learned classifiers[J]. Bioinformatics, 2004, 20(4):547-556.
|
[54] |
Cokol M, Nair R, Rost B. Finding nuclear localization signals[J]. EMBO Rep, 2000, 1(5):411-415.
|
[55] |
Hiller K, Grote A, Scheer M, Münch R, Jahn D. PrediSi:prediction of signal peptides and their cleavage positions[J]. Nucleic Acids Res, 2004, 32:W375-W379.
|
[56] |
Small I, Peeters N, Legeai F, Lurin C. Predotar:a tool for rapidly screening proteomes for N-terminal targeting sequences[J]. Proteomics, 2004, 4(6):1581-1590.
|
[57] |
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, et al. PSORTb 3.0:improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes[J]. Bioinformatics, 2010, 26(13):1608-1615.
|
[58] |
Almagro Armententeros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, et al. SignalP 5.0 improve signal peptide predictions using deep neural networks[J]. Nat Biotechnol, 2019, 37(4):420-423.
|
[59] |
Zhang YZ, Shen HB. Signal-3L 2.0:A hierarchical mixture model for enhancing protein signal peptide prediction by incorporating residue-domain cross-level features[J]. J Chem Inf Model, 2017, 57(4):988-999.
|
[60] |
Peters C, Tsirigos KD, Shu N, Elofsson A. Improved topology prediction using the terminal hydrophobic helices rule[J]. Bioinformatics, 2016, 32(8):1158-1162.
|
[61] |
Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence[J]. J Mol Biol, 2000, 300(4):1005-1016.
|
[62] |
Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides[J]. Nucleic Acids Res, 2015, 43:W401-W407.
|
[63] |
Abe S, Nagai T, Masukawa M, Okumoto K, Homma Y, et al. Localization of protein kinase NDR2 to peroxisomes and its role in Ciliogenesis[J]. J Biol Chem, 2017, 292(10):4089-4098.
|
[64] |
K hler S, Delwiche CF, Denny PW, Tilney LG, Webster P, et al. A plastid of probable green algal origin in apicomplexan parasites[J]. Science, 1997, 275(5305):1485-1489.
|
[65] |
Lee MH, Min MK, Lee YJ, Jin JB, Shin DH, et al. ADP-ribosylation factor 1 of Arabidopsis plays a critical role in intracellular trafficking and maintenance of endoplasmic reticulum morphology in Arabidopsis[J]. Plant Physiol, 2002, 129(4):1507-1520.
|
[66] |
Brandizzi F, Hanton S, DaSilva LLP, Boevink P, Evans D, et al. ER quality control can lead to retrograde transport from the ER lumen to the cytosol and the nucleoplasm in plants[J]. Plant J, 2003, 34(3):269-281.
|
[67] |
Irons SL, Evans DE, Brandizzi F. The first 238 amino acids of the human lamin B receptor are targeted to the nuclear envelope in plants[J]. J Exp Bot, 2003, 54(384):943-950.
|
[68] |
Saint-Jore-Dupa C, Nebenführ A, Boulaflous A, Follet-Gueye ML, Plasson C, et al. Plant N-glycan processing enzymes employ different targeting mechanisms for their spatial arrangement along the secretory pathway[J]. Plant Cell, 2006, 18(11):3182-3200.
|
[69] |
Ito Y, Uemura T, Nakano A. The Golgi entry core compartment functions as a COPII-independent scaffold for ER-to-Golgi transport in plant cells[J]. J Cell Sci, 2018, 131(2):jcs203893.
|
[70] |
Baldwin TC, Handford MG, Yuseff M, Orellana A, Dupree P. Identification and characterization of GONST1, a Golgi-localized GDP-mannose transporter in Arabidopsis[J]. Plant Cell, 2001, 13(10):2283-2295.
|
[71] |
Renna L, Hanton SL, Stefano G, Bortolotti L, Misra V, Brandizzi F. Identification and characterization of AtCASP, a plant transmembrane Golgi matrix protein[J]. Plant Mol Biol, 2005, 58(1):109-122.
|
[72] |
Sato K, Nishikawa S, Nakano A. Membrane protein retrieval from the Golgi apparatus to the endoplasmic reticulum(ER):characterization of the RER1 gene product as a component involved in ER localization of Sec12p[J]. Mol Biol Cell, 1995, 6(11):1459-1477.
|
[73] |
Leung KP, Luo M, Gao C, Zeng Y, Zhao Q, et al. Arabidopsis ENDOMEMBRANE PROTEIN 12 contributes to the endoplasmic reticulum stress response by regulating K/HDEL receptor trafficking[J]. Plant Cell, 2019, 31(7):1669.
|
[74] |
Wang T, Li L, Hong W. SNARE protein in membrane trafficking[J]. Traffic, 2017, 18(12):767-775.
|
[75] |
Parsons HT, Stevens TJ, McFarlane HE, Vidal-Melgosa S, Griss J, et al. Separating Golgi proteins from cis to trans reveals underlying properties of cisternal localization[J]. Plant Cell, 2019, 31(9):2010-2034.
|
[76] |
Feeney M, Frigerio L, Kohalmi SE, Cui Y, Menassa R. Reprogramming cells to study vacuolar development[J]. Front Plant Sci, 2013, 3(4):493.
|
[77] |
Gattolin S, Sorieul M, Frigerio L. Mapping of tonoplast intrinsic proteins in maturing and germinating Arabidopsis seeds reveals dual localization of embryonic TIPs to the tonoplast and plasma membrane[J]. Mol Plant, 2011, 4(1):180-189.
|
[78] |
Sato MH, Nakamura N, Ohsumi Y, Kouchi H, Kondo M, et al. TheAtVAM3 encodes a syntaxin-related molecule implicated in the vacuolar assembly in Arabidopsis thaliana[J]. J Biol Chem, 1997, 272(39):24530-24535.
|
[79] |
Uemura T, Yoshimura SH, Takeyasu K, Sato MH. Vacuolar membrane dynamics revealed by GFP-AtVam3 fusion protein[J]. Genes Cells, 2002, 7(7):743-753.
|
[80] |
Dettmer J, Hong-Hermesdorf A, Stierhof YD, Schumacher K. Vacuolar H+-ATPase activity is required for endocytic and secretory trafficking in Arabidopsis[J]. Plant Cell, 2006, 18(3):715-730.
|
[81] |
Wang X, Cai Y, Wang H, Zeng Y, Zhuang X, Li B, et al. Trans-Golgi network-located AP1 gamma adaptins me-diate dileucine motif-directed vacuolar targeting in Arabidopsis[J]. Plant Cell, 2014, 26(10):4102-4118.
|
[82] |
Robinson DG, Jiang L, Schumacher K. The endosomal system of plants:charting new and familiar territories[J]. Plant Physiol, 2008, 147(4):1482-1492.
|
[83] |
Rymer Ł, Kempiński B, Chelstowska A, Skoneczny M. The budding yeast Pex5p receptor directs Fox2 and Cta1p into peroxisomes via its N-terminal region near the FxxxW domain[J]. J Cell Sci, 2018, 131(17):jcs216986.
|
[84] |
Chu Y, Dodiya H, Aebischer P, Olanow CW, Kordower JH. Alterations in lysosomal and proteasomal markers in Parkinson's disease:relationship to alpha-synuclein inclusions[J]. Neurobiol Dis, 2009, 35(3):385-398.
|
[85] |
Okamoto K, SakoY. Recent advances in FRET for the study of protein interactions and dynamics[J]. Curr Opin Struct Biol, 2017, 46:16-23.
|
[86] |
Deal J, Pleshinger DJ, Johnson SC, Leavesley SJ, Rich TC. Milestones in the development and implementation of FRET-based sensors of intracellular signals:a biological perspective of the history of FRET[J]. Cell Signal, 2020, 75:109769.
|
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