Advancement of Protein Subcellular Localization in Plants

doi:10.3321/j.issn:1000-7091.2006.z2.001

Abstract

Abstract: Cell is the fundamental unit of living organism,proteins with different functions distributed in cellular compartments,including plasmolemma,nucleus,cytoplasm and organelles like mitochondria,chloroplast,Golgi,and endoplasmic reticulum etc.Protein subcellular localization is one of the key questions for functional genomics.The techniques used for subcellular localization of plants protein include fusion reporter gene localization,immunohistochemical localization,2D combined with mass spectrometry,marker enzyme-assisted localization and bioinformatics prediction.The development and application of high-throughtput protein subcellular localization technology stimulated the establishment of protein subcellular localization database.In model plant Arabidopsis thaliana,the number of proteins with localization data is over 4000.

Key words: Protein, Subcellular localization, Cellular compartment, Proteomics, High_throughput

CLC Number:

XING Hao-ran, LIU Li-juan, LIU Guo-zhen. Advancement of Protein Subcellular Localization in Plants[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2006, 21(S2): 1-6. doi: 10.3321/j.issn:1000-7091.2006.z2.001.

/ / Recommend / Download Citations

URL: http://www.hbnxb.net/EN/10.3321/j.issn:1000-7091.2006.z2.001

http://www.hbnxb.net/EN/Y2006/V21/IS2/1

References

[1] Kaul S,Koo H L,Jenkins J,et al.Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J].Nature,2000,408:796-815.
[2] Goff S A,Ricke D,Lan T H,et al.A draft sequence of the rice genome (Oryza sativa L.ssp.japonica)[J].Science,2002,296:92-100.
[3] Emanuelsson O,von Heijne G.Prediction of organellar targeting signals[J].Biochim Biophys Acta,2001,1541:114-119.
[4] Sullivan K F,Kay S A.Green fluorescent proteins[J].Methods in Cell Biology,1998,58:386.
[5] Abelson J,Simon M.Green fluorescent protein[J].Methods in Enzymology,1999,302:449.
[6] Cinelli R A,Ferrari A,Pellegrini V,et al.The enhanced green fluorescent protein as a tool for the analysis of protein dynamics and localization:local fluorescence study at the single-molecule level[J].Photochem Photobiol,2000,71(6):771-776.
[7] Hadjantonakis A K,Nagy A.The color of mice:in the light of GFP-variant reporters[J].Histochem Cell Biol,2001,115(1):49-58.
[8] Lansford R,Bearman G,Fraser S E.Resolution of multiple green fluorescent protein color variants and dyes using two-photon microscopy and imaging spectroscopy[J].J Biomed,2001,6(3):311-318.
[9] Goldenkova I V,Musiichuk K A,Piruzian E S.Bifunctional reporter genes:construction and expression in prokaryotic and eukaryotic cells[J].Mol Biol,2003,37(2):356-364.
[10] Mantis J,Tague B W.Comparing the utility of h-glucuronidase andgreen fluorescent protein for detection of weak promoter activity inArabidopsis thaliana[J].Plant Mol Biol Reporter,2000,18:319-330.
[11] Quaedvlieg N E,Schlaman H R,Admiraal P C,et al.Fusions between green fluorescent protein and beta-glucuronidase as sensitive and vital bifunctional reporters in plants[J].Plant Mol Biol,1998,38(5):861-873.
[12] Escobar N M,Haupt S,Thow G,et al.High-throughput viral expression of cDNA-green fluorescent protein fusions reveals novel subcellular addresses and identifies unique proteins that interact with plasmodesmata[J].Plant Cell,2003,15(7):1507-1523.
[13] Nakashima J,Endo S,Fukuda H.Immunocytochemical localization of polygalacturonase during tracheary element differentiation in Zinnia elegans[J].Planta,2004,218(5):729-739.
[14] brummell D A,Catala C,Lashbrook C C,et al.A membrane-anchored E-type endo-1,4-beta-glucanase is localized on Golgi and plasma membranes of higher plants[J].Proc Natl Acad Sci U S A,1997,94(9):4794-4799.
[15] Tanaka N,Fujita M,Handa H,et al.Proteomics of the rice cell:systematic identification of the protein populations in subcellular compartments[J].Mol Genet Genomics,2004,271(5):566-576.
[16] Shan L,Thara V K,Martin G B,et al.The pseudomonas AvrPto protein is differentially recognized by tomato and tobacco and is localized to the plant plasma membrane[J].Plant Cell,2000,12(12):2323-2338.
[17] Bhushan S,Stahl A,Nilsson S,et al.Catalysis,subcellular localization,expression and evolution of the targeting peptides degrading protease,AtPreP2,2005,46(6):985-996.
[18] Fujiwara Y,Asogawa M.Prediction of subcellular localizations using amino acid composition and order[J].Genome Inform Ser Workshop Genome Inform,2001,12:103-112.
[19] Chou K C,Cai Y D.Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition[J].J Cell Biochem,2004,91(6):1197-203.
[20] Cui Q,Jiang T,Liu B,et al.Esub8:a novel tool to predict protein subcellular localizations in eukaryotic organisms[J].BMC Bioinformatics,2004,5:66.
[21] Feng Zhi Ping.An overview on predicting the subcellular location of a protein[J].In Silico Biol,2002,2(3):291-303.
[22] Donnes P,Hoglund A.Predicting protein subcellular localization:past,present,and future[J].Genomics Proteomics Bioinformatics,2004,2(4):209-215.
[23] http://www.bioinfo.tsinghua.edu.cn/~shenjc/SPPI/Document.htm#statis2.
[24] Michael B Sheahan,Chris J Rose,David W McCurdy.A Green Fluorescent Protein Fusion to Actin-Binding Domain 2 of Arabidopsis Fimbrin Highlights New Features of a Dynamic Actin Cytoskeleton in Live Plant Cell[J].Plant physiology,2004,136 (4):3968-3977.
[25] Lee J Y,Taoka K,Yoo B C,et al.Plasmodesmal-associated protein kinase in tobacco and Arabidopsis recognizes a subset of non-cell-autonomous proteins[J].Plant Cell,2005,17(10):2817-2831.
[26] Cutler S R,Ehrhardt D W,Griffitts J S,et al.Random GFP::cDNA fusions enable visualization of subcellular structures in cells of Arabidopsis at a high frequency[J].Proc Natl Acad Sci U S A,2000,97(7):3718-3723.
[27] Tian G W,Mohanty A,Chary S N.High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta[J].Plant Physiol,2004,135(1):25-38.
[28] Koroleva O A,Tomlinson M L,Leader D,et al.High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions[J].The Plant Journal,2005,41(1):162-174.
[29] Komatsu S,Kojima K,Suzuki K,et al.Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis:its status in 2003[J].Nucleic Acids Res,2004,32:D388-D392.
[30] Millar A H.Location,location,location:surveying the intracellular real estate with proteomics in plants[J].Funct Plant Biol,2004,31:563-571.
[31] Kleffmann T,Russenberger D,von Zychlinski A,et al.The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions[J].Curr Biol,2004,14:354-362.
[32] Herald V L,Heazlewood J L,Day D A,et al.Proteomic identification of divalent metal cation binding proteins in plant mitochondria[J].FEBS Lett,2003,537:96-100.
[33] Millar A H,Heazlewood J L.Genomic and proteomic analysis of mitochondrial carrier proteins in Arabidopsis[J].Plant Physiol,2003,131:443-453.
[34] Heazlewood J L,Tonti-Filippini J S,Gout A M,et al.Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components,provides assessment of targeting prediction programs and points to plant specific mitochondrial proteins[J].Plant Cell,2004,16:241-256.
[35] Bae M S,Cho E J,Choi E Y,et al.Analysis of the Arabidopsis nuclear proteome and its response to cold stress[J].Plant J,2003,36:652-663.
[36] Calikowski T T,Meulia T,Meier I.A proteomic study of the Arabidopsis nuclear matrix[J].J Cell Biochem,2003,90:361-378.
[37] Pendle A F,Clark G P,Boon R,et al.Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions[J].Mol Biol Cell,2005,16:260-269.
[38] Fukao Y,Hayashi M,Nishimura M.Proteomic analysis of leaf peroxisomal proteins in greening cotyledons of Arabidopsis thaliana[J].Plant Cell Physiol,2002,43:689-696.
[39] Fukao Y,Hayashi M,Hara_Nishimura I,et al.Novel glyoxysomal protein kinase,GPK1,identified by proteomic analysis of glyoxysomes in etiolated cotyledons of Arabidopsis thaliana[J].Plant Cell Physiol,2003,44:1002-1012.
[40] Mano S,Nishimura M.Plant peroxisomes[J].Vitam Horm,2005,72:111-154.
[41] Alexandersson E,Saalbach G,Larsson C,et al.Arabidopsis plasma membrane proteomics identifies components of transport,signal transduction andmembrane trafficking[J].Plant Cell Physiol,2004,45:1543-1556.
[42] Haslam R P,Downie A L,Raveton M,et al.The assessment of enriched apoplastic extracts using proteomic approaches[J].Ann Appl Biol,2003,143:81-91.
[43] Joshua L Heazlewood,Julian Tonti-Filippini,Robert E.Verboom,et al.Combining Experimental and Predicted Datasets for Determination of the Subcellular Location of Proteins in Arabidopsis[J].Plant Physiology,2005,139:598-609.
[44] Heijnen H F,Waaijenborg S,Crapo J D,et al.Colocalization of eNOS and the catalytic subunit of PKA in endothelial cell junctions:a clue for regulated NO production[J].J Histochem Cytochem,2004,52(10):1277-1285.
[45] Voss T C,Demarco I A,Day R N.Quantitative imaging of protein interactions in the cell nucleus[J].Biotechniques.2005,38(3):413-424.

Please choose a citation manager

Content to export