Comprehensive proteome analysis using quantitative proteomic technologies
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With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS),and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.
Abstract
With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS),and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.
참고문헌 (51)
- Aghaei K, "Proteome analysis of soybean hypocotyl and root under salt stress", Amino acids, 36, pp.91~98 (2009)
- Anderson OD, "The characterization and comparative analysis of high-molecular-weight glutenin genes from genomes A and B of a hexaploid bread wheat", Theor Appl Genet, 77, pp.689~700 (1989)
- Anderson OD, "Nucleotide sequences of the two high-molecular weight glutenin genes from the D-genome of a hexaploid bread wheat, Triticum aestivum L. cv Cheyenne", Nucleic Acids Res, 17, pp.461~462 (1989)
- Bardi JS, "Scientists Identify Thousands of Proteins Associated with the Deadliest Form of Malaria", The scripps research institute, 2, pp.29~
- Bietz JA, "Wheat gluten subunits: Molecular weights determined by sodium sulfate-polyacrylamide gel electrophoresis", Cereal Chem, 49, pp.416~430 (1972)
- Butow BJ, "Molecular discrimination of Bx7 alleles demonstrates that a highly expressed high-molecularweight glutenin allele has a major impact on wheat flour dough strength", Theor Appl Genet, 107, pp.1524~1532 (2003)
- Choi JS, "Proteome analysis of light-induced proteins in Synechocystis sp. PCC 6803: Identification of proteins separated by 2D-PAGE using N-terminal sequencing and MALDI-TOF-MS", Mol Cells, 10, pp.705~711 (2000)
- D’Amici GM, "Separation of Thylakoid Membrane proteins by Sucrose Gradient Ultracentrifuge or Blue Native-SDS-PAGE Two-Dimensional Electrophoresis", Membrane Proteomics:methods and protocols, 528, pp.61~70 (2009)
- DeRisi JL, "Exploring the metabolic and genetic control of gene expression in a genomic scale", Science, 278, pp.680~686 (1997)
- Edman P, "A method for the determination of the amino acid sequence in peptides", Arch Biochem, 22, pp.475~476 (1949)
- Fields S, "Proteomics. Proteomics in genomeland", Science, 291, pp.1221~1224 (2001)
- Gooley AA, "A role of Edman degradation in proteome studies", Electrophoresis, 18, pp.1068~1072 (1997)
- Görg A, "Approach to staionary two-dimensional pattern: influence of focusing time and immbiline", carrier ampholytes concentrations, 1988, pp.9, 37~46
- Gygi SP, "Quantitative analysis of complex protein mixtures using isotope-coded affinity tags", Nature Biotech, 17, pp.994~999 (1999)
- Gygi SP, "Aebersold R (1999b) Correlation between protein and mRNA abundance in yeast", Mol Cell Biol, 19, pp.1720~1730 (1999)
- Haezewood JL, "Towards an analysis of the rive mitochondrial proteome", Plant physiol, 132, pp.230~242 (2003)
- Hansen KC, "Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotopecoded affinity tag and multidimensional chromatography", Mol Cell Proteomics, 2, pp.299~314 (2003)
- Hoogland C, "Two-dimensional electrophoresis resources available from ExPASy", Electrophoresis, 20, pp.3568~3571 (1999)
- Hunter T, "Protein kinases and posphatases: the yin and yang of protein phosphorylation and signaling", Cell, 80, pp.225~236 (1995)
- Islam N, "Exploring protein–protein interactions in wheat proteome by manipulating genome composition: a perspective", J Electrophoresis, 47, pp.33~42 (2003)
- Issaq HJ, "The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification", Biochem Biophys Res Commun, 292, pp.587~592 (2002)
- Jonas K, "Protein complexes of the plant plasma membrane resolved by Blue Native PAGE", Physiol Plantarum, 121, pp.546~555 (2004)
- Kamal AHM, "Proteomics profile of pre-harvest sprouting wheat by using MALDI-TOF Mass Spectrometry", Plant Omics J, 2, pp.110~119 (2009)
- Abu Hena Mostafa Kamal, "Diversity of Novel Glutenin Subunits in Bread Wheat (Triticum aestivum L.)", Journal of Plant Biology(한국식물학회지), 52(6), pp.533~542 (2009), 한국식물학회
- Abu Hena Mostafa Kamal, "Proteomics Approach on Puroindoline Gene of Pre-harvest Sprouting Wheat", 한국육종학회지, 41(3), pp.205~212 (2009), 한국육종학회
- Kaufmann H, "Use of antibodies for detection of phosphorylated proteins separated by twodimensional gel electrophoresis", Proteomics, 1, pp.194~199 (2001)
- Kislinger T, "Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling", Cell, 125, pp.173~186 (2006)
- Klose J, "Protein mapping by combined isoelectric focusing and electrophoresis in mouse tissues. A novel approach to testing for induced point mutations in mammals", Humangenetik, 26, pp.231~243 (1975)
- Lewis TS, "Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry", Mol Cell, 6, pp.1343~1354 (2000)
- MacCoss MJ, "Shotgun identification of protein modifications from protein complexes and lens tissue", Proc Nat’l Acad Sci USA, 통권 : 99, pp.7900~7905 (2002)
- O`Farrell PH, "High resolution two-dimensional electrophoresis of proteins", J Biol Chem, 250, pp.4007~4021 (1975)
- Ong SE, "Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics", Mol Cell Proteomics, 1, pp.376~386 (2002)
- Pappin DJ, "Rapid identification of proteins by peptide-mass fingerprinting", Curr Biol, 3, pp.327~332 (1993)
- Payne PI, "Correlation between the inheritance of certain high-molecular-weight subunits of glutenin and bread making quality in progenies of six crosses of bread wheat", J Sci Food Agric, 32, pp.51~60 (1981)
- Peltier JB, "Proteomics of the chloroplast: Systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins", Plant Cell, 12, pp.319~342 (2000)
- Peng Z, "Aproteomics study of the response to salinity and drought stress in an introgression strain of bread wheat", Mol Cell Proteomics, 8, pp.2676~2686 (2009)
- Rakwal R, "Rice proteomics: current status and future perspectives", Electrophoresis, 24, pp.3378~3389 (2003)
- Ross PL, "Multiplexed protein quantitation in Saccharomyces cervisiae using amine-reactive isobaric tagging reagents", Mol Cell Proteomics, 3, pp.1154~1169 (2004)
- Schlessinger J, "Cellular signaling by receptor tyrosine kinases", Harvey Lect, 89, pp.105~123 (1993)
- Schützendübel A, "Plant responses to abiotic stresses:heavy metal-induced oxidative stress and protection by mycorrhization", J Exp Bot, 53, pp.1351~1365 (2002)
- Skylas DJ, "Proteomics of wheat grain", Cereal Sci, 41, pp.165~179 (2005)
- The C. elegans Sequencing Consortium, "Genome sequence of the nematode Caenorhabditis elegans. A platform for investigating biology", Science, 282, pp.2012~2018 (1998)
- Thiellement H, "Combining proteomic and genetic studies in plants", J Chromatogr B Analyt Technol Biomed Life Sci, 782, pp.137~149 (2002)
- Unlu M, "Difference gel electrophoresis:a single gel method for detecting changes in protein extracts", Electrophoresis, 18, pp.2071~2077 (1997)
- van Wijk KJ, "Challenges and prospects of plant proteomics", Plant Physiol, 126, pp.501~508 (2001)
- Venter JC, "The sequence of the human genome", Science, 291, pp.1304~1351 (2001)
- Wang Y, "Differential proteomic analysis of proteins in wheat spikes induced by Fusarium graminearum", Proteomics, 5, pp.4496~4503 (2005)
- Washburn MP, "Large-scale analysis of the yeast proteome by multidimensional protein identification technology", Nat Biotechnol, 19, pp.242~247 (2001)
- Wilkins MR, "Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it", Biotechnol Genet Eng Rev, 13, pp.19~50 (1996)
- Woo SH, "Efficient peptide mapping and its application to identification of embryo proteins in the rice proteome analysis", Electrophoresis, 23, pp.647~654 (2002)
- Woo SH, "Proteome analysis of wheat lemma", Biosci Biotechnol Biochem, 67, pp.2486~2491 (2003)