Genetic variability of proteome expression and metabolic control

Plant Physiology and Biochemistry - Tập 39 - Trang 271-283 - 2001
Dominique de Vienne1, Bruno Bost2, Julie Fiévet1, Michel Zivy1, Christine Dillmann1
1Station de génétique végétale, Inra/University Paris XI/INA PG, Ferme du Moulon, 91190 Gif-sur-Yvette, France
2Institut de génétique et microbiologique, University Paris XI, 91405 Orsay cedex, France

Tài liệu tham khảo

Albe, 1990, Cellular concentrations of enzymes and their substrates, J. Theor. Biol., 143, 163, 10.1016/S0022-5193(05)80266-8 Atkinson, 1969, Limitation of metabolite concentrations and the conservation of solvent capacity in living cells, Curr. Top. Cell. Regul., 1, 29, 10.1016/B978-0-12-152801-0.50007-9 Bahrman, 1995, Genetic polymorphism in maritime pine (Pinus pinaster Ait.) assessed by two-dimensional gel electrophoresis of needle, bud and pollen proteins, J. Mol. Evol., 41, 231, 10.1007/BF00170677 Bahrman, 1985, Two-dimensional gel electrophoresis of proteins for genetic studies in Douglas fir (Pseudotsuga menziesii), Biochem. Genet., 23, 247, 10.1007/BF00504322 Bailey, 2000, Control of C4 photosynthesis: effects of reduced activities of PEPC on CO2 assimilation in Amaranthus edulis L., J. Exp. Bot., 51, 339, 10.1093/jexbot/51.suppl_1.339 Bhattacharyya, 1990, The wrinkled seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme, Cell, 60, 115, 10.1016/0092-8674(90)90721-P Boon Chock, 1980, Interconvertible enzyme cascades in cellular regulation, Ann. Rev. Biochem., 49, 813, 10.1146/annurev.bi.49.070180.004121 Burness, 1999, Allometric scaling of RNA, DNA, and enzyme levels: an intraspecific study, Am. J. Physiol., 277, R1164 Burstin, 1994, Molecular markers and protein quantities as genetic descriptors in maize, Theor. Appl. Genet., 89, 943, 10.1007/BF00224522 Burstin, 1993, Analysis of scaling methods to minimize the experimental variations in 2-D PAGE quantitative data. Application to the comparison of maize inbred lines, Electrophoresis, 14, 1067, 10.1002/elps.11501401170 Canel, 1998, Effects of over-expression of strictosidine synthase and tryptophan decarboxylase on alkaloid production by cell cultures of Catharanthus roseus, Planta, 205, 414, 10.1007/s004250050338 Cornish-Bowden, 1995, Strategies for manipulating metabolic fluxes in biotechnology, Bioorg. Chem., 23, 439, 10.1006/bioo.1995.1030 Costa, 1999, Genetic analysis of needle proteins in Maritime Pine. 2. Variations in protein accumulation, Silvae Genet., 48, 146 Damerval, 1994, Quantification of silver-stained proteins resolved by two-dimensional electrophoresis: genetic variability as related to abundance and solubility in two maize lines, Electrophoresis, 15, 1573, 10.1002/elps.11501501226 Damerval, 1998, Characterization of novel proteins affected by the o2 mutation and expressed during maize endosperm development, Mol. Gen. Genet., 257, 354, 10.1007/s004380050657 Damerval, 1994, Quantitative trait loci underlying gene product variation - a novel perspective for analyzing regulation of genome expression, Genetics, 137, 289, 10.1093/genetics/137.1.289 de Vienne, 1990, Comparison of leaflets and tendrils in wildtype and homeotic mutant morphs of pea by two-dimensional electrophoresis of proteins, J. Her, 81, 117 de Vienne, 1988, Genetic aspects of variation of protein amounts in maize and pea, Electrophoresis, 9, 742, 10.1002/elps.1150091110 de Vienne, 1996, Two-dimensional electrophoresis of proteins as a source of monogenic and codominant markers for population genetics and mapping the expressed genome, Heredity, 76, 166, 10.1038/hdy.1996.24 de Vienne, 1999, Genetics of proteome variation for QTL characterization: application to drought-stress responses in maize, J. Exp. Bot., 50, 303, 10.1093/jexbot/50.332.303 Dieuaide-Noubhani, 1995, Quantification of compartmented metabolic fluxes in maize root tips using isotope distribution from 13C- or 14C-labeled glucose, J. Biol. Chem., 270, 13147, 10.1074/jbc.270.22.13147 Dong, 1995, Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction, J. Bacteriol., 177, 1497, 10.1128/jb.177.6.1497-1504.1995 Droux, 1998, Interactions between serine acetyltransferase and O-acetylserine (thiol) lyase in higher plants – structural and kinetic properties of the free and bound enzymes, Eur. J. Biochem., 255, 235, 10.1046/j.1432-1327.1998.2550235.x Fell, 1992, Metabolic control analysis: a survey of its theoretical and experimental background, Biochem. J., 286, 313, 10.1042/bj2860313 Fiehn, 2000, Metabolite profiling for plant functional genomics, Nature Biotech., 18, 1157, 10.1038/81137 Gauss, 1999, Analysis of mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation, Electrophoresis, 20, 575, 10.1002/(SICI)1522-2683(19990301)20:3<575::AID-ELPS575>3.0.CO;2-3 Geldermann, 1975, Investigations on inheritance of quantitative characters in animals by gene markers I, Theor. Appl. Genet., 46, 319, 10.1007/BF00281673 Gerber, 1998, Relation between protein markers and quantitative traits in maritime pine (Pinus pinaster AIT), Silvae Genet., 46, 286 Giersch, 1995, Determining elasticities from multiple measurements of flux rates and metabolite concentrations. Application of the multiple modulation method to a reconstituted pathway, Eur. J. Biochem., 227, 194, 10.1111/j.1432-1033.1995.tb20376.x Goldman, 1987, A molecular phylogeny of the hominoid primates as indicated by two-dimensional protein electrophoresis, Proc. Natl. Acad. Sci. USA, 84, 3307, 10.1073/pnas.84.10.3307 Gottlieb, 1988, Assessment of pleiotropic effects of a gene substitution in Pea by two-dimensional polyacrylamide gel electrophoresis, Genetics, 119, 705, 10.1093/genetics/119.3.705 Hardie, 1999, Plant protein serine/threonine kinases: classification and functions, Annu. Rev. Plant Physiol. Plant Mol. Biol., 50, 97, 10.1146/annurev.arplant.50.1.97 Hauf, 2000, Simultaneous genomic overexpression of seven glycolytic enzymes in the yeast Saccharomyces cerevisiae, Enzyme Microb. Technol., 26, 688, 10.1016/S0141-0229(00)00160-5 Heinrich, 1974, A linear steady-state treatment of enzymatic chains. General properties, control and effector strength, Eur. J. Biochem., 42, 89, 10.1111/j.1432-1033.1974.tb03318.x Heinrich, 1991, Mathematical analysis of enzymic reaction systems using optimization principles, Eur. J. Biochem., 201, 1, 10.1111/j.1432-1033.1991.tb16251.x Herbik, 1996, Iron and copper nutrition-dependent changes in protein expression in a tomato wild type and the nicotianamine-free mutant chloronerva, Plant Physiol., 111, 533, 10.1104/pp.111.2.533 Higginbotham, 1991, Quantitative analysis of two-dimensional protein profiles of inbred lines of maize (Zea mays L.), Electrophoresis, 12, 425, 10.1002/elps.1150120608 Hunter, 1987, A thousand and one protein kinases, Cell, 50, 823, 10.1016/0092-8674(87)90509-5 Jones, 1986, Intracellular diffusion gradients of oxygen and ATP, Am. J. Physiol., 250, 663, 10.1152/ajpcell.1986.250.5.C663 Jorgensen, 1995, Genetic analysis of heat-shock proteins in maize, Theor. Appl. Genet., 91, 38, 10.1007/BF00220856 Kacser, 1973, The control of flux, Symp. Soc. Exp. Biol., 27, 65 Kacser, 1981, The molecular basis of dominance, Genetics, 97, 639, 10.1093/genetics/97.3-4.639 Klose, 1975, Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals, Humangenetik, 26, 231, 10.1007/BF00281458 Klose, 1982, Genetic variability of soluble proteins studied by two-dimensional electrophoresis on different inbred mouse strains and on different mouse organs, J. Mol. Evol., 18, 315, 10.1007/BF01733898 Klose, 1981, Genetic variability of proteins from plasma membranes and cytosols of mouse organs, Biochem. Genet., 19, 859, 10.1007/BF00504251 Koehn, 1991, The cost of enzyme synthesis in the genetics of energy balance and physiological performance, Biol. J. Lin. Soc., 44, 231, 10.1111/j.1095-8312.1991.tb00618.x Leonardi, 1988, Organ specific variability and inheritance of maize proteins revealed by two-dimensional electrophoresis, Genet. Res. Camb., 52, 97, 10.1017/S0016672300027464 Leonardi, 1991, Association of protein amount polymorphism (PAP) among maize lines with performance of their hybrids, Theor. Appl. Genet., 82, 552, 10.1007/BF00226790 Leymarie, 1996, Two-dimensional protein patterns of Arabidopsis wild-type and auxin insensitive mutants, axr1, axr2, reveal interactions between drought and hormonal responses, Plant Cell Physiol., 37, 966, 10.1093/oxfordjournals.pcp.a029046 McConkey, 1982, Molecular evolution, intracellular organization, and the quinary structure of proteins, Proc. Natl. Acad. Sci. USA, 79, 3236, 10.1073/pnas.79.10.3236 Müller, 1986, Quantification of ATP-producing and consuming process of Ehrlich ascites tumour cells, Eur. J. Biochem., 161, 701, 10.1111/j.1432-1033.1986.tb10496.x Niederberger, 1992, A strategy for increasing an in vivo flux by genetic manipulations. The tryptophane system of yeast, Biochem. J., 287, 473, 10.1042/bj2870473 Norbeck, 1997, Two-dimensional electrophoretic separation of yeast proteins using a non-linear wide range (pH 3-10) immobilized pH gradient in the first dimension; reproducibility and evidence for isoelectric focusing of alkaline (pI > 7) proteins, Yeast, 13, 1519, 10.1002/(SICI)1097-0061(199712)13:16<1519::AID-YEA211>3.0.CO;2-U O'Farrell, 1975, High resolution two-dimensional electrophoresis of proteins, J. Biol. Chem., 250, 4007, 10.1016/S0021-9258(19)41496-8 Pandey, 2000, Proteomics to study genes and genomes, Nature, 405, 837, 10.1038/35015709 Puigjaner, 1997, Comparison of control analysis data using different approaches: modelling and experiments with muscle extract, FEBS Lett., 418, 47, 10.1016/S0014-5793(97)01347-1 Quick, 1992, Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with ‘antisense’ rbcS. IV. Impact on photosynthesis in conditions of altered nitrogen supply, Planta, 188, 522, 10.1007/BF00197044 Ramagopal, 1990, Protein polymorphism in sugarcane revealed by two-dimensional gel analysis, Theor. Appl. Genet., 79, 297, 10.1007/BF01186071 Riccardi, 1998, Protein changes in response to progressive water deficit in maize: quantitative variations and polypeptide identification, Plant Physiology, 117, 1253, 10.1104/pp.117.4.1253 Santoni, 1997, A comparison of two-dimensional electrophoresis data with phenotypical traits in Arabidopsis leads to the identification of a mutant (cri1) that accumulates cytokinins, Planta, 202, 62, 10.1007/s004250050103 Schellenberger, 1981, Selforganization of a glycolytic reconstituted enzyme system: alternate stable stationary states, hysteretic transitions and stabilization of the energy charge, Adv. Enzyme Regul., 18, 257, 10.1016/0065-2571(81)90019-4 Schmidt, 1990, Nucleotide Maize regulatory gene opaque-2 encodes a protein with a ‘leucine-zipper' motif that binds to zein DNA, Proc. Natl. Acad. Sci. USA, 87, 46, 10.1073/pnas.87.1.46 Siems, 1984, Accounting for the ATP-consuming processes in rabbit reticulocytes, Eur. J. Biochem., 139, 101, 10.1111/j.1432-1033.1984.tb07982.x Singh, 1982, Genic variation in abundant soluble proteins of Drosophila melanogaster and Drosophila pseudoobscura, Genetics, 102, 437, 10.1093/genetics/102.3.437 Smits, 2000, Simultaneous overexpression of enzymes of the lower part of glycolysis can enhance the fermentative capacity of Saccharomyces cerevisiae, Yeast, 16, 1325, 10.1002/1097-0061(200010)16:14<1325::AID-YEA627>3.0.CO;2-E Snoep, 1995, Protein burden in Zymomonas mobilis: negative flux and growth control due to overproduction of glycolytic enzymes, Microbiology, 141, 2329, 10.1099/13500872-141-9-2329 Soller, 1976, On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines, Theor. Appl. Genet., 47, 35, 10.1007/BF00277402 Suarez, 1996, Upper limits to mass-specific metabolic rates, Annu. Rev. Physiol., 58, 583, 10.1146/annurev.ph.58.030196.003055 Thiellement, 1999, Proteomics for genetical and physiological studies in plants, Electrophoresis, 20, 2013, 10.1002/(SICI)1522-2683(19990701)20:10<2013::AID-ELPS2013>3.0.CO;2-# Touzet, 1996, Amino acid analysis of proteins separated by two-dimensional electrophoresis in maize: isoform detection and function identification, Electrophoresis, 17, 1393, 10.1002/elps.1150170819 Touzet, 1996, The maize two-dimensional gel protein database: towards an integrated genome analysis program, Theoret. Appl. Genet., 93, 997, 10.1007/BF00224104 Tretheway, 1999, Metabolic profiling: a Rosetta stone for genomics?, Curr. Opin. Plant Biol., 2, 83, 10.1016/S1369-5266(99)80017-X Vind, 1993, Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels, J. Mol. Biol., 231, 678, 10.1006/jmbi.1993.1319 Wasinger, 1995, Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium, Electrophoresis, 16, 1090, 10.1002/elps.11501601185 Waterlow, 1984, Protein turnover with special reference to man, Q. J. Expl. Physiol., 69, 409, 10.1113/expphysiol.1984.sp002829 Welle, 1990, Relationship of resting metabolic rate to body composition and protein turnover, Am. J. Physiol., 258, E990 Wilkins, 1996, From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis, Biotechnol. Genet. Eng. Rev., 13, 19, 10.1080/02648725.1996.10647923 Zivy, 2000, Proteomics: a link between genomics, genetics and physiology, Plant Mol. Biol., 44, 575, 10.1023/A:1026525406953 Zivy, 1983, Study on nuclear and cytoplasmic genome expression in wheat by two-dimensional gel electrophoresis. 1. First results on 18 alloplasmic lines, Theor. Appl. Genet., 66, 1, 10.1007/BF00281838 Zivy, 1984, Study on nuclear and cytoplasmic genome expression in wheat by two-dimensional gel electrophoresis. 2. Genetic differences between two lines and two groups of cytoplasms at five developmental stages or organs, Theor. Appl. Genet., 68, 335, 10.1007/BF00267887 Zuckerkandl, 1986, Quantitative protein profiling: determining lexotypes, J. Theor. Biol., 121, 185, 10.1016/S0022-5193(86)80092-3