Proteomics for genetic and physiological studies in plants

Proteomics is becoming a necessity in plant biology, as it is in medicine, zoology and microbiology, for deciphering the function and role of the genes that are or will be sequenced. In this review we focus on the various, mainly genetic, applications of the proteomic tools that have been developed in recent years: characterization of individuals or lines, estimation of genetic variability within and between populations, establishment of genetic distances that can be used in phylogenetic studies, characterization of mutants and localization of the genes encoding the revealed proteins. Improvements in specifically devoted software have permitted precise quantification of the variation in amounts of proteins, leading to the concept of “protein quantity loci” which, combined with the “quantitative trait loci” approach, results in testable hypotheses regarding the role of “candidate proteins” in the metabolism or phenotype under study. This new development is exemplified by the reaction of plants to drought, a trait of major agronomic interest. The accumulation of data regarding genomic and cDNA sequencing will be connected to the protein databases currently developed in plants.

[1]  A. Görg,et al.  Genetic variability of pepper (Capsicum annuum L.) seed proteins studied by 2‐D electrophoresis with immobilized pH gradients , 1992, Electrophoresis.

[2]  P Dupree,et al.  Use of a proteome strategy for tagging proteins present at the plasma membrane. , 1998, The Plant journal : for cell and molecular biology.

[3]  A. Görg,et al.  Genetic variability of carrot seed proteins analyzed by one‐ and two‐dimensional electrophoresis with immobilized pH gradients , 1995, Electrophoresis.

[4]  N. Iusem,et al.  Tomato (Lycopersicon esculentum) Transcript Induced by Water Deficit and Ripening , 1993, Plant physiology.

[5]  D. Rouquié,et al.  Construction of a directory of tobacco plasma membrane proteins by combined two‐dimensional gel electrophoresis and protein sequencing , 1997, Electrophoresis.

[6]  P. O’Farrell.  High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[7]  N. Bahrman,et al.  Linkage relationships of loci controlling protein amounts in maritime pine (Pinus pinaster Ait.) , 1989, Heredity.

[8]  A. Görg,et al.  Two–dimensional polyacrylamide gel electrophoresis, with immobilized pH gradients in the first dimension, of barley seed proteins: Discrimination of cultivars with different malting grades , 1992, Electrophoresis.

[9]  R. Nowak.  Entering the Postgenome Era , 1995, Science.

[10]  N. Bahrman,et al.  Variability of 3 cytoplasmically encoded proteins in the Triticum genus , 1988, Heredity.

[11]  M. Caboche,et al.  The PASTICCINO genes of Arabidopsis thaliana are involved in the control of cell division and differentiation. , 1998, Development.

[12]  A. Görg,et al.  Two‐dimensional electrophoresis with immobilized pH gradients of leaf proteins from barley (Hordeum vulgare): Method, reproducibility and genetic aspects , 1988, Electrophoresis.

[13]  D. Hochstrasser,et al.  Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. , 1996, Biotechnology & genetic engineering reviews.

[14]  C. Damerval,et al.  Characterization of novel proteins affected by the o2 mutation and expressed during maize endosperm development , 1998, Molecular and General Genetics MGG.

[15]  N. Anderson,et al.  Two-Dimensional Electrophoretic Analysis of Wheat Seed Proteins 1 , 1985 .

[16]  A. Tsugita,et al.  Two‐dimensional electrophoresis of plant proteins and standardization of gel patterns , 1996, Electrophoresis.

[17]  M. Van Montagu,et al.  Molecular and Physiological Responses to Abscisic Acid and Salts in Roots of Salt-Sensitive and Salt-Tolerant Indica Rice Varieties , 1995, Plant physiology.

[18]  J. Giraudat,et al.  A Brassica napus transcript encoding a protein related to the Künitz protease inhibitor family accumulates upon water stress in leaves, not in seeds. , 1992, The Plant journal : for cell and molecular biology.

[19]  T. Sasahara,et al.  Variations in glutelin and high molecular weight endosperm proteins among subspecies of rice (Oryza sativa L.) detected by two-dimensional gel electrophoresis. , 1996, Genes & genetic systems.

[20]  B. Burr,et al.  Maize regulatory gene opaque-2 encodes a protein with a "leucine-zipper" motif that binds to zein DNA. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Distance indices in a comparison between the A, D, I and R genomes of the Triticeae tribe , 1995, Electrophoresis.

[22]  Philippe Picard,et al.  Potential of two‐dimensional electrophoresis in routine identification of closely related durum wheat lines , 1997, Electrophoresis.

[23]  J. David,et al.  Protein evolution in dynamically managed populations of wheat: adaptive responses to macro-environmental conditions , 1997, Theoretical and Applied Genetics.

[24]  M. Kearsey,et al.  QTL analysis in plants; where are we now? , 1998, Heredity.

[25]  S. Lin,et al.  A 300 kilobase interval genetic map of rice including 883 expressed sequences , 1994, Nature Genetics.

[26]  C. Adessi,et al.  Two‐dimensional electrophoresis of membrane proteins: A current challenge for immobilized pH gradients , 1997, Electrophoresis.

[27]  J. Josse,et al.  Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. , 1994, Genetics.

[28]  J. Wall,et al.  Improved Two-Dimensional Electrophoretic Separation of Zein Proteins: Application to Study of Zein Inheritance in Corn Genotypes , 1984 .

[29]  D. de Vienne,et al.  Assessment of pleiotropic effects of a gene substitution in pea by two-dimensional polyacrylamide gel electrophoresis. , 1988, Genetics.

[30]  C. Plomion,et al.  Genetic analysis of needle proteins in maritime pine. 1. Mapping dominant and codominant protein markers assayed on diploid tissue, in a haploid-based genetic map , 1997 .

[31]  D. de Vienne,et al.  Analysis of Leaf Proteins by Two-Dimensional Gel Electrophoresis: Protease Action as Exemplified by Ribulose Bisphosphate Carboxylase/ Oxygenase Degradation and Procedure to Avoid Proteolysis during Extraction. , 1985, Plant physiology.

[32]  J. Huet,et al.  Characterization of a Novel Protein Induced by Progressive or Rapid Drought and Salinity in Brassica napus Leaves. , 1992, Plant physiology.

[33]  H. Hirano.  Varietal differences of leaf protein profiles in mulberry , 1982 .

[34]  D. Rouquié,et al.  Four root plasmalemma polypeptides under-represented in the maize mutant ys1 accumulate in a Fe-efficient genotype in response to iron-deficiency , 1997 .

[35]  M. Caboche,et al.  A comparison of two-dimensional electrophoresis data with phenotypical traits in Arabidopsis leads to the identification of a mutant (cri1) that accumulates cytokinins , 1997, Planta.

[36]  M. Rossignol,et al.  Basic plasticity of protein expression in tobacco leaf plasma membrane , 1995 .

[37]  C. Durel,et al.  Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers , 1995, Heredity.

[38]  P. Rey,et al.  A novel thioredoxin-like protein located in the chloroplast is induced by water deficit in Solanum tuberosum L. plants. , 2002, The Plant journal : for cell and molecular biology.

[39]  D. Vienne,et al.  Inheritance of protein amounts: comparison of two-dimensional electrophoresis patterns of leaf sheaths of two maize lines ( Zea mays L.) and their hybrids , 1987 .

[40]  C. Damerval.  Quantification of silver‐stained proteins resolved by two‐dimensional electrophoresis: Genetic variability as related to abundance and solubility in two maize lines , 1994, Electrophoresis.

[41]  H. Greppin,et al.  Analysis of leaf proteins in late flowering mutants of Arabidopsis thaliana , 1995 .

[42]  M. Bon.  A two‐dimensional electrophoresis procedure for single meristems of different forest species , 1989, Electrophoresis.

[43]  Finn Larsen,et al.  The value of parallel analysis of uni- and bi-parental inherited loci: the North Atlantic humpback whale (Megaptera novaeangliae) , 1998 .

[44]  N. Bahrman,et al.  Comparison of genetic differentiation in maritime pine (Pinus pinaster Ait.) estimated using isozyme, total protein and terpenic loci , 1995, Heredity.

[45]  A. Leone,et al.  Comparative Analysis of Short- and Long-Term Changes in Gene Expression Caused by Low Water Potential in Potato (Solanum tuberosum) Cell-Suspension Cultures , 1994, Plant physiology.

[46]  T. Sasaki,et al.  Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. , 1994, The Plant journal : for cell and molecular biology.

[47]  F Quigley,et al.  Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. , 1996, The Plant journal : for cell and molecular biology.

[48]  I. Humphery-Smith,et al.  Proteomic ‘contigs’ of Ochrobactrum anthropi, application of extensive pH gradients , 1997, Electrophoresis.

[49]  G. Galili,et al.  Intergenomic suppression of endosperm protein genes in common wheat , 1984 .

[50]  A. Tsugita,et al.  Separation and characterization of Arabidopsis thaliana proteins by two‐dimensional gel electrophoresis , 1995, Electrophoresis.

[51]  M. Zivy,et al.  Technical improvements in two‐dimensional electrophoresis increase the level of genetic variation detected in wheat‐seedling proteins , 1986 .

[52]  T. Helentjaris,et al.  Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. , 1988, Genetics.

[53]  M. Zivy,et al.  Protein changes in response to progressive water deficit in maize . Quantitative variation and polypeptide identification , 1998, Plant physiology.

[54]  R. Sederoff,et al.  Analysis of xylem formation in pine by cDNA sequencing. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[55]  A. Görg,et al.  Identification and characterization of wheat grain albumin/globulin allergens , 1997, Electrophoresis.

[56]  G. Hagen,et al.  Two-dimensional gel analysis of the zein proteins in maize. , 1980 .

[57]  W. Blackstock,et al.  Proteome research: Complementarity and limitations with respect to the RNA and DNA worlds , 1997, Electrophoresis.

[58]  U. W. Stephan,et al.  Iron and Copper Nutrition-Dependent Changes in Protein Expression in a Tomato Wild Type and the Nicotianamine-Free Mutant chloronerva , 1996, Plant physiology.

[59]  M. Zivy,et al.  Characterizing allelic proteins for genome mapping in maize , 1995, Electrophoresis.

[60]  J. Burstin,et al.  Two-dimensional electrophoresis of proteins as a source of monogenic and codominant markers for population genetics and mapping the expressed genome , 1996, Heredity.

[61]  J. Leymarie,et al.  Two-dimensional protein patterns of Arabidopsis wild-type and auxin insensitive mutants, axr1, axr2, reveal interactions between drought and hormonal responses. , 1996, Plant & cell physiology.

[62]  S. Apte,et al.  Transient expression of multiple genes in salinity-stressed young seedlings of rice (Oryza sativa L.) cv. bura rata. , 1997, Biochemical and biophysical research communications.

[63]  L. C. Loon,et al.  Two-dimensional gel electrophoretic analysis of chromatin-associated proteins from leaves of different species and varieties of Nicotiana , 1985 .

[64]  D. de Vienne,et al.  Genetic aspects of variation of protein amounts in maize and pea , 1988, Electrophoresis.

[65]  A. Görg,et al.  Polymorphism of pepper (Capsicum annuum L.) seed proteins studied by two‐dimensional electrophoresis with immobilized pH gradients: Methodical and genetic aspects , 1994, Electrophoresis.

[66]  G. Foster,et al.  Plant gene isolation: principles and practice. , 1996 .

[67]  N. Bahrman,et al.  Genetic relationships in the Sitopsis section of Triticum and the origin of the B genome of polyploid wheats , 1988, Heredity.

[68]  James L. Winkler,et al.  Accessing Genetic Information with High-Density DNA Arrays , 1996, Science.

[69]  A. Mirzabekov,et al.  DNA analysis and diagnostics on oligonucleotide microchips. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[70]  C. Baysdorfer,et al.  Partial Sequence Analysis of 130 Randomly Selected Maize cDNA Clones , 1993, Plant physiology.

[71]  I. Humphery-Smith,et al.  ‘Proteomic contigs’ of Mycobacterium tuberculosis and Mycobacterium bovis (BCG) using novel immobilised pH gradients , 1997, Electrophoresis.

[72]  H. Hirano,et al.  Analysis of adzuki bean seed protein by partial amino acid sequencing of polypeptide separated on two-dimensional gel , 1992 .

[73]  E. Lander,et al.  Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. , 1989, Genetics.

[74]  D. Rouquié,et al.  New zwitterionic detergents improve the analysis of membrane proteins by two‐dimensional electrophoresis , 1998, Electrophoresis.

[75]  D. Rouquié,et al.  Towards the recovery of hydrophobic proteins on two‐dimensional electrophoresis gels , 1999, Electrophoresis.

[76]  A Tsugita,et al.  Separation and characterization of rice proteins , 1994, Electrophoresis.

[77]  Separation and characterization of needle and xylem maritime pine proteins , 1999, Electrophoresis.

[78]  E. Pennisi.  From Genes to Genome Biology , 1996, Science.

[79]  C. Damerval,et al.  Quantification of dominance for proteins pleiotropically affected by opaque-2 in maize , 1993, Heredity.