Genetic variability of pepper (Capsicum annuum L.) seed proteins studied by 2-D electrophoresis with immobilized pH gradients

Combining proteomic and genetic studies in plants

Plant proteomics is still in its infancy, although numerous experiments have been undertaken since the end of the 1970s. In this review we focus on the interactions between proteomics and genetics. A given genome can express various proteomes according to differentiation, development, tissues, cells and subcellular compartments, and proteomes are modified in function of biotic and abiotic environment. These different proteomes and the way they respond to environment can be compared between genotypes, allowing the characterization of mutants or lines, the study of mutation pleiotropic effects, the genetic mapping of expressed genes. These comparisons also permit to hypothesize for "candidate proteins" that might be involved in the genetic variation of traits of economic or agronomic interest.

Quantitative analysis of two-dimensional gel electrophoresis protein patterns: a method for studying genetic relationships among Globodera pallida populations

A method based in two-dimensional protein gel electrophoresis has been developed in order to improve the analysis of genetic relationships among populations of Globodera. It has been used to estimate genetic divergence among nine Globodera pallida nematode populations. Sixty-one anonymous polypeptide spots were resolved using silver-stained high-resolution 2D gels and they were quantified in each population to establish genetic variation among G. pallida populations. The results of this analysis were compared with those obtained after a study of allelic frequency variation, which was carried out using seven previously described loci. Genetic distances among populations were calculated by means of both studies, the quantitative analysis and the allelic frequency variation, and phylogenetic trees were constructed for each type of analysis. A correlation analysis between the two distance matrices was carried out and a bootstrap analysis was performed to determine the strength of the clusters obtained with each method. The results obtained support the idea that quantitative protein analysis can be successfully applied to phylogenetic analysis of G. pallida populations.

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.

Isoelectric focusing in the vegetable seed industry

Different types of electrophoretic procedures were developed for hybrid purity testing based on starch gel electrophoresis (SGE), vertical polyacrylamide gel electrophoresis (PAGE), and isoelectric focusing (IEF). For the most important vegetables these methods are much faster than plant grow-outs and relatively inexpensive. Compared to SGE and PAGE methods, horizontal IEF proved to be more efficient for large-scale hybrid purity testing. These developments were made possible by the basic work of Harry Rilbe and improvements that were initiated as a result of Rilbe's work. The present paper describes a number of milestones during this developmental period, starting with the isoelectric focusing concept of Harry Rilbe up to the large-scale application of IEF. Further, a comparison of IEF with DNA fingerprinting methods along with the future of both techniques is discussed with respect to hybrid purity testing in the vegetable seed industry. When it comes to a choice between the use of either IEF or a DNA-based method, efficiency and efficacy determines the method which is best suited for hybrid purity testing. It is also concluded that in the future we will see an increased use of both IEF as well as DNA-based methods for hybrid purity testing because expectations of growers has increased; consequently they will accept fewer inbreds in a hybrid variety, especially when growing in a greenhouse.

State of the art of large-scale genetic purity testing of hybrid vegetable seeds using isoelectric focusing at PetoSluis

During the past ten years we have been engaged in developing and applying isoelectric focusing techniques to test the genetic quality of vegetable seeds. We started with isoelectric focusing using carrier ampholytes (IEF-CA), and continued research with isoelectric focusing in immobilized pH gradients (IEF-IPG) and two-dimensional electrophoresis (IPG-DALT). In addition, we have developed equipment and procedures for large-scale seed and seedling homogenization, sample preparation and semi-automatic gel staining. Moreover, we have optimized the sample application and gel running setup for large-scale analysis. We have developed hybrid purity (inbred) testing methods for all important vegetables, e.g., melon, cole crops, tomato, pepper, watermelon, squash, cucumber, radish etc. using either IEF-CA or IEF-IPG of seed or seedling proteins, followed by specific or general protein staining. To indicate the efficiency of the equipment and procedures developed we present results of two of our hybrid purity test methods, namely for brassica using polymorphism for phosphoglucomutase (PGM) from dry seeds, and for tomato using polymorphism for alcohol dehydrogenase (ADH) from imbibed seeds. We show that one person can routinely analyze 1536 individual seeds per day at a cost of about US +0.11 per seed for chemicals, materials, and electrophoresis equipment.

Effects of cyclosporine A on the rat liver and kidney protein pattern, and the influence of vitamin E and C coadministration

The effects of cyclosporine A (CsA), a potent immunosuppressive drug, were examined in rat liver and kidney samples using two-dimensional electrophoretic protein analysis. Of a total of 370 liver and 336 kidney spots analyzed, 8% (29 spots) and 6% (19 spots), respectively, showed a significant drug-induced change (p < 0.01), which was predominantly reflected in increased protein abundance (62% and 74% of the changes, respectively). Of the 48 proteins changed in either organ, 14 were most probably common to both tissues and one of these was significantly increased in both the liver and the kidney. Most of the other 13 showed similar trends (either increases or decreases) in both organs. However, the most striking drug effect seen in this study concerned an unidentified protein present only in the kidney, which completely disappeared upon CsA treatment. It was also investigated whether the drug-induced changes could be prevented by the coadministration of the radical scavengers vitamin E and C with CsA. Spots changed by the administration of the drug were classified according to three different categories, based on their response profiles in rats treated with CsA in combination with the vitamins: (i) spots which were changed by CsA as well as by CsA in combination with the vitamins (12 liver and 4 kidney spots), (ii) spots which were changed by CsA and showed an additional increase of this change by CsA plus the vitamins (no liver and 4 kidney spots), and (iii) spots which were changed by CsA but not by CsA in combination with the vitamins (8 liver and 6 kidney spots). These results showed that in both organs the vitamins were able to prevent around 30% of the effects caused by CsA, and that two-dimensional gel electrophoresis is an excellent tool to demonstrate such drug interactions at the molecular level.

Protein mutations revealed by two-dimensional electrophoresis

High-resolution two-dimensional electrophoresis (2DE) can resolve many hundreds of proteins present in complex mixtures depending on the method of detection. These proteins can be characterised qualitatively, with respect to their electrophoretic mobilities (i.e. charge and apparent molecular mass) and quantitatively, using densitometry, to determine their amounts. There has been a widespread application of 2DE in the analysis and characterisation of protein mutations for a range of organisms. This review presents examples of the use of 2DE to study naturally occurring protein mutations and polymorphisms as well as the characterisation of induced protein mutations in prokaryotes and eukaryotes. Examples are presented to illustrate the use of 2DE to detect mutations affecting the electrophoretic mobility and biosynthesis of individual proteins as well as mutations leading to global alterations in cellular protein synthesis. The advantages and disadvantages of 2DE in the detection of protein mutations are discussed.