Polymorphism of pepper (Capsicum annuum L.) seed proteins studied by two-dimensional electrophoresis with immobilized pH gradients: methodical and genetic aspects

Identification of Anoectochilus based on rDNA ITS sequences alignment and SELDI-TOF-MS

The internal transcribed spacer (ITS) sequences alignment and proteomic difference of Anoectochilus interspecies have been studied by means of ITS molecular identification and surface enhanced laser desorption ionization time of flight mass spectrography. Results showed that variety certification on Anoectochilus by ITS sequences can not determine species, and there is proteomic difference among Anoectochilus interspecies. Moreover, proteomic finger printings of five Anoectochilus species have been established for identifying species, and genetic relationships of five species within Anoectochilus have been deduced according to proteomic differences among five species.

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.

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.

Horizontal ultrathin-layer multi-zonal electrophoresis of DNA: an efficient tool for large-scale polymerase chain reaction (PCR) fragment analysis

A rapid and efficient procedure for large-scale analysis of polymerase chain reaction (PCR) fragments in the range of 200-3000 base pairs is presented. The procedure is based on horizontal ultrathin-layer multi-zonal (HUME) electrophoresis of PCR fragments in polyacrylamide gels followed by silver staining. HUME gels can be prepared rapidly using a simple procedure called the flap technique. The electrophoretic set-up allows the use of multi-channel pipettes for sample loading. Separation and detection of the PCR fragments from sample preparation to silver staining can be carried out in 2 h. Using four electrophoresis units, one technician can analyze 400 PCR fragment samples in 2 h.

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.

Genetic variability of carrot seed proteins analyzed by one- and two-dimensional electrophoresis with immobilized pH gradients

The genetic variability of eight carrot populations representing commercially important morphological types was analyzed for seed protein polymorphism by one- and two-dimensional electrophoresis using immobilized pH gradients (IPG) in order to assess the potential of both techniques in carrot hybrid breeding as well as genetic quality testing of carrot trade seeds. The digitized silver-stained one- and two-dimensional gels of the urea/detergent-soluble seed proteins were subjected to computer analysis to estimate both the inter- and intrapopulation genetic variability. The results indicated that isoelectric focusing (IEF-IPG) of seed proteins is a powerful tool for quick screening of the genetic variability present between and within carrot populations, while two-dimensional polyacrylamide gel electrophoresis (IPG-DALT) can be employed to establish detailed genetic relationships of carrot populations selected by initial IEF-IPG screening in order to use genetic distant and homogeneous populations for successful carrot hybrid breeding. However, the applicability of IEF-IPG in genetic quality testing of carrot seeds seems to be restricted to hybrid purity testing. IPG-DALT is a far more powerful tool to profile unambiguously all carrot varieties commercially used in order to test the genetic quality of trade seeds, because this technique exhibits protein spots or spot combinations exclusively found in each of the eight varieties investigated.

Characterization of aspen isoprene synthase, an enzyme responsible for leaf isoprene emission to the atmosphere

Isoprene (2-methyl-1,3-butadiene) is a volatile hydrocarbon emitted from many plant species to the atmosphere, where it plays an important role in atmospheric chemistry. An enzyme extracted from aspen (Populus tremuloides) leaves was previously found to catalyze the Mg(2+)-dependent elimination of pyrophosphate from dimethylallyl diphosphate (DMAPP) to form isoprene (Silver, G. M., and Fall, R. (1991) Plant Physiol. 97, 1588-1591). This enzyme, isoprene synthase, has now been purified 4000-fold to near homogeneity. The enzyme had a native molecular mass of 98-137 kDa and isoelectric point of 4.7 and contained 58- and 62-kDa subunits, implying that it is a heterodimer. Partial amino acid sequences of the two subunits indicated they are closely related to each other and that they do not share a strong homology with any other reported proteins. The isoprene synthase reaction was dependent on Mg2+ or Mn2+, and the reaction products were shown to be isoprene and pyrophosphate with a stoichiometry close to 1:1. The Km for DMAPP was high at 8 mM, and the kcat of 1.7 s-1 was low, but similar to those of other allylic diphosphate-utilizing enzymes. It is argued that the isoprene synthase reaction may be much more efficient in vivo, where it is under light-dependent control. It seems probable that this unique enzyme, rather than non-enzymatic reactions, can account for the emission of hundreds of millions of metric tons of isoprene from plants to the global atmosphere each year.

Association of protein polymorphism among pepper (Capsicum annuum L.) inbred lines with agronomic performance of their crosses

The genetic variation of 10 morphologically similar pepper (Capsicum annuum L.) inbred lines has been analyzed by two-dimensional electrophoresis with immobilized pH gradient (IPG-DALT) of seed proteins. For all pairs of inbred lines genetic distance indices were calculated on the basis of the IPG-DALT analysis and a genetic tree was constructed. The protein polymorphism data of the 10 inbred lines were integrated into a pepper breeding program to validate the assumption that there is a higher chance of achieving better hybrid performance when the genetic distance between the parents is as great as possible. Field trials were performed in Turkey and consisted of a total of 27 crossings based on 9 inbred lines. Fifteen hybrids exceeded the crop yield of the better parent and 8 additional hybrids exceeded the mean crop yield of both parents. The genetic distance indices of the parental inbred lines based on protein polymorphism data were not significantly correlated to heterosis performance of the experimental hybrids (r = 0.20), indicating that protein polymorphism data add little to the prediction of single cross hybrid performance. Nevertheless, protein polymorphism data support the breeder in being more effective in finding out the best inbred combinations, because most of the less promising crossings can be omitted from the expensive and time-consuming performance tests. Those hybrids whose distance indices exceeded the mean of all 27 distance values (0.52) were superior to the mean value of all heterosis performances by 19%.(ABSTRACT TRUNCATED AT 250 WORDS)

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.