Qualitative and quantitative variability in different classes of proteins: comparison of mouse and rat

Accounting for biological variation in differential display two-dimensional electrophoresis experiments

Variation of protein expression levels was investigated in the heart, lung and liver from an inbred (C57/BL6) and an outbred (CD-1) mouse line. Based on the measured inter-individual variation, optimal sample sizes for two-dimensional electrophoresis experiments were determined by means of power analysis. For both lines, the level of protein expression variation was in the range of technical variation. Thus, although the differences in protein expression variation were significant between organs and mouse lines, optimal sample sizes were very similar (between 8 for heart proteins from C57/BL6 and 10 for liver proteins of the same line). Proteins with organ expression bias (higher expression in one organ as compared to the other two organs) exhibited higher variation of expression and the proportion of these proteins in each organ explained at least partly inter-organ differences in protein expression variation. The results suggest that proteomic experiments using more heterogeneous mouse samples would not require much larger sample sizes than those using narrowly standardized samples. Experiment designs encompassing a broader genetic variation and thus affording increased relevance of the results can be accessible to proteomics researchers at still affordable sample sizes.

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.

Analysis of the mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation

The total protein of the mouse brain was fractionated into three fractions, supernatant, pellet extract and rest pellet suspension, by a procedure that avoids any loss of groups or classes of proteins. The supernatant proteins were resolved to a maximum by large-gel two-dimensional electrophoresis. Two-dimensional patterns from ten individual mice of the commonly used inbred strain C57BL/6 (species: Mus musculus) were prepared. The master pattern was subjected to densitometry, computer-assisted image analysis and treatment with our spot detection program. The resulting two-dimensional pattern, a standard pattern for mouse brain supernatant proteins, was divided into 40 squares, calibrated, and specified by providing each spot with a number. The complete pattern and each of the 40 squares are shown in our homepage (http://www.charite.de/ humangenetik). The standard pattern comprises 8767 protein spots. To identify the proteins known so far in the brain fraction investigated, a first set of 200 spots was analyzed by matrix-assisted laser desorption/ionization - mass spectrometry (MALDI-MS) after in-gel digestion. By screening protein databases 115 spots were identified; by extending the analysis to selected, genetically variant protein spots, 166 spots (including some spot series) were identified in total. This number was increased to 331 by adding protein spots identified indirectly by a genetic approach. By comparing the two-dimensional patterns from C57BL/6 mice with those of another mouse species (Mus spretus), more than 1000 genetically variant spots were detected. The genetic analysis allowed us to recognize spot families, i.e., protein spots that represent the same protein but that are post-translationally modified. If some members of the family were identified, the whole family was considered as being identified. Spot families were investigated in more detail, and interpreted as the result of protein modification or degradation. Genetic analysis led to the interesting finding that the size of spot families, i.e., the extent of modification or degradation of a protein, can be genetically determined. The investigation presented is a first step towards a systematic analysis of the proteome of the mouse. Proteome analysis was shown to become more efficient, and, at the same time, linked to the genome, by combining protein analytical and genetic methods.

Proteins of rat serum: I. Establishing a reference two-dimensional electrophoresis map by immunodetection and microbore high performance liquid chromatography-electrospray mass spectrometry

In the present investigation, we have identified 56 major spots, or spot rows, corresponding to 22 proteins, in the 2-DE pattern of adult male rats. This was done mainly by applying two complementary techniques, namely immunoblotting and high performance liquid chromatography-mass spectrometry (HPLC-MS) peptide mapping. Glycoproteins were characterized by affinity blotting with six lectins. We have also detailed how rat serum differs from human serum in two main respects: (i) relative abundance of individual proteins, which amounts in some cases to a complete absence in either sample, and (ii) varying molecular parameters for homologous proteins. It was thus possible to establish a first-generation reference map of rat serum proteins, which can be accessed through http://weber.u.washington.edu/ruedilab/aebersold++ +.html. We hope the present database will be a useful reference for the evaluation of changes in serum protein distribution in the course of pharmacological and toxicological studies. The recognition of species-specific proteins appears of special relevance in this respect.

Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome

The two-dimensional electrophoresis (2-DE) technique developed by Klose in 1975 (Humangenetik 1975, 26, 211-234), independently of the technique developed by O'Farrell (J. Biol. Chem. 1975, 250, 4007-4021), has been revised in our laboratory and an updated protocol is presented. This protocol is the result of our experience in using this method since its introduction. Many modifications and suggestions found in the literature were also tested and then integrated into our original method if advantageous. Gel and buffer composition, size of gels, use of stacking gels or not, necessity of isoelectric focusing (IEF) gel incubation, freezing of IEF gels or immediate use, carrier ampholytes versus Immobilines, regulation of electric current, conditions for staining and drying the gels - these and other problems were the subject of our concern. Among the technical details and special equipment which constitute our 2-DE method presented here, a few features are of particular significance: (i) sample loading onto the acid side of the IEF gel with the result that both acidic and basic proteins are well resolved in the same gel; (ii) use of large (46 x 30 cm) gels to achieve high resolution, but without the need of unusually large, flat gel equipment; (iii) preparation of ready-made gel solutions which can be stored frozen, a prerequisite, among others, for high reproducibility. Using the 2-DE method described we demonstrate that protein patterns revealing more than 10 000 polypeptide spots can be obtained from mouse tissues. This is by far the highest resolution so far reported in the literature for 2-DE of complex protein mixtures. The 2-DE patterns were of high quality with regard to spot shape and background. The reproducibility of the protein patterns is demonstrated and shown to be thoroughly satisfactory. An example is given to show how effectively 2-DE of high resolution and reproducibility can be used to study the genetic variability of proteins in an interspecific mouse backcross (Mus musculus x Mus spretus) established by the European Backcross Collaborative Group for mapping the mouse genome. We outline our opinion that the structural analysis of the human genome, currently pursued most intensively on a worldwide scale, should be accompanied by a functional analysis of the genome that starts from the proteins of the organism.

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.

Composition and genetic variability of proteins from nuclear fractions of mouse (DBA/2J and C57BL/6J) liver and brain

Proteins from nuclear plasma of mouse liver and brain and from the nuclear membranes of mouse liver were separated by two-dimensional electrophoresis. For the purpose of comparison, liver cytosol proteins were also investigated. The protein samples were prepared from two inbred strains of the mouse (DBA/2J, C57BL/6J) and their hybrids. The patterns obtained were compared with regard to the composition and genetic variability (qualitative and quantitative variants) of proteins from different nuclear fractions and organs. The percentage (greater than 30%) of spots common to different organs (liver, brain), but from the same nuclear fraction (plasma) was greater than the percentage (less than 20%) of spots common to different cell and nuclear fractions (cytosol, nuclear plasma and nuclear membranes) of the same organ (liver). Quantitative genetic variants occurred much more frequently than qualitative genetic variants (5.1% vs. 0.2%; liver nuclear plasma). The incidence of genetic variants was much higher in liver (5.3%) than in brains (0.0%), and higher in solubilized nuclear proteins (5.3%) than in structure-bound nuclear proteins (2.1%).

Systematic analysis of the total proteins of a mammalian organism: principles, problems and implications for sequencing the human genome

High-resolution two-dimensional electrophoresis (2-DE) has reached a technological level that allows us to resolve most of the numerous unknown protein species of a mammalian organism if appropriate strategies are used. We will discuss the problems of classification and characterization of proteins and propose a systematic approach to the analysis of the total protein complex. Both a comprehensive as well as a pragmatic approach towards systematic analysis have been considered. A "complex protein database" is suggested and considered with regard to various uses. A systematic analysis of the mouse proteins has been started and some of the preliminary results are summarized here. In particular, genetic properties of the proteins were investigated and are presented in order to demonstrate the significance of a systematic analysis of proteins for research and practical application (e.g. mutagenicity testing). A concept is presented for sequencing the coding DNA of mouse and man, starting with a systematic analysis of mouse proteins and then using two recently developed methods - microsequencing of proteins from spots of 2-DE protein patterns, and utilization of the relatively short N-terminal sequences obtained - to produce the corresponding cDNA's of these proteins.

Genetic aspects of variation of protein amounts in maize and pea

Using high-resolution two-dimensional polyacrylamide gel electrophoresis we studied the polymorphism of protein amounts in some genotypes of maize and pea. This type of variability seems to be rather common and insensitive to environmental conditions, as attested by the comparison of the patterns of two maize lines harvested in two different years. A large-scale experiment involving 5 lines, 7 of their hybrids, and 6 organs (or physiological stages) of maize allowed us to examine numerous polypeptides regarding their genetic variability, their amount differences between organs and the inheritance of their abundance. Genetic and organ variations are not independent: polypeptides whose amount varies from one organ to another are, for the most part, genetically variable (59%), while the stable polypeptides are not often genetically variable (18%). We found a striking organ specificity for (i) the extent of quantitative variability (from 2.3-15.4% of the polypeptides), (ii) the occurrence and the type of variation for a given polypeptide (an intensity difference seen in an organ can disappear or even be reversed in another one), (iii) the kind of inheritance (additive/non-additive): combining the 6 organs and the 7 hybrids we found 101 cases of non-additivity (4% of the total) which concern as many as 72 different spots, that is to say that in most cases a polypeptide displaying nonadditivity in an organ seems to display additivity in the other ones. Moreover, for most of the polypeptides with nonadditive inheritance the hybrid spot presents an intensity similar to that of the most intense parental spot.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of protein patterns from different organs and cell fractions of trisomy 19 mice

Proteins were extracted from liver, brain, and skin of 6-day-old mice with trisomy (Ts) 19 and fractionated into solubilized cell proteins and structure-bound cell proteins. The proteins were separated by two-dimensional electrophoresis, and protein patterns were compared in the combinations Ts/normal and normal/normal. Analysis of the protein patterns revealed protein spots (variants) with densities higher (h-type) or lower (l-type) in trisomies than in normal mice. Some of these variants were found in all Ts individuals investigated for a particular protein class. These variants, termed regular Ts-variants, constituted 0.8%-1.6% of the total number of spots. The proteins of the regular Ts variants were in most cases organ-nonspecific. However, in almost all cases a given quantitative variation was expressed in only one of the three organs investigated. To explain our results, we have presented models for the control of protein levels on the basis of gene regulation. New aspects in the conception of studies on trisomies in man could be gained.