Effects of aroclor 1254 on proteins of mouse liver: Application of two-dimensional electrophoretic protein mapping

The impact of proteomics on products and processes

Not much more than 15 years ago a handful of visionary scientists around the world suggested to sequence and analyze not only the human genome but also as many genomes as possible in order to compare DNA as well as to deduce protein sequences. By that means they expected to get an idea about the organization of life. However, after now having now sequenced the human genome and at least identified around 40,000 genes as coding regions, we are still left with the fundamental questions of how genes are regulated, and what is the rationale of genetic regulatory networks. The basic knowledge and methodologies to elucidate functional regulatory networks of cells and organisms on the protein level had been around for much longer than DNA-based discovery tools. This was mainly due to the fact that proteins have to fulfill universal functions in nature and, unlike DNA polynucleotides, proteins differ not only in their amino acid sequences; they come in nearly all shapes and sizes and have all kinds of physical as well as chemical properties. They can be highly water soluble, e.g., serum and milk proteins, or nearly insoluble in any solvent, e.g., keratin and some other structural proteins. In addition, structure, function, as well as the respective stability of proteins inside and outside of a biological system, are individual features of any given polypeptide. On one hand, the individuality of proteins allows adaptation of any life form to the environment, and on the other it is still a real challenge for biotech R&D and production. The present review is actually the first approach to evaluate and judge the achievements made by Applied Proteome Analysis and Proteomics over the last 27 years.

Effects of oltipraz and related chemoprevention compounds on gene expression in rat liver

One promising approach to cancer chemoprevention involves the induction of phase II xenobiotic metabolism enzymes. Since this approach requires drugs specifically intended to alter tissue gene expression patterns over long periods, it will be important to determine experimentally which proteins are increased or decreased by treatment, and how such alterations may (or may not) be related to the postulated chemopreventive mechanism. We have employed two-dimensional electrophoresis to detect and quantitate gene expression effects of candidate chemoprevention compounds in the livers of treated rats. Oltipraz, an inducer of several phase II enzymes, affected a series of at least 26 proteins, most of which were slightly decreased by treatment. Several proteins were increased, the prime example being rat liver spot 693, which was induced more than 7-fold by oltipraz. This protein was excised from multiple 2-D gels and subjected to in situ tryptic digestion followed by microchemical sequence analysis. The resulting multiple peptide sequences match perfectly with the cDNA-derived sequence of rat aflatoxin B1 aldehyde reductase (AFAR). Using quantitative measurements of AFAR from 2-D gels, we compared a series of dose regimens. Oltipraz administration by gavage or in diet appeared equally effective, while recovery studies indicated a half-time of 5.5 days for disappearance of the AFAR protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of scaling methods to minimize experimental variations in two-dimensional electrophoresis quantitative data: application to the comparison of maize inbred lines

The analysis of two-dimensional (2-D) electrophoresis quantitative data from a design involving 21 maize genotypes revealed a significant experimental variation. In order to minimize this variation, we investigated the possible causes and found that it was essentially due to global effects, affecting all the spots in a gel in a similar way, and occurring during the 2-D run/staining procedure. Three scaling methods to discard these experimental variations were analyzed: the linear scaling method, a method based on principal component analysis, and a combined method that unites the advantages of both of the former. Comparing these three methods, we found that they led to consistent results with regard to the factor under study, i.e. the genetic factor in our case. However, the combined scaling method was the most efficient in reducing experimental variations.

Comparisons of protein changes in human and rodent hepatocytes induced by the rat-specific carcinogen, methapyrilene

There is a growing concern that the rodent bioassay may not always serve as an appropriate model to assess the carcinogenic risk for humans exposed to certain compounds. Mechanistic research that examines the effects of a compound in rodent and man could help in the interpretation of bioassay results. This paper reports a novel use of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) technology to assess similarities and differences in the response of rodents and humans to the rat-specific hepatocarcinogen, methapyrilene (MP). A sequential examination of rodent and human hepatic proteins was conducted following in vivo exposure of rats and mice and in vitro exposure of rat, mouse, and human hepatocytes to MP. Results showed that covalent modifications observed in rats and mice in vivo were duplicated both qualitatively and quantitatively in the corresponding in vitro systems and that these modifications correlated with carcinogenic susceptibility. Covalent modifications in human hepatocytes were minimal despite exposure to concentrations of MP that were 6-fold higher than those used in rodent hepatocytes. These studies suggest that in the case of MP the rat is not the most appropriate model for assessing the human situation. Furthermore, these data show that in vitro-in vivo comparisons based on 2-D PAGE may provide adjunctive information for extrapolating rodent toxicity/bioassay results to human risk assessment.

Human liver protein map: a reference database established by microsequencing and gel comparison

This publication establishes a reference human liver protein map obtained with immobilized pH gradients. By microsequencing, 57 spots or 42 polypeptide chains were identified. By protein map comparison and matching (liver, red blood cell and plasma sample maps), 8 additional proteins were identified. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing a human liver two-dimensional gel database. This reference map can be used to identify protein spots on other samples such as rectal cancer biopsies.

Global changes in gene expression related to antibiotic synthesis in Streptomyces hygroscopicus

Two-dimensional gel electrophoresis was used to follow changes in gene expression associated with antibiotic (bialaphos) biosynthesis in Streptomyces hygroscopicus. Cultures were pulse-labelled with [35S]-methionine before, during, and after the switch from primary to secondary metabolism in order to compare kinetic profiles of bialaphos (antibiotic) production (bap) genes during this metabolic transition. Separation of gene products on two-dimensional gels revealed that 27 were dependent on brpA for optimal expression and were activated as the culture approached stationary phase. Genes which encoded 10 brpA-dependent proteins were mapped to a 10 kb SstI fragment of the 35 kb bap gene cluster by expressing them in Streptomyces lividans using the thiostrepton-inducible tipA promoter. N-terminal amino acid sequences of two brpA-dependent proteins, obtained by direct microsequencing of protein spots excised from two-dimensional gels, identified them as gene products mapping to the same region and involved in secondary metabolic conversions of the bap pathway. The kinetics of synthesis of 16 brpA-dependent gene products were characterized using QUEST computer software. Cluster analysis performed on the kinetics of synthesis of 346 of the most highly expressed gene products of HP5-29, including 16 brpA-dependent ones, identified 75 families having distinct patterns of expression. Many brpA-dependent proteins were clustered together; 10 were found in one kinetic family. These kinetic families also included brpA-independent gene products perhaps subject to similar regulatory mechanisms and thus possibly involved in bialaphos biosynthesis. The activation/derepression of bap expression took place as cultures approached stationary phase and was temporally related to synthesis of ppGpp.

A two-dimensional gel database of rat liver proteins useful in gene regulation and drug effects studies

A standard two-dimensional (2-D) protein map of Fischer 344 rat liver (F344MST3) is presented, with a tabular listing of more than 1200 protein species. Sodium dodecyl sulfate (SDS) molecular mass and isoelectric point have been established, based on positions of numerous internal standards. This map has been used to connect and compare hundreds of 2-D gels of rat liver samples from a variety of studies, and forms the nucleus of an expanding database describing rat liver proteins and their regulation by various drugs and toxic agents. An example of such a study, involving regulation of cholesterol synthesis by cholesterol-lowering drugs and a high-cholesterol diet, is presented. Since the map has been obtained with a widely used and highly reproducible 2-D gel system (the Iso-Dalt system), it can be directly related to an expanding body of work in other laboratories.

Biomedical relevance of two-dimensional protein mapping

State-of-the-art and future perspectives are discussed for the application of two-dimensional protein maps to basic medical research and routine clinical chemistry problems. Despite the technical advances that allow effective processing of a large number of samples and the refinement of devices and procedures for image analysis, at present two-dimensional maps are mostly confined to research purposes, i.e. to the inventory of normal constituents of body fluids and tissues on the one hand, and to qualitative-quantitative alterations of some protein spots in a number of instances (genetic, degenerative, infectious or xenobiotic diseases) on the other. It is hoped that in some instances a single primarily affected component will be able to be identified and then specifically tested (for instance by immunological means) as a diagnostic marker, but complex pathological patterns would still require the analysis of a large number of peptides at the resolution level only afforded by two dimensions. Further simplification of the protocols, for example with ready-made gels, and data reduction systems might then allow the application of the technique to be extended to general clinical laboratories.

The use of quantitative two-dimensional gel electrophoresis to analyze changes in alveolar macrophage proteins in humans exposed to ozone

Acute exposure of humans to 0.4 ppm ozone is known to cause production of components that mediate inflammation and damage in the lung. However, ozone may cause even more extensive changes in the lung than those currently measured by traditional enzymatic or immunologic methods. The contribution of alveolar macrophages to these processes is not well understood. Therefore we have used molecular techniques to measure changes in the total spectrum of alveolar macrophage proteins in humans exposed to ozone. In this study, 8 human volunteers were each exposed to 0.4 ppm ozone and to filtered air for 2 h with intermittent exercise. Eighteen hours later, bronchoalveolar lavage was performed and alveolar macrophages were isolated. Changes in proteins made by these cells after air or ozone exposure were analyzed by high-resolution two-dimensional gel electrophoresis, using computerized densitometry to quantify changes in individual proteins. Of the nearly 900 proteins analyzed, 45 (5.1%) were synthesized at a significantly increased rate following ozone exposure, while 78 (8.8%) were synthesized at a significantly reduced rate. These results indicate that exposure of humans to ozone causes extensive changes in the spectrum of macrophage proteins being produced. Quantitative two-dimensional gel electrophoresis is a highly sensitive technique that may reveal much more information about the in vivo effects of a pollutant than has previously been available. Furthermore, the ability to survey large numbers of macrophage proteins after exposure to various inhaled pollutants may allow a better understanding of the mechanisms of action of these agents, as well as provide new biomarkers of pollutant exposure.