DNA microarray-based gene expression profiling of estrogenic chemicals

We summarize updated information about DNA microarray-based gene expression profiling by focusing on its application to estrogenic chemicals. First, estrogenic chemicals, including natural/industrial estrogens and phytoestrogens, and the methods for detection and evaluation of estrogenic chemicals were overviewed along with a comprehensive list of estrogenic chemicals of natural or industrial origin. Second, gene expression profiling of chemicals using a focused microarray containing estrogen-responsive genes is summarized. Third, silent estrogens, a new type of estrogenic chemicals characterized by their estrogenic gene expression profiles without growth stimulative or inhibitory effects, have been identified so far exclusively by DNA microarray assay. Lastly, the prospect of a microarray assay is discussed, including issues such as commercialization, future directions of applications and quality control methods.     

Oxygen intervention in the regulation of gene expression: the photosynthetic bacterial paradigm

The means by which oxygen intervenes in gene expression has been examined in considerable detail in the metabolically versatile bacterium Rhodobacter sphaeroides. Three regulatory systems are now known in this organism, which are used singly and in combination to modulate genes in response to changing oxygen availability. The outcome of these regulatory events is that the molecular machinery is present for the cell to obtain energy by means that are best suited to prevailing conditions, while at the same time maintaining cellular redox balance. Here, we explore the dangers associated with molecular oxygen relative to the various metabolisms used by R. sphaeroides, and then present the most recent findings regarding the features and operation of each of the three regulatory systems which collectively mediate oxygen control in this organism.Received 26 June 2003; received after revision 30 July 2003; accepted 8 August 2003     

Interaction of platinum compounds with bacterial DNA

Summary The cis and trans isomer of PtCl₂(NH₃)₂, cis-Pt(cpa)₂Cl₂ and 2 platinum pyrimidine blues have been used in a number of bacterial tests indicative of their interaction with bacterial DNA.This investigation was supported by a grant from C.N.R., Rome. We thank Mrs S. Saincich for skilful technical assistance.     

Polyamine-dependent gene expression

The polyamines spermidine and spermine along with the diamine putrescine are involved in many cellular processes, including chromatin condensation, maintenance of DNA structure, RNA processing, translation and protein activation. The polyamines influence the formation of compacted chromatin and have a well-established role in DNA aggregation. Polyamines are used in the posttranslational modification of eukaryotic initiation factor 5A, which regulates the transport and processing of specific RNA. The polyamines also participate in a novel RNA-decoding mechanism, a translational frameshift, of at least two known genes, the TY1 transposon and mammalian antizyme. Polyamines are crucial for their own regulation and are involved in feedback mechanisms affecting both polyamine synthesis and catabolism. Recently, it has become apparent that the polyamines are able to influence the action of the protein kinase casein kinase 2. Here we address several roles of polyamines in gene expression.Received 27 November 2002; received after revision 9 January 2003; accepted 31 January 2003     

Transcription of bacterial DNA by isolated plant nuclei.

Plant nuclei prepared from protoplasts can be used as a cell-free system for testing their template activity of procaryotic DNA for plant polymerases. We were able to demonstrate that plant polymerases of Petunia hybrida are capable of transcribing linear bacterial DNA, whereas supercoiled DNA could not be used as a template.     

Memory formation and the regulation of gene expression

On a cellular level, formation of memory is based on a selective change in synaptic efficacy that is both fast and, in case of important information, long-lasting. Rapidity of cellular changes is achieved by modifying preexisting synaptic molecules (receptors, ion channels), which instantaneously alters the efficacy of synaptic transmission. Endurance, that is the formation of long-term memory (LTM), is based on transient and perhaps also long-lasting changes in protein synthesis. A number of different methods exist to interfere with the synthesis of specific proteins or proteins in general. Other methods, in turn, help to identify proteins whose synthesis is changed following learning. These mostly molecular methods are briefly described in the present review. Their successful application in a variety of memory paradigms in invertebrates and vertebrates is illustrated. The data support the importance of selective changes in gene expression for LTM. Proteins newly synthesized during memory consolidation are likely to contribute to restructuring processes at the synapse, altering the efficiency of transmission beyond the scope of STM. Increased or, less often, decreased synthesis of proteins appears during specific time windows following learning. Recent evidence supports older data suggesting that two or even more waves of protein synthesis exist during the consolidation period. It is expected that the new molecular methods will help to identify and characterize molecules whose expression changes during LTM formation even in complex vertebrate learning paradigms.     

Altered proteoglycan gene expression and the tumor stroma

Tumor stroma is a specialized form of tissue that is associated with epithelial neoplasms. Recent evidence indicates that significant changes in proteoglycan content occur in the tumor stroma and that these alterations could support tumor progression and invasion as well as tumor growth. Our main hypothesis is that the generation of tumor stroma is under direct control of the neoplastic cells and that, via a feedback loop, altered proteoglycan gene expression would influence the behavior of tumor cells. In this review, we will focus primarily on the work from our laboratory related to the altered expression of chondroitin sulfate proteoglycan and its role in tumor development and progression. The connective tissue stroma of human colon cancer is enriched in chondroitin sulfate and the stromal cell elements, primarily colon fibroblasts and smooth muscle cells, are responsible for this biosynthetic increase. These changes can be reproduced in vitro by using either tumor metabolites or co-cultures of human colon carcinoma cells and colon mesenchymal cells. The levels of decorin, a leucine-rich proteoglycan involved in the regulation of matrix assembly and cell proliferation, are markedly elevated in the stroma of colon carcinoma. These changes correlate with a marked increase in decorin mRNA levels and a concurrent hypomethylation of decorin gene, a DNA alteration associated with enhanced gene expression. Elucidation of decorin gene structure has revealed an unexpected degree of complexity in the 5 untranslated region of the gene with two leader exons that are alternatively spliced to the second coding exon. Furthermore, a transforming growth factor beta (TGF-)-negative element is present in the promoter region of decorin gene. This regulatory domain is likely to be implicated in the silencing of decorin gene by TGF- and may contribute to the regulation of this matrix gene in the tumor stroma.     

Effects of light on the translocation of bacterial DNA inSolanum lycopersicum esc

Résumé Nous avons étudié l'influence de la lumière sur la translation de l'ADN d'origine bactérienne chez des plantules de tomate. La lumière augmente la prise d'ADN étranger. Cet ADN est, par contre, dans un état moins polymérisé que chez les plantules exposées à l'obscurité. Dans les mêmes conditions expérimentales, la lumière n'a aucune influence sur la synthèse de l'ADN endogène, réalisée à partir de petits précurseurs.     

Effect of temperature on the translocation of bacterial DNA inSolanum lycopersicum esc

Résumé Nous avons étudié l'influence de différentes températures sur la translation de l'ADN d'origine bactérienne chez les plantules de tomate. La température n'a aucune influence en elle-même. Néanmoins des variations de température diminuent la dépolymérisation de l'ADN étranger migré dans la plante.

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This work was done under a Euratom/C.E.N. contract, and was supported by grants from the Belgian Fonds de la Recherche Scientifique Fondamentale Collectye.

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Boursier Euratom.

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Boursier au Fonds national suisse de la recherche scientifique.     

Restriction endonucleases that resemble a component of the bacterial DNA repair machinery

It has long been known that most Type II restriction endonucleases share a conserved core fold and similar active-sites. The same core folding motif is also present in the MutH protein, a component of the bacterial DNA mismatch repair machinery. In contrast to most Type II restriction endonucleases, which assemble into functional dimers and catalyze double-strand breaks, MutH is a monomer and nicks hemimethylated DNA. Recent biochemical and crystallographic studies demonstrate that the restriction enzymes BcnI and MvaI share many additional features with MutH-like proteins, but not with most other restriction endonucleases. The structurally similar monomers all recognize approximately symmetric target sequences asymmetrically. Differential sensitivities to slight substrate asymmetries, which could be altered by protein engineering, determine whether the enzymes catalyze only single-strand nicks or double-strand breaks. M. Sokolowska, M. Kaus-Drobek: These authors contributed equally to this work. Received 12 March 2007; received after revision 28 April 2007; accepted 3 May 2007