Robust transmission of information despite the presence of variation is a fundamental problem in cellular functions. However, the capability and characteristics of information transmission in signaling pathways remain poorly understood. We describe robustness and compensation of information transmission of signaling pathways at the cell population level. We calculated the mutual information transmitted through signaling pathways for the growth factor-mediated gene expression. Growth factors appeared to carry only information sufficient for a binary decision. Information transmission was generally more robust than average signal intensity despite pharmacological perturbations, and compensation of information transmission occurred. Information transmission to the biological output of neurite extension appeared robust. Cells may use information entropy as information so that messages can be robustly transmitted despite variation in molecular activities among individual cells.
The erythropoietin (Epo) gene is regulated by hypoxia-inducible cis-acting elements in the promoter and in a 3 enhancer, both of which contain consensus hexanucleotide hormone receptor response elements which are important for function. A group of 11 orphan nuclear receptors, transcribed and translated in vitro, were screened by the electrophoretic mobility shift assay. Of these, hepatic nuclear factor 4 (HNF-4), TR2-11, ROR␣1, and EAR3/COUP-TF1 bound specifically to the response elements in the Epo promoter and enhancer and, except for ROR␣1, formed DNA-protein complexes that had mobilities similar to those observed in nuclear extracts of the Epo-producing cell line Hep3B. Moreover, both anti-HNF-4 and anti-COUP antibodies were able to supershift complexes in Hep3B nuclear extracts. Like Epo, HNF-4 is expressed in kidney, liver, and
We have studied the transcriptional regulatory mechanism of the human histo-blood group ABO genes, and identified DNA cis-elements and trans-activating protein that control the expression of these genes which are important in blood transfusion and organ transplantation. We introduced the 5 -upstream sequence of ABO genes into the promoterless reporter vector and characterized the promoter activity of deletion constructs using transient transfection assays with gastric cancer cell line KATO III cells. The sequence just upstream of the transcription start site (cap site), and an enhancer element, which is located further upstream (between ؊3899 and ؊3618 base pairs ( Histo-blood group ABH(O) antigens, the major alloantigens in humans (1), have been characterized as defined trisaccharide determinants GalNAc␣133(Fuc␣132)Gal13 R, Gal␣133(Fuc␣132)Gal13 R, and disaccharide determinant Fuc␣132Gal13 R for A, B, and H, respectively (2, 3). These structures represent the secondary gene products which are synthesized from the precursor H substrate by ␣133GalNAc (A transferase) and ␣133Gal transferase (B transferase), the primary gene products coded by the functional alleles at the ABO locus (4, 5). Molecular genetic studies of the ABO genotypes have identified two critical single-base substitutions between A and B genes, the resultant 2-amino acid substitutions being responsible for the different donor nucleotide-sugar substrate specificity between A and B transferases. A single base deletion, which shifts the codon reading frame and abolishes the function of A transferase, has been identified in O allelic cDNAs (6, 7).ABH antigens are known to undergo drastic changes during development, differentiation, and maturation. Studies of these antigens in stratified squamous epithelia provided one of the clearest examples of differential expression during cell maturation (8). In non-keratinized stratified squamous epithelia, the immature cells in the basal layers are characterized by the expression of sialylated or unsubstituted precursor peripheral cores, while differentiated and mature cells in the upper layers sequentially express ␣132-fucosylated H structures, and A and B antigens depending on the ABO genotype of the individual. This sequential expression of carbohydrate antigens is associated with the differentiation pattern of the epithelium. An interesting question is how these changes are controlled during cell differentiation. Since keratinocytes are known to greatly change their gene expression during terminal cell differentiation (9), the switch-on of the ABO genes during the maturation may be governed by the same factor(s). To fill in the gap between the expression of the ABO genes and the appearance of the ABO phenotypes in the terminal differentiation of epithelial cells, it is essential to understand the transcriptional regulatory mechanism of the ABO genes. In addition to the normal cell differentiation process, the changes of ABH antigen expression have also been documented in abnormal processes such as tumorig...
We have investigated the regulatory role of DNA methylation in the expression of the human histo-blood group ABO genes. The ABO gene promoter region contains a CpG island whose methylation status correlates well with gene expression in the cell lines tested. The CpG island was found hypomethylated in some cell lines that expressed ABO genes, whereas the other cell lines that did not express ABO genes were hypermethylated. The ABO blood group system discovered by Karl Landsteiner (1) at the beginning of this century is of great importance in blood transfusions and organ transplantations. Two carbohydrate antigens, A-and B-antigens, and their antibodies constitute this system. The A and B functional alleles at the ABO genetic locus encode glycosyltransferases ␣133GalNAc transferase (designated A-transferase) and ␣133Gal transferase (designated B-transferase), respectively. A-transferase transfers a GalNAc residue from UDP-GalNAc to the precursor H substrate, producing A antigens as defined by the trisaccharide determinant structure, GalNAc␣133(Fuc␣132)Gal13 R. Similarly, B-transferase catalyzes the transfer of a Gal from UDP-Gal to the same H substrate, producing B antigens defined by Gal␣133(Fuc␣132)Gal13 R (2-5). Molecular genetic studies of the human ABO genes have identified two critical single base substitutions that result in amino acid substitutions responsible for the different donor nucleotidesugar substrate specificity between A-and B-transferases. A single base deletion, which shifts the reading frame of codons and abolishes the function of A-transferase, has been identified in most O alleles (6, 7).The ABO genes are expressed in a cell type-specific manner; the isoantigens A, B, and H of blood groups A, B, and O are not confined to red cells only but are also found in most secretions and on some epithelial cells. However, they are absent in connective tissues and the central nervous system (8). ABH antigens are known to undergo drastic changes during development, differentiation, and maturation of normal cells (9). In addition to these physiological processes, profound changes have also been documented in pathological processes such as tumorigenesis. Reduction or complete deletion of A/B antigen expression in bladder and oral cancers has been documented, as well as the apparent onco-developmental expression of the ABH antigens in gastric and distal colon tumors (10 -12). Moreover, the loss of ABH antigens has been correlated with tumor progression of various carcinomas including lung and bladder carcinomas (13-16). Thus, delineation of regulatory mechanism is essential to understand these complicated expression patterns of the ABO genes.In an initial attempt to elucidate the molecular mechanism controlling the expression of the human ABO genes, we isolated several genomic clones that covered the ABO genes over 18 kb 1 (17). A 4.7-kb EcoRI/NcoI 5Ј-upstream fragment flanking the coding sequence in exon 1 of the human ABO gene was subcloned into the promoterless pGL3-basic vector upstream of the lucifer...
The x-ray photoelectron spectra of tetraphenylporphin, phthalocyanine and their copper complexes were measured. The copper complexes show a single nitrogen 1s photoline, whereas the metal free bases give rise to a doublet nitrogen 1s photoline. The central pyrrole and aza nitrogens in the metal free bases could be identified, whereas the central and meso-bridging aza nitrogens in phthalocyanine could not be discriminated. Each of the central two protons in the metal free bases is localized on one of the central four porphinato nitrogens. The shifts in N 1s binding energy observed in the present work could be reproduced by the shifts in the charge density on nitrogen obtained for the bonded structure by an extended Hückel molecular orbital calculation.
Impaired glucose tolerance associated with obesity causes postprandial hyperglycemia and can lead to type 2 diabetes. To study the differences in liver metabolism in healthy and obese states, we constructed and analyzed transomics glucose-responsive metabolic networks with layers for metabolites, expression data for metabolic enzyme genes, transcription factors, and insulin signaling proteins from the livers of healthy and obese mice. We integrated multiomics time course data from wild-type and leptin-deficient obese (ob/ob) mice after orally administered glucose. In wild-type mice, metabolic reactions were rapidly regulated within 10 min of oral glucose administration by glucose-responsive metabolites, which functioned as allosteric regulators and substrates of metabolic enzymes, and by Akt-induced changes in the expression of glucose-responsive genes encoding metabolic enzymes. In ob/ob mice, the majority of rapid regulation by glucose-responsive metabolites was absent. Instead, glucose administration produced slow changes in the expression of carbohydrate, lipid, and amino acid metabolic enzyme–encoding genes to alter metabolic reactions on a time scale of hours. Few regulatory events occurred in both healthy and obese mice. Thus, our transomics network analysis revealed that regulation of glucose-responsive liver metabolism is mediated through different mechanisms in healthy and obese states. Rapid changes in allosteric regulators and substrates and in gene expression dominate the healthy state, whereas slow changes in gene expression dominate the obese state.
SummaryCellular signaling processes can exhibit pronounced cell-to-cell variability in genetically identical cells. This affects how individual cells respond differentially to the same environmental stimulus. However, the origins of cell-to-cell variability in cellular signaling systems remain poorly understood. Here, we measure the dynamics of phosphorylated MEK and ERK across cell populations and quantify the levels of population heterogeneity over time using high-throughput image cytometry. We use a statistical modeling framework to show that extrinsic noise, particularly that from upstream MEK, is the dominant factor causing cell-to-cell variability in ERK phosphorylation, rather than stochasticity in the phosphorylation/dephosphorylation of ERK. We furthermore show that without extrinsic noise in the core module, variable (including noisy) signals would be faithfully reproduced downstream, but the within-module extrinsic variability distorts these signals and leads to a drastic reduction in the mutual information between incoming signal and ERK activity.
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