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PubMed2005

cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network.

Expression of the wnt8 gene is the key transcriptional motivator of an intercellular signaling loop which drives endomesoderm specification forward early in sea urchin embryogenesis. This gene was predicted by network perturbation analysis to be activated by inputs from the blimp1/krox gene, itself expressed zygotically in the endomesoderm during cleavage; and by a Tcf1/beta-catenin input. The implication is that zygotic expression of wnt8 is stimulated in neighboring cells by its own gene product, since reception of the Wnt8 ligand causes beta-catenin nuclearization. Here, the modular cis-regulatory system of the wnt8 gene of Strongylocentrotus purpuratus was characterized functionally, and shown to respond to blockade of both Blimp1/Krox and Tcf1/beta-catenin inputs just as does the endogenous gene. The genomic target sites for these factors were demonstrated by mutation in one of the cis-regulatory modules. The Tcf1/beta-catenin and Blimp1/Krox inputs are both necessary for normal endomesodermal expression mediated by this cis-regulatory module; thus, the genomic regulatory code underlying the predicted signaling loop thus resides in the wnt8 cis-regulatory sequence. In a second regulatory region, which initiates expression in micromere and macromere descendant cells early in cleavage, Tcf1 sites act to repress ectopic transcription in prospective ectoderm cells.

Animals↗

PubMed1996

The pilA regulatory gene modulates the pilus-mediated adhesion of Neisseria meningitidis by controlling the transcription of pilC1.

Adherence to eukaryotic cells is essential in the pathogenesis of Neisseria meningitidis. Pilus-mediated adhesion has been shown to play an essential role in this process. Pilin, the pilus major subunit, and two pilus associated proteins, PilC1 and PilC2, are key components in meningococcal adhesiveness. Phase and/or antigenic variation of these molecules are the only identified means by which N. meningitidis modulates pilus-mediated adhesion. PilA/PilB is a pleiotropic regulatory system first characterized in Neisseria gonorrhoeae where it controls pilin gene transcription. Similar alleles are found in N. meningitidis. To address the role of this regulatory pathway in N. meningitidis, we engineered a meningococcal pilA mutant strain and analysed the consequences of this mutation on pilus-mediated adhesion using epithelial Hec-1-B cells. This mutation resulted in a threefold reduction in adhesiveness. As no change in the amount of pilin nor in pilin gene mRNA was detected, we compared the expression of the pilC genes in both pilA and parental strains. Two transcriptional fusions pilC1-lacZ and pilC2-lacZ were constructed. A threefold reduction in beta-galactosidase activity was observed in the pilA mutant strain harbouring the pilC1-lacZ fusion. No effect of the pilA mutation on beta-galactosidase activity was observed in the strain carrying the pilC2-lacZ fusion. Gel retardation experiments confirmed that the PilA protein binds to the promoter region of pilC1 but not of pilC2. Taken together, these data demonstrate that PilA modulates meningococcal adhesiveness via the transcription of pilC1. Thus, in addition to phase variation, a more co-ordinate and responsive system may allow a fine adaptation of adhesiveness of meningococci to various environmental signals.

Bacterial Adhesion↗

PubMed1996

Quantitative functional interrelations within the cis-regulatory system of the S. purpuratus Endo16 gene.

Embryonic expression of the Endo16 gene of Strongylocentrotus purpuratus is controlled by interactions with at least 13 different DNA-binding factors. These interactions occur within a cis-regulatory domain that extends about 2300 bp upstream from the transcription start site. A recent functional characterization of this domain reveals six different subregions, or cis-regulatory modules, each of which displays a specific regulatory subfunction when linked with the basal promoter and in some cases various other modules (C.-H. Yuh and E. Davidson (1996) Development 122, 1069-1082). In the present work, we analyzed quantitative time-course measurements of the CAT enzyme output of embryos bearing expression constructs controlled by various Endo16 regulatory modules, either singly or in combination. Three of these modules function positively in that, in isolation, each is capable of promoting expression in vegetal plate and adjacent cell lineages, though with different temporal profiles of activity. Models for the mode of interaction of the three positive modules with one another were tested by assuming mathematical relations that would generate, from the measured single module time courses, the experimentally observed profiles of activity obtained when the relevant modules are physically linked in the same construct. The generated and observed time functions were compared, and the differences were minimized by least squares adjustment of a scale parameter. When the modules were tested in context of the endogenous promoter region, one of the positive modules (A) was found to increase the output of the others (B and G), by a constant factor. In contrast, a solution in which the time-course data of modules A and B are multiplied by one another was required for the interrelations of the positive modules when a minimal SV40 promoter was used. One interpretation is that, in this construct, each module independently stimulates the basal transcription complex. We used a similar approach to analyze the repressive activity of the three Endo16 cis-regulatory modules that act negatively in controlling spatial expression. The evidence obtained confirms that the repressive modules act only by affecting the output of module A (C.-H. Yuh and E. Davidson (1996) Development 122, 1069-1082). A new hierarchical model of the cis-regulatory system was formulated in which module A plays a central integrating role, and which also implies specific functions for certain DNA-binding sites within the basal promoter fragment of the gene. Additional kinetic experiments were then carried out, and key aspects of the model were confirmed.

Animals↗

PubMed1986

Gastrointestinal regulatory peptides modulate in vitro immune reactions of mouse lymphoid cells.

The effects of six gastrointestinal regulatory peptides (beta-endorphin, substance P, metenkephalin, vasoactive intestinal peptide, bombesin, and somatostatin) on mouse lymphocytes stimulated with concanavalin A, lipopolysaccharide, phytohemagglutinin, or alloantigens were evaluated. Lymphocytes were stimulated in vitro and the influences of exogenously adding varying concentrations of neuropeptides (10(-6)-10(-11) M) on the incorporation of [methyl-3H-]thymidine were determined. The roles of cell density and antigen concentration on neuropeptide induced immunomodulation were also assessed. We observed that vasoactive intestinal peptide (VIP) would significantly inhibit the response of B10 lymphocytes to concanavalin A (54%) and phytohemagglutinin (56%) but not to lipopolysaccharide (16%). The VIP-induced inhibition was progressively diminished as the neuropeptide concentration was reduced to 10(-11) M. By 24 hr after stimulation the lymph node cells were refractory to the inhibitory effects of VIP. In addition, VIP would not inhibit B10 lymph node cells from responding to B10. K spleen cells in mixed, one-way lymphocyte cultures. The other five peptides did not influence the in vitro responses. The potential role of neuropeptides in the pathophysiology of immunologic-based disorders is discussed.

Animals↗

PubMed1995

A new regulatory element modulates homoserine lactone-mediated autoinduction of Ti plasmid conjugal transfer.

Conjugal transfer of the Agrobacterium tumefaciens nopaline-type Ti plasmid pTiC58 is induced by agrocinopines A and B, opines secreted by crown gall tumors induced by the bacterium. This regulation functions through the transcriptional repressor, AccR. However, actual transcription of the tra genes is regulated by autoinduction through the activator TraR and the substituted homoserine lactone second messenger, Agrobacterium autoinducer (AAI). We have identified a new regulatory element that modulates the response of TraR to AAI. The gene, called traM, suppresses TraR-AAI activation of transcription of tra genes carried on recombinant clones. The suppression could be relieved by increasing the expression of TraR but not by increasing AAI levels. traM is located between traR and traAF on pTiC58 and is transcribed in the clockwise direction. The 306-bp gene encodes an 11.2-kDa protein showing no significant relatedness to other proteins in the databases. Mutations in traM in pTiC58 conferred a transfer-constitutive phenotype, and strains harboring the Ti plasmid produced easily detectable amounts of AAI. These same mutations engineered into the transfer-constitutive Ti plasmid pTiC58 delta accR conferred a hyperconjugal phenotype and very high levels of AAI production. Expression of traM required TraR, indicating that transcription of the gene is regulated by the autoinduction system. TraM had no effect on the expression of traR, demonstrating that the suppressive effect is not due to repression of the gene encoding the activator. These results suggest that TraM is not a direct transcriptional regulator. Since the suppressive effect is demonstrable only when traM is overexpressed with respect to traR, we suggest that TraM functions to sequester TraR from the very small amounts of AAI produced under conditions when the agrocinopines are not present.

4-Butyrolactone↗

PubMed1996

Developmental expression of synthetic cis-regulatory systems composed of spatial control elements from two different genes.

Synthetic cis-regulatory systems consisting of positively and negatively acting cis-regulatory modules of the Endo16 gene were combined with the lineage-specific regulatory element of the SM50 gene associated with a reporter and injected into eggs of sea urchins. We show here that synthetic cis-regulatory systems consisting of the positive Endo16 regulatory elements linked with the SM50 regulatory element are expressed spatially exactly as the sum of the individual endodermal and skeletogenic expression patterns. In combination, both lineage-specific positive regulatory elements function autonomously. However, addition of the Endo16 regulatory module that represses ectopic skeletogenic expression of Endo16 receptor constructs does not affect expression driven by the SM50 regulatory elements in the same skeletogenic cells. The repression function of this element is thus dedicated to control of the positive spatial output of the Endo16 regulatory system.

Animals↗

PubMed1995

cDNA structure of rabbit C4b-binding protein alpha-chain. Preserved sequence motive in complement regulatory protein modules which bind C4b.

A full length cDNA clone for the alpha-chain of the rabbit complement regulatory protein C4b-binding protein (C4BP) was isolated from a liver cDNA library. The clone encoded an open reading frame of 597 amino acids, which included a signal peptide, eight short consensus repeats (SCR) and a carboxy terminal non-repeat region. Gel filtration of rabbit plasma and testing of fractions for factor I cofactor activity (C4BP-like) revealed two peaks of activity, the one with highest molecular weight corresponding in size to that of human C4b-binding protein. Comparison of the rabbit C4BP alpha-chain sequence with other SCR containing C3b/C4b binding proteins revealed highest sequence similarities between the second SCRs in C4BP from rabbit, human and murine species and SCRs at corresponding position in complement receptor 1 (CR1) whereas in decay accelerating factor (DAF), the third SCR was most similar. A conserved sequence motive was identified in these C4b-binding SCRs.

Amino Acid Sequence↗

PubMed1991

The effect of high hydrostatic pressure on the modulation of regulatory enzymes from spinach chloroplasts.

High hydrostatic pressure enhanced the specific activity of regulatory enzymes of the Benson-Calvin cycle (fructose-1,6-bisphosphatase, glyceraldehyde-3-P dehydrogenase, phosphoribulokinase) which are modulated by the ferredoxin-thioredoxin system. High activity of chloroplast fructose-1,6-bisphosphatase required dithiothreitol, fructose 1,6-bisphosphate, and Ca2+. At 100 bar the A0.5 for fructose 1,6-bisphosphate (0.3 mM) was lower than that at 1 bar (1.5 mM), whereas similar variations of pressure did not alter the A0.5 for Ca2+ (55 microM). The response of chloroplast glyceraldehyde-3-P dehydrogenase exposed to 500 bar was a 4-fold increase in the NADP-linked activity; conversely, the NAD-dependent activity remained unchanged. The concerted action of high pressure and Pi (or ATP), both activators of chloroplast glyceraldehyde-3-P dehydrogenase, led to inactivation. On the other hand, the activity of phosphoribulokinase increased 10-fold when the enzyme was incubated at 1500 bar; the activation process was strictly dependent on the presence of dithiothreitol. At variance with these enzymes, bovine liver fructose-1,6-bisphosphatase, yeast glyceraldehyde-3-P dehydrogenase, and chloroplast ribulose 1,5-bisphosphate carboxylase, whose activities are not modulated by reduced thioredoxin, were inactivated by high pressure. The comparison of oligomeric enzymes revealed that the stimulation of specific activity by high pressure correlated with thioredoxin-mediated activation, and it did not depend on a particular subunit composition. Present results show that high pressure resembled thioredoxin, cosolvents, and chaotropic anions in its action on regulatory enzymes of the Benson-Calvin cycle. The comparison of physiological and non-physiological modulators suggested that thioredoxin-mediated modifications of noncovalent interactions is an important event in light-dependent regulation of chloroplast enzymes.

Animals↗

PubMed2003

Conservation of regulatory elements between two species of Drosophila.

BACKGROUND: One of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arrangement are poorly understood. However, the genomes of suitably diverged species help to predict regulatory elements based on the generally accepted assumption that conserved blocks of genomic sequence are likely to be functional. To judge the efficacy of strategies that prefilter by sequence conservation it is important to know to what extent the converse assumption holds, namely that functional elements common to both species will fall within these conserved blocks. The recently completed sequence of a second Drosophila species provides an opportunity to test this assumption for one of the experimentally best studied regulatory networks in multicellular organisms, the body patterning of the fly embryo. RESULTS: We find that 50%-70% of known binding sites reside in conserved sequence blocks, but these percentages are not greatly enriched over what is expected by chance. Finally, a computational genome-wide search in both species for regulatory modules based on clusters of binding sites suggests that genes central to the regulatory network are consistently recovered. CONCLUSIONS: Our results indicate that binding sites remain clustered for these "core modules" while not necessarily residing in conserved blocks. This is an important clue as to how regulatory information is encoded in the genome and how modules evolve.

Algorithms↗

PubMed2006

Regulatory peptides modulate adhesion of polymorphonuclear leukocytes to bronchial epithelial cells through regulation of interleukins, ICAM-1 and NF-kappaB/IkappaB.

A complex network of regulatory neuropeptides controls airway inflammation reaction, in which airway epithelial cells adhering to and activating leukocytes is a critical step. To study the effect of intrapulmonary regulatory peptides on adhesion of polymorphonuclear leukocytes (PMNs) to bronchial epithelial cells (BECs) and its mechanism, several regulatory peptides including vasoactive intestinal peptide (VIP), epidermal growth factor (EGF), endothelin-1 (ET-1) and calcitonin gene-related peptide (CGRP), were investigated. The results demonstrated that VIP and EGF showed inhibitory effects both on the secretion of IL-1, IL-8 and the adhesion of PMNs to BECs, whereas ET-1 and CGRP had the opposite effect. Anti-intercellular adhesion molecule-1 (ICAM-1) antibody could block the adhesion of PMNs to ozone-stressed BECs. Using immunocytochemistry and reverse transcription-polymerase chain reaction (RT-PCR), it was shown that VIP and EGF down-regulated the expression of ICAM-1 in BECs, while ET-1 and CGRP up-regulated ICAM-1 expression. NF-kappaB inhibitor MG132 blocked ICAM-1 expression induced by ET-1 and CGRP. Furthermore, in electric mobility shift assay (EMSA), VIP and EGF restrained the binding activity of NF-kappaB to the NF-kappaB binding site within the ICAM-1 promoter in ozone-stressed BECs, while CGRP and ET-1 promoted this binding activity. IkappaB degradation was consistent with NF-kappaB activation. These observations indicate that VIP and EGF inhibit inflammation, while ET-1 and CGRP enhance the inflammation reaction.

Animals↗

PubMed2001

The MHC-specific enhanceosome and its role in MHC class I and beta(2)-microglobulin gene transactivation.

The promoter regions of MHC class I and beta(2)-microglobulin (beta(2)m) genes possess a regulatory module consisting of S, X, and Y boxes, which is shared by MHC class II and its accessory genes. In this study we show that, similar to MHC class II, the SXY module in MHC class I and beta(2)m promoters is cooperatively bound by a multiprotein complex containing regulatory factor X, CREB/activating transcription factor, and nuclear factor Y. Together with the coactivator class II transactivator this multiprotein complex drives transactivation of these genes. In contrast to MHC class II, the multiprotein complex has an additional function in the constitutive transactivation of MHC class I and beta(2)m genes. The requirement for all transcription factors in the complex and correct spacing of the binding sites within the SXY regulatory module for complex formation and functioning of this multiprotein complex strongly suggests that this complex can be regarded as a bona fide enhanceosome. The general coactivators CREB binding protein, p300, general control nonderepressible-5, and p300/CREB binding protein-associated factor exert an ancillary function in MHC class I and beta(2)m transactivation, but exclusively through the class II transactivator component of this enhanceosome. Thus, the SXY module is the basis for a specific enhanceosome important for the constitutive and inducible transactivation of MHC class I and beta(2)m genes.

Cyclic AMP Response Element-Binding Protein↗

PubMed1998

Functional characterization of the human CYP1A1 negative regulatory element: modulation of Ah receptor mediated transcriptional activity.

The mechanisms that underly the regulation of human CYP1A1 have merited considerable attention because of their association both with toxic outcomes and the etiology of several cancers. Previous work conducted in this laboratory has identified a negative regulatory element (NRE) in the 5' region of this gene that appeared to modulate CYP1A1 transcriptional activity. This NRE is present in two functional copies, a high affinity 21-bp palindrome centered at position -784, and an additional element found within a GC-rich region between position -728 and -558. In this report, the regulatory function of the NREs in the context of the CYP1A1 promoter was evaluated. This was accomplished by substituting mutated elements for the corresponding wild-type element in a vector that contained human CYP1A1 sequences positions -1140 to +59 directing the transcription of the chloramphenicol acetyltransferase reporter gene. Expression vectors containing specific mutations in each or both NREs were characterized. We show that eliminating the binding of the CYP1A1 repressor protein to one or both repressor motifs results in a significant 2- to 3-fold increase in the inducibility of CYP1A1 promoter activity. Although mutation of both sites appeared to result in an increase in inducibility over that observed with only one site mutated, the effect was not additive. Such aberrant transcriptional activity correlates with the highly inducible aryl hydrocarbon hydroxylase phenotype that is a reported marker for individuals predisposed to lung cancer. Mutation of the NRE, or more likely, the cognate repressor protein(s), may provide a genetic basis for this phenotype.

Base Sequence↗

PubMed2004

cis-Regulatory control circuits in development.

During development, an organism undergoes many rounds of pattern formation, generating ever-greater complexity with each ensuing round of cell division and specification. The instructions for executing this process are encoded in the cis-regulatory modules that direct the expression of developmental transcription factors and signaling molecules. Each transcription factor binding site within a cis-regulatory module contributes information about when, where, or how much a gene is turned on, and by dissecting the modules driving a given gene, all the inputs governing expression of the gene can be accurately identified. Furthermore, by mapping the output of each gene to the inputs of other genes, it is possible to reverse engineer developmental circuits and even whole networks. At this higher level of organization, common bilaterian strategies for specifying progenitor fields, locking down regulatory states, and driving development forward emerge.

Animals↗

PubMed2005

Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.

BACKGROUND: This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. Experimental procedures for this are slow and costly, and computational methods are hard, because they lack positional information. RESULTS: We present a novel statistical method, the "fluffy-tail test", to recognise regulatory DNA. We exploit one of the basic informational properties of regulatory DNA: abundance of over-represented transcription factor binding site (TFBS) motifs, although we do not look for specific TFBS motifs, per se . Though overrepresentation of TFBS motifs in regulatory DNA has been intensively exploited by many algorithms, it is still a difficult problem to distinguish regulatory from other genomic DNA. CONCLUSION: We show that, in the data used, our method is able to distinguish cis-regulatory modules by exploiting statistical differences between the probability distributions of similar words in regulatory and other DNA. The potential application of our method includes annotation of new genomic sequences and motif discovery.

Algorithms↗

PubMed2000

Modular regulation of cGATA-5 gene expression in the developing heart and gut.

The evolutionarily conserved GATA-5 transcription factor is an early and persistent marker of heart and gut development in diverse vertebrate species. To search for control regions that might regulate the chicken GATA-5 (cGATA-5) gene, we assayed a set of cGATA-5/lacZ constructs in transgenic mice and found evidence for two functionally conserved control regions that regulate different facets of cGATA-5 gene expression. The more distal control region is activated in embryonic endoderm at the head-fold stage, whereas the other control region contains a regulatory module that is activated in a restricted region of endoderm following closure of the gut tube. Remarkably, the latter control region also contains a complex regulatory module that is activated in the cardiac crescent at the head-fold stage and subsequently functions in several mesodermal components of the developing heart, including the outer (epicardial) layer. We discuss these results in terms of possible contributions of epicardial-derived cells to the formation of heart valves, conduction tissue, and compact myocardium. These transgenes thus reveal, and provide a means to further analyze, transcriptional programs for several facets of heart morphogenesis and gut development.

Animals↗

PubMed1986

Gastrointestinal regulatory peptides modulate mouse lymphocyte functions under serum-free conditions in vitro.

Conditions are described for performing mitogen (Concanavalin A, Con A; lipopolysaccharide, LPS) and mixed lymphocyte reaction (MLR) cultures using serum-free medium. The effects of exogenously adding several gastrointestinal regulatory peptides (beta-endorphin, substance P, met-enkephalin, vasoactive intestinal peptide, bombesin and somatostatin) on the incorporation of 3H-methyl-thymidine was determined. It was observed that mitogen stimulation of lymph node cells with Con A was inhibited (70% of control) by vasoactive intestinal peptide (VIP) but spleen cells stimulated by LPS were insensitive to immunomodulation (98% of control). The ability of VIP to inhibit Con A induced thymidine incorporation was concentration dependent (10(-6) to 10(-18) M) and was not attributable to kinetic shifts or cell toxicity. None of the other tested neuropeptides affected Con A or LPS induced blastogenesis. MLR cultures were inhibited by VIP, beta-endorphin and somatostatin in a biphasic manner with maximal inhibition observed at 10(-8) to 10(-12) M. Both substance P and bombesin exhibited slight immunoenhancing properties at 10(-14) to 10(-18) M. Met-enkephalin was ineffective as an immunomodulator of MLR cultures. The utility of using serum-free medium in identifying neuropeptides with immunomodulatory properties are discussed.

Animals↗

PubMed2005

Modulation of regulatory factors involved in cholesterol metabolism in response to feeding of pravastatin- or cholesterol-supplemented diet in chickens.

mRNA transcripts encoding multiple proteins from the cholesterol biosynthetic and uptake pathways in livers are controlled by sterol regulatory element binding protein-2 (SREBP-2), a membrane-bound mammalian transcription factor. The aims of the present study were to investigate whether SREBP-2 responds to plasma cholesterol levels and modulates expression of factors involved in the cholesterol metabolism of chickens. Supplementing the diets of chickens with 0.1% pravastatin, a drug used to control hypercholesterolemia, decreased plasma LDL-cholesterol concentrations. It also increased levels of the nuclear forms of SREBP-2 and increased gene expression of 3-hydroxy-3-methylglutaryl CoA reductase (HMGR) and low-density lipoprotein receptor (LDLr) in livers, relative to a control group. In contrast, feeding of 3% cholesterol-supplemented diet increased plasma total- and LDL-cholesterol concentrations but decreased levels of nuclear forms of SREBP-2 and reduced gene expression of HMGR and LDLr. However, the LDL-binding activities of chicken liver membranes were not affected by plasma cholesterol concentrations or by hepatic levels of the nuclear form of SREBP-2. LDL-binding proteins were detected as bands of 90 and 515 kDa on a ligand blot and the intensity of these bands was unaffected by pravastatin and cholesterol supplementation. These findings suggest that the cholesterol biosynthetic pathway is regulated by the nuclear form of SREBP-2 in chickens as well as in mammals, but that there may be species-specific differences in the regulatory mechanisms of hepatic cholesterol uptake.

Animals↗

PubMed1980

Molecular interactions in biomedicine: modulation of regulatory behavior by cross reactivity: relevance to analysis of receptor function.

The influence of cross reactivity on biomolecular regulation is not frequently incorporated into theoretical analysis and is often eliminated by experimental design. Nonetheless, cross reactive molecules produce effects on binding which may considerably modulate their behavior in quite diverse systems, i.e., drug-tissue receptor, antigen-antibody, substrate-enzyme, protein-DNA and hormone-tumor receptor interactions. In particular, certain effects vary at different concentrations suggesting a simple control mechanism.

Allosteric Regulation↗