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Evidence for the separate regulation of the human papillomavirus type 11 E7 and E6 promoters by Viral cis sequences near the E6 promoter.

The human papillomavirus type 11 (HPV-11) E7 protein can modulate host cell functions and is required for papilloma formation, but little is known concerning the regulation of its expression. This study was designed to determine whether the viral upstream regulatory region controlled expression from the E7 promoter and whether cis sequences differentially regulated E6 and E7 expression in laryngeal mucosal keratinocytes, the natural target cells for this virus. Reporter constructs were designed to study expression of the luciferase gene from the HPV-11 E7 promoter in its natural position downstream of a functional E6 promoter. E7 expression, like E6 expression, required upstream regulatory sequences. However, E7 expression was less sensitive to repression by viral E2 protein and to mutation of the Spl binding site adjacent to the E2 binding site. Moreover, there was differential sensitivity of the two promoters to mutation of the E6 TATA box, with E7 expression more affected than E6 expression. These findings show that, in the normal host cells for this virus, the E6 and E7 promoters can be independently regulated by the cis regulatory region adjacent to the E6 promoter.

DNA Transposable Elements↗

Promoter and leader sequences of the spinach PsaD and PsaF genes direct an opposite light response in tobacco cotyledons: PsaD sequences downstream of the ATG codon are required for a positive light response.

Subunits II and III of the photosystem I reaction centre are encoded by the nuclear genes PsaD and PsaF, respectively. In spinach, the expression of both genes is highly synchronized with regard to time, space and in response to stimulators such as light. Nevertheless, promoter sequences as well as the design and location of regulatory elements are strikingly different. Promoter and leader of PsaF, when fused to the GUS reporter gene, direct a positive light response in the cotyledons of transgenic tobacco seedlings. In contrast, the equivalent PsaD regions confer a negative-light regulation to the GUS gene. If a 6-kb fragment that contains 1802 bp of the promoter, the transcription unit as well as additional 2.5 kb downstream of the PsaD gene is introduced into tobacco, the transcript level from the PsaD transgene is positively light-regulated in tobacco cotyledons. Thus, regulatory elements of the spinach PsaD and PsaF promoters are arranged in a very different way and essential cis-determinants for the positive light response of the PsaD gene can be located within the coding region and/or even further downstream.

Base Sequence↗

Kinetics and characteristics of replication-competent revertants derived from self-inactivating foamy virus vectors.

In this study, self-inactivating (SIN) retroviral vectors based on feline foamy virus (FFV) were constructed and analysed. The FFV SIN vectors were devoid of the core FFV long terminal repeat promoter plus upstream sequences but contained all structural and regulatory genes. This design allowed sensitive detection of replication-competent revertants (RCRs). The FFV SIN vectors efficiently transduced the green fluorescence protein into recipient cells. However, RCRs appeared after serial passages of transduced cells. In all RCR clones analysed, parts of the heterologous cytomegalovirus immediate early promoter, originally driving expression of the FFV vector genome, were taken up to restore the deleted SIN promoter function required for replication competence. The RCRs were strongly reduced in replication capacity compared with the parental replication-competent vectors containing the FFV promoter. In all RCR genomes analysed, the uptake of the heterologous promoter was accompanied by deletion of almost the complete marker gene. Although the RCRs described in this study may not have the capacity to spread in humans and animals, they may pose a theoretical risk, for instance during transduction of haematopoietic stem cells. Thus, FV-based SIN vectors require additional genetic modifications in order to avoid RCRs.

Base Sequence↗

Cloning, sequencing and characterization of the ccpA gene from Enterococcus faecalis.

Enzymes involved in the metabolism of complex carbon and energy sources are unnecessary under conditions of abundant, readily metabolisable nutrients such as glucose or fructose. The repression of these enzymes by glucose has been termed carbon catabolite repression. Mechanisms involved in the carbon catabolite repression in gram-positive bacteria are known to differ from those of gram-negative bacteria such as Escherichia coli. It appears to be mediated by transcriptional repression, requiring trans-acting CcpA, a member of the LacI-GalR family of bacterial regulatory proteins and a cis-acting consensus sequence, designated cre. Here, we report the cloning and characterisation of the chromosomal ccpA gene from Enterococcus faecalis JH2-2. This gene is predicted to encode a 333 amino acids protein with nearly 75% identity to CcpA of Lactobacillus casei.

Amino Acid Sequence↗

An ATF/CREB binding site is required for virus induction of the human interferon beta gene [corrected].

We report the characterization of a distinct regulatory element of the human interferon beta (HuIFN-beta) gene promoter, which we designate PRDIV (positive regulatory domain IV). In previous studies, sequences between -104 and -91 base pairs upstream from the start site of transcription were shown to be required for maximal levels of virus induction in mouse L929 cells. We have localized the essential sequence in this region extending from -99 to at least -91, and we show that this sequence is a binding site for a protein of the activating transcription factor/cAMP response element binding protein (ATF/CREB) family of transcription factors. Mutations in PRDIV that decrease the affinity of one member of this family (ATF-2/CRE-BP1) decrease the level of virus induction in vivo. Moreover, multiple copies of PRDIV can confer both virus and cAMP inducibility upon a minimal promoter in L929 cells, while it is constitutively active in HeLa cells. We conclude that PRDIV is a distinct regulatory element of the HuIFN-beta promoter and that the signal transduction pathways involved in virus and cAMP induction may partially overlap.

Animals↗

clpC and clpP1P2 gene expression in Corynebacterium glutamicum is controlled by a regulatory network involving the transcriptional regulators ClgR and HspR as well as the ECF sigma factor sigmaH.

The ATP-dependent protease Clp plays important roles in the cell's protein quality control system and in the regulation of cellular processes. In Corynebacterium glutamicum, the levels of the proteolytic subunits ClpP1 and ClpP2 as well as of the corresponding mRNAs were drastically increased upon deletion of the clpC gene, coding for a Clp ATPase subunit. We identified a regulatory protein, designated ClgR, binding to a common palindromic sequence motif in front of clpP1P2 as well as of clpC. Deletion of clgR in the DeltaclpC background completely abolished the increased transcription of both operons, indicating that ClgR activates transcription of these genes. ClgR activity itself is probably controlled via ClpC-dependent regulation of its stability, as ClgR is only present in DeltaclpC and not in wild-type cells, whereas the levels of clgR mRNA are comparable in both strains. clpC, clpP1P2 and clgR expression is induced upon severe heat stress, however, independently of ClgR. Identification of the heat-responsive transcriptional start sites in front of these genes revealed the presence of sequence motifs typical for sigmaECF-dependent promoters. The ECF sigma factor sigmaH could be identified as being required for transcriptional activation of clpC, clpP1P2 and clgR in response to severe heat stress. A second heat-responsive but sigmaH-independent promoter in front of clgR could be identified that is subject to negative regulation by the transcriptional repressor HspR. Taken together, these results show that clpC and clpP1P2 expression in C. glutamicum is subject to complex regulation via both independent and hierarchically organized pathways, allowing for the integration of multiple environmental stimuli. Both the ClgR- and sigmaH-dependent regulation of clpC and clpP1P2 expression appears to be conserved in other actinomycetes.

Adenosine Triphosphatases↗

Na+/H+ exchanger 1 deficiency alters gene expression in mouse brain.

Na(+)/H(+) exchanger 1 (NHE1) is well known to function as a major regulator of intracellular pH (pH(i)). It is activated by low pH(i) and exchanges extracellular Na(+) for intracellular H(+) to maintain cellular homeostasis. Despite the fact that we now have evidence suggesting other roles for NHE1, there has been no comprehensive study investigating its role as a signaling molecule. Toward this aim, we used in this study NHE1 null mutant mice and cDNA microarrays to investigate the effects of NHE1 on global gene expression in various regions of the brain, e.g., cortex, hippocampus, brain stem-diencephalon, and cerebellum. We found that a total of 35 to 79 genes were up- or downregulated in each brain region, with the majority being downregulated. The effect of NHE1 null mutation on gene expression is region specific, and only 11 genes were changed in all brain regions studied. Further analysis of the cis-regulatory regions of downregulated genes revealed that transcription suppressors, BCL6 and E4BP4, were probable candidates that mediated the inhibitory effect of NHE1 null mutation. One of the genes, MCT-13, was not only downregulated in the NHE1 null mutant brain but also in tissue cultures treated with an NHE1 inhibitor. We conclude that 1) a relatively small number of genes were altered in the NHE1 null mouse brain; 2) the effects of NHE1 null mutation on gene expression are region specific; and 3) several genes implicated in neurodegeneration have altered expression, potentially offering a molecular explanation for the phenotype of the NHE1 null mouse.

Acidosis↗

High-throughput PCR screening of genes for three-component regulatory system putatively involved in quorum sensing from low-G + C gram-positive bacteria.

Quorum sensing of gram-positive bacteria is often regulated by three-component regulatory system composed of autoinducing peptide, sensor kinase and response regulator. We used PCR to study a gene cassette encoding this three-component regulatory system. Degenerate primers were designed from consensus amino acid sequences in the HPK10 subfamily, mostly involved in quorum sensing. Products amplified from genomic DNA of Lactobacillus, Enterococcus, and Clostridium species were cloned and sequenced; their deduced amino acid sequences were similar to those of members of the HPK10 subfamily. Complete genes for the putative gene cassette were cloned by inverse PCR from L. paracasei E93490 and L. plantarum WCFS6. Phylogenetic analysis grouped the cloned putative HPKs into the HPK10 subfamily. These results indicated the usefulness of this high-throughput gene screening and suggested that the three-component regulatory gene cassette are widely present.

Amino Acid Sequence↗

Mapping Dmef2-binding regulatory modules by using a ChIP-enriched in silico targets approach.

Mapping the regulatory modules to which transcription factors bind in vivo is a key step toward understanding of global gene expression programs. We have developed a chromatin immunoprecipitation (ChIP)-chip strategy for identifying factor-specific regulatory regions acting in vivo. This method, called the ChIP-enriched in silico targets (ChEST) approach, combines immunoprecipitation of cross-linked protein-DNA complexes (X-ChIP) with in silico prediction of targets and generation of computed DNA microarrays. We report the use of ChEST in Drosophila to identify several previously unknown targets of myocyte enhancer factor 2 (MEF2), a key regulator of myogenic differentiation. Our approach was validated by demonstrating that the identified sequences act as enhancers in vivo and are able to drive reporter gene expression specifically in MEF2-positive muscle cells. Presented here, the ChEST strategy was originally designed to identify regulatory modules in Drosophila, but it can be adapted for any sequenced and annotated genome.

Animals↗

Differential expression of CYP102 in Bacillus megaterium by 17-beta-estradiol and 4-sec-butylphenol.

Previously we have reported the induction of CYP102 in Bacillus megaterium by 17beta-estradiol (E2) and 4-sec-butylphenol (4-sBP). Electrophoretic mobility shift assay analyses demonstrated that E2 and 4-sBP both cause a dose-dependent disassociation of the Bm3R1 repressor protein from its binding site on the operator sequence of the CYP102 gene. Equimolar combinations of E2 and 4-sBP demonstrated additive induction of CYP102 compared to equivalent samples of E2 and 4-sBP added alone. Two gene constructs were used in this investigation. One construct designated BMC143 contained the entire regulatory region of CYP102. The other gene construct, designated BMA45, had the "Barbie box" sequence deleted. While the induction of CYP102 by 4-sBP was much higher in the BMC 143 construct, E2 induced CYP102 in both constructs to the same extent. This difference in induction of CYP102 by these two inducers indicates that they act at different sites, either on the Bm3R1 repressor protein or on positive regulatory sites, or that they act, in part, through different mechanisms.

Bacillus megaterium↗

A bifunctional genetic regulatory element of the rat dopamine beta-hydroxylase gene influences cell type specificity and second messenger-mediated transcription.

Dopamine beta-hydroxylase, the enzyme which converts dopamine to norepinephrine, is expressed in a cell type-restricted pattern in neuroendocrine tissue. A segment of the rat gene containing 395 bases of 5'-flanking sequence regulates expression of a reporter gene in a cell type-selective pattern in mammalian cell cultures. Using deletion mutants of the 5'-flanking sequence, we have identified a 30-base genetic regulatory element, designated DB1, which enhances transcription from a heterologous promoter 5-20-fold in neuroendocrine cell lines. DB1-specific DNA-protein complexes are found in nuclear extracts from all cell lines examined, but the migration pattern differs between cell lines. The 5'-flanking region of the dopamine beta-hydroxylase gene is also responsive to cyclic AMP and phorbol ester treatment of SHSY-5Y neuroblastoma cells. The simultaneous presence of both effectors results in synergistic increases in DBH1 mRNA and reporter gene activity. The second messenger regulatory element was localized to the region containing the DB1 element, and reporter plasmids containing multiple copies of the DB1 element are responsive to treatment with inducers. The results of this study identify a cis-acting regulatory element which influences both cell type selectivity and second messenger responsiveness of the rat dopamine beta-hydroxylase gene.

Animals↗

The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli.

The tRNA(m5U54)methyltransferase, whose structural gene is designated trmA, catalyzes the formation of 5-methyluridine in position 54 of all tRNA species in Escherichia coli. The synthesis of this enzyme has previously been shown to be both growth rate dependent and stringently regulated, suggesting regulatory features similar to those of rRNA. We have determined the complete nucleotide sequence of the trmA operon in E. coli and the sequence of the trmA promoter region in Salmonella typhimurium and also analyzed the transcriptional regulation of the gene. The trmA and the btuB (encoding the vitamin B12 outer membrane receptor protein) promoters are divergent promoters separated by 102 bp between the transcriptional start sites. The trmA promoters of both E. coli and S. typhimurium share promoter elements with the rRNA P1 promoter. The sequence downstream from the -10 region of the trmA promoter is homologous to the discriminatory region found in stringently regulated promoters. Next to and upstream from the -10 region is a sequence, TCCC, in the trmA promoter that is present in all of the seven rRNA P1 promoters and in some tRNA promoters but not in any other sigma 70 promoter. However, a similar motif is also found in promoters transcribed by the heat shock sigma factor sigma 32. The trmA gene is transcribed as a monocistronic operon, and the 3' end of the transcript is shown to be located downstream from a dyad symmetry region not followed by a poly(U) stretch. Using a trmA-cat operon fusion, we show that the growth rate-dependent regulation of trmA resembles that of rRNA and operates at the level of transcription.

Amino Acid Sequence↗

Detection of genes that are differentially expressed during mouse embryogenesis by genetic trapping strategies.

OBJECTIVE: Our objective was to identify novel genes that are expressed in temporally and spatially restricted patterns during mouse embryonic development and organogenesis. STUDY DESIGN: Two genetic trapping reporter constructs that lack transcriptional regulatory sequences were introduced independently into transcriptionally active gene loci by electroporation into mouse embryonic stem cells. Patterns of host gene-reporter construct expression were investigated in differentiated embryonic stem cells, embryoid bodies, and chimeric embryos at various stages of development. RESULTS: Three patterns of host gene-reporter construct expression were observed from the developmental analysis of four vector-integrated cell lines. Reporter expression patterns reflecting developmental regulation, constitutive activity, and developmental inactivation of the host genes were observed. CONCLUSIONS: Two vector-integrated gene loci from cell lines CCE-1C1 and D3-B44 have expression patterns not previously described by genetic trapping. Molecular characterization of these interrupted genes will shed light on their developmental function.

Animals↗

Integrated databases and computer systems for studying eukaryotic gene expression.

MOTIVATION: The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. RESULTS: The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. AVAILABILITY: GeneExpress is available at http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.

Algorithms↗

A gene from Aspergillus nidulans with similarity to URE2 of Saccharomyces cerevisiae encodes a glutathione S-transferase which contributes to heavy metal and xenobiotic resistance.

Aspergillus nidulans is a saprophytic ascomycete that utilizes a wide variety of nitrogen sources. We identified a sequence from A. nidulans similar to the glutathione S-transferase-like nitrogen regulatory domain of Saccharomyces cerevisiae Ure2. Cloning and sequencing of the gene, designated gstA, revealed it to be more similar to URE2 than the S. cerevisiae glutathione S-transferases. However, creation and analysis of a gstA deletion mutant revealed that the gene does not participate in nitrogen metabolite repression. Instead, it encodes a functional theta class glutathione S-transferase that is involved in resistance to a variety of xenobiotics and metals and confers susceptibility to the systemic fungicide carboxin. Northern analysis showed that gstA transcription is strongly activated upon exposure to 1-chloro-2,4-dinitrobenzene and weakly activated by oxidative stress or growth on galactose as a carbon source. These results suggest that nitrogen metabolite repression in A. nidulans does not involve a homolog of the S. cerevisiae URE2 gene and that the global nitrogen regulatory system differs significantly in these two fungi.

Aspergillus nidulans↗

Silencing of gene expression: implications for design of retrovirus vectors.

Transcriptional silencing of retroviruses poses a major obstacle to their use as gene therapy vectors. Silencing is most pronounced in stem cells which are desirable targets for therapeutic gene delivery. Many vector designs combat silencing through cis-modifications of retroviral vector sequences. These designs include mutations of known retroviral silencer elements, addition of positive regulatory elements and insulator elements to protect the transgene from negative position effects. Similar strategies are being applied to lentiviral vectors that readily infect non-dividing quiescent stem cells. Collectively these cis-modifications have significantly improved vector design but optimal expression may require additional intervention to escape completely the trans-factors that scan for foreign DNA, establish silencing in stem cells and maintain silencing in their progeny. Cytosine methylation of CpG sites was proposed to cause retroviral silencing over 20 years ago. However, several studies provide evidence that retrovirus silencing acts through methylase-independent mechanisms. We propose an alternative silencing mechanism initiated by a speculative stem cell-specific "somno-complex". Further understanding of retroviral silencing mechanisms will facilitate better gene therapy vector design and raise new strategies to block transcriptional silencing in transduced stem cells.

Chromatin↗

CPRF4a, a novel plant bZIP protein of the CPRF family: comparative analyses of light-dependent expression, post-transcriptional regulation, nuclear import and heterodimerisation.

Several DNA-binding proteins with conserved basic region/leucine zipper domains (bZIP) have been isolated from parsley. They all recognise defined ACGT-containing elements (ACEs), including ACE(PcCHSII) in the Light Regulatory Unit LRU1 of the CHS promoter which confers light responsiveness. A new member of this Common Plant Regulatory Factor (CPRF) family, designated CPRF4a, has been cloned, which displays sequence similarity to HBP-1a from wheat, as well as to other plant bZIP proteins. CPRF4a specifically binds as a homodimer to ACE(PcCHSII) and forms heterodimers with CPRF1 but not with CPRF2. In adult parsley plants, CPRF2 and CPRF4a mRNAs are found in all tissues and organs in which the chalcone synthase gene CHS is expressed. In protoplasts from suspension cultured cells, UV irradiation (290-350 nm) did not cause an increase in levels of CPRF1, CPRF2, or CPRF4a mRNA, whereas the corresponding CPRF proteins accumulated within 15 min of light treatment. Furthermore, the rapid light-mediated increase of CPRF proteins was insensitive to transcriptional inhibitors, suggesting that a post-transcriptional mechanism controls CPRF accumulation. CPRFs as well as Arabidopsis thaliana G-box binding factors (GBFs) are selectively transported from the cytosol into the nucleus, as shown in an in vitro nuclear transport system prepared from evacuolated parsley protoplasts, indicating that cytosolic compounds are involved in regulated nuclear targeting of plant bZIP factors.

Acyltransferases↗