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PubMed2005

The Influence of Mycobacterium tuberculosis sigma factors on the promotion efficiency of ptpAt promoter in Mycobacterium smegmatis.

It was found in a previous study that Mycobacterium tuberculosis protein tyrosine phosphatase ptpAt promoter is a highly active promoter in slow-growing species of mycobacteria, such as M. tuberculosis and M. bovis BCG, but inert in fast-growing mycobacterial species, such as M. smegmatis. This difference is presumed to be due to the differences between sigma factors systems of slow-growing pathogenic mycobacteria and the fast-growing saprophyte M. smegmatis. Therefore, we constructed a series of plasmids, named pOLYG-13x, which can express various M. tuberculosis sigma factors and also contain a P(ptpAt)-gfp reporter gene construct. By inducing different sigma factor genes of M. tuberculosis in M. smegmatis, we were able to explore the influences of various sigma factors on the expression efficiency of the ptpAt promoter. The result show that of the 10 sigma factors evaluated, only sigF and sigL were able to weakly drive the ptpAt promoter in M. smegmatis and other sigma factors were unable to drive the promoter.

Bacterial Proteins↗
PubMed1998

The UP element of the promoter for the flagellin gene, hag, stimulates transcription from both SigD- and SigA-dependent promoters in Bacillus subtilis.

DNA sequences upstream (UP element) of the core promoter (-10, -35 region) of the Bacillus subtilis flagellin gene hag stimulate transcription in vivo and in vitro. We constructed a number of hybrids, placing the UP element of hagp upstream of the core of one SigD-dependent (fliDp) and two SigA-dependent (tmsp, vegp) B. subtilis promoters. The hybrid promoters were fused to a lacZ reporter gene and their activity tested in vivo. The presence of the UP module enhanced transcription at both types of promoters. We conclude that the hagp UP sequence can act as a promoter module independently of the core sequence.

Bacillus subtilis↗
PubMed1987

Molecular analysis of the promoter region of the Escherichia coli K-12 phoE gene. Identification of an element, upstream from the promoter, required for efficient expression of phoE protein.

The phoE gene of Escherichia coli codes for an outer membrane pore protein whose expression is induced under phosphate limitation. The promoter of this gene contains a 17 base-pair fragment, designated a pho box, which is present also in other phosphate-controlled promoters. The mRNA start site was determined and found to be located downstream from the pho box, such that this element is located in the -35 region of the phoE promoter. A set of promoter deletions was generated in vitro and analysis of these deletions revealed that sequences upstream from the pho box are required for the efficient expression of phoE. The required upstream region is located (in part) between positions -106 and -121 relative to the mRNA start site, and contains sequences homologous to a pho box and a correctly spaced Pribnow box, but in the reversed orientation relative to the regular -35 and -10 regions. A proper spacing between this upstream region and the -35 region appears to be important, since an oligonucleotide insertion in the intervening region interferes with phoE expression. By cloning the upstream region in a lacZ operon fusion vector, a weak phosphate limitation-inducible promoter activity could be detected.

Bacterial Outer Membrane Proteins↗
PubMed1990

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences.

Optimized weight matrices defining four major eukaryotic promoter elements, the TATA-box, cap signal, CCAAT-, and GC-box, are presented; they were derived by comparative sequence analysis of 502 unrelated RNA polymerase II promoter regions. The new TATA-box and cap signal descriptions differ in several respects from the only hitherto available base frequency Tables. The CCAAT-box matrix, obtained with no prior assumption but CCAAT being the core of the motif, reflects precisely the sequence specificity of the recently discovered nuclear factor NY-I/CP1 but does not include typical recognition sequences of two other purported CCAAT-binding proteins, CTF and CBP. The GC-box description is longer than the previously proposed consensus sequences but is consistent with Sp1 protein-DNA binding data. The notion of a CACCC element distinct from the GC-box seems not to be justified any longer in view of the new weight matrix. Unlike the two fixed-distance elements, neither the CCAAT- nor the GC-box occurs at significantly high frequency in the upstream regions of non-vertebrate genes. Preliminary attempts to predict promoters with the aid of the new signal descriptions were unexpectedly successful. The new TATA-box matrix locates eukaryotic transcription initiation sites as reliably as do the best currently available methods to map Escherichia coli promoters. This analysis was made possible by the recently established Eukaryotic Promoter Database (EPD) of the EMBL Nucleotide Sequence Data Library. In order to derive the weight matrices, a novel algorithm has been devised that is generally applicable to sequence motifs positionally correlated with a biologically defined position in the sequences. The signal must be sufficiently over-represented in a particular region relative to the given site, but need not be present in all members of the input sequence collection. The algorithm iteratively redefines the set of putative motif representatives from which a weight matrix is derived, so as to maximize a quantitative measure of local over-representation, an optimization criterion that naturally combines structural and positional constancy. A comprehensive description of the technique is presented in Methods and Data.

Algorithms↗
PubMed1992

Supercoiling, integration host factor, and a dual promoter system, participate in the control of the bacteriophage lambda pL promoter.

The high level of efficiency of the bacteriophage lambda pL promoter is dependent upon the topological state of the promoter DNA and the binding of a DNA-bending protein, IHF, to a site centered -86 base-pairs upstream from the pL transcription start site. Abortive initiation assays indicate that DNA supercoiling stimulates open complex formation, whereas IHF enhances promoter recognition. IHF stimulates promoter recognition to the same extent on linear and supercoiled templates. We found that the pL region contains a second promoter, pL2, that initiates transcription 42 base-pairs upstream from pL. Although competitive with pL and inhibited by IHF, mutations in pL2 do not affect the regulation of pL. Stimulation by IHF is helix-face-dependent. IHF inhibits pL when the IHF binding site is displaced a helical half-turn upstream. The pL sequences protected against DNase I digestion by bound IHF and RNA polymerase do not overlap. However, DNase I-hypersensitive sites appear in the region between the two bound proteins. In addition, IHF enhances RNA polymerase binding to pL. These data suggest that stimulation of pL by IHF involves the interaction of IHF and RNA polymerase to form a loop or otherwise distort the DNA between their binding sites.

Bacterial Proteins↗
PubMed1989

Regulation of JCVL promoter function: transactivation of JCVL promoter by JCV and SV40 early proteins.

To better understand the basis of cell type specificity of JCV replication, we have analyzed the expression of the viral late promoter in glial cells. Using transient transfection procedures, we show that the late gene expression, like that of the early gene, is restricted to glial cells. However, cotransfection with a plasmid producing the JCV early protein, T-antigen, stimulates expression from the JCV late promoter in both glial and non-glial cells. The SV40-encoded T-antigen acts similarly on transcription of JCV late promoter in both cell types. This transacting effect occurs at the level of RNA synthesis, as measured by the rate of transcription, stability of the message, and translation. These results indicate that basal JCV late promoter activity is restricted to glial cells, whereas in the presence of viral early protein this promoter functions in both glial and non-glial cells.

Antigens, Polyomavirus Transforming↗
PubMed1996

An upstream region of the H2AZ gene promoter modulates promoter activity in different cell types.

Human H2AZ gene promoter fragments that included sequences upstream from the core promoter resulted in decreased activity of reporter constructs transfected into several human cell lines, but increased activity in the undifferentiated human embryonal carcinoma cell line Tera-2. Differentiation of Tera-2 cells in media containing retinoic acid restored the ability of the upstream region to downregulate H2AZ gene promoter activity. Levels of endogenous H2AZ mRNA were also found to be 2.5-fold higher in undifferentiated Tera-2 cells than in differentiated Tera-2 cells. A 128 bp region located 234 to 361 bp upstream from the transcription start site of the H2AZ gene was found to be responsible for the modulation of reporter activity. The upstream region also functioned similarly when removed from the H2AZ gene promoter and inserted upstream of the SV40 promoter in reporter constructs. Gel mobility shift studies of fragments of this region revealed two sequence elements, CTCCTCC and CACGTG, that bound nuclear factors in vitro.

Base Sequence↗
PubMed1989

Investigation into the nature of a Bacillus promoter cloned into a promoter-probe plasmid.

The alpha-amylase-coding gene (amy) of Bacillus amyloliquefaciens NCP1 was cloned into the Bacillus subtilis promoter probe vector pPL603b.1, using a BglII digest of chromosomal DNA. The resulting plasmid, pVC102, was shown to have a BglII site within the insert. It was determined that this was the result of the fortuitous co-cloning of 2.88-kb and 0.92-kb BglII fragments separated in NCP1 DNA by approx. 3 kb. Unexpectedly, this co-cloning was readily repeated. Subcloning showed that while the 2.88-kb amy-bearing fragment was sufficient for amylase production, it might not have been capable of promoting sufficient levels of chloramphenicol resistance under the conditions used in the cloning experiments. The promoter on the 0.92-kb BglII fragment was more efficient, although its sequence differed from the canonical promoter sequence recognised by B. subtilis RNA polymerase E.sigma 43. As other promoter-bearing fragments from NCP1 DNA operated equally efficiently when cloned into pPL603b.1, the reason for the repeated co-cloning of the 2.88-kb and 0.92-kb NCPI BglII fragments may well be due to structural parameters, whereby certain nucleotide sequences are more readily cloned than others.

Bacillus↗
PubMed2004

Cloning of the rat beta-catenin gene (Ctnnb1) promoter and its functional analysis compared with the Catnb and CTNNB1 promoters.

Considerable recent interest has focused on the stabilization and accumulation of beta-catenin protein in human and animal tumors and the corresponding activation of downstream beta-catenin/TCF/LEF target genes. However, there is only sparse information on the regulation of beta-catenin expression at the transcriptional level and its possible involvement in physiological and pathophysiological processes. We report here the cloning and characterization of a 3.6-kb promoter fragment from the rat beta-catenin gene, Ctnnb1, and its comparison with corresponding promoters from the mouse and human genes, Catnb and CTNNB1. Several AP1 binding sites were confirmed in the promoters of all three species using mobility shift and reporter assays, and one putative TCF/LEF site also was observed in the promoter of CTNNB1. Subsequently, protein/DNA array analyses identified numerous other transcription factors through their high-affinity binding to the Ctnnb1 promoter, including E2F1, NFkappaB, MEF1, Pax5, ISRE2, Smad3/4, GATA, and ZIC. The strong binding of E2F1 and NFkappaB is especially noteworthy, because the former transcription factor is regulated by cyclin D1, a downstream target of beta-catenin/TCF/LEF signaling, whereas the latter transcription factor has been implicated in "cross talk" between the Wnt and the NFkappaB signaling pathways. These results are discussed in terms of their implications for human cancer development and specifically the various tumors in which beta-catenin mRNA is overexpressed, as well as for embryonic development, when reversible changes in beta-catenin expression occur in response to secreted Wnt ligands. The findings reported here should provide important avenues for further research focused on the regulation of Ctnnb1 activity, including the ability of beta-catenin/Tcf downstream targets to modulate beta-catenin expression at the transcriptional level.

5' Flanking Region↗
PubMed2003

Regulation of the human tumor necrosis factor-alpha promoter by angiotensin II and lipopolysaccharide in cardiac fibroblasts: different cis-acting promoter sequences and transcriptional factors.

We recently showed that angiotensin (ANG) II as well as mechanical stretch stimulated production of tumor necrosis factor (TNF) in cardiac fibroblasts. Presently, we examined the molecular mechanisms by which ANGII and lipopolysaccharide (LPS) upregulate TNF-alpha gene expression. In neonatal rat cardiac fibroblasts, increased transcription of TNF-alpha mRNA was detected as luciferase activity associated with activity of the TNF-alpha promoter. Progressive deletion from this promoter located the LPS-responsive region between -200 and -120 bp from the transcription initiation site, while the sequence between -120 and -70 bp was required for ANGII-induced expression. Next, we examined which cis-acting sequences in the TNF-alpha promoter region were essential for induction of TNF-alpha transcription. Competition analysis by electrophoretic mobility shift assay with and without specific antibodies showed that LPS increased binding of Sp1 and Sp3 to the Sp1-binding site, while Egr-1 was unimportant. With ANGII, binding of ATF-2/c-jun to the CRE site was required for TNF-alpha gene induction; neither Ets nor NF-kappaB was essential. Mutation analysis confirmed that response to LPS relied upon the Sp1 site in the TNF-alpha promoter, while the CRE-binding site was essential for stimulation by ANGII. We concluded that since TNF-alpha gene expression is transcriptionally activated by ANGII or LPS in cardiac fibroblasts via different cis-acting sequences in the TNF-alpha promoter and different transcriptional factors, mechanisms inducing TNF production differ between heart failure or cardiac hypertrophy and infectious disease.

Animals↗
PubMed1997

Comparison between cytomegalovirus promoter and elongation factor-1 alpha promoter-driven constructs in the establishment of cell lines expressing hepatitis C virus core protein.

The establishment of stable cell lines expressing the hepatitis C virus (HCV) core protein may be important for studies of HCV pathogenesis. Human and mouse cell lines were generated expressing the HCV core protein using expression vectors driven by either the cytomegalovirus (CMV) or elongation factor-1 alpha (EF-1 alpha) promoters. Following transient transfection, HCV core protein was expressed in all cell lines. However, stable human hepatocellular carcinoma (HCC) and murine myeloma cell lines expressing the HCV core protein were only established using constructs driven by the EF-1 alpha promoter. In contrast, stable expression of the hepatitis B virus (HBV) middle envelope protein (MHBs) was obtained successfully in these cell lines using an expression vector driven by the CMV promoter. Inhibitory activity of the first 69 amino acids of the HCV core protein on the CMV promoter was found by using chimeric MHBs/HCV core protein constructs. Growth of cloned cell lines expressing the HCV core protein was slower than that of nonexpressing cell lines. However, morphological changes and cell death were not observed in the stable cell lines expressing HCV core protein. These results indicate that the HCV core protein was not directly cytotoxic to HCC and myeloma cell lines but that specific promoter elements are required to establish stable expression of the nucleocapsid structural protein.

Animals↗
PubMed2001

The rainbow trout metallothionein-B gene promoter: contributions of distal promoter elements to metal and oxidant regulation.

In this report, the contributions of the distal 5'-regulatory sequences of the rainbow trout (Oncorhynchus mykiss) metallothionein (tMT)-B gene promoter (-738 to +5) were studied. Transfection of the -738 promoter fragment in a rainbow trout hepatoma cell line (RTH-149) resulted in 4- to 5-fold greater activity compared to the proximal -137 promoter region. Mutation of the proximal MREa abolishes the basal activity of the -738 fragment indicating that the distal regulatory elements require a cooperative interaction with MREa. However, the fragments containing both distal MREs, c and d (positioning -570 and -680, respectively), or MREc alone could confer basal and metal-induced activity when fused to the TATA box. This suggests that these distal elements are functional and therefore may play a role as basal elements in their natural state. The trout MT genes are also induced by oxidants including H2O2, tBHP and tBHQ. The larger promoter fragment -738 responds to H2O2, while the -137 fragment does not. However, fusion of the isolated MREc fragment (-648 to -533) in its native orientation, upstream of the -137 promoter elicits a response to H2O2, although no response is seen with MREc in reverse. These data suggest that this distal fragment contains functional oxidant responsive elements which have resemblance to the mammalian antioxidant responsive element (AREs).

Animals↗
PubMed1998

Activation of the iNOS gene promoter by Brn-3 POU family transcription factors is dependent upon the octamer motif in the promoter.

The promoter of the gene encoding the inducible nitric oxide synthase (iNOS) contains an octamer motif which is of importance for its activation by specific stimuli. We show that in contrast to the promoter of the neuronal nitric oxide synthase gene (nNOS) which is strongly activated by the Oct-2 octamer-binding POU family transcription factor, the iNOS gene is only weakly activated by Oct-2 via its octamer motif. Unlike the nNOS promoter, however, the iNOS promoter is strongly activated by the POU family transcription factors Brn-3a and Brn-3b. This activation is dependent upon the octamer motif in the iNOS promoter and requires the activation domain located within the POU domain of Brn-3a or Brn-3b but not the N-terminal activation domain of Brn-3a. Thus different but related POU proteins play important roles in the regulation of the genes encoding different forms of nitric oxide synthase.

Animals↗
PubMed2000

The 5'2 promoter of the neuronal nitric oxide synthase dual promoter complex mediates inducibility by nerve growth factor.

Neuronal nitric oxide synthase (nNOS) is induced by nerve growth factor (NGF) in pheochromocytoma PC12 cells. Previous studies from our laboratory identified two closely linked promoters (designated 5'1 and 5'2) that mediate transcription of the human nNOS gene in the brain [J. Xie, P. Roddy, T.K. Rife, F. Murad, A.P. Young, Two closely linked but separable promoters for human neuronal nitric oxide synthase gene transcription, Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 1242-1246]. In this report, we demonstrate that luciferase fusion genes under transcriptional control by the 5'1 and 5'2 dual promoter complex are inducible by NGF in stably transformed PC12 cells. In sharp contrast, neither epidermal growth factor (EGF) nor fibroblast growth factor 2 (FGF2) are able to significantly enhance the expression of NOS-luciferase fusion genes. Deletion studies indicate that the 5'2 promoter plays a major role in mediating NGF inducibility. The 5'2 promoter contains six potential Ets binding sites as well as four potential AP1 binding sites. Thus, it is possible that activation of Ets and/or AP1 transcription factors by the Ras-Raf-MAP kinase cascade contributes to the NGF-mediated induction of nNOS.

Animals↗
PubMed2002

Structure of the human carboxypeptidase M gene. Identification of a proximal GC-rich promoter and a unique distal promoter that consists of repetitive elements.

The human carboxypeptidase M (CPM) gene was found to encompass about 112.6 kb of genomic sequence, containing 11 exons of which eight (exons 2-9) are common to all transcripts and contain the entire coding region. We have cloned several alternative variants of CPM transcripts that result from differential promoter usage and alternative splicing. Although CPM belongs to the same metallocarboxypeptidase subfamily as CPE, their intron/exon structures differ significantly. Multiple transcription start sites were found in the CPM gene that cluster in two regions separated by about 30 kb and are flanked by two unique functional promoters. One ('proximal') is immediately upstream of the coding region and contains GC-rich sequences and a typical TATA box whereas the other ('distal') consists almost entirely of repetitive elements. Luciferase reporter assays with constructs of the promoter regions showed they were both quite active in several cell lines. However, the proximal promoter was much stronger than the distal one in two of the human cell lines tested (HepG2 and HEK293) whereas both promoters were highly and equally active in the human monocytic cell line THP-1, which has high constitutive expression of CPM.

3' Untranslated Regions↗
PubMed1998

Identification of mycoplasmal promoters in Escherichia coli using a promoter probe vector with Green Fluorescent Protein as reporter system.

A promoter probe vector, pGFPUV2, with Green Fluorescent Protein (GFP) as the reporter system was constructed to identify potential mycoplasmal promoter-containing regulatory sequences in E. coli. Libraries of M. pneumoniae and M. genitalium DNA constructed in pGFPUV2 and transformed into E. coli resulted in GFP-expressing clones. Primer extension analysis with E. coli RNA from five M. pneumoniae clones and two M. genitalium clones indicated that transcription originated from the insert DNA fragments of these promoter constructs. Primers based on the insert DNA sequences were used in primer extension reactions with total RNA isolated from M. pneumoniae or M. genitalium. Of the seven primers used, three generated products by primer extension with mycoplasmal RNA. However, only one of the DNAs had a 5' end similar to that obtained in a comparable reaction with E. coli RNA, and the start site of this transcript appeared to originate one base prior to the predicted open reading frame. These results indicate that E. coli can identify mycoplasmal promoters which have transcriptional elements resembling E. coli promoters.

Base Sequence↗
PubMed2002

The Brome mosaic virus subgenomic promoter hairpin is structurally similar to the iron-responsive element and functionally equivalent to the minus-strand core promoter stem-loop C.

In the Bromoviridae family of plant viruses, trinucleotide hairpin loops play an important role in RNA transcription. Recently, we reported that Brome mosaic virus (BMV) subgenomic (sg) transcription depended on the formation of an unusual triloop hairpin. By native gel electrophoresis, enzymatic structure probing, and NMR spectroscopy it is shown here that in the absence of viral replicase the hexanucleotide loop 5'C1AUAG5A3' of this RNA structure can adopt a pseudo trinucleotide loop conformation by transloop base pairing between C1 and G5. By means of in vitro replication assays using partially purified BMV RNA-dependent RNA polymerase (RdRp) it was found that other base pairs contribute to sg transcription, probably by stabilizing the formation of this pseudo triloop, which is proposed to be the primary element recognized by the viral replicase. The BMV pseudo triloop structure strongly resembles iron-responsive elements (IREs) in cellular messenger RNAs and may represent a general protein-binding motif. In addition, in vitro replication assays showed that the BMV sg hairpin is functionally equivalent to the minus-strand core promoter hairpin stem-loop C at the 3' end of BMV RNAs. Replacement of the sg hairpin by stem-loop C yielded increased sg promoter activity whereas replacement of stem-loop C by the sg hairpin resulted in reduced minus-strand promoter activity. We conclude that AUA triloops represent the common motif in the BMV sg and minus-strand promoters required for recruitment of the viral replicase. Additional sequence elements of the minus-strand promoter are proposed to direct the RdRp to the initiation site at the 3' end of the genomic RNA.

Base Pairing↗
PubMed1997

A 146 bp fragment of the tobacco Lhcb1*2 promoter confers very-low-fluence, low-fluence and high-irradiance responses of phytochrome to a minimal CaMV 35S promoter.

The occurrence of very-low-fluence responses (VLFR), low-fluence responses (LFR) and high-irradiance responses (HIR) of phytochrome was investigated for the expression of the gene of beta-glucuronidase (gusA) under the control of the tobacco Lhcb1*2 promoter, in etiolated transgenic tobacco seedlings. The activity of beta-glucuronidase (GUS) showed biphasic responses to the calculated proportion of Pfr provided by light pulses. The first phase (i.e. the VLFR) showed a maximum for Pfr levels characteristic of far-red light. The second phase (i.e. the LFR) was observed at higher Pfr levels and was reversible by far-red light pulses. The strong effect of continuous far-red light (i.e. HIR) was fluence-rate-dependent and could not be replaced either by hourly pulses of the same spectral composition and total fluence or by very low fluences of red light. Deletion of the Lhcb1*2 promoter to -453 caused little loss of GUS activity. The -453 to -31, -270 to -31 and -176 to -31 fragments of the Lhcb1*2 promoter conferred proportionally normal VLFR, LFR and HIR to a truncated (-46 to +8) CaMV 35S minimal promoter. This is the first demonstration of the presence of three phytochrome action modes in the control of the transcriptional activity of a single gene. The cis-acting regulatory elements necessary for VLFR, LFR and HIR are present in a 146 bp fragment of the tobacco Lhcb1*2 promoter.

Base Sequence↗