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PubMed2003

G-box binding coincides with increased Solanum melongena cysteine proteinase expression in senescent fruits and circadian-regulated leaves.

We have previously shown that SmCP, the gene encoding Solanum melongena cysteine proteinase, is expressed during developmental events associated with programmed cell death (PCD) suggesting its involvement in protein degradation during these events (Xu and Chye, Plant Journal 17 (1999) 321-327). Here, we investigated the regulation of SmCP expression and showed that it is ethylene-inducible and is under circadian control. This circadian rhythm is entrained by light/dark (LD) cycling with peak expression in the late light period, as opposed to that in early light for rbcS, suggesting that protein degradation and photosynthesis are temporally separated by circadian control. Northern blot analysis shows that the pattern of ethylene induction of SmCP is consistent with our previous observation of its significantly increased expression at leaf senescence and fruit ripening when endogenous ethylene is abundant. To further understand SmCP regulation, we have cloned the SmCP promoter and identified a G-box (CACGTG) at -85/-80 by DNase I footprinting analysis of the -221/+17 region. Its specific interaction with nuclear proteins in S. melongena leaves and fruits was confirmed by competitive electrophoretic mobility shift assays using oligonucleotides containing the G-box and mutant derivatives. G-box binding activity was stronger in senescent than young fruits. In circadian-regulated leaves, stronger binding activity coincided with peak circadian expression of SmCP. This correlation between binding activity and expression suggests that G-box binding factors enhance SmCP transcription and that the G-box likely plays a role in circadian regulation of genes affected by LD cycling.

Aging↗

PubMed2001

Polymorphism in the Y box controls level of cytokine-mediated expression of HLA-DRB1 genes.

The HLA class II molecules play an important role in immune response. The quality of immune response is dependent not only on the polymorphisms in the class II molecules, but also on the level of their cell-surface expression. In fact, it has been demonstrated that differences in the level of expression of DRB1 and DRB3 genes restricted and activated distinct CD4+ T lymphocytes. We and others have previously described allelic polymorphisms in the upstream regulatory regions of DRB genes, which affected DNA-protein interactions and resulted in significantly different promoter strengths. We showed that polymorphisms in both the X1 and Y box motifs affect level of constitutive expression of DRB1 genes in the DR1, DR51 and DR53 haplotype groups. In the present study, we examined the effect polymorphisms in the X1 box and the Y box on the cytokine (interferon-gamma (IFNgamma), tumor necrosis factor-alpha (TNFalpha) and granulocyte macrophage-colony-stimulating factor (GM-CSF))-mediated transcriptional activities of DRB1 promoters in these, i.e. DR1, DR51 and DR53, haplotype groups. The results demonstrate that the polymorphism in the X1 box does not affect cytokine-mediated strength of DRB1 gene promoters. In contrast, the polymorphism in the Y box, which affects the inverted CCAAT sequence, plays a dominant role on the cytokine-mediated transcriptional activity of DRB1 promoters.

Base Sequence↗

PubMed2004

Object retrieval in the 1st year of life: learning effects of task exposure and box transparency.

Before 12 months of age, infants have difficulties coordinating and sequencing their movements to retrieve an object concealed in a box. This study examined (a) whether young infants can discover effective retrieval solutions and consolidate movement coordination earlier if exposed regularly to such a task and (b) whether different environments, indexed by box transparency, would impact the rate of learning and time of discovery of these solutions. Infants (N=12) were presented with an object retrieval task every week from 6 1/2 months of age until they were able to retrieve the toy from the box using coordinated two-handed patterns for 3 weeks. To reach that criterion, infants tested with an opaque box took 2 1/2 months and infants tested with a semitransparent box took 1 1/2 months. Both groups outperformed age-matched controls who received a one-time exposure to the task. Repeated exposure to the task and vision of the toy significantly enhanced this process of solution discovery.

Female↗

PubMedDate not supplied

G to A substitution in the distal CCAAT box of the A gamma-globin gene in Greek hereditary persistence of fetal haemoglobin.

The sequence 5'TTGGPyCAAT 3' (the 'CCAAT box') is a constituent of the promoter region of many eukaryotic and prokaryotic genes and is believed to play a part in promoter function. A characteristic of the two fetal human globin genes (A gamma and G gamma) is a duplication of a 12-base pair (bp) sequence containing the CCAAT box. Here we report a G----A substitution in the TTG sequence of the distal CCAAT box of the A gamma-globin gene in an individual with the A gamma (Greek) type of hereditary persistence of fetal haemoglobin (HPFH). This represents the first report of a natural mutation of the CCAAT box in a eukaryotic gene. The fact that this transition is associated with inappropriate expression of the A gamma gene in adult life suggests that the CCAAT box (or its surrounding sequences) may have a role in the developmental control of gamma-globin genes.

Base Sequence↗

PubMed1990

Functional heterogeneity of mammalian TATA-box sequences revealed by interaction with a cell-specific enhancer.

A regulatory element upstream of the human myoglobin gene functions as a muscle-specific enhancer (MSE) in conjunction with core promoter elements of the myoglobin gene, but not in combination with the simian virus 40 (SV40) early promoter. These two promoters differ in the sequences of their 'TATA boxes': for the myoglobin gene, the sequence is TATAAAA, whereas for SV40, the sequence is TATTTAT. We have now tested the hypothesis that this sequence difference is responsible for the differential response of the promoters to the MSE. We found that when the TATA box sequence of the myoglobin promoter was changed to that of the SV40 promoter, responsiveness to the MSE was abolished; conversely, when the SV40 TATA box sequence was changed to that of the myoglobin promoter, the promoter became responsive to the MSE. We conclude that mammalian TATA-box elements are functionally heterogeneous, and suggest that this heterogeneity reflects differential interactions with distinctive TATA box-binding factors, only some of which can act cooperatively with MSE-binding proteins to generate an active transcriptional complex.

Chloramphenicol O-Acetyltransferase↗

PubMed2001

A new twist on RNA helicases: DExH/D box proteins as RNPases.

DExH/D box proteins are required for the major transactions of RNA, including mRNA synthesis, pre-mRNA splicing, ribosome biogenesis, translation and RNA decay. In the popular imagination, DExH/D box proteins have become synonymous with 'RNA helicases', which are enzymes that unwind duplex RNAs in concert with the hydrolysis of nucleoside triphosphates (NTPs). But all DExH/D box proteins may not be RNA helicases and the energy of NTP hydrolysis by DExH/D box proteins may be harnessed for other purposes. Cellular RNAs are associated with proteins, often in large ribonucleoprotein (RNP) complexes. This review focuses on recent progress suggesting a role for DExH/D box proteins as 'RNPases' that use chemical energy to remodel the interactions of RNA and proteins.

Adenosine Triphosphatases↗

PubMed2006

The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase.

We have identified the S(MK) box as a conserved RNA motif in the 5' untranslated leader region of metK (SAM synthetase) genes in lactic acid bacteria, including Enterococcus, Streptococcus and Lactococcus species. This RNA element bound SAM in vitro, and binding of SAM caused an RNA structural rearrangement that resulted in sequestration of the Shine-Dalgarno (SD) sequence. Mutations that disrupted pairing between the SD region and a sequence complementary to the SD blocked SAM binding, whereas compensatory mutations that restored pairing restored SAM binding. The Enterococcus faecalis S(MK) box conferred translational repression of a lacZ reporter when cells were grown under conditions where SAM pools are elevated, and mutations that blocked SAM binding resulted in loss of repression, demonstrating that the S(MK) box is functional in vivo. The S(MK) box therefore represents a new SAM-binding riboswitch distinct from the previously identified S box RNAs.

5' Untranslated Regions↗

PubMed2006

The CRY box: a second APCcdh1-dependent degron in mammalian cdc20.

Cdc20 and cdh1 are coactivators of the anaphase-promoting complex (APC). APC(cdc20) is necessary for the metaphase-anaphase transition and, at the end of mitosis, vertebrate cdc20 itself becomes a target for degradation through KEN-box-dependent APC(cdh1) activity. By studying the degradation of fluorescent protein chimaeras in mammalian oocytes and early embryos, we found that cdc20 was degraded through two independent degradation signals (degrons), the KEN box and a newly described CRY box. In both oocytes and G1-stage embryos, the rate of degradation through the CRY box was greater than through the KEN box, although both were mediated by APC(cdh1). Thus, mammalian oocytes and embryos have the capacity to recognize two degrons in cdc20.

Anaphase-Promoting Complex-Cyclosome↗

PubMed2001

Functional roles and efficiencies of the thioredoxin boxes of calcium-binding proteins 1 and 2 in protein folding.

The rat luminal endoplasmic-recticulum calcium-binding proteins 1 and 2 (CaBP1 and CaBP2 respectively) are members of the protein disulphide-isomerase (PDI) family. They contain two and three thioredoxin boxes (Cys-Gly-His-Cys) respectively and, like PDI, may be involved in the folding of nascent proteins. We demonstrate here that CaBP1, similar to PDI and CaBP2, can complement the lethal phenotype of the disrupted Saccharomyces cerevisiae PDI gene, provided that the natural C-terminal Lys-Asp-Glu-Leu sequence is replaced by His-Asp-Glu-Leu. Both the in vitro RNase AIII-re-activation assays and in vivo pro-(carboxypeptidase Y) processing assays using CaBP1 and CaBP2 thioredoxin (trx)-box mutants revealed that, whereas the three trx boxes in CaBP2 seem to be functionally equivalent, the first trx box of CaBP1 is significantly more active than the second trx box. Furthermore, only about 65% re-activation of denatured reduced RNase AIII could be obtained with CaBP1 or CaBP2 compared with PDI, and the yield of PDI-catalysed reactions was significantly reduced in the presence of either CaBP1 or CaBP2. In contrast with PDI, neither CaBP1 nor CaBP2 could catalyse the renaturation of denatured glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is a redox-independent process, and neither protein had any effect on the PDI-catalysed refolding of GAPDH. Furthermore, although PDI can bind peptides via its b' domain, a property it shares with PDIp, the pancreas-specific PDI homologue, and although PDI can bind malfolded proteins such as 'scrambled' ribonuclease, no such interactions could be detected for CaBP2. We conclude that: (1) both CaBP2 and CaBP1 lack peptide-binding activity for GAPDH attributed to the C-terminal region of the a' domain of PDI; (2) CaBP2 lacks the general peptide-binding activity attributed to the b' domain of PDI; (3) interaction of CaBP2 with substrate (RNase AIII) is different from that of PDI and substrate; and (4) both CaBP2 and CaBP1 may promote oxidative folding by different kinetic pathways.

Amino Acid Sequence↗

PubMed2003

Upstream stimulatory factor (USF) and neurogenic differentiation/beta-cell E box transactivator 2 (NeuroD/BETA2) contribute to islet-specific glucose-6-phosphatase catalytic-subunit-related protein (IGRP) gene expression.

Islet-specific glucose-6-phosphatase (G6Pase) catalytic-subunit-related protein (IGRP) is a homologue of the catalytic subunit of G6Pase, the enzyme that catalyses the final step of the gluconeogenic pathway. The analysis of IGRP-chloramphenicol acetyltransferase (CAT) fusion-gene expression through transient transfection of islet-derived beta TC-3 cells revealed that multiple promoter regions, located between -306 and -97, are required for maximal IGRP-CAT fusion-gene expression. These regions correlated with trans -acting factor-binding sites in the IGRP promoter that were identified in beta TC-3 cells in situ using the ligation-mediated PCR (LMPCR) footprinting technique. However, the LMPCR data also revealed additional trans -acting factor-binding sites located between -97 and +1 that overlap two E-box motifs, even though this region by itself conferred minimal fusion-gene expression. The data presented here show that these E-box motifs are important for IGRP promoter activity, but that their action is only manifest in the presence of distal promoter elements. Thus mutation of either E-box motif in the context of the -306 to +3 IGRP promoter region reduces fusion-gene expression. These two E-box motifs have distinct sequences and preferentially bind NeuroD/BETA2 (neurogenic differentiation/beta-cell E box transactivator 2) and upstream stimulatory factor (USF) in vitro, consistent with the binding of both factors to the IGRP promoter in situ, as determined using the chromatin-immunoprecipitation (ChIP) assay. Based on experiments using mutated IGRP promoter constructs, we propose a model to explain how the ubiquitously expressed USF could contribute to islet-specific IGRP gene expression.

Animals↗

PubMed1998

The first high-mobility-group box of upstream binding factor assembles across-over DNA junction by basic residues.

Upstream binding factor (UBF) is a eukaryotic RNA polymerase I-specific transcription factor. Its predominant DNA-binding motif, ubfHMG box 1, preserves DNA assembling activity that can bind two or more DNA duplexes simultaneously to form a crossover DNA junction. Here we investigate the basis of crossover DNA-assembling activity of ubfHMG box 1 by extensive mutagenesis analyses and mobility shift assay. Although the ubfHMG box 1 preserves a high mobility group (HMG) core structure, changing a number of the consensus hydrophobic and aromatic residues to alanine did not inhibit its crossover-assembling activity. This indicates that these residues do not directly participate in protein-DNA interaction. However, altering a series of basic residues in the helices 1 and 2 regions or the N-terminal extended strand of the ubfHMG box 1 motif had severe effects on DNA-assembling activity; however, certain non-specific DNA binding activity still remained. This suggests that the ubfHMG box 1 motif might extensively contact the backbone of a crossover junction through its multiple basic residues. Mutating a hydrophobic residue in the terminal dimerization domain inhibited the association of truncated Xenopus UBF, but had little effect on its crossover-assembling activity. This indicates that the UBF-crossover DNA complex is not established by the association of individual DNA-bound peptides.

Amino Acid Sequence↗

PubMed2004

Flavonoids induce temporal shifts in gene-expression of nod-box controlled loci in Rhizobium sp. NGR234.

Rhizobia, soil bacteria of the Rhizobiales, enter the roots of homologous legumes, where they induce the formation of nitrogen-fixing nodules. Signals emanating from both symbiotic partners control nodule development. Efficient nodulation requires precise, temporal regulation of symbiotic genes. Roots continuously release flavonoids that interact with transcriptional activators of the LysR family. NodD proteins, which are members of this family, act both as sensors of the environment and modulate the expression of genes preceded by conserved promoter sequences called nod-boxes. The symbiotic plasmid of the broad host-range Rhizobium sp. NGR234 caries 19 nod-boxes (NB1 to NB19), all of which were cloned upstream of a lacZ-reporter gene. A flavonoid, daidzein was able to induce 18 of the 19 nod-boxes in a NodD1-dependent manner. Interestingly, induction of four nod-boxes (NB6, NB15, NB16 and NB17) is highly dependent on NodD2 and was delayed in comparison with the others. In turn, NodD2 is involved in the repression of the NB8 nodABCIJnolOnoeI operon. Activation of transcription of nodD2 is also dependent on flavonoids despite the absence of a nod-box like sequence in the upstream promoter region. Mutational analysis showed that syrM 2 (another member of the LysR family), which is controlled by NB19, is also necessary for expression of nodD 2. Thus, NodD1, NodD2 and SyrM2 co-modulate a flavonoid-inducible regulatory cascade that coordinates the expression of symbiotic genes with nodule development.

Base Sequence↗

PubMed1984

Upstream activation sites of the CYC1 gene of Saccharomyces cerevisiae are active when inverted but not when placed downstream of the "TATA box".

The ability of the upstream activation sites (UASs) of the yeast CYC1 gene to function when inverted or when positioned downstream of the "TATA box" is investigated. Inversion of a 130-base-pair DNA fragment bearing the UASs leaves the activity of the sites almost completely intact. In contrast, positioning the sites downstream of the TATA box or in the intron of a CYC1-ribosomal protein 51-lacZ tribrid gene almost totally abolishes their activity. In the latter construct, the separation between the UASs and TATA box is roughly equivalent to that between the elements in the intact CYC1 promoter region. The UASs are shown not to interrupt transcription of splicing in this construct since a GAL10 UAS positioned upstream of the TATA box gives rise to galactose-inducible expression of the tribrid gene. The inability of the UASs to function in the intron is partly due to sequences between the intron and the TATA box that block the activation signal. However, a large component of the inactivity of the sites in the intron appears to be their downstream location. This result is discussed in light of possible mechanisms of upstream activation in yeast.

Base Composition↗

PubMed1987

Conserved major histocompatibility complex class II boxes--X and Y--are transcriptional control elements and specifically bind nuclear proteins.

A conserved sequence motif exists at the 5' end of all major histocompatibility complex class II genes. This motif consists of the 14-base X and Y boxes separated by a short stretch of variable sequence. In this report, we provide evidence that the X and Y boxes play an important role in controlling transcription of the murine class II gene E kappa alpha. We have developed transgenic mouse lines that carry E alpha genes cleanly deleted for either the X or Y box and have compared the expression of these mutant transgenes with that of a nondeleted control. Both the X and Y segments appear critical for accurate and efficient transcription of E kappa alpha. The most drastic effect is seen with gamma-interferon-treated macrophages, where deletion of the Y box completely abrogates transcription initiated by the normal promoter. In addition, we identify proteins from nuclear extracts that bind specifically to the X or Y box.

Animals↗

PubMed1999

Induction of utrophin gene expression by heregulin in skeletal muscle cells: role of the N-box motif and GA binding protein.

The modulation of utrophin gene expression in muscle by the nerve-derived factor agrin plausibly involves the trophic factor ARIA/heregulin. Here we show that heregulin treatment of mouse and human cultured myotubes caused a approximately 2.5-fold increase in utrophin mRNA levels. Transient transfection experiments with utrophin promoter-reporter gene constructs showed that this increase resulted from an enhanced transcription of the utrophin gene. In the case of the nicotinic acetylcholine receptor delta and epsilon subunit genes, heregulin was previously reported to stimulate transcription via a conserved promoter element, the N-box, which binds the multimeric Ets-related transcription factor GA binding protein (GABP). Accordingly, site-directed mutagenesis of a single N-box motif in the utrophin gene promoter abolished the transcriptional response to heregulin. In addition, overexpression of heregulin, or of the two GABP subunits in cultured myotubes, caused an N-box-dependent increase of the utrophin promoter activity. In vivo, direct gene transfer into muscle confirmed that heregulin regulates utrophin gene expression. Finally, electrophoretic mobility shift assays and supershift experiments performed with muscle extracts revealed that the N-box of the utrophin promoter binds GABP. These findings suggest that the subsynaptic activation of transcription by heregulin via the N-box motif and GABP are conserved among genes expressed at the neuromuscular junction. Because utrophin can functionally compensate for the lack of dystrophin, the elucidation of the molecular mechanisms regulating utrophin gene transcription may ultimately lead to therapies based on utrophin expression throughout the muscle fibers of Duchenne muscular dystrophy patients.

Animals↗

PubMed1996

The role of an E box binding basic helix loop helix protein in the cardiac muscle-specific expression of the rat cytochrome oxidase subunit VIII gene.

We have characterized the rat gene for muscle-specific cytochrome oxidase VIII (COX VIII(H)) and mapped the distal promoter region responsible for transcription activation in C2C12 skeletal myocytes and H9C2 cardiomyocytes. In both cell types, the promoter elements responding to the induced differentiation of myocytes map to two E boxes, designated as E1 and E2 boxes with a core sequence of CAGCTG. Gel mobility shift analysis showed that both E1 and E2 box motifs form complexes with nuclear extracts from H9C2 cardiomyocytes that were supershifted with monoclonal antibody to E2A but not with antibody to myo-D. Extracts from induced and uninduced H9C2 cardiomyocytes yielded different gel mobility patterns and also different E2A antibody supershifts suggesting a difference in the DNA-bound protein complexes cross-reacting with the E2A antibody. Transcriptional activity of the promoter construct containing intact E boxes was inhibited by coexpression with Id in differentiated H9C2 cardiomyocytes. Our results show the involvement of an E box binding basic helix loop helix protein in the cardiac muscle-specific regulation of the COX VIII(H) promoter.

Animals↗

PubMed1997

Upstream stimulatory factor binding to the E-box at -65 is required for insulin regulation of the fatty acid synthase promoter.

Fatty acid synthase (FAS) plays a central role in de novo lipogenesis in mammals. We have shown that FAS transcription rate is induced dramatically when fasted animals are refed with a high carbohydrate diet or when streptozotocin-diabetic mice are given insulin. We also reported that FAS gene transcription was up-regulated by insulin through the proximal promoter region from -71 to -50 and that upstream stimulatory factors (USFs), including USF1 and USF2, interact with this region in vitro. In the present study, by using site-directed mutagenesis of the -71/-50 region and correlating functional assays of the mutated promoter with USF binding activities, we demonstrate that the -65/-60 E-box motif (5'-CATGTG-3') is functionally required for insulin regulation and that USFs are in vivo components of the insulin response complex. Mutation of the -65/-60 E-box sequence abolished insulin response in both transiently and stably transfected 3T3-L1 adipocytes in the -2. 1 kb promoter context, which contains all the necessary regulatory elements of the promoter based on our previous transgenic mice studies, and in the minimal -67 promoter context. Gel mobility shift assays demonstrated that USFs can no longer bind to the -71/-50 promoter region when the E-box is mutated. Cotransfection of USF1 and USF2 expression vectors with the FAS promoter-luciferase reporter constructs increased insulin-stimulated FAS promoter activity. Moreover, cotransfection of dominant negative USF1 and USF2 mutants lacking the DNA binding domain inhibited the insulin stimulation of the FAS promoter activity. On the other hand, site-directed mutagenesis of the -65/-60 E-box surrounding sequences within the overlapped tandem copies of sterol regulatory element-binding protein (SREBP) binding sites prevented SREBP from binding to -71/-50 promoter region in vitro but had no effect on insulin regulation of the FAS promoter in vivo. When rat liver nuclear extracts were used in gel mobility shift assays, only USF-containing protein-DNA complexes that can be supershifted by specific USF antibodies were observed. These results demonstrate that upstream stimulatory factor binding to the E-box at -65 is required for insulin regulation of the fatty acid synthase promoter.

3T3 Cells↗

PubMed2000

Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei. Sequence conservation and implications for 2'-O-ribose methylation of rRNA.

We report the identification of 17 box C/D fibrillarin-associated small nucleolar RNAs (snoRNAs) from the ancient eukaryote, Trypanosoma brucei. To systematically isolate and characterize these snoRNAs, the T. brucei cDNA for the box C/D snoRNA common protein, fibrillarin, was cloned and polyclonal antibodies to the recombinant fibrillarin protein were generated in rabbits. Immunoprecipitations from T. brucei extracts with the anti-fibrillarin antibodies indicated that this trypanosomatid has at least 30 fibrillarin-associated snoRNAs. We have sequenced seventeen of them and designated them TBR for T. brucei RNA 1-17. All of them bear conserved box C, D, C', and D' elements, a hallmark of fibrillarin-associated snoRNAs in eukaryotes. Fourteen of them are novel T. brucei snoRNAs. Fifteen bear potential guide regions to mature rRNAs suggesting that they are involved in 2'-O-ribose methylation. Indeed, eight ribose methylations have been mapped in the rRNA at sites predicted by the snoRNA sequences. Comparative genomics indicates that six of the seventeen are the first trypanosome homologs of known yeast and vertebrate methylation guide snoRNAs. Our results indicate that T. brucei has many fibrillarin-associated box C/D snoRNAs with roles in 2'-O-ribose methylation of rRNA and that the mechanism for targeting the nucleotide to be methylated at the fifth nucleotide upstream of box D or D' originated in early eukaryotes.

Amino Acid Sequence↗