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At least 811 records · Page 45Linked to original sources

PubMed1993

The CAGTCACA box in the fission yeast Schizosaccharomyces pombe functions like a TATA element and binds a novel factor.

Fourteen ribosomal protein genes from the fission yeast Schizosaccharomyces pombe contain a highly conserved sequence, CAGTCACA, in the proximal promoter. This sequence, which was also conserved in its location, was found where the TATA element usually resides. Deletion and point mutations in the CAGTCACA box reduced the expression of these genes to almost zero and caused aberrant transcriptional start sites. Insertions between this box and the original transcriptional start sites led to new start sites which were the same distance from the CAGTCACA box as the original start sites. The results presented provide evidence that this box, like a TATA sequence, is involved in basal expression and fixing the transcriptional start sites of these genes. Furthermore, the CAGTCACA sequence is the target of a binding protein which appears to be different from the TATA-binding protein.

Base Sequence↗

PubMed2006

Binding and functional characteristics of two E-box motifs within the S100A6 (calcyclin) gene promoter.

S100A6 (calcyclin) is a small calcium-binding protein of the S100 family often associated with cancer and metastasis. We have previously shown that the E-box sequence at position -283/-278 of the S100A6 gene promoter interacts with USF transcription factor and contributes to promoter transcriptional activity. We now present evidence that a second E-box motif at position -593/-588 of the promoter also binds USF and that the USF1/USF2 heterodimer is the prevailing dimeric form of the transcription factor bound. Using the chromatin immunoprecipitation assay (ChIP), we show that USF is bound in vivo to the E-box regulatory element(s). Depletion of the endogenous USF pool by means of a decoy oligonucleotide evokes a severe inhibition of S100A6 gene promoter activity. Furthermore, we show that S100A6 gene promoter activity can be stimulated by palmitate and that mutation of the -283/-278 E-box sequence completely blocks this stimulation.

Binding Sites↗

PubMed1997

Synergism of the ATF/CRE site and GC box in the housekeeping Na,K-ATPase alpha1 subunit gene is essential for constitutive expression.

Na,K-ATPase alpha1 subunit gene is constitutively expressed in a wide variety of tissues. Our previous studies revealed that the promoter region between -77 and +17 of the transcription initiation site of the rat Na,K-ATPase alpha1 subunit gene (Atp1a1) is sufficient for the promoter activity. In this region, an ATF/CRE site with an adjacent GC box exists. To elucidate how these sites are involved in the promoter activity, we analyzed effects of point mutations at these sites on transcription by in vitro transcription assays using nuclear extracts prepared from various rat tissues. Mutation at either site resulted in dramatic reduction of the promoter activity in all nuclear extracts, while mutation at both sites did not lead to further reduction. These results indicate that the ATF/CRE site and GC box are both essential for promoter activity and show synergistic activation. Electrophoretic mobility shift assay indicated that Sp1 and/or Sp3 bind to the GC box, and ATF1-CREB heterodimer binds to the ATF/CRE site. Since an element, ATF/CRE site-GC box, is conserved in mammalian Na,K-ATPase alpha1 subunit genes and in other constitutive promoters, we propose that this element is a critical unit for constitutive expression.

Activating Transcription Factors↗

PubMed1998

Hoechst 33342 induces apoptosis and alters tata box binding protein/DNA complexes in nuclei from BC3H-1 myocytes.

Hoechst 33342 and Hoechst 33258 bind to adenine-thymine rich regions of the minor groove of DNA. Hoechst 33342, but not Hoechst 33258, induces BC3H-1 myocyte cell death and DNA fragmentation into an internucleosomal pattern characteristics of apoptosis. Hoechst 33342 has been shown to inhibit endogenous nuclear topoisomerase I activity. Another enzymatic activity utilizing the minor groove of DNA, the initiation of RNA polymerase II activity by formation of a TATA box binding protein/TATA box promoter complex, is shown to be altered using a gel mobility shift assay. A [32P]-labeled 24-oligonucleotide containing a TATA box element formed one molecular weight complex in control and Hoechst 33258 treated cells. The presence of Hoechst 33342 (26.7 microM) decreased the amount of the control complex and increased the presence of lower molecular weight species suggesting degradation of nuclear TBP and/or release of other transcription factors from the complex creating a smaller sized molecular complex which retains TATA box binding capacity. These results suggest that the pathway utilized to induce apoptosis in BC3H-1 myocytes may also involve the alteration of normal TBP/DNA complex formation and reduction in the initiation of new transcription.

Animals↗

PubMed1999

A novel human gene encoding an F-box/WD40 containing protein maps in the SHFM3 critical region on 10q24.

We report the cloning and characterization of a new human gene, Dactylin, encoding a novel member of the F-box/WD40 protein family. The Dactylin gene comprises nine exons distributed in more than 85 kb of genomic DNA and encoding a protein with four WD40 repeats and an F-box motif. Northern blot analysis demonstrates a single 2.8 kb transcript in brain, kidney, lung and liver. FISH hybridization localized Dactylin to 10q24.3. Using an Msc I SNP identified in the first exon of the gene, we were able to assign Dactylin within the critical region for Split Hand Split Foot malformation (SHFM3) that has been mapped to 10q24. The SHFM3 phenotype includes absence or hypoplasia of the central digital rays, a deep median cleft and syndactyly of the remaining digits. Recent studies have demonstrated the importance of F-box/WD40 proteins in the regulation of developmental processes, by a mechanism of specific ubiquitinization and subsequent proteolysis of target proteins belonging to the Wnt, Hh and NF-kappaB signaling pathways. The chromosomal location of Dactylin and its putative function as an F-box/WD40 repeat protein, likely to be involved in key signaling pathways crucial for normal limb development, make it a promising candidate gene for SHFM3.

Amino Acid Sequence↗

PubMed1996

Tbx6, a mouse T-Box gene implicated in paraxial mesoderm formation at gastrulation.

The T-box genes constitute an evolutionarily conserved family of putative transcription factors which are expressed in discrete domains during embryogenesis, suggesting that they may play roles in inductive interactions. Members have been identified by virtue of their homology to the prototypical T-box gene, T or Brachyury, which is required for mesoderm formation and axial elongation during embryogenesis. We have previously reported the discovery of six new mouse T-box genes, Tbx1-Tbx6, and described the expression patterns of Tbx1-Tbx5 (Bollag et al., 1994; Agulnik et al., 1996; Chapman et al., 1996; Gibson-Brown et al., 1996). We have obtained cDNA clones encoding the full-length Tbx6 protein from screens of gastrulation-stage mouse cDNA libraries and determined the spatial and temporal distribution of Tbx6 transcripts during embryogenesis. The gene codes for a 1.9-kb transcript with an open reading frame coding for a 540-amino acid protein, with a predicted molecular weight of 59 kDa. Tbx6 maps to chromosome 7 and does not appear to be linked to any known mutation. Unlike other members of the mouse T-box gene family which are expressed in a wide variety of tissues derived from all germ layers, Tbx6 expression is quite restricted. Tbx6 transcripts are first detected in the gastrulation stage embryo in the primitive streak and newly recruited paraxial mesoderm. Later in development, Tbx6 expression is restricted to presomitic, paraxial mesoderm and to the tail bud, which replaces the streak as the source of mesoderm. Expression in the tail bud persists until 12. 5 days postcoitus. Tbx6 expression thus overlaps that of Brachyury in the primitive streak and tail bud, although Brachyury is expressed earlier in the primitive streak. Brachyury is also expressed in a second domain, the node and notochord, that is not shared with Tbx6. The onset of Tbx6 expression is not affected in homozygous null Brachyury mutant embryos at 7.5 days postcoitus. However, Tbx6 expression is extinguished in mutant embryos as soon as the Brachyury phenotype becomes evident at 8.5 days postcoitus, indicating that the continued expression of Tbx6 is directly or indirectly dependent upon Brachyury expression.

Amino Acid Sequence↗

PubMed1998

Cloning, mapping, and expression analysis of TBX15, a new member of the T-Box gene family.

The T-box gene family has been conserved throughout metazoan evolution and codes for putative transcription factors that share a uniquely defining DNA-binding domain. We have previously uncovered six mouse T-box genes with discrete spatial and temporal patterns of expression during embryogenesis. Here, we report a novel mouse T-box gene, Tbx15. The Tbx15 gene produces a 3.7-kb transcript with an open reading frame coding for a polypeptide with 602 amino acid residues. Phylogenetic analysis places the Tbx15 gene into a T-box subfamily that also includes mouse Tbx1, Drosophila H15, and nematode Ce-tbx-12 genes. We have mapped mouse Tbx15 to chromosome 3, at a position 49 cM from the centromere. During development, Tbx15 transcripts are first detected at embryonic day 9.5. The gene is expressed primarily in the cranio-facial region and in the developing limbs. An isolated human homolog, TBX15, has been mapped by in situ hybridization to chromosomal band 1p13. TBX15 appears to be an excellent candidate for the dominantly expressed acromegaloid facial appearance syndrome, which also maps to the short arm of human chromosome 1 and, like TBX15, is expressed prominently in the eyebrow regions.

Animals↗

PubMed1999

Identification, mapping, and phylogenomic analysis of four new human members of the T-box gene family: EOMES, TBX6, TBX18, and TBX19.

Brachyury(T) is a mouse mutation, first described over 70 years ago, that causes defects in mesoderm formation. Recently several related genes, the T-box gene family, that encode a similar N-terminal DNA binding domain, the T-box, and that play critical roles in human embryonic development have been identified. It has been shown that human TBX5 and TBX3, if mutated, cause developmental disorders, Holt-Oram syndrome (OMIM 142900) and ulnar-mammary syndrome (OMIM 181450), respectively. We have identified four new human members of the T-box gene family, EOMES, TBX6, TBX18, and TBX19, and these genes have been mapped to different chromosomal regions by radiation hybrid mapping. The four T-box genes were classified into four different subfamilies and have also been subjected to phylogenomic analysis. Human EOMES maps at 3p21.3-p21.2. This Tbr1-subfamily gene is likely to play a significant role in early embryogenesis similar to that described for Xenopus eomesodermin. Human TBX6 maps at 16p12-q12. This Tbx6-subfamily gene is likely to participate in paraxial mesoderm formation and somitogenesis in human embryo. TBX18 is a novel member of the Tbx1 subfamily that maps at 6q14-q15. Two subgroups, TBX1/10 and TBX15/18 subgroups, could be distinguished within the Tbx1 subfamily. TBX19 is an orthologue of chick TbxT and maps at 1q23-q24. The genomic organization of TBX19 is highly similar to that of human T(Brachyury), another human member of the same subfamily.

Adult↗

PubMed2000

Cloning and characterization of human DDX24 and mouse Ddx24, two novel putative DEAD-Box proteins, and mapping DDX24 to human chromosome 14q32.

DEAD-box proteins are a large group of putative RNA helicases that exist ubiquitously in organisms ranging from bacteria to humans. They are likely to play important roles in many different RNA metabolic processes. In this paper, we report the cloning of human DDX24, a putative DEAD-box protein, and its ortholog, Ddx24 in mouse. The deduced proteins encoded by these two cDNAs share 78.7% identity at the amino acid level and possess all the well-conserved motifs of DEAD-box proteins. However, little homology can be found between them and other DEAD-box proteins, even in their core region (identity <40%). Northern blot analysis showed that a 3.0-kb transcript of human DDX24 exists ubiquitously in the 16 human tissues examined and was most abundant in heart and brain, but with lowest levels in thymus and small intestine. The mouse Ddx24, whose transcript is 4.0 kb, was also expressed widely in 10 tissues tested with the highest level in heart and testis. By radiation hybrid mapping, the human DDX24 gene was localized to human chromosome 14q32 between the markers D14S81 and D14S265. Moreover, the gene structure of DDX24 was determined by comparing its cDNA and genomic sequence from BAC R-1089B7, which showed that the gene spanned a 30-kb region and consisted of at least nine exons.

Amino Acid Sequence↗

PubMed2000

Cloning and characterization of a new member of the T-box gene family.

The T-box is a strongly conserved protein domain, 174 to 186 amino acids in length, that binds DNA. Many genes from many species have been shown to encode T-box domain-containing proteins. Here we report the cloning and characterization of a novel T-box gene, TBX21. The human cDNA contains an open reading frame encoding a 535-amino-acid protein with a predicted molecular mass of 58.3 kDa. Except for the T-box sequence, database searches revealed no significant homology to any known sequences at the nucleotide or protein level. In addition to the human cDNA sequence, we report the cDNA sequence of the murine homologue, the structure and organization of the murine Tbx21 gene, and its localization to mouse chromosome 11. TBX21 expression was detected in peripheral blood lymphocytes, spleen, lung, and natural killer cells.

Amino Acid Sequence↗

PubMed2004

Boxing as a sport activity associated with isolated GH deficiency.

Traumatic brain injury (TBI) has long been known as a cause of hypopituitarism, and it is characterized by a high prevalence of neuroendocrine abnormalities. Boxing, one of the most common combative sports, may also result in TBI. As far as we know, pituitary functions including GH status have not been investigated in boxers. Therefore, in this preliminary study, we have assessed the pituitary functions in boxers. Eleven actively competing or retired male boxers with a mean age of 38.0 +/- 3.6 yr and 7 age-, sex- and BMI-matched healthy non-boxing controls were included in the study. Biochemical and basal hormonal parameters including IGF-I levels were measured. To assess GH secretory status in boxers and healthy controls, GHRH (1 microg/kg)+GHRP-6 (1 microg/kg) test was performed. After GHRH+GHRP-6 test, mean peak GH level in boxers and in controls were 10.9 +/- 1.7 and 41.4 +/- 6.7 microg/l, respectively (p < 0.05). Peak GH levels in 5 (45%) boxers were found to be lower than 10 microg/l and considered as severe GH deficient. In the control group, mean IGF-1 levels (367 +/- 18.8 ng/ml) were significantly higher than that obtained in boxers (237 +/- 23.3 ng/dl) (p < 0.01). All the other pituitary hormones were normal including ADH as no signs and symptoms of diabetes insipidus. There was a significant negative correlation between peak GH levels and boxing duration, and between peak GH levels and number of bouts. In conclusion, we think that boxing is a cause of TBI, and GH deficiency is very common among boxers. Further studies including large number of boxers, both professional and amateur, are needed to clarify pituitary dysfunction in boxers.

Adult↗

PubMed2026

Comparative transcriptomics reveals hormone signaling and MADS-box genes in divergent development of inflorescences and tendrils in grapevine lateral shoots.

Hormone signaling and MADS-box genes regulate grapevine tendril and inflorescence growth divergence, offering molecular insights for managing tendril growth. Grapevine (Vitis vinifera L.) tendrils and inflorescences are homologous organs; however, their divergent development has important agronomic consequences because excessive tendril growth increases vineyard management costs. To explore the regulatory mechanisms, we compared the inflorescence-prone cultivar 'Einset Seedless' (ENT) with the tendril-prone cultivar 'Pinot Noir' (PN) using anatomical observation, transcriptome analysis of specific tendril nodes, and functional characterization of MADS-box genes. ENT exhibited a higher flowering rate at tendril nodes 1-4 than PN. Transcriptome profiling of specific tendril nodes uncovered 549 differentially expressed genes (DEGs) through an intersection/exclusion strategy, with Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicating that hormone and mitogen-activated protein kinase (MAPK) signaling were the primary candidates driving the divergence. To assess the spatiotemporal dynamics of these DEGs, we performed Mfuzz clustering, which revealed that multiple expression trajectories were highly consistent with the flowering gradient across different ENT and PN nodes. Plant hormone signal transduction was the predominantly enriched pathway across all dynamic clusters, highlighting the centrality of phytohormones in this process. Guided by this transcriptional evidence, we measured endogenous zeatin and gibberellin (GA₃) contents in the nodal tissues. Remarkably, the zeatin-to-GA₃ ratio not only paralleled the flowering gradient but also correlated with the cluster expression trajectories, providing physiological evidence for a cytokinin-gibberellin interaction model governing organ divergence. Additionally, we analyzed the differentially expressed transcription factors among the DEGs and identified a MADS-box gene, FRUITFULL-LIKE (VvFUL-L), which was markedly upregulated in PN tendrils. Heterologous overexpression of VvFUL-L in arabidopsis promoted early flowering and reduced inflorescence branching, suggesting its potential role in regulating lateral meristem development and affecting tendril formation. Collectively, these findings establish that Hormone Signaling, particularly cytokinin-GA crosstalk, and MADS-box regulators, such as VvFUL-L, are key regulators of inflorescence versus tendril growth in grapevines, providing a basis for future molecular and breeding studies.

Vitis↗

PubMed2005

Fluorescence resonance energy transfer studies of aminoglycoside binding to a T box antiterminator RNA.

The T box transcription antitermination mechanism is found in many Gram-positive bacteria. The T box genes are typically tRNA synthetase, amino acid biosynthesis, and amino acid transport genes that have a common transcriptional control mechanism in which a unique RNA-RNA interaction occurs between an uncharged tRNA and the 5' leader region of the nascent mRNA, leading to antitermination of transcription. The tRNA binds the mRNA in at least two regions: the specifier sequence and the antiterminator. If the latter interaction does not occur, then transcription is terminated. The binding of eight different aminoglycosides to a model of the Bacillus subtilis tyrS T box antiterminator RNA has been studied using fluorescence resonance energy transfer. The observed single-site binding dissociation constants were in the low to mid micromolar range. The structure-activity relationship of aminoglycoside binding indicates that selective binding of small molecules to T box antiterminator RNA can be achieved.

Aminoglycosides↗

PubMed2005

T-box and homeobox genes from the ctenophore Pleurobrachia pileus: comparison of Brachyury, Tbx2/3 and Tlx in basal metazoans and bilaterians.

Most animals are classified as Bilateria and only four phyla are still extant as outgroups, namely Porifera, Placozoa, Cnidaria and Ctenophora. These non-bilaterians were not considered to have a mesoderm and hence mesoderm-specific genes. However, the T-box gene Brachyury could be isolated from sponges, placozoans and cnidarians. Here, we describe the first Brachyury and a Tbx2/3 homologue from a ctenophore. In addition, analysing T-box and homeobox genes under comparable conditions in all four basal phyla lead to the discovery of novel T-box genes in sponges and cnidarians and a Tlx homeobox gene in the ctenophore Pleurobrachia pileus. The conservation of the T-box and the homeobox genes suggest that distinct subfamilies with different roles in bilaterians were already split in non-bilaterians.

Amino Acid Sequence↗

PubMed2006

Unraveling the 'DEAD-box' helicases of Plasmodium falciparum.

The causative agent for the most fatal form of malaria, Plasmodium falciparum, has developed insecticide and drug resistance with time. Therefore combating this disease is becoming increasingly difficult and this calls for finding alternate ways to control malaria. One of the feasible ways could be to find out inhibitors/drugs specific for the indispensable enzymes of malaria parasite such as helicases. These helicases, which contain intrinsic nucleic acid-dependent ATPase activity, are capable of enzymatically unwinding energetically stable duplex nucleic acids into single-stranded templates and are required for all the nucleic acid transactions. Most of the helicases contain a set of nine extremely conserved amino acid sequences, which are called 'helicase motifs'. Due to the presence of the DEAD (Asp-Glu-Ala-Asp) in one of the conserved motifs, this family is also known as the 'DEAD-box' family. In this review, using bioinformatic approach, we describe the 'DEAD-box' helicases of malaria parasite P. falciparum. An in depth analysis shows that the parasite contains 22 full-length genes, some of which are homologues of well-characterized helicases of this family from other organisms. Recently we have cloned and characterized the first member of this family, which is a homologue of p68 and is expressed during the schizont stage of the development of the parasite [Pradhan, A., Chauhan, V.S., Tuteja, R., 2005a. A novel 'DEAD-box' DNA helicase from Plasmodium falciparum is homologous to p68. Mol. Biochem. Parasitol. 140, 55-60.; Pradhan A., Chauhan V.S., Tuteja R., 2005b. Plasmodium falciparum DNA helicase 60 is a schizont stage specific, bipolar and dual helicase stimulated by PKC phosphorylation. Mol. Biochem. Parasitol. 144, 133-141.]. It will be really interesting to clone and characterize other members of the 'DEAD-box' family and understand their role in the replication and transmission of the parasite. These detailed studies may help to identify a parasite-specific enzyme, which could be a potential drug target to treat malaria. The various steps at which this probable drug can act are also discussed.

Animals↗

PubMed2004

DNA binding and bending by HMG boxes: energetic determinants of specificity.

To clarify the physical basis of DNA binding specificity, the thermodynamic properties and DNA binding and bending abilities of the DNA binding domains (DBDs) of sequence-specific (SS) and non-sequence-specific (NSS) HMG box proteins were studied with various DNA recognition sequences using micro-calorimetric and optical methods. Temperature-induced unfolding of the free DBDs showed that their structure does not represent a single cooperative unit but is subdivided into two (in the case of NSS DBDs) or three (in the case of SS DBDs) sub-domains, which differ in stability. Both types of HMG box, most particularly SS, are partially unfolded even at room temperature but association with DNA results in stabilization and cooperation of all the sub-domains. Binding and bending measurements using fluorescence spectroscopy over a range of ionic strengths, combined with calorimetric data, allowed separation of the electrostatic and non-electrostatic components of the Gibbs energies of DNA binding, yielding their enthalpic and entropic terms and an estimate of their contributions to DNA binding and bending. In all cases electrostatic interactions dominate non-electrostatic in the association of a DBD with DNA. The main difference between SS and NSS complexes is that SS are formed with an enthalpy close to zero and a negative heat capacity effect, while NSS are formed with a very positive enthalpy and a positive heat capacity effect. This indicates that formation of SS HMG box-DNA complexes is specified by extensive van der Waals contacts between apolar groups, i.e. a more tightly packed interface forms than in NSS complexes. The other principal difference is that DNA bending by the NSS DBDs is driven almost entirely by the electrostatic component of the binding energy, while DNA bending by SS DBDs is driven mainly by the non-electrostatic component. The basic extensions of both categories of HMG box play a similar role in DNA binding and bending, making solely electrostatic interactions with the DNA.

Amino Acid Sequence↗

PubMed2005

Belle is a Drosophila DEAD-box protein required for viability and in the germ line.

DEAD-box proteins are ATP-dependent RNA helicases that function in various stages of RNA processing and in RNP remodeling. Here, we report identification and characterization of the Drosophila protein Belle (Bel), which belongs to a highly conserved subfamily of DEAD-box proteins including yeast Ded1p, Xenopus An3, mouse PL10, human DDX3/DBX, and human DBY. Mutations in DBY are a frequent cause of male infertility in humans. Bel can substitute in vivo for Ded1p, an essential yeast translation factor, suggesting a requirement for Bel in translation initiation. Consistent with an essential cellular function, strong loss of function mutations in bel are recessive lethal with a larval growth defect phenotype. Hypomorphic bel mutants are male-sterile. Bel is also closely related to the Drosophila DEAD-box protein Vasa (Vas), a germ line-specific translational regulator. We find that Bel and Vas colocalize in nuage and at the oocyte posterior during oogenesis, and that bel function is required for female fertility. However, unlike Vas, Bel is not specifically enriched in embryonic pole cells. We conclude that the DEAD-box protein Bel has evolutionarily conserved roles in fertility and development.

Amino Acid Sequence↗

PubMed2004

Identification and distinct regulation of yeast TATA box-containing genes.

Despite being one of the first eukaryotic transcriptional regulatory elements identified, the sequence of a native TATA box and its significance remain elusive. Applying criteria associated with TATA boxes we queried several Saccharomyces genomes and arrived at the consensus TATA(A/T)A(A/T)(A/G). Approximately 20% of yeast genes contain a TATA box. Strikingly, TATA box-containing genes are associated with responses to stress, are highly regulated, and preferentially utilize SAGA rather than TFIID when compared to TATA-less promoters. Transcriptional regulation in yeast appears to be mechanistically bipolar, possibly reflecting a need to balance inducible stress-related responses with constitutive housekeeping functions.

Chromatin↗