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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The nucleotide sequence of the 3' external transcribed spacer (3' ETS) region in Schizosaccharomyces pombe rDNA was determined to define structural features which mediate the termination of RNA transcription and subsequent rRNA maturation. S1 nuclease protection studies suggest three alternative termination sites and four cleavage sites in the processing of the 3' ETS sequence. Each of the termination sites precedes a "Sal box"-like sequence which has been demonstrated to mediate the termination of rRNA transcription in mammalian cells. A highly conserved extended hairpin structure in the ETS sequence was deleted by PCR-mediated mutagenesis and the mutant rDNA was expressed in vivo to determine its role in rRNA maturation. Despite an efficient expression of the mutant gene, mature 5.8 S or 25 S rRNA was not observed. Labelling kinetics and S1 nuclease protection analyses indicate that the deletion not only fully inhibits the removal of the 3' ETS but also fully inhibits the processive excision of the second internal transcribed spacer (ITS2). Instead, a relatively stable 27 S nRNA precursor remains easily detectable in the whole cell RNA population. The results demonstrate a critical dependence of ITS processing on the 3' ETS raising the possibility that these sequences interact in a common processing domain.
J Mol Biol 1994 Jun 03
PMID:Intragenic processing in yeast rRNA is dependent on the 3' external transcribed spacer. 819 52

Directly repeated elements have been characterized downstream of the transcription initiation site (TIS) in the 5' external transcribed spacer (5' ETS) of the rRNA genes of cucumber (Cucumis sativus). In order to show that these repeated elements are also involved in transcriptional regulation processes of RNA polymerase I while being single-stranded during transcription, DNA-protein binding assays were performed with synthetic oligonucleotides prepared from the promoter region as well as from the repeated elements. The single-stranded DNA of the upstream binding element (from -164 to -105), the core promoter (from -41 to +16) and a loop-forming sequence (LRE) of the repeated elements interact with the same nuclear proteins whereas another region of the repeated elements (XRE) cooperates with a different nuclear protein. Remarkably, both complementary strands show identical protein binding.
Plant Mol Biol 1993 Sep
PMID:Nuclear proteins interact with RNA polymerase I promoter and repeated elements of the 5' external transcribed spacer of the rDNA of cucumber in a single-stranded stage. 840 Jan 31

The intergenic spacer (IGS) of a 10-kbp repeat (clone pRZ7D) of the nuclear 18S, 5.8S, and 25S ribosomal RNA genes of Cucurbita pepo (zucchini) was sequenced and compared to the IGS sequences of two other Cucurbitaceae, Curcurbita maxima (squash), and Cucumis sativus (cucumber). The nucleotide sequence and the structural organization of the IGS of C. pepo and C. maxima are rather similar (between 75 and 100% sequence similarity depending on the region compared). The IGS are mainly composed of three different repeated elements interspersed into unique sequences: GC-rich clusters, a 422-bp AT-rich element including the transcription initiation site (TIS) for RNA polymerase I, and 260-bp repeats in the 5' external transcribed spacer (D repeats). The TIS is duplicated in the 10-kbp repeat class of C. pepo, as it is also described for the 11.5-kbp rDNA repeat of C. maxima. The IGS of Cucumis sativus is also composed of different repeated elements; however, obvious sequence identity to the Cucurbita species only occurs around the TIS and the preceding AT-rich region. GC-rich clusters with different primary sequences are present in the IGS of all three plants. Remarkably, the repeated elements in the 5'ETS accumulate TpG and TpNpG motifs, whereas CpG and CpNpG motifs less frequently occur. This accumulation might be caused by the transition of methylated cytosines (in mCpG or mCpNpG motifs) into thymidine via deamination in a previously GC-rich ancestor. The following singular region exhibits 50% G + C in C. pepo, 53% G+C in C. maxima, and 63% G + C in C. sativus.(ABSTRACT TRUNCATED AT 250 WORDS)
J Mol Evol 1993 Feb
PMID:Molecular evolution of the intergenic spacer in the nuclear ribosomal RNA genes of cucurbitaceae. 843 83

E4TF1 was originally identified as one of the transcription factors responsible for adenovirus E4 gene transcription. It is composed of two subunits, a DNA binding protein with a molecular mass of 60 kDa and a 53-kDa transcription-activating protein. Heterodimerization of these two subunits is essential for the protein to function as a transcription factor. In this study, we identified a new E4TF1 subunit, designated E4TF1-47, which has no DNA binding activity but can associate with E4TF1-60. We then cloned the cDNAs for each of the E4TF1 subunits. E4TF1 was purified, and the partial amino acid sequence of each subunit was determined. The predicted amino acid sequence of each cDNA clone revealed that E4TF1-60 had an ETS domain, which is a DNA binding domain common to ets-related transcription factors. E4TF1-53 had four tandemly repeated notch-ankyrin motifs. The putative cDNA of E4TF1-47 coded almost the same amino acid sequences as E4TF1-53. Three hundred and thirty-two amino acids of the N termini of E4TF1-47 and -53 were identical except for one amino acid insertion in E4TF1-53, and they differ from each other at the C terminus. These three recombinant cDNA clones were expressed in Escherichia coli, and the proteins behaved in the same manner as purified proteins in a gel retardation assay. Nucleotide and predicted amino acid sequences were highly homologous to GABP-alpha and -beta, which is further supported by the observation that GABP-specific antibody can recognize human E4TF1.
Mol Cell Biol 1993 Mar
PMID:cDNA cloning of transcription factor E4TF1 subunits with Ets and notch motifs. 844 84

A plethora of extracellular signals leads to the stimulation of Ras, which triggers intracellular protein kinase cascades, resulting in activation of transcription factors and thus in enhanced gene activity. In this report, it is demonstrated that the ETS transcription factor ER81, which appears to be localized within the cell nucleus by virtue of its DNA binding domain, is transcriptionally activated by oncogenic Ras. Since this activation was dependent on the presence of Raf-1 and ERK-1, ER81 is a target of the Ras/Raf/MEK/ERK signaling cascade. Consistently, activated ERK-1 is capable to phosphorylate ER81. However, the carboxy-terminal region of ER81, which contains no potential ERK phosphorylation sites, is also transcriptionally activated by ERK-1, suggesting that an ERK-stimulated protein kinase phosphorylates and thus stimulates ER81 activity. Two acidic stretches of amino acids, which are conserved in the related PEA3 and ERM proteins, are localized within the amino-and carboxy-terminal transactivation domains of ER81. In addition, an inhibitory domain may dampen the activation function of these two domains. In conclusion, ER81 is a target of Ras-dependent signaling cascades and may thus contribute to the nuclear response upon stimulation of cells and also to cellular transformation due to oncogenic Ras.
Mol Cell Biol 1996 Apr
PMID:Analysis of the ERK-stimulated ETS transcription factor ER81. 865 29

Several mechanisms are employed by members of transcription factor families to achieve sequence-specific DNA recognition. In this study, we have investigated how members of the ETS-domain transcription factor family achieve such specificity. We have used the ternary complex factor (TCF) subfamily as an example. ERK2 mitogen-activated protein kinase stimulates serum response factor-dependent and autonomous DNA binding by the TCFs Elk-1 and SAP-la. Phosphorylated Elk-1 and SAP-la exhibit specificities of DNA binding similar to those of their isolated ETS domains. The ETS domains of Elk-1 and SAP-la and SAP-2 exhibit related but distinct DNA-binding specificities. A single residue, D-69 (Elk-1) or V-68 (SAP-1), has been identified as the critical determinant for the differential binding specificities of Elk-1 and SAP-1a, and an additional residue, D-38 (Elk-1) or Q-37 (SAP-1), further modulates their DNA binding. Creation of mutations D38Q and D69V is sufficient to confer SAP-la DNA-binding specificity upon Elk-1 and thereby allow it to bind to a greater spectrum of sites. Molecular modelling indicates that these two residues (D-38 and D-69) are located away from the DNA-binding interface of Elk-1. Our data suggest a mechanism in which these residues modulate DNA binding by influencing the interaction of other residues with DNA.
Mol Cell Biol 1996 Jul
PMID:Determinants of DNA-binding specificity of ETS-domain transcription factors. 866 49

Nucleolin is an abundant nucleolar protein, which plays an essential, but largely unknown role in ribosome biogenesis. Nucleolin contains four consensus RNA-binding domains (CS-RBD), the presence of which suggests that the molecular function of this protein is likely reflected by its RNA-binding properties. Indeed, by immunocytological analysis performed on ribosomal transcription units, we have found several nucleolin molecules associated with nascent pre-rRNA. In mouse, two high-affinity binding sites with an apparent dissociation constant (Kd) of 50 to 100 nM have been mapped in the 5' ETS upstream from the early pre-rRNA processing site. Interestingly, nucleolin of mouse origin has recognized analogous sequences in the 5' ETS of human pre-rRNA. In parallel, selection-amplification (SELEX) experiments have identified an 18-nucleotide long RNA sequence that binds nucleolin with high affinity (Kd 5 to 20 nM) and shares a common UCCCGA motif with the characterized pre-rRNA binding sites. By mutagenesis and a structural analysis, we have characterized the nucleolin RNA binding site and found that it is constituted by a minimal 18-nucleotide long stem-loop structure. The sequence UCCCGA that is found within the hairpin loop is necessary for the specific interaction. Mutation of any of the C or G residues within this motif abolishes nucleolin interaction. Furthermore, point mutation in the stem that completely disrupt the hairpin structure also prevents nucleolin binding. By determining the minimal 5' and 3' ends of the RNA that is bound to the protein we concluded that nucleolin binding site is constituted by a short four to five-base-pair stem and an eight-nucleotide loop. This structural motif is very similar to hairpins recognized by two other CS-RBD-containing proteins (U1 snRNP A and U2 snRNP B"). Possible functional implications of our findings are discussed.
J Mol Biol 1996 Jul 05
PMID:Nucleolin is a sequence-specific RNA-binding protein: characterization of targets on pre-ribosomal RNA. 867 91

The U3 nucleolar RNA has a remarkably wide phyletic distribution extending from the Eukarya to the Archaea. It functions in maturation of the small subunit (SSU) rRNA through a mechanism which is as yet unknown but which involves base-pairing with pre-rRNA. The most conserved part of U3 is within 30 nucleotides of the 5' end, but as yet no function for this domain has been proposed. Elements within this domain are complementary to highly conserved sequences in the SSU rRNA which, in the mature form, fold into a universally conserved pseudoknot. The nature of the complementarity suggests a novel mechanism for U3 function whereby U3 facilitates correct folding of the pseudoknot. Wide phylogenetic comparison provides compelling evidence in support of the interaction in that significant complementary changes have taken place, particularly in the archaeon Sulfolobus, which maintain the base-pairing. Base-substitution mutations in yeast U3 designed to disrupt the base-pairing indicate that the interaction is probably essential. These include cold-sensitivity mutations which exhibit phenotypes similar to U3-depletion, but without impairment of the AO processing step, which occurs within the 5' ETS. These phenotypes are consistent with the destabilization of SSU precursors and partial impairment of the processing steps A1, at the 5' ETS/18 S boundary, and A2, within the ITS1.
J Mol Biol 1996 Jun 21
PMID:Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. 868 71

The lymphocyte-specific immunoglobulin mu heavy-chain gene intronic enhancer is regulated by multiple nuclear factors. The previously defined minimal enhancer containing the muA, muE3, and muB sites is transactivated by a combination of the ETS-domain proteins PU.1 and Ets-1 in nonlymphoid cells. The core GGAAs of the muA and muB sites are separated by 30 nucleotides, suggesting that ETS proteins bind to these sites from these same side of the DNA helix. We tested the necessity for appropriate spatial alignment of these elements by using mutated enhancers with altered spacings. A 4- or 10-bp insertion between muE3 and muB inactivated the mu enhancer in S194 plasma cells but did not affect in vitro binding of Ets-1, PU.1, or the muE3-binding protein TFE3, alone or in pairwise combinations. Circular permutation and phasing analyses demonstrated that PU.1 binding but not TFE3 or Ets-1 bends mu enhancer DNA toward the major groove. We propose that the requirement for precise spacing of the muA and muB elements is due in part to a directed DNA bend induced by PU.1.
Mol Cell Biol 1996 Aug
PMID:Precise alignment of sites required for mu enhancer activation in B cells. 875 55

Hughes (1996, J Mol Biol 259:645-654) proposed that the box A region of U3 snoRNA interacts by complementary base pairing with small subunit (ss) rRNA sequences within precursor (pre-) rRNA and through rearrangement and displacement mediates the formation of the universally conserved 5' end pseudoknot. We wondered how this conserved pseudoknot might be formed in the ss rRNAs of archaeal and bacterial organisms that lack a U3 RNA. In examining the 5' external transcribed spacer (5' ETS) region in pre-rRNA transcripts from some of these organisms, we noted the presence of U3 box A-like sequences. By analogy with the U3-ss rRNA intermolecular interaction, we suggest that the box A-like 5' ETS sequence interacts through intramolecular complementary base pairing with the 5' end pseudoknot sequences within pre-rRNA; rearrangement of this structure mediates the formation of the conserved 5' end pseudoknot. If correct, this means that some of the pre-rRNA maturation-folding functions provided in trans by snoRNAs in eukaryotic organisms may be provided in cis by the spacer sequences in pre-rRNA transcripts in some bacterial or archaeal organisms lacking snoRNAs.
 ...
PMID:Formation of the 5' end pseudoknot in small subunit ribosomal RNA: involvement of U3-like sequences. 908 41


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