Purification and assay of Saccharomyces cerevisiae phosphatase that acts on the C-terminal domain of the largest subunit of RNA polymerase II.
Explore the source record for details and available documents.
Baculoviridae↗
SEARCH · PubMed Health
Results for “RNA tertiary structure”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Backbone 1H, 15N and 13C resonance assignments of the NTPase subdomain of the hepatitis C virus NS3 RNA helicase.
Explore the source record for details and available documents.
Acid Anhydride Hydrolases↗
Functional genomics: RNA sets the standard.
Explore the source record for details and available documents.
Animals↗
Biochemistry. If the RNA fits, use it.
Explore the source record for details and available documents.
Apoferritins↗
The role of the largest RNA polymerase subunit lid element in preventing the formation of extended RNA-DNA hybrid.
Analysis of multi-subunit RNA polymerase (RNAP) structures revealed several distinct elements that may perform partial functions of the enzyme. One such element, the "lid", is formed by an evolutionarily conserved segment of the RNAP largest subunit (beta' in bacterial RNAP). The beta' lid contacts the nascent RNA at the upstream edge of the RNA-DNA hybrid, where the RNA gets separated from the DNA template-strand and double-stranded upstream DNA is formed. To test the beta' lid functions, we generated bacterial RNAP lacking the lid and studied the mutant enzyme's properties in vitro. Our results demonstrate that removal of the lid has minimal consequences on transcription elongation from double-stranded DNA. On single-stranded DNA, the mutant RNAP generates full-sized transcripts that remain annealed to the DNA throughout their length. In contrast, the wild-type enzyme produces short, 18-22 nucleotide transcripts that remain part of the transcription complex but cannot be further elongated. The cessation of transcription is apparently triggered by a clash between the lid and the nascent RNA 5' end. The results show that the lid's function is redundant in the presence of the non-template DNA strand, which alone can control the proper geometry of nucleic acids at the upstream edge of the transcription complex. Structural considerations suggest that in the absence of the non-template strand and the lid, a new channel opens within the RNAP molecule that allows continuous DNA-RNA hybrid to exit RNAP.
Amino Acid Sequence↗
SRprises along a messenger's journey.
SR (serine/arginine-rich) proteins were originally identified as essential splicing factors. Recent work, however, has implicated these proteins in numerous additional steps of mRNA metabolism, including nuclear export, RNA stability, mRNA quality control, and translation.
Animals↗
RNA-dependent RNA polymerase gene sequence from foot-and-mouth disease virus in Hong Kong.
A foot-and-mouth disease virus (FMDV, HKN/2002) was isolated in Hong Kong in 2002. The nucleotide sequence of the 3D(pol) gene encoding the viral RNA-dependent RNA polymerase was determined and compared with that of the same gene from other FMDVs. The 3D(pol) gene was 1410 nucleotides in length encoding a protein of 470 amino acid residues. Sequence comparisons indicated that HKN/2002 belonged to serotype O. An evolutionary tree based on the 3D(pol) sequences of 20 FMDV isolates revealed that the nucleotide sequence of the HKN/2002 3D(pol) gene was most similar to those of isolates found in Taiwan in 1997, suggesting that they share a common ancestor. The amino acid sequence of the HKN/2002 3D(pol) gene was determined and aligned with those of representative isolates from seven other Picornaviridae genera. Eight highly conserved regions were detected, indicating a conserved functional relevance for these motifs. Alignment of 20 FMDV 3D(pol) amino acid sequences revealed a hypermutation region near the N-terminus that may help the virus evade host immune systems.
Amino Acid Motifs↗
Structural domains involved in the RNA folding activity of RNA helicase II/Gu protein.
RNA helicase II/Gu (RH II/Gu) is a nucleolar protein that unwinds dsRNA in a 5' to 3' direction, and introduces a secondary structure into a ssRNA. The helicase domain is at the N-terminal three-quarters of the molecule and the foldase domain is at the C-terminal quarter. The RNA folding activity of RH II/Gu is not a mere artifact of its binding to RNA. This study narrows down the RNA foldase domain to amino acids 749-801 at the C-terminus of the protein. Dissection of this region by deletion and site-directed mutagenesis shows that the four FRGQR repeats, as well as the C-terminal end bind RNA independently. These juxtaposed subdomains are both important for the RNA foldase activity of RH II/Gu. Mutation of either repeat 2 or repeat 4, or simultaneous mutation of Lys792, Arg793 and Lys797 at the C-terminal end of RH II/Gu to alanines inhibits RNA foldase activity. The last 17 amino acids of RH II/Gu can be replaced by an RNA binding motif from nucleolar protein p120 without a deleterious effect on its foldase activity. A model is proposed to explain how RH II/Gu binds and folds an RNA substrate.
Amino Acid Sequence↗
Interaction between Not1p, a component of the Ccr4-not complex, a global regulator of transcription, and Dhh1p, a putative RNA helicase.
The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor IID function. Two components of this complex, Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex. In this work, we tried to determine whether Dhh1p might interact with the Ccr4-Not complex. We found that, first, not mutations displayed severe synthetic phenotypes when combined with a dhh1-null mutation. Second, overexpression of Not1p was toxic in dhh1-null cells. Third, a not mutant phenotype was suppressed by deletion of DHH1 and mimicked by overexpression of DHH1. Fourth, dhh1-null mutants displayed resistance to heat shock, a phenotype observed for all mutants that affect the Ccr4-Not complex. Finally, like Caf1p and Ccr4p, Dhh1p co-immunoprecipitated with the nonessential N-terminal domain of Not1p, and the levels of Caf1p and Dhh1p were dependent upon this Not1p domain. Taken together, our results suggest that the Ccr4-Not complex, via the N-terminal region of Not1p, is necessary for the maintenance of stable cellular levels of Dhh1p and Caf1p, thus contributing to regulation of mRNA decay in addition to transcription.
Blotting, Western↗
Cell-specific and hormone-regulated expression of gonadotropin-regulated testicular RNA helicase gene (GRTH/Ddx25) resulting from alternative utilization of translation initiation codons in the rat testis.
Gonadotropin-regulated testicular RNA helicase (GRTH) is a novel DEAD-box protein with ATPase and RNA helicase activities. GRTH gene transcription is stimulated by human chorionic gonadotropin (hCG) via cyclic AMP-induced androgen formation in testicular Leydig cells. In this study, immunocytochemical and Western analyses identified GRTH as a developmentally regulated protein in Leydig cells and in germ cells (pachytene spermatocytes and round spermatids) of the rat testis. Three ATGs with the potential for generation of multiple protein species were identified. Germ cells primarily utilized the 1st ATG codon (+1) and contained major proteins of 61/56 kDa, whereas Leydig cells utilized preferentially the 2nd ATG codon (+ 343) with expression of 48/43 kDa species. A 3rd ATG was weakly utilized and yielded a 33-kDa protein only in germ cells. The increase in GRTH 43-kDa protein in Leydig cells caused by hCG treatment was prevented by the androgen receptor antagonist, flutamide. In round spermatids, hCG caused a significant decrease of 61 kDa species and an induction 48/43 kDa species, whereas no changes were observed in pachytene spermatocytes. Reversal of this hormone-induced switch of expression by flutamide indicated a role of androgen in utilization of the 2nd ATG. These studies have demonstrated a cell-specific and hormone-dependent alternative usage of ATG codons in the testis. They have also revealed that the androgen-dependent transcription of GRTH expression in Leydig cells is accompanied by a marked increase of 43-kDa species. The findings indicate that expression of GRTH proteins is regulated by gonadotropin/androgen at the translational level.
Amino Acid Sequence↗
Structure of the RNA polymerase domain of E. coli primase.
All cellular organisms use specialized RNA polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication. The high-resolution crystal structure of a primase, comprising the catalytic core of the Escherichia coli DnaG protein, was determined. The core structure contains an active-site architecture that is unrelated to other DNA or RNA polymerase palm folds, but is instead related to the "toprim" fold. On the basis of the structure, it is likely that DnaG binds nucleic acid in a groove clustered with invariant residues and that DnaG is positioned within the replisome to accept single-stranded DNA directly from the replicative helicase.
Amino Acid Motifs↗
Structural and functional studies on the leukemia inhibitory factor receptor (LIF-R): gene and soluble form of LIF-R, and cytoplasmic domain of LIF-R required for differentiation and growth arrest of myeloid leukemic cells.
The leukemia inhibitory factor receptor (LIF-R) subunit is a component of cell-surface receptor complexes for the multifunctional cytokines, LIF, cardiotrophin-1, ciliary neurotrophic factor, and human oncostatin M. The structure of the human LIF-R gene is similar to that of the mouse gene. The transmembrane receptor is encoded by 19 exons. Two distinct 5' non-coding exons are present, indicating the existence of alternative promoters. An extra-exon specific to the mouse soluble receptor contains a stop codon and polyadenylation signals in a B2 repetitive element. On the other hand, LIF-R mRNAs containing unspliced introns are abundantly present in human tissues. These intronic sequences introduce a termination codon before the transmembrane domain. Human choriocarcinoma cells expressing these mRNAs release soluble LIF-R. The cytoplasmic domain of LIF-R can generate the signals for growth arrest and differentiation of mouse myeloid leukemic cells when they are induced to form a homodimer of the cytoplasmic domain independently of gp130. Two membrane-distal tyrosines on the YXXQ motif of LIF-R are critical not only for STAT3 activation but also for growth arrest and macrophage differentiation of WEHI-3B D+ cells.
Amino Acid Motifs↗
The theoretical analysis of the process of RNA molecule self-assembly.
The Kinetic approach to the problem of the RNA structure prediction based on the analysis of the molecule self-formation is proposed. Re-structurization that occurs during processing is described in terms of Markov processes. A new formalism designating nucleotides by complex numbers is proposed, leading to the complex unitary space of nucleic vectors. Properties of structure and transition matrices are discussed in relation to the analysis of RNA structural formation processes. The non-linear dynamic behavior of secondary structure transition is analyzed. Soliton-like oscillations of RNA and DNA tertiary structures are predicted. The Monte-Carlo simulation of the RNA structure self-formation is used to calculate the ensemble of the secondary structures of the tRNA(Ala) precursor from Bombix mori formed during processing.
Animals↗
RNA ligase; picking up the pieces.
In the current issue of Structure, Ho and coworkers report the crystal structure and mechanism of a T4 RNA ligase. These studies provide valuable insights on the mechanism and origin of RNA and DNA ligases, and RNA capping enzymes.
Adenosine Triphosphate↗
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
DEAD-box RNA helicases, which regulate various processes involving RNA, have two RecA-like domains as a catalytic core to alter higher-order RNA structures. We determined the 2.2 A resolution structure of the core of the Drosophila DEAD-box protein Vasa in complex with a single-stranded RNA and an ATP analog. The ATP analog intensively interacts with both of the domains, thereby bringing them into the closed form, with many interdomain interactions of conserved residues. The bound RNA is sharply bent, avoiding a clash with a conserved alpha helix in the N-terminal domain. This "wedge" helix should disrupt base pairs by bending one of the strands when a duplex is bound. Mutational analyses indicated that the interdomain interactions couple ATP hydrolysis to RNA unwinding, probably through fine positioning of the duplex relative to the wedge helix. This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures.
Adenosine Triphosphate↗
Overexpression of a protein fragment of RNA helicase A causes inhibition of endogenous BRCA1 function and defects in ploidy and cytokinesis in mammary epithelial cells.
The breast- and ovarian-specific tumor suppressor, BRCA1, has been implicated to function in many nuclear processes, including DNA damage repair, recombination, transcription, ubiquitination, cell cycle checkpoint enforcement, and centrosome regulation. Utilizing a previously described interaction between BRCA1 and RNA helicase A (RHA), we have developed a dominant-negative approach to block BRCA1 function in human breast epithelial cells. Overexpression of a truncated RHA peptide that can bind to the BRCA1 carboxy-terminus prevents normal BRCA1 function, such as BRCA1 association with nuclear foci following DNA damage. Overexpression of this dominant-negative protein induces pleomorphic nuclei, aberrant mitoses with extra centrosomes, and tetraploidy. This model system allows us to observe changes to mammary epithelial cells that occur acutely following loss of BRCA1 function. Furthermore, inhibition of BRCA1 via overexpressing the RHA fragment coincides with a reduction in PARP-1 protein expression, suggesting a possible mechanism for BRCA1 in the maintenance of genomic integrity.
Aneuploidy↗
Intrinsic promoter recognition by a "core" RNA polymerase.
Two classes of RNA polymerases transcribe RNA from promoters on DNA templates: promoter recognition-competent single polypeptides and multisubunit enzymes that require separable promoter recognition factors. Eukaryotic mitochondria utilize an unusual hybrid of these classes composed of a "core" RNA polymerase related to the single polypeptide enzymes plus a "specificity factor" necessary for promoter utilization. Using supercoiled or premelted templates, we have discovered that the yeast core mitochondrial RNA polymerase (Rpo41) has the intrinsic ability to initiate from promoters without its specificity factor (Mtf1). Rpo41 requires the mitochondrial promoter sequence (ATATAAGTA) for this activity. On premelted templates addition of Mtf1 actually inhibits the promoter selective activity of Rpo41. Mtf1 increases abortive relative to productive transcription by Rpo41, possibly by stabilizing the promoter complex and reducing escape into elongation. The requirement for Mtf1 on closed but not open templates indicates that Mtf1 facilitates melting but not recognition of promoters.
Base Sequence↗
Interactions of regulated and deregulated forms of the sigma54 holoenzyme with heteroduplex promoter DNA.
The bacterial sigma54 RNA polymerase holoenzyme binds to promoters as a stable closed complex that is silent for transcription unless acted upon by an enhancer-bound activator protein. Using DNA binding and transcription assays the ability of the enhancer-dependent sigma54 holoenzyme to interact with promoter DNA containing various regions of heteroduplex from -12 to -1 was assessed. Different DNA regions important for stabilising sigma54 holoenzyme-promoter interactions, destabilizing binding, limiting template utilisation in activator-dependent transcription and for stable binding of a deregulated form of the holoenzyme lacking sigma54 Region I were identified. It appears that homoduplex structures are required for early events in sigma54 holoenzyme promoter binding and that disruption of a repressive fork junction structure only modestly deregulates transcription. DNA opening from -5 to -1 appears important for stable engagement of the holoenzyme following activation. The regulatory Region I of sigma54 was shown to be involved in interactions with the sequences in the -5 to -1 area.
Bacterial Proteins↗