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At least 901 records · Page 50Linked to original sources
PubMed2006

Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli.

Adaptation to extracytoplasmic stress in Escherichia coli depends on the activation of sigmaE, normally sequestered by the membrane protein RseA. SigmaE is released in response to stress through the successive RseA cleavage by DegS and the RIP protease RseP. SigmaE and proteases that free it from RseA are essential. We isolated a multicopy suppressor that alleviated RseP and DegS requirement. The suppressor encodes a novel small RNA, RseX. Its activity required the RNA-binding protein Hfq. We used the property that small RNAs are often involved in RNA-RNA interactions to capture RseX putative partners; ompA and ompC mRNA, which encode two major outer membrane proteins, were identified. RseX activity was shown to confer an Hfq-dependent coordinate OmpA and OmpC down-regulation. Because RseP is shown to be no longer essential in a strain lacking OmpA and OmpC, we conclude that RseP, which is required for normal sigmaE activation, prevents toxicity due to the presence of two specific outer membrane proteins that are down-regulated by RseX.

Bacterial Outer Membrane Proteins↗
PubMed2002

Crystal structure of TB-RBP, a novel RNA-binding and regulating protein.

The testis/brain-RNA-binding protein (TB-RBP) spatially and temporally controls the expression of specific mRNAs in developing male germ cells and brain cells, and is implicated in DNA recombination and repair events. We report the 2.65 A crystal structure of mouse TB-RBP. The structure is predominantly alpha-helical and exhibits a novel protein fold and mode of assembly. Crystal symmetry and molecular symmetry combine to form an octet of TB-RBP monomers in the shape of an elongated spherical particle with a large cavity at its center. Amino acid residues that affect RNA and DNA binding are located on the interior surface of the assembled particle, and a putative nucleotide-binding domain that controls RNA binding is located at a dimer interface. Other modes of assembly are suggested for TB-RBP based on our structure and recently reported electron microscopic reconstructions of human TB-RBP.

Amino Acid Sequence↗
PubMed1998

RNA recognition and regulation of HIV-1 gene expression by viral factor Tat.

Viral transcription factor Tat is a small nuclear protein containing a large number of basic amino acids. The tat gene consists of two exons but only the first encoding 72-amino acid polypeptide is necessary for protein activity. Since the second exon is poorly conservative the total number of amino acids among Tat proteins from different strains of HIV-1 varies from 86 to 130. Tat protein acts as trans-activator of HIV genome transcription. It is absolutely required for viral functioning. Tat increases processivity of RNA-polymerase II by abolition of transcription blockade, which appears after polycondensation of the first 60-70 nucleotides of either HIV mRNA, i.e., it acts as antiterminator. For manifestation of its activity Tat specifically binds to the double stranded RNA fragment called TAR which is located at the 5'-terminus of all HIV mRNAs. The TAR structure contains a hairpin and a side loop. The Tat-binding region includes only a site of the loop; manifestation of Tat activity in vivo requires the full TAR and additional cellular co-factors.

Amino Acid Sequence↗
PubMed1994

Cell-specific regulation of agrin RNA splicing in the chick ciliary ganglion.

Alternative splicing results in production of four agrin proteins (agrin0, agrin8, agrin11, and agrin19) with different AChR aggregating activities. However, the cellular origin of mRNAs encoding each agrin isoform remains unknown. Using single-cell PCR, we demonstrate that in the chick ciliary ganglion, nonneuronal cells express only mRNA encoding agrin0, whereas neurons express one or any combination of agrin mRNAs. Moreover, significant differences were observed between the agrin mRNA profiles of ciliary and choroid neurons in the ganglion. The abundance of each agrin mRNA, the fraction of neurons expressing each transcript, and the combinations of transcripts expressed by neurons also change during development. Our results demonstrate that transcripts encoding agrin proteins with high AChR aggregating activity are expressed exclusively by neurons in the ciliary ganglion and that alternative splicing of agrin mRNA is regulated during development and in a cell-specific manner.

Agrin↗
PubMed1997

Structural analysis of the human BIN1 gene. Evidence for tissue-specific transcriptional regulation and alternate RNA splicing.

BIN1 is a putative tumor suppressor that was identified through its interaction with the MYC oncoprotein. To begin to identify elements of BIN1 whose alteration may contribute to malignancy, we cloned and characterized the human BIN1 gene and promoter. Nineteen exons were identified in a region of >54 kilobases, six of which were alternately spliced in a cell type-specific manner. One alternately spliced exon encodes part of the MYC-binding domain, suggesting that splicing controls the MYC-binding capacity of BIN1 polypeptides. Four other alternately spliced exons encode amphiphysin-related sequences that were included in brain-specific BIN1 species, also termed amphiphysin isoforms or amphiphysin II. The 5'-flanking region of BIN1 is GC-rich and lacks a TATA box but directs transcriptional initiation from a single site. A approximately 0. 9-kilobase fragment from this region was sufficient for basal transcription and transactivation by MyoD, which may account for the high levels of BIN1 observed in skeletal muscle. This study lays the foundation for genetic and epigenetic investigations into the role of BIN1 in normal and neoplastic cell regulation.

Adaptor Proteins, Signal Transducing↗
PubMedDate not supplied

DNA damage regulation of the RNA components of the translational apparatus: new biology and mechanisms.

It was shown more than 30 years ago that expression of ribosomal (r) RNAs processed from the large precursor rRNA is repressed when eukaryotic cells are exposed to genotoxic stress. More recently it has been found that other RNA components of the translational machinery, the tRNAs and 5S rRNA transcribed by RNA polymerase (pol) III, are also downregulated in cells that have experienced DNA damage. In other words, the DNA damage response involves coordinate repression of genes whose products comprise the heart of the translational machinery. This repression could be due to blockage of polymerase elongation, and indeed this mechanism was originally invoked to explain repression of pol I-transcribed rRNAs under conditions of genotoxic stress. Recent work however reveals the existence of a DNA damage signaling pathway that directly contributes to downregulation of the pol III and probably the pol I transcription initiation machinery. This pathway involves a highly conserved protein kinase, CK2. Its likely target is the TATA Binding Protein, which in most eukaryotes is required for transcription by both pol I and pol III. Here I consider the implications of these findings for our understanding of the physiology of the DNA damage response, and for the prospect of developing a comprehensive molecular model of how cells cope with genotoxic stress.

Animals↗
PubMed1987

Regulation of c-myc RNA and its proteins in Daudi cells by interferon-beta.

It has been shown previously that interferons (IFNs) -alpha and -beta cause a reduction in the steady-state level of poly(A) c-myc RNA in the Burkitt lymphoma, Daudi. In this report we show that the c-myc RNA reduction is not mediated by simple changes in the poly-adenylation of either nascent or existing c-myc transcripts, since similar reductions of c-myc sequences were observed in poly(A) and total cellular RNA preparations from IFN-beta-treated cells. Furthermore, the first exon of c-myc RNA in Daudi cells contains several mutations, suggesting that the germ line configuration of the first exon is not essential for the IFN-beta-mediated regulation. The c-myc RNA reduction was also detected in cells whose protein synthesis was inhibited by more than 95% with cycloheximide or emetine. We surmise that neither sustained nor IFN-induced protein synthesis is required for the c-myc RNA regulation. Antisera raised against either the carboxy- or amino-terminal c-myc peptides precipitate in Daudi cells proteins of 66,000 and 63,000 daltons. In cells treated with IFN-beta, the amounts of these proteins are reduced by 46-74% which is in agreement with the reduction detected at the level of c-myc RNA.

Burkitt Lymphoma↗
PubMed1993

Sequences downstream of the RNA initiation site regulate human T-cell lymphotropic virus type I basal gene expression.

Sequences which control basal human T-cell lymphotropic virus type I (HTLV-I) transcription probably play an important role in initiation and maintenance of virus replication. We have identified and analyzed a 45-nucleotide sequence (downstream regulatory element 1 [DRE 1]) at the boundary of the R/U5 region of the long terminal repeat which is required for HTLV-I basal transcription. The basal promoter strength of constructs that contained deletions in the R/U5 region of the HTLV-I long terminal repeat were analyzed by chloramphenicol acetyltransferase assays following transfection of Jurkat T cells. We consistently observed a 10-fold decrease in basal promoter activity when sequences between +202 to +246 were deleted. By reverse transcriptase polymerase chain reaction RNA analysis, we confirmed that the drop in chloramphenicol acetyltransferase activity was paralleled by a decrease in the level of steady-state RNA. DRE 1 did not affect the level of Tax1 transactivation. Using a gel shift assay, we have purified a highly enriched fraction that could specifically bind DRE 1. This DNA affinity column fraction contained four detectable proteins on sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis: p37, p50, p60, and p100. The affinity column fraction stimulated HTLV-I transcription approximately 12-fold in vitro. No effect was observed with the human immunodeficiency virus or adenovirus major late promoters. Following renaturation of the proteins isolated from an SDS-containing gel, p37, but not the other protein fractions, was able to specifically bind to DRE 1.

Animals↗
PubMed1993

Intratumor gene expression after adoptive immunotherapy in a murine tumor model. Regulation of messenger RNA levels associated with the differential expansion of tumor-infiltrating lymphocytes.

The aim of this paper was to show that the adoptive immunotherapy (AIT) of established tumors resulted in the activation of defined lymphocyte-associated genes at the site of rejection. C57BL/6J mice bearing the moderately immunogenic syngeneic MCA/76-9 sarcoma received combination therapy 10 days after tumor cell implantation. This consisted of a single i.p. injection of cyclophosphamide (CY) followed by the i.v. injection of tumor-sensitized T cells (CY/AIT). The previously observed in situ differential expansion of tumor-infiltrating lymphocytes (TIL) was associated with a parallel modulation of CD4 (L3T4) and CD8 Ag expression. Flow cytometric analysis indicated that the CD8+ TIL appeared to contain two subpopulations during the reported proliferative phase, but by day 8 after CY/AIT the cells were composed of a single bright population. The CD4+ TIL similarly appeared to show two subpopulations, but in contrast to the CD8+ TIL there was a shift to a predominantly less bright single population by day 8. The expression of lymphocyte genes (Ly-2 and Ly-4 encoding the CD8 and CD4 Ag, respectively, IL-2, IL-2R, IFN-gamma, and IL-6) was analyzed by Northern hybridization using RNA extracted from whole tumor tissue. Progressing tumors expressed only low and relatively constant levels of mRNA for all of the genes except Ly-2 over a 19-day period. In contrast, there were considerable temporal fluctuations in mRNA levels depending on whether the mice had received CY or CY/AIT, but it was apparent that CY/AIT induced the more dramatic changes as far as Ly-2, Ly-4, IL-2, and IFN-gamma mRNA levels were concerned. A preliminary survey of cytokine bioactivity released by tumor-associated cells isolated 9 days after CY/AIT indicated that both IFN-gamma and IL-6 activities were released by the cells, but not IL-2, despite the relatively high levels of IL-2 mRNA. These data provide evidence that the differential expansion of TIL after CY/AIT is accompanied by well defined changes in the levels of mRNA-encoding TIL membrane Ag and lymphokine genes and are concordant with the view that amplified anti-tumor immune responses occur after AIT.

Animals↗
PubMed1991

An A + U-rich element RNA-binding factor regulates c-myc mRNA stability in vitro.

Transient expression of some proto-oncogenes, cytokines, and transcription factors occurs as a cellular response to growth factors, 12-O-tetradecanoylphorbol-13-acetate, antigen stimulation, or inflammation. Expression of these genes is mediated in part by the rapid turnover of their mRNAs. A + U-rich elements in the 3' untranslated regions of these mRNAs serve as one recognition signal targeting the mRNAs for rapid degradation. I report the identification of a cytosolic factor that both binds to the proto-oncogene c-myc A + U-rich element and specifically destabilizes c-myc mRNA in a cell-free mRNA decay system which reconstitutes mRNA decay processes found in cells. Proteinase K treatment of the factor abolishes its c-myc mRNA degradation activity without affecting its RNA-binding capacity. Thus, RNA substrate binding and degradation appear to be separable functions. These findings should aid in understanding how the cell selectively targets mRNAs for rapid turnover.

Adenine↗
PubMed1988

Hormonal regulation of somatostatin messenger RNA.

The ability of gonadal steroids to regulate the expression of the somatostatin gene in several regions of the CNS was investigated with in situ hybridization histochemistry. The amount of somatostatin mRNA was found to be significantly decreased 2-3 weeks after ovariectomy or orchidectomy in the periventricular hypothalamus, the ventromedial nucleus of the hypothalamus, and the medial and central nuclei of the amygdala. Treatment of gonadectomized rats with estradiol benzoate or testosterone enanthate reversed this decrease in somatostatin mRNA. No significant effect was noted in the cerebral cortex or bed nucleus of the stria terminalis. In some regions, there was a high degree of convergence between the distribution of neurons containing estrogen/androgen receptors and somatostatin neurons that were responsive to gonadectomy. These results suggest that sex steroids regulate the expression of somatostatin through an action at the level of transcription.

Amygdala↗
PubMed2002

The dominance of alleles controlling self-incompatibility in Brassica pollen is regulated at the RNA level.

Self-incompatibility (SI) in Brassica is controlled sporophytically by the multiallelic S-locus. The SI phenotype of pollen in an S-heterozygote is determined by the relationship between the two S-haplotypes it carries, and dominant/recessive relationships often are observed between the two S-haplotypes. The S-locus protein 11 (SP11, also known as the S-locus cysteine-rich protein) gene has been cloned from many pollen-dominant S-haplotypes (class I) and shown to encode the pollen S-determinant. However, SP11 from pollen-recessive S-haplotypes (class II) has never been identified by homology-based cloning strategies, and how the dominant/recessive interactions between the two classes occur was not known. We report here the identification and molecular characterization of SP11s from six class II S-haplotypes of B. rapa and B. oleracea. Phylogenetic analysis revealed that the class II SP11s form a distinct group separated from class I SP11s. The promoter sequences and expression patterns of SP11s also were different between the two classes. The mRNA of class II SP11, which was detected predominantly in the anther tapetum in homozygotes, was not detected in the heterozygotes of class I and class II S-haplotypes, suggesting that the dominant/recessive relationships of pollen are regulated at the mRNA level of SP11s.

Alleles↗
PubMed2005

The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression.

The RNA recognition motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is one of the most abundant protein domains in eukaryotes. Based on the comparison of more than 40 structures including 15 complexes (RRM-RNA or RRM-protein), we reviewed the structure-function relationships of this domain. We identified and classified the different structural elements of the RRM that are important for binding a multitude of RNA sequences and proteins. Common structural aspects were extracted that allowed us to define a structural leitmotif of the RRM-nucleic acid interface with its variations. Outside of the two conserved RNP motifs that lie in the center of the RRM beta-sheet, the two external beta-strands, the loops, the C- and N-termini, or even a second RRM domain allow high RNA-binding affinity and specific recognition. Protein-RRM interactions that have been found in several structures reinforce the notion of an extreme structural versatility of this domain supporting the numerous biological functions of the RRM-containing proteins.

Amino Acid Sequence↗
PubMed2004

Regulation of glutamate receptor RNA editing and ADAR mRNA expression in developing human normal and Down's syndrome brains.

In human brain, developmental up-regulation in RNA editing at the Q/R site was evident in GluR5 and GluR6, but GluR2 editing in the white matter was down-regulated. Each ADAR mRNA expression was up-regulated in the gray matter, whereas differently regulated in the white matter. ADAR2 mRNA was not overexpressed in the brains of Down's syndrome subjects, nor was there any evidence of changes in the RNA editing efficiency of their GluRs.

Adenosine Deaminase↗
PubMed1999

Embryonic lethal abnormal vision-like RNA-binding proteins regulate neurite outgrowth and tau expression in PC12 cells.

The embryonic lethal abnormal vision (ELAV)-like proteins are mRNA-binding proteins that regulate mRNA stability. The neuronal members of this family are required for neuronal differentiation. We identified the binding region of purified HuD protein to a target neuronal mRNA encoding for the tau microtubule-associated protein and demonstrated an in vivo interaction between the ELAV-like protein and its target tau mRNA. We show that treatment of neuronal cells with antisense oligodeoxynucleotides directed against HuD blocks the induction of neurite outgrowth and decreases the levels of tau mRNAs, indicating that the ELAV-like proteins are required for neuronal differentiation.

Animals↗
PubMed1995

Requirements for iron-regulated degradation of the RNA binding protein, iron regulatory protein 2.

Iron regulatory proteins (IRPs) regulate the expression of genes involved in iron metabolism whose transcripts contain RNA stem-loop motifs known as iron-responsive elements (IREs). When iron concentrations are low, IRPs bind to IREs in the 5' untranslated region (UTR) of transcripts where they repress translation, or the 3' UTR of transcripts where they inhibit degradation. The RNA binding activities of the homologous proteins IRP1 and IRP2 are both regulated post-translationally. The binding activity of IRP2 is regulated by the degradation of the protein when cells are iron-replete. Here, we demonstrate that a 73 amino acid sequence that corresponds to a unique exon in IRP2 contains a sequence required for rapid degradation in iron-replete cells. The deletion of this sequence eliminates the rapid turnover of IRP2, whereas the transfer of this sequence to the corresponding position in the homologous protein IRP1 confers the capacity for iron-dependent degradation upon IRP1. Site-directed mutagenesis has demonstrated that specific cysteines within the IRP2 exon are required for iron-dependent degradation. The degradation of IRP2 appears to be mediated by the proteasome in iron-replete cells. When degradation is prevented, the RNA binding activity of IRP2 is not regulated by iron concentration. Thus, degradation is required for the regulation of the RNA binding activity of IRP2.

Amino Acid Sequence↗