ON THE ROLE OF S-RNA IN REGULATING THE RATES OF AMINO ACID-DEPENDENT PYROPHOSPHATE EXCHANGE REACTIONS: A POSSIBLE "ALLOSTERIC CONTROL" PHENOMENON.
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Adenosine Triphosphate↗
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Autogenous regulation of RNA polymerase beta subunit synthesis in vitro.
The effects of Escherichia coli RNA polymerase and its subassemblies and subunits on the in vitro synthesis of beta subunit directed by DNA from a lambda transducing phage lambdadrif+-6 were investigated. This phage carries the structural gene (rpoB) for beta subunit as well as the genes for EF (translation elongation factor)-Tu, some ribosomal proteins, and stable RNAs of the E. coli chromosome. Among the RNA polymerase proteins examined, the two oligomers, holoenzyme and alpha2beta complex, repressed the synthesis of only the beta subunit but not of other proteins encoded by the phage DNA. The results indicate that the expression of at least the betabeta' (rpoBC) operon is under autogenous regulation, in which both holoenzyme and alpha2beta complex function as regulatory molecules with repressor activity.
Bacterial Proteins↗
Cell-type-specific regulation of RNA polymerase I transcription: a new frontier.
Ribosomal RNA transcription was one of the first model systems for molecular characterization of a transcription regulatory mechanism and certainly one of the best studied in the widest range of organisms. In multicellular organisms, however, the issue of cell-type-specific regulation of rRNA transcription has not been well addressed. Here I propose that a systematic study of cell-type-specific regulation of rRNA transcription may reveal new regulatory mechanisms that have not been previously realized. Specifically, issues concerning the cell-type-specific requirement for rRNA production, the universality of Pol I transcription complex and the division of rDNA into regulatory subdomains are discussed.
Animals↗
A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II.
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Genes, Regulator↗
[DNA replication and RNA transcription regulated by c-myc protein].
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Animals↗
The expression of androgen receptor messenger RNA is regulated by tri-iodothyronine in lizard testis.
The network of hormonal and non-hormonal signals required for testicular activity during the reproductive cycle of the seasonal breeding lizard, Podarcis sicula, are not yet well understood. Androgens are significantly involved in meiosis and spermiogenesis, and such an effect is mediated through their receptor (AR). Estrogens also affect the testicular activity down-regulating the expression of AR mRNA. Since over the last few years, extensive works have reported, in mammals, a clear influence of tri-iodothyronine (T(3)), the biologically active thyroid hormone, on Sertoli cell activities, we carried out a study to shead light on the effect/s exerted by T(3) in lizard testis. A thyroid hormone receptor mRNA (TR mRNA) has been found in the testis indicating that T(3) might be involved in the regulation of gonadal activity. In in vivo experiments, injection of T(3) to male lizards, captured during the recrudescence period (March) and maintained under experimental photothermal conditions (24 degrees C and 15 h daylight), increased the expression of AR mRNA. The in vitro results confirmed the stimulatory effect of T(3) on AR mRNA levels. Thus, in testosterone (T) exposed cells, the highest values of AR mRNA were observed in T(3)-primed animals, indicating that T and T(3) increase AR gene transcription independently. The present data suggest that, in lizards, the combined action of androgens, estrogen and T(3) might regulate testicular activity, modulating AR mRNA levels.
Actins↗
The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis.
Escherichia coli and Bacillus subtilis use different mechanisms of sensing and responding to tryptophan and uncharged tRNA(Trp) as regulatory signals. In E. coli, tryptophan activates a repressor that binds to the trp promoter- operator, inhibiting transcription initiation. In B. subtilis, tryptophan activates an RNA-binding protein, TRAP, which binds to the trp operon leader RNA, causing transcription termination. In E. coli uncharged tRNA(Trp) accumulation stalls the ribosome attempting translation of tandem Trp codons in the leader-peptide coding region of the operon. This stalling permits the formation of an RNA antiterminator structure, preventing transcription termination. In B. subtilis uncharged tRNA(Trp) accumulation activates transcription and translation of the at operon. AT protein inhibits tryptophan-activated TRAP, thereby preventing TRAP-mediated transcription termination. These differences might reflect the unique organizational features of the respective trp operons and their ancestry.
Bacillus subtilis↗
A partial sequence of nuclear events in regenerating rat liver (gene regulation-chromosomal RNA).
When two lobes of the liver of the adult rat are removed, the cells of the remaining lobe are aroused to renewed cell division. We have studied the early events in such regeneration. The first observable response to such partial hepatectomy is the production in the liver nuclei of rapidly-labeled high-molecular-weight RNA of sequences not produced by normal liver. This is followed, with a lag of about 1 hr, by the appearance of increased (above normal) amounts of chromosomal RNA, again of sequences not produced by normal liver. With a lag of another hour, the template activity in support of RNA synthesis of the liver chromatin increases substantially. These events occur before initiation of DNA synthesis in the cells of the regenerating liver.
Animals↗
Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors.
In eukaryotes, transcription of the diverse array of tens of thousands of protein-coding genes is carried out by RNA polymerase II. The control of this process is predominantly mediated by a network of thousands of sequence-specific DNA binding transcription factors that interpret the genetic regulatory information, such as in transcriptional enhancers and promoters, and transmit the appropriate response to the RNA polymerase II transcriptional machinery. This review will describe some early advances in the discovery and characterization of the sequence-specific DNA binding transcription factors as well as some of the properties of these regulatory proteins.
Animals↗
[DNA replication and RNA transcription regulated by c-myc protein].
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Animals↗
Developmentally regulated alternative RNA splicing of rat brain sodium channel mRNAs.
Two rat brain Na channel alpha-subunit cDNAs, named RII and RIIA, have almost identical coding regions, with a divergence of only 36 nucleotides (0.6%) over a total length of 6015 residues. A cluster of 20 divergent residues occurs within a 90 nucleotide segment of cDNA sequence. We now demonstrate that this 90 nucleotide segment is encoded twice in the RII/RIIA genomic sequence. Furthermore, the mutually exclusive selection of these two exons is developmentally regulated. RII mRNAs are relatively abundant at birth but are gradually replaced by RIIA mRNAs as development proceeds. The two mRNAs also appear to have different regional distributions in the developing rat brain. Strikingly, although 30 amino acids are encoded by each alternative exon, only amino acid position 209 is altered between the two, specifying asparagine in RII and aspartate in RIIA. Alternative RNA splicing may modulate the RII/RIIA sodium channel properties during neuronal development.
Amino Acid Sequence↗
FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition.
The nuclear RNA binding protein, FCA, promotes Arabidopsis reproductive development. FCA contains a WW protein interaction domain that is essential for FCA function. We have identified FY as a protein partner for this domain. FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. We propose that FCA controls 3' end formation of specific transcripts and that in higher eukaryotes, proteins homologous to FY may have evolved as sites of association for regulators of RNA 3' end processing.
Amino Acid Sequence↗
Developmental regulation of RNA transcript destabilization by A + U-rich elements is AUF1-dependent.
The developmental immaturity of neonatal phagocytic function is associated with decreased accumulation and half-life (t((1)/(2))) of granulocyte/macrophage colony-stimulating factor (GM-CSF) mRNA in mononuclear cells (MNC) from the neonatal umbilical cord compared with adult peripheral blood. The in vivo t((1)/(2)) of GM-CSF mRNA is 3-fold shorter in neonatal (30 min) than in adult (100 min) MNC. Turnover of mRNA containing a 3'-untranslated region (3'-UTR) A + U-rich element (ARE), which regulates GM-CSF mRNA stability, is accelerated in vitro by protein fractions enriched for AUF1, an ARE-specific binding factor. The data reported here demonstrate that the ARE significantly accelerates in vitro decay of the GM-CSF 3'-UTR in the presence of either neonatal or adult MNC protein. Decay intermediates of the GM-CSF 3'-UTR are generated that are truncated at either end of the ARE. Furthermore, the t((1)/(2)) of the ARE-containing 3'-UTR is 4-fold shorter in the presence of neonatal (19 min) than adult (79 min) MNC protein, reconstituting developmental regulation in a cell-free system. Finally, accelerated ARE-dependent decay of the GM-CSF 3'-UTR in vitro by neonatal MNC protein is significantly attenuated by immunodepletion of AUF1, providing new evidence that this accelerated turnover is ARE- and AUF1-dependent.
3' Untranslated Regions↗
Evidence for a mechanism of demyelination by human JC virus: negative transcriptional regulation of RNA and protein levels from myelin basic protein gene by large tumor antigen in human glioblastoma cells.
Human JC virus (JCV) is a neurotropic human polyomavirus that was found in the plaques and oligodendroglial cells of the brains of patients with the fatal demyelinating disease, progressive multifocal leukoencephalopathy (PML). Transgenic mice expressing JCV large tumor (T)-antigen from integrated DNA showed dysmyelination in the central nervous system. However, the role of T-antigen from episomal DNA in the demyelination in PML remains unclear. In this report, we examined the effect of episomally expressed JCV T-antigen on the expression of myelin basic protein (MBP) in U-87 MG human glioblastoma cells to study the mechanism of demyelination. Expression assays of the MBP promoter in U-87 MG detected a 2.5-fold reduction in cells expressing intact T-antigen. Next, U-87 MG expressing T-antigen were examined by RNase protection assays for mRNA accumulation from the endogenous MBP promoter. Also, the expression of the MBP promoter plasmid was determined using in vitro transcription assays with extracts from T-antigen expressing cells. Both assays found a similar down-regulation of the MBP promoter by T-antigen, confirming that negative regulation occurred at the transcriptional level for the endogenous and exogenous MBP promoters. Furthermore, in situ immunofluorescence assays and quantitative Western blot analysis provided convincing evidence of a similar reduction in the level of MBP produced from the functional endogenous gene in U-87 MG glioblastoma cells expressing T-antigen. Thus, we provide evidence for the role of T-antigen in a transcriptional control mechanism for the demyelination that is caused by JCV in PML patients.
Antigens, Polyomavirus Transforming↗
Developmentally regulated, alternative RNA splicing-generated pectoral muscle-specific troponin T isoforms and role of the NH2-terminal hypervariable region in the tolerance to acidosis.
The structure-function relationship of the alternative RNA splicing-generated NH2-terminal variable region of troponin T (TnT) is essential for understanding the physiological significance of developmental or muscle-specific TnT isoforms. Representing the hypervariable nature of the NH2-terminal region, a repeating transition metal-binding sequence (H(E/A)EAH)4-7 (Tx) has been found in chicken fast skeletal muscle TnT. In the present study, the developmentally regulated pectoral muscle-specific expression of this novel TnT isoform has been characterized. It was found that the variable amino terminus determined the isoelectric points of the TnT isoforms expressed, and the adult muscle-specific inclusion of the Tx sequence resulted in pectoralis TnTs, which were significantly more acidic in their NH2-terminal segment versus gastrocnemius TnTs. Experiments testing the effect of pH on TnT interaction with troponin I and tropomyosin indicated that although the interaction of acidic TnT isoforms with troponin I was less sensitive to the decrease of pH than the basic TnTs, the binding affinity of acidic TnT isoforms with tropomyosin was minimally affected by the decreased pH in contrast to basic TnT isoforms. Given that the majority of adult skeletal muscles express basic fast TnT isoforms, the switching between acidic and basic TnT isoforms may play a role in the functional adaptation of muscle to acidosis.
Acidosis↗
Stimulation of poly(A) polymerase through a direct interaction with the nuclear poly(A) binding protein allosterically regulated by RNA.
During polyadenylation of mRNA precursors in metazoan cells, poly(A) polymerase is stimulated by the nuclear poly(A) binding protein PABPN1. We report that stimulation depends on binding of PABPN1 to the substrate RNA directly adjacent to poly(A) polymerase and results in an approximately 80-fold increase in the apparent affinity of poly(A) polymerase for RNA without significant effect on catalytic efficiency. PABPN1 associates directly with poly(A) polymerase either upon allosteric activation by oligo(A) or, in the absence of RNA, upon deletion of its N-terminal domain. The N-terminal domain of PABPN1 may function to inhibit undesirable interactions of the protein; the inhibition is relieved upon RNA binding. Tethering of poly(A) polymerase is mediated largely by the C-terminal domain of PABPN1 and is necessary but not sufficient for stimulation of the enzyme; an additional interaction dependent on a coiled-coil structure located within the N-terminal domain of PABPN1 is required for a productive interaction.
Allosteric Regulation↗
Interactions among regulators of RNA abundance characterized using RNA fingerprinting by arbitrarily primed PCR.
Using RNA fingerprinting by arbitrarily primed PCR it is possible to infer convergent transcript regulatory pathways from the coordinate behavior of subsets of anonymous transcripts without cloning any genes. The number of transcripts in each response category can be estimated. The same may be true for differential display. We demonstrate these claims by treating a cell line with two known modulators of RNA abundance, transforming growth factor-beta (TGF beta) and cycloheximide (CX), used together and alone. The responses of over 1700 anonymous transcripts were monitored under these three conditions and in an untreated control. Eight of the twenty-seven [3(3)] possible transcript response categories were observed among 86 differentially expressed transcripts. For example, CX stabilizes or induces as many as 2.7% of transcripts of which about one third do not accumulate when TGF beta is also present. This intersection may reflect CX stabilization or induction of an important class of RNAs that otherwise usually have short half-lives. We predict that RNAs in this class constitute the majority of transcripts targeted for rapid down regulation in response to TGF beta and perhaps most other natural transcriptional modulators.
Animals↗
Expression of bacteriophage T4 gene 25 is regulated via RNA secondary structure in the translational initiation region.
Analysis of the nucleotide sequence in the 5' flanking region of bacteriophage T4 gene 25 revealed three potential Shine and Dalgarno sequences, SD1, SD2 and SD3, with a spacing of 8, 17 and 27 nucleotides from the initiation codon of this gene, respectively. Results of our experiments in the bacteriophage T7 expression system clearly demonstrate that the SD3 sequence is required for efficient expression of gene 25. We propose the existence of a stem-loop structure that includes SD1 and SD2 sequences and brings the SD3 sequence to a favourable spacing with the initiation codon of gene 25. Since the predicted secondary structure in the translational initiation region of gene 25 is relatively unstable and the SD3 sequence, GAGG, is more typical than the SD1 sequence, GAG, we suggest that this structure could control the level of gene expression.
Bacteriophage T4↗