Correlations between transcription of a yeast tRNA gene and transcription factor-DNA interactions

Structural rearrangements of the RNA polymerase III machinery during tRNA transcription initiation

RNA polymerase III catalyses the synthesis of tRNAs in eukaryotic organisms. Through combined biochemical and structural characterisation, multiple auxiliary factors have been identified alongside RNA Polymerase III as critical in both facilitating and regulating transcription. Together, this machinery forms dynamic multi-protein complexes at tRNA genes which are required for polymerase recruitment, DNA opening and initiation and elongation of the tRNA transcripts. Central to the function of these complexes is their ability to undergo multiple conformational changes and rearrangements that regulate each step. Here, we discuss the available biochemical and structural data on the structural plasticity of multi-protein complexes involved in RNA Polymerase III transcriptional initiation and facilitated re-initiation during tRNA synthesis. Increasingly, structural information is becoming available for RNA polymerase III and its functional complexes, allowing for a deeper understanding of tRNA transcriptional initiation. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.

Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization

DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases and other pathways highlights the potential of DNA glycosylase inhibitors for future medicinal chemistry development in cancer therapy. By combining biochemical and structural approaches, the physical target of 2-thioxanthine (2TX), an uncompetitive inhibitor of Fpg, was identified. 2TX interacts with the zinc finger (ZnF) DNA binding domain of the enzyme. This explains why the zincless hNEIL1 enzyme is resistant to 2TX. Crystal structures of the enzyme bound to DNA in the presence of 2TX demonstrate that the inhibitor chemically reacts with cysteine thiolates of ZnF and induces the loss of zinc. The molecular mechanism by which 2TX inhibits Fpg may be generalized to all prokaryote and eukaryote ZnF-containing Fpg/Nei-DNA glycosylases. Cell experiments show that 2TX can operate in cellulo on the human Fpg/Nei DNA glycosylases. The atomic elucidation of the determinants for the interaction of 2TX to Fpg provides the foundation for the future design and synthesis of new inhibitors with high efficiency and selectivity.

The acetaminophen-derived bioactive N-acylphenolamine AM404 inhibits NFAT by targeting nuclear regulatory events

AM404 is a synthetic TRPV1/CB(1) hybrid ligand with inhibitory activity on the anandamide transporter and is used for the pharmacological manipulation of the endocannabinoid system. It has been recently described that acetaminophen is metabolised in the brain to form the bioactive N-acylphenolamine AM404 and therefore, we have evaluated the effect of this metabolite in human T cells, discovering that AM404 is a potent inhibitor of TCR-mediated T-cell activation. Moreover, we found that AM404 specifically inhibited both IL-2 and TNF-alpha gene transcription and TNF-alpha synthesis in CD3/CD28-stimulated Jurkat T cells in a FAAH independent way. To further characterize the biochemical inhibitory mechanisms of AM404, we examined the signaling pathways that regulate the activation of the transcription factors NF-kappaB, NFAT and AP-1 in Jurkat cells. We found that AM404 inhibited both the binding to DNA and the transcriptional activity of endogenous NFAT and the transcriptional activity driven by the over expressed fusion protein Gal4-NFAT (1-415). However, AM404 did not affect early steps in NFAT signaling such as CD3-induced calcium mobilization and NFAT1 dephosphorylation. The NFAT inhibitory activity of AM404 seems to be quite specific since this compound did not interfere with the signaling pathways leading to AP-1 or NF-kappaB activation. These findings provide new mechanistic insights into the immunological effects of AM404 which in part could explain some of the activities ascribed to the widely used acetaminophen.

The viral protein A238L inhibits cyclooxygenase-2 expression through a nuclear factor of activated T cell-dependent transactivation pathway

Cyclooxygenase-2 is transiently induced upon cell activation or viral infections, resulting in inflammation and modulation of the immune response. Here we report that A238L, an African swine fever virus protein, efficiently inhibits cyclooxygenase-2 gene expression in Jurkat T cells and in virus-infected Vero cells. Transfection of Jurkat cells stably expressing A238L with cyclooxygenase-2 promoter-luciferase constructs containing 5'-terminal deletions or mutations in distal or proximal nuclear factor of activated T cell (NFAT) response elements revealed that these sequences are involved in the inhibition induced by A238L. Overexpression of a constitutively active version of the calcium-dependent phosphatase calcineurin or NFAT reversed the inhibition mediated by A238L on cyclooxygenase-2 promoter activation, whereas overexpression of p65 NFkappaB had no effect. A238L does not modify the nuclear localization of NFAT after phorbol 12-myristate 13-acetate/calcium ionophore stimulation. Moreover, we show that the mechanism by which the viral protein down-regulates cyclooxygenase-2 activity does not involve inhibition of the binding between NFAT and its specific DNA sequences into the cyclooxygenase-2 promoter. Strikingly, A238L dramatically inhibited the transactivation mediated by a GAL4-NFAT fusion protein containing the N-terminal transactivation domain of NFAT1. Taken together, these data indicate that A238L down-regulates cyclooxygenase-2 transcription through the NFAT response elements, being NFAT-dependent transactivation implicated in this down-regulation.

Activation of transcription factor IIIC by the adenovirus E1A protein

The factor(s) responsible for the adenovirus E1A-stimulated transcription of RNA polymerase III genes was localized previously in a chromatographic fraction containing transcription factor IIIC (TFIIIC). In further studies, two distinct forms of TFIIIC, which were chromatographically separable, generated VA gene-protein complexes that were distinguished by gel shift assays. The form of TFIIIC that generated the more slowly migrating promoter complex had greater transcriptional activity in vitro, associated more rapidly with the promoter, and formed a more salt-resistant complex. Greater amounts of this more active form of TFIIIC resulted from either E1A expression during infection or growth of the cells in a higher concentration of serum, whereas template commitment assays indicated that overall TFIIIC concentrations remained unchanged during viral infection. The in vitro interconversion of the two forms of TFIIIC by phosphatase treatment suggests that transcriptional activation of RNA polymerase III genes can be mediated by phosphorylation of TFIIIC.

Functional dissection of 5' and 3' extragenic control regions of human tRNA(Val) genes reveals two different regulatory effects

Two natural human tRNA(Val) genes, pHtV1 and pHtV3, differ in their transcription efficiency by an order of magnitude. The extragenic control regions (ECRs) responsible for this effect were compared with respect to the kinetics and thermodynamics of transcription complex formation. The 5' ECR of pHtV1 acts by increasing both the rate of stable complex formation and the equilibrium constant of association between tDNA and at least one transcription factor present in the stable complex. The stability of the preinitiation complexes is not affected by ECRs. For the formation of a stable preinitiation complex, we suggest a two-step mechanism, comprising (i) the ECR-controlled association of at least one transcription factor (TFIIIC) with the tDNA, and (ii) an ECR-independent conformational change of this tDNA-protein complex. The function of 3' ECRs could be discriminated from the 5' ECR-mediated effects by transcriptional analysis of two chimeric constructs derived from pHtV1 and pHtV3. Surprisingly, the pHtV1 3' ECR causes an eight-fold increase of transcription efficiency, although it has only minor influence on stable preinitiation complex formation. Instead, this ECR stimulates transcription by promoting the transition of the preinitiation complex into an activity synthesizing transcription complex. This novel function of a 3' ECR contributes an additional regulatory level for tRNA gene expression.

Selective proteolysis defines two DNA binding domains in yeast transcription factor tau

Transcription of eukaryotic transfer RNA genes involves, as a primary event, the stable binding of a protein factor to the intragenic promoter. The internal control region is composed of two non-contiguous conserved sequence elements, the A and B blocks. These are variably spaced depending on the genes. tau, a large transcription factor purified from yeast cells, interacts with these two control elements as shown by DNase I footprinting, exonuclease digestion, dimethyl sulphate protection experiments and by analysis of point mutations. Here we used a limited proteolysis treatment to obtain a smaller form of tau with drastically altered DNA binding properties. A protease-resistant domain interacts solely with the B block region of tRNA genes.

Yeast class III gene transcription factors and homologous RNA polymerase III form ternary transcription complexes stable to disruption by N-lauroyl-sarcosine (sarcosyl)

Yeast Class III gene transcription factors and RNA polymerase III were used to form ternary transcription complexes on a tRNASer gene in vitro under UTP-limiting transcription conditions. These ternary transcription complexes were composed of template DNA, proteins, and RNA. We have shown that the RNAs contained in these complexes represented specifically initiated nascent pre-tRNASer transcripts. These nascent RNAs could be very efficiently elongated to full-length pre-tRNASer molecules, even in the presence of the ionic detergent sarcosyl. Partial purification (greater than 100-fold) of these sarcosyl-resistant ternary transcription complexes could be achieved in a single step via sucrose gradient sedimentation. Comparable sarcosyl-resistant ternary transcription complexes could not be formed using purified yeast RNA polymerase III as the only protein component of the complex.

Electron-microscopic examination of the binding of a large RNA polymerase III transcription factor to a tRNA gene

A Saccharomyces cerevisiae RNA polymerase III transcription factor was previously shown to bind stably to tRNA genes. This transcription factor has been further purified on the basis of its large size and its binding to a S. cerevisiae tRNALeu3 gene has been examined by electron microscopy. Site-specific binding of the factor to the tRNALeu3 gene sharply bends the DNA.

A large region controls tRNA gene transcription

We find that tRNA gene transcription is controlled by a region much larger than the previously described internal segments known as A and B boxes. In a Bombyx mori silkworm tRNA2Ala gene, transcriptionally important sequences extend at least from -13 to +146, and thus include sequences both upstream and downstream from the 98 base-pair primary transcription unit. We show that the apparent size of this control region can be manipulated by the conditions used to measure transcription in vitro. Specifically, the use of high concentrations of templates to overcome the effect of an inhibitory substance in crude extracts can make the control region appear smaller. We propose that this finding explains much of the observed variability in the sequence requirements for transcription of different tRNA genes. If so, large size is likely to be a general feature of tRNA gene control regions.

Eukaryotic RNA polymerases

This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.

Transcription of tRNA gene fragments by HeLa cell extracts

Promoter elements for tRNA genes from several eukaryotes have been identified in the coding regions of the DNA. There are two non-contiguous sequences, an A-block or D-control region and a B-block or T-control region, located in the 5'- and 3'-halves of the tRNA sequence respectively. Both sequences are about 12 bp in length and are strongly conserved in all tRNA genes. We and others have recently shown that some tRNA genes from yeast and insects have a third control region located in the 5'-flanking sequences adjacent to tDNA. The tRNALeu3 genes from yeast have such a sequence. It is strongly conserved in non-allelic copies of tRNALeu3 genes as well as several other yeast tRNA genes. This 5'-flanking sequence is indispensable for transcription of the gene in an in vitro system derived from yeast cells. Further, the transcription apparatus from yeast will recognize and transcribe gene fragments including the 5'-flanking sequence in conjunction with either the A or B-blocks. Neither the 5'-flanking sequence alone nor the A and B-blocks lacking the 5'-flanking region can act as promoters in the yeast system. We have used these tRNALeu3 gene fragments to analyze the promoter activity of the three control regions with a Hela cell extract which actively transcribes class III genes. We find that the Hela cell system requires the presence of both A and B-block sequences and is insensitive to 5'-flanking DNA.