Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5'-flanking region

Differential Phosphorylation of RNA Polymerase III and the Initiation Factor TFIIIB in Saccharomyces cerevisiae

The production of ribosomes and tRNAs for protein synthesis has a high energetic cost and is under tight transcriptional control to ensure that the level of RNA synthesis is balanced with nutrient availability and the prevailing environmental conditions. In the RNA polymerase (pol) III system in yeast, nutrients and stress affect transcription through a bifurcated signaling pathway in which protein kinase A (PKA) and TORC1 activity directly or indirectly, through downstream kinases, alter the phosphorylation state and function of the Maf1 repressor and Rpc53, a TFIIF-like subunit of the polymerase. However, numerous lines of evidence suggest greater complexity in the regulatory network including the phosphoregulation of other pol III components. To address this issue, we systematically examined all 17 subunits of pol III along with the three subunits of the initiation factor TFIIIB for evidence of differential phosphorylation in response to inhibition of TORC1. A relatively high stoichiometry of phosphorylation was observed for several of these proteins and the Rpc82 subunit of the polymerase and the Bdp1 subunit of TFIIIB were found to be differentially phosphorylated. Bdp1 is phosphorylated on four major sites during exponential growth and the protein is variably dephosphorylated under conditions that inhibit tRNA gene transcription. PKA, the TORC1-regulated kinase Sch9 and protein kinase CK2 are all implicated in the phosphorylation of Bdp1. Alanine substitutions at the four phosphosites cause hyper-repression of transcription indicating that phosphorylation of Bdp1 opposes Maf1-mediated repression. The new findings suggest an integrated regulatory model for signaling events controlling pol III transcription.

Regulation of pol III transcription by nutrient and stress signaling pathways

Transcription by RNA polymerase III (pol III) is responsible for ~15% of total cellular transcription through the generation of small structured RNAs such as tRNA and 5S RNA. The coordinate synthesis of these molecules with ribosomal protein mRNAs and rRNA couples the production of ribosomes and their tRNA substrates and balances protein synthetic capacity with the growth requirements of the cell. Ribosome biogenesis in general and pol III transcription in particular is known to be regulated by nutrient availability, cell stress and cell cycle stage and is perturbed in pathological states. High throughput proteomic studies have catalogued modifications to pol III subunits, assembly, initiation and accessory factors but most of these modifications have yet to be linked to functional consequences. Here we review our current understanding of the major points of regulation in the pol III transcription apparatus, the targets of regulation and the signaling pathways known to regulate their function. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Stimulation of direct-repeat recombination by RNA polymerase III transcription

Eukaryotic cells have to regulate the progression and integrity of DNA replication forks through concomitantly transcribed genes. A transcription-dependent increase of recombination within protein-coding and ribosomal genes of eukaryotic cells is well documented. Here we addressed whether tRNA transcription and tRNA-dependent transcription-associated replication pausing leads to genetic instability. Thus, we designed a plasmid based, LEU2 direct-repeat containing system for the analysis of factors that contribute to tRNA(SUP53)-dependent genetic instability. We show that tRNA(SUP53) transcription is recombinogenic and that recombination can be further stimulated by deletion of the 5' to 3' helicase Rrm3. Furthermore, tRNA(SUP53)-dependent recombination was markedly increased in the presence of 4-NQO in rrm3Delta cells only. The frequency of recombination events mediated by tRNA(SUP53) transcription does not correlate with the appearance and intensity of replication fork pausing sites. Our results provide evidence that the convergent encounter of replication and RNA polymerase III transcription machineries stimulates recombination, although to a lesser extent than RNA polymerase I or II transcription. However, there is no correlation between recombination and the specific replication fork pausing sites found at the tRNA (SUP53) gene. Our results indicate that tRNA-specific replication fork pausing sites are poorly recombinogenic.

Increased recombination between active tRNA genes

Transfer RNA genes are distributed throughout eukaryotic genomes, and are frequently found as multicopy families. In Saccharomyces cerevisiae, tRNA gene transcription by RNA polymerase III suppresses nearby transcription by RNA polymerase II, partially because the tRNA genes are clustered near the nucleolus. We have tested whether active transcription of tRNA genes might also suppress recombination, since recombination between identical copies of the repetitive tRNA genes could delete intervening genes and be detrimental to survival. The opposite proved to be the case. Recombination between active tRNA genes was elevated, but only when both genes are transcribed. We also tested the effects of tRNA genes on recombination between the direct terminal repeats of a neighboring retrotransposon, since most Ty retrotransposons reside next to tRNA genes, and the selective advantage of this arrangement is not known.

Two steps in Maf1-dependent repression of transcription by RNA polymerase III

In Saccharomyces cerevisiae, Maf1 is essential for mediating the repression of transcription by RNA polymerase (pol) III in response to diverse cellular conditions. These conditions activate distinct signaling pathways that converge at or above Maf1. Thus, Maf1-dependent repression is thought to involve a common set of downstream inhibitory effects on the pol III machinery. Here we provide support for this view and define two steps in Maf1-dependent transcriptional repression. We show that chlorpromazine (CPZ)-induced repression of pol III transcription is achieved by inhibiting de novo assembly of transcription factor (TF) IIIB onto DNA as well as the recruitment of pol III to preassembled TFIIIB.DNA complexes. Additionally Brf1 was identified as a target of repression in extracts of CPZ-treated cells. Maf1-Brf1 and Maf1-pol III interactions were implicated in the inhibition of TFIIIB.DNA complex assembly and polymerase recruitment by recombinant Maf1. Co-immunoprecipitation experiments confirmed these interactions in yeast extracts and demonstrated that Maf1 does not differentially sequester Brf1 or pol III under repressing conditions. The results suggest that Maf1 functions by a non-stoichiometric mechanism to repress pol III transcription.

A composite upstream sequence motif potentiates tRNA gene transcription in yeast

Transcription of eukaryotic tRNA genes relies on the TFIIIC-dependent recruitment of TFIIIB on a approximately 50 bp region upstream of the transcription start site (TSS). TFIIIC specifically interacts with highly conserved, intragenic promoter elements, while the contacts between TFIIIB and the upstream DNA have long been considered as largely non-specific. Through a computer search procedure designed to detect shared, yet degenerate sequence features, we have identified a conserved sequence pattern upstream of Saccharomyces cerevisiae tDNAs. This pattern consists of four regions in which particular sequences are over-represented. The most downstream of these regions surrounds the TSS, while the other three districts of sequence conservation (appearing as a centrally located TATA-like sequence flanked by T-rich elements on both sides) are located across the DNA region known to interact with TFIIIB. Upstream regions whose sequence conforms to this pattern were found to potentiate tRNA gene transcription, both in vitro and in vivo, by enhancing TFIIIB binding. A conserved pattern of DNA bendability was also revealed, with peaks of bending propensity centered on the TATA-like and the TSS regions. Sequence analysis of other eukaryotic genomes further revealed the widespread occurrence of conserved sequence patterns upstream of tDNAs, with striking lineage-specific differences in the number and sequence of conserved motifs. Our data strongly support the notion that tRNA gene transcription in eukaryotes is modulated by composite TFIIIB binding sites that may confer responsiveness to variation in TFIIIB activity and/or concentration.

Detours and shortcuts to transcription reinitiation

Gene transcription is repetitive, enabling the synthesis of multiple copies of identical RNA molecules from the same template. The cyclic process of RNA synthesis from active genes, referred to as transcription reinitiation, contributes significantly to the level of RNAs in living cells. Contrary to the perception that multiple transcription cycles are a mere iteration of mechanistically identical steps, a large body of evidence indicates that, in most transcription systems, reinitiation involves highly specific and regulated pathways. These pathways influence the availability for reinitiation of template DNA and/or transcription proteins, and represent an important yet poorly characterized aspect of gene regulation.

Mutational analysis of the transcription factor IIIB-DNA target of Ty3 retroelement integration

The Ty3 retrovirus-like element inserts preferentially at the transcription initiation sites of genes transcribed by RNA polymerase III. The requirements for transcription factor (TF) IIIC and TFIIIB in Ty3 integration into the two initiation sites of the U6 gene carried on pU6LboxB were previously examined. Ty3 integrates at low but detectable frequencies in the presence of TFIIIB subunits Brf1 and TATA-binding protein. Integration increases in the presence of the third subunit, Bdp1. TFIIIC is not essential, but the presence of TFIIIC specifies an orientation of TFIIIB for transcriptional initiation and directs integration to the U6 gene-proximal initiation site. In the current study, recombinant wild type TATA-binding protein, wild type and mutant Brf1, and Bdp1 proteins and highly purified TFIIIC were used to investigate the roles of specific protein domains in Ty3 integration. The amino-terminal half of Brf1, which contains a TFIIB-like repeat, contributed more strongly than the carboxyl-terminal half of Brf1 to Ty3 targeting. Each half of Bdp1 split at amino acid 352 enhanced integration. In the presence of TFIIIB and TFIIIC, the pattern of integration extended downstream by several base pairs compared with the pattern observed in vitro in the absence of TFIIIC and in vivo, suggesting that TFIIIC may not be present on genes targeted by Ty3 in vivo. Mutations in Bdp1 that affect its interaction with TFIIIC resulted in TFIIIC-independent patterns of Ty3 integration. Brf1 zinc ribbon and Bdp1 internal deletion mutants that are competent for polymerase III recruitment but defective in promoter opening were competent for Ty3 integration irrespective of the state of DNA supercoiling. These results extend the similarities between the TFIIIB domains required for transcription and Ty3 integration and also reveal requirements that are specific to transcription.

Kinetic analysis of segmentation gene interactions in Drosophila embryos

A major challenge for developmental biologists in coming years will be to place the vast number of newly identified genes into precisely ordered genetic and molecular pathways. This will require efficient methods to determine which genes interact directly and indirectly. One of the most comprehensive pathways currently under study is the genetic hierarchy that controls Drosophila segmentation. Yet, many of the potential interactions within this pathway remain untested or unverified. Here, we look at one of the best-characterized components of this pathway, the homeodomain-containing transcription factor Fushi tarazu (Ftz), and analyze the response kinetics of known and putative target genes. This is achieved by providing a brief pulse of Ftz expression and measuring the time required for genes to respond. The time required for Ftz to bind and regulate its own enhancer, a well-documented interaction, is used as a standard for other direct interactions. Surprisingly, we find that both positively and negatively regulated target genes respond to Ftz with the same kinetics as autoregulation. The rate-limiting step between successive interactions (<10 minutes) is the time required for regulatory proteins to either enter or be cleared from the nucleus, indicating that protein synthesis and degradation rates are closely matched for all of the proteins studied. The matching of these two processes is likely important for the rapid and synchronous progression from one class of segmentation genes to the next. In total, 11 putative Ftz target genes are analyzed, and the data provide a substantially revised view of Ftz roles and activities within the segmentation hierarchy.

Transcriptional silencing of a tRNA1Gly copy from within a multigene family is modulated by distal cis elements

Individual copies of tRNA1Gly from within the multigene family in Bombyx mori could be classified based on in vitro transcription in homologous nuclear extracts into three categories of highly, moderately, or weakly transcribed genes. Segregation of the poorly transcribed gene copies 6 and 7, which are clustered in tandem within 425 base pairs, resulted in enhancement of their individual transcription levels, but the linkage itself had little influence on the transcriptional status. For these gene copies, when fused together generating a single coding region, transcription was barely detectable, which suggested the presence of negatively regulating elements located in the far flanking sequences. They exerted the silencing effect on transcription overriding the activity of positive regulatory elements. Systematic analysis of deletion, chimeric, and mutant constructs revealed the presence of a sequence element TATATAA located beyond 800 nucleotides upstream to the coding region acting as negative modulator, which when mutated resulted in high level transcription. Conversely, a TATATAA motif reintroduced at either far upstream or far downstream flanking regions exerted a negative effect on transcription. The location of cis-regulatory sequences at such farther distances from the coding region and the behavior of TATATAA element as negative regulator reported here are novel. These element(s) could play significant roles in activation or silencing of genes from within a multigene family, by recruitment or sequestration of transcription factors.

In vitro evidence for growth regulation of tRNA gene transcription in yeast. A role for transcription factor (TF) IIIB70 and TFIIIC

We report in vitro studies showing that tRNA gene transcription in yeast is down-regulated during the transition from logarithmic to stationary phase growth. Transcription in a postdiauxic (early stationary) phase extract of a wild-type strain decreased 3-fold relative to a log phase extract. This growth stage-related difference in transcription was amplified to 20-fold in extracts of a strain containing a mutation (pcf1-4) in the 131-kDa subunit of TFIIIC. The reduction in transcription activity in both wild-type and mutant postdiauxic phase extracts was correlated with a decrease in the amount of TFIIIB70, the limiting factor in these extracts. However, the 3.7 +/- 0.5-fold decrease in amount of TFIIIB70 in mutant extracts does not, by itself, account for the 20-fold decrease in transcription. Accordingly, transcription in the mutant postdiauxic phase extract could be reconstituted to a level equal to the mutant log phase extract by the addition of two components, TFIIIB70 and TFIIIC. Addition of TFIIIB70 increased transcription 10-fold, while a 2-fold effect of TFIIIC was seen at saturating levels of TFIIIB70. The data suggest that both TFIIIB70 and TFIIIC play a role in coordinating the level of polymerase III transcription with cell growth rate.

Developmental stage-specific regulation of Xenopus tRNA genes by an upstream promoter element

Typically the internal promoter elements of tRNA genes are necessary and sufficient to support transcription. Here a sequence element preceding a Xenopus tRNA gene is shown to be required for transcription in late stage, but not early stage oocyte extracts. The constitutive tyrD gene is expressed in both early and late oocyte extracts, whereas the early oocyte-specific tyrCooc gene is only expressed in early extracts. An upstream promoter element (URR), between positions -42 and -14 of the tyrD gene, mediates this differential expression. The URR is required for tyrD transcription in late oocyte extracts. Placing the URR upstream of the tyrCooc gene allows this gene to be transcribed in late extracts. The URR is irrelevant to transcription in early extracts; transcription of tyrD or tyrCooc requires only the internal promoter sequences. This indicates the polymerase III transcriptional machinery changes during oogenesis, resulting in a stringent upstream sequence requirement. Mutations within the URR are shown to alter the preferred site of initiation by RNA polymerase III. Shifting the position of the URR upstream by one-half helical turn also repositioned the site of initiation, suggesting the URR directs the placement of the initiation factor complex or polymerase itself.

RNA polymerase III. Genes, factors and transcriptional specificity

Recent studies on RNA polymerase III (pol III) gene transcription have provided a new awareness of the molecular complexity of this process. Fortunately, while the number of transcription components has been increasing, fundamental similarities have emerged regarding the function of eukaryotic promoter elements and the factors that bind them to form preinitiation complexes. Among these, the ability of transcription factor IIIB (TFIIIB) and pol III to transcribe the Saccharomyces cerevisiae U6 gene suggests that the concept of a minimal pol II promoter comprising a TATA box and an initiator region has a parallel in the pol III system. Furthermore, for each of the three classes of eukaryotic RNA polymerase, the assembly of transcription preinitiation complexes and, to some extent, the nature of these complexes appears to be more similar than was previously anticipated. This work highlights the novel functions and transcriptional properties of newly identified pol III genes, discusses the diversity of pol III promoter structures and presents the notion that the exclusive use of extragenic promoters by some pol III genes (so-called type-3 genes) may have evolved since the divergence of yeast and higher eukaryotes. Additionally, recent progress is reviewed on the identification and cloning of subunits for TFIIIC and TFIIIB. Particular emphasis is given to two components of TFIIIB, the TATA-binding protein and a protein with TFIIB homology (PCF4), since the properties of these molecules suggest a model whereby the polymerase specificity of transcription complexes is determined.

RNA polymerase III (C) and its transcription factors

Transcription of small genes by RNA polymerase III or C (pol III) involves many of the strategies that are used for transcription complex formation and occasionally the same components as those used by RNA polymerase II or B (pol II). Transcription complex formation is a multistep process that leads to the binding of a single initiation factor, TFIIIB, which in turn directs the selection of pol III. The general transcription factor TFIID can be involved in both pol II and pol III transcription. These and other similarities point towards a unifying mechanism for eukaryotic transcription initiation.

RNA polymerase III transcription

Remarkable progress has been made in defining the functional significance of the protein-DNA interactions involved in transcription complex formation on yeast tRNA and 5S RNA genes. This new information leads to a re-evaluation of how the class III gene transcription machinery operates.

Binding of yeast TFIIIC to tRNA gene bipartite internal promoters: analysis of physical effects on the intervening DNA

Complexes between transcription factor TFIIIC and eukaryotic tRNA gene internal promoter A and B boxes are unusual in that the binding to the two distinct sites tolerates considerable variation in both distance and helical orientation between the sites. Electrophoretic mobility of Saccharomyces cerevisiae TFIIIC complexes with circularly permuted tRNA gene fragments and sensitivity of the complexes to a single stranded-specific reagent, potassium permanganate, indicated that no significant bend or distortion was introduced into the DNA by simultaneous binding to both internal promoters. These data support a model in which variability in the relative positions of the two binding sites is compensated by flexibility in the structure of TFIIIC.

Unraveling the complexities of transcription by RNA polymerase III

The biosynthesis of proteins and nucleic acids in eukaryotes requires the participation of numerous small RNAs, many of which are products of RNA polymerase III transcription. How cells are able to coordinate the synthesis of these RNAs during growth and replication has been the subject of recent exciting and thought-provoking studies. We review the progress in this area, and focus upon shared properties between transcription systems having different functions.

S. cerevisiae TFIIIB is the transcription initiation factor proper of RNA polymerase III, while TFIIIA and TFIIIC are assembly factors

The S. cerevisiae RNA polymerase III (pol III) transcription factor TFIIIB binds to DNA upstream of the transcription start site of the SUP4 tRNA(Tyr) gene in a TFIIIC-dependent reaction and to the major 5S rRNA gene in a reaction requiring TFIIIC and TFIIIA. It is shown here that TFIIIB alone correctly positions pol III for repeated cycles of transcription on both genes, with the same efficiency as fully assembled transcription complexes. Thus, TFIIIB is the sole transcription initiation factor of S. cerevisiae pol III; TFIIIC and TFIIIA are assembly factors for TFIIIB. The TFIIIB-dependent binding of pol III to the SUP4 tRNA and 5S rRNA genes has been analyzed in binary (protein and DNA only) and precisely arrested ternary (protein, DNA, and RNA) transcription complexes. Pol III unwinds at least 14 bp of DNA at the SUP4 transcription start in a temperature-dependent process. The unwound DNA segment moves downstream with nascent RNA as a transcription bubble of approximately the same size.

Sequences preceding the minimal promoter of the Xenopus somatic 5S RNA gene increase binding efficiency for transcription factors

Sequences preceding the minimal promoter play a role in the differential expression of the Xenopus somatic and oocyte-type 5S RNA genes. In this report, the somatic sequences between -32 and +37 are shown to increase transcriptional activity in microinjected embryos, yet have little to no effect in microinjected oocyte nuclei. In vitro, these sequences increase activity in whole oocyte S150 extracts, but not in oocyte nuclear extracts. In S150 extracts, these somatic sequences facilitate binding by a commonly required factor(s), other than TFIIIA, which forms a stable complex with the 5S gene. This transcriptional enhancement is also apparent in a reconstituted system using purified TFIIIA and partially purified TFIIIB and TFIIIC.