Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III

Possible interaction between the bacterial transcription factor ArtA and the eukaryotic RNA polymerase III promoter

Eukaryotic RNA polymerase III (RNAP III) transcribes tRNA genes and short interspersed elements that have internal promoters consisting of A- and B-blocks. The B-block binding subunit of the transcription initiation factor TFIIIC binds to the B-block. The mobile bacterial insertion sequence (IS) 1 contains a RNAP III promoter-like sequence, which stimulates bacterial transcription along with the bacterial ArtA protein. Here, the DNA-binding ability of ArtA was examined in vitro using a simple, newly developed method. Various DNA fragments, including RNAP III promoter fragments, were separately incubated with purified ArtA, and then loaded onto a polyacrylamide gel. Since DNAs bound by ArtA remain in the gel wells during electrophoresis, SDS was added into the wells at the electrophoresis halfway point. It was hypothesized that SDS would dissociate the DNA-ArtA complexes in the wells, and then the DNAs would begin to migrate. In fact, new bands appeared in all of the lanes at similar intensities, indicating that ArtA binds nonspecifically to DNA. Therefore, labeled wild-type RNAP III promoter fragments were incubated with either the unlabeled wild-type or mutant fragments and ArtA, and electrophoresed. The B-block(-like) sequences of IS1, a human Alu element, and an anuran tRNA gene were important for binding to ArtA. Additionally, in silico analyses revealed the presence of the RNAP III promoter-like structures in the IS1 isoforms and the IS3 family elements. These results suggest the presence of parts of the RNAP III transcription machinery in bacteria, and might imply that its prototype existed in the common ancestor.

Evolution of the B-Block Binding Subunit of TFIIIC That Binds to the Internal Promoter for RNA Polymerase III

Eukaryotic RNA polymerase III transcribes tRNA genes, and this requires the transcription factor TFIIIC. Promoters are within genes, with which the B-block binding subunit of TFIIIC associates to initiate transcription. The binding subunits are more than 1000 amino acids in length in various eukaryotic species. There are four regions with conserved sequence similarities in the subunits. The helix-turn-helix motif is included in one of these regions and has been characterized as the B-block_TFIIIC family in the Pfam database. In the NCBI and EMBL translated protein databases, there are archaeal proteins (approximately 100 amino acids in length) referred to as B-block binding subunits. Most of them contain a B-block_TFIIIC motif. DELTA-BLAST searches using these archaeal proteins as queries showed significant multiple blast hits for many eukaryotic B-block binding subunits on the same proteins. This result suggests that eukaryotic B-block binding subunits were constituted by repeating a small unit of B-block_TFIIIC over a long evolutionary period. Bacterial proteins have also been annotated as B-block binding subunits in the databases. Here, some of them were confirmed to have significant similarities to B-block_TFIIIC. These results may imply that part of the RNAP III transcription machinery existed in the common ancestry of prokaryotes and eukaryotes.

Yeast RNA polymerase III transcription factors and effectors

Recent data indicate that the well-defined transcription machinery of RNA polymerase III (Pol III) is probably more complex than commonly thought. In this review, we describe the yeast basal transcription factors of Pol III and their involvements in the transcription cycle. We also present a list of proteins detected on genes transcribed by Pol III (class III genes) that might participate in the transcription process. Surprisingly, several of these proteins are involved in RNA polymerase II transcription. Defining the role of these potential new effectors in Pol III transcription in vivo will be the challenge of the next few years. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Plastid endosymbiosis, genome evolution and the origin of green plants

Evolutionary relationships among complex, multicellular eukaryotes are generally interpreted within the framework of molecular sequence-based phylogenies that suggest green plants and animals are only distantly related on the eukaryotic tree. However, important anomalies have been reported in phylogenomic analyses, including several that relate specifically to green plant evolution. In addition, plants and animals share molecular, biochemical and genome-level features that suggest a relatively close relationship between the two groups. This article explores the impacts of plastid endosymbioses on nuclear genomes, how they can explain incongruent phylogenetic signals in molecular data sets and reconcile conflicts among different sources of comparative data. Specifically, I argue that the large influx of plastid DNA into plant and algal nuclear genomes has resulted in tree-building artifacts that obscure a relatively close evolutionary relationship between green plants and animals.

Possible presence and role of the promoter sequence for eukaryotic RNA polymerase III in bacteria

The bacterial repetitive sequence IS1, is a translocatable DNA segment. The internal region of IS1 acts as a cis-element to stimulate RNA synthesis from the upstream promoter. The product of the bacterial artA gene works with this cis-element to stimulate transcription. Eukaryotic genes for small RNAs and short interspersed repetitive elements (SINEs) have internal promoters, transcribed by RNA polymerase III (RNAP III). RNAP III requires the multisubunit protein factor TFIIIC in transcription initiation. TFIIIC contains the B-block binding subunit which recognizes the internal promoter. Here, I report that the eukaryotic RNAP III promoter-like sequence was found in the cis-element of bacterial IS1. Mutations in the cis-element which affect transcription were present in the RNAP III promoter-like sequence. The RNAP III promoter sequence of Alu, which is a human SINE, was cloned into Escherichia coli, and was shown to stimulate bacterial transcription like the cis-element of IS1. Furthermore, the primary structures of ArtA protein and B-block binding subunits were compared. The amino acid sequence of ArtA appeared to be similar to the N- and C-terminal regions conserved in many B-block binding subunits. Prokaryotes and eukaryotes have been thought to have inherent transcription machineries. The results shown here, however, suggest a new aspect of the evolution of the RNAP III transcription machinery.

Distinct modes of TATA box utilization by the RNA polymerase III transcription machineries from budding yeast and higher plants

The TATA box is a key upstream control element for basal tRNA gene transcription by RNA polymerase III in some eukaryotes, such as the fission yeast (Schizosaccharomyces pombe) and higher plants, but not in others such as the budding yeast (Saccharomyces cerevisiae). To gain information on this differential TATA box requirement, we examined side-by-side the in vitro transcription properties of TATA-containing and TATA-mutated plant and S. cerevisiae tDNAs in homologous in vitro transcription systems from both organisms and in a hybrid system in which yeast TBP was replaced by its plant homologue. The data support the general conclusion that specific features of the plant transcription machinery, rather than upstream region architecture per se, are responsible for the much stronger TATA box dependence of the plant system. In both systems, however, a strong influence of the TATA box on transcription start site selection was observed. This was particularly striking in the case of plant tDNAs, where TATA-rich upstream regions were found to favour the use of alternative initiation sites. Replacement of yeast TBP with its plant counterpart did not confer any general TATA box responsiveness to the yeast transcription machinery. Interactions involving components other than TBP are thus responsible for the strong TATA box requirement of plant tDNA transcription.

The growing pre-mRNA recruits actin and chromatin-modifying factors to transcriptionally active genes

In the dipteran Chironomus tentans, actin binds to hrp65, a nuclear protein associated with mRNP complexes. Disruption of the actin-hrp65 interaction in vivo by the competing peptide 65-2CTS reduces transcription drastically, which suggests that the actin-hrp65 interaction is required for transcription. We show that the inhibitory effect of the 65-2CTS peptide on transcription is counteracted by trichostatin A, a drug that inhibits histone deacetylation. We also show that actin and hrp65 are associated in vivo with p2D10, an evolutionarily conserved protein with histone acetyltransferase activity that acts on histone H3. p2D10 is recruited to class II genes in a transcription-dependent manner. We show, using the Balbiani ring genes of C. tentans as a model system, that p2D10 is cotranscriptionally associated with the growing pre-mRNA. We also show that experimental disruption of the actin-hrp65 interaction by the 65-2CTS peptide in vivo results in the release of p2D10 from the transcribed genes, reduced histone H3 acetylation, and a lower level of transcription activity. Furthermore, antibodies against p2D10 inhibit run-on elongation. Our results suggest that actin, hrp65, and p2D10 are parts of a positive feedback mechanism that contributes to maintaining the active transcription state of a gene by recruiting HATs at the RNA level.

Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms

Sequence-based molecular phylogenies have provided new models of early eukaryotic evolution. This includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the Opisthokonta. Although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. The alternative tree-building signal is especially intriguing in light of emerging data from genomic and proteomic studies that indicate striking and potentially synapomorphic similarities between plants and animals. This paper reviews these new lines of evidence, which have yet to be incorporated into models of broad scale eukaryotic evolution.