Component H of the DNA-dependent RNA polymerases of Archaea is homologous to a subunit shared by the three eucaryal nuclear RNA polymerases (original) (raw)

An archaebacterial RNA polymerase binding site and transcription initiation of the his A gene in Methanococcus vannielii

Nucleic Acids Research, 1988

Transcription initiation of the tisfi sent in aiua. in the archaebacterium MuthinnrnmiT uannlitlii. as determined by nuclease Sj and primer extension analyses, occurs 73 base pairs <bp) upstream of the translation initiation >ita. Binding of U. uannlalii RHA polymerase protects 43 bp of DNA. from 33 bp upstream (-35) to 8 bp downstream <+8) of the hisP mRNA initiation site, from digestion by DNase I and exonuclease III. An fi+T rich region, with a sequence ujhich conforms to the consensus sequence for promoters of stable RNA-encoding genes in methanogens, is found at the same location <-25> upstream of the polgpeptide-encoding bisfi gene. It appears therefore that a TATA-lika sequence is also an element of promoters which direct transcription of polypeptide-encoding genes in this archaebacterium.

Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA

Nucleic Acids Research, 2012

Multi-subunit RNA polymerases (RNAPs) in all three domains of life share a common ancestry. The composition of the archaeal RNAP (aRNAP) is not identical between phyla and species, with subunits Rpo8 and Rpo13 found in restricted subsets of archaea. While Rpo8 has an ortholog, Rpb8, in the nuclear eukaryal RNAPs, Rpo13 lacks clear eukaryal orthologs. Here, we report crystal structures of the DNA-bound and free form of the aRNAP from Sulfolobus shibatae. Together with biochemical and biophysical analyses, these data show that Rpo13 C-terminus binds non-specifically to double-stranded DNA. These interactions map on our RNAP-DNA binary complex on the downstream DNA at the far end of the DNA entry channel. Our findings thus support Rpo13 as a RNAP-DNA stabilization factor, a role reminiscent of eukaryotic general transcriptional factors. The data further yield insight into the mechanisms and evolution of RNAP-DNA interaction.

An archaebacterial promoter sequence assigned by RNA polymerase binding experiments

Canadian Journal of Microbiology, 1989

sequence assigned by RNA Polymerase binding experiments. Can. J. Microbiol. 35: 30-35. To identify an archaebacterial promoter sequence, nuclease protection studies with the purified RNA Polymerase of Methanococcus vannielii were performed. The enzyme binds specifically both at protein-encoding (hisA and methyl CoM reductase, component C) and tRNA-rRNA genes. The binding region of the RNA Polymerase extends from 30 base pairs (bp) upstream (-30) to 20 bp downstream (+20) from the in vivo transcription start site. This finding indicates that the archaebacterial enzyme recognizes promoters without transacting transcription factors. The DNA segment protected from nuclease digestion by bound RNA Polymerase contains an octanucleotide sequence centered at -25, which is conserved between the protein-encoding and the stable RNA genes. According to the specific binding of the enzyme to only DNA-fragments harbouring this motif, we propose the sequence TTTATATA as the major recognition signal of the Methanococcus RNA Polymerase. Comparison of this motif with published archaebacterial DNA sequences revealed the presence of homologous sequences at the same location upstream of 36 genes. We therefore consider the overall consensus TTTAjATA as a general element of Promoters in archaebacteria. In spite of the specific binding of the enzyme, most preparations of the Methanococcus vannielii RNA Polymerase are unable to initiate transcription at the correct sites in vitro. Here we present first evidence for the possible existence of a transcription factor conferring the ability to the enzyme to initiate and terminate transcription specifically in vitro. THOMM, M., WICH, G , BROWN, J. W., FREY, G., SHERF, B. A., et BECKLER, G. S. 1989. An archaebacterial promoter sequence assigned by RNA Polymerase binding experiments. Can. J. Microbiol. 35 : 30-35. Dans le but d'identifier une sequence archaebacterienne de promoteur, des etudes sur la protection contre la nuclease ont ete entreprises avec de TARN Polymerase purifiee de Methanococcus vannielii. Cette enzyme se lie specifiquement ä la fois aux genes qui encodent la proteine (hisA et methyle CoM reductase, composant C) et aux genes ARN t -ARN r . La region d'attachement de TARN Polymerase s'etend depuis 30 bp en amont (-30) ä 20 bp en aval (+20) du site de debut de transcription in vivo. Cette decouverte indique que l'enzyme archaebacterienne reconnait les promoteurs sans Fintervention de facteurs de transcription. Le segment d'ADN protege contre la digestion par la nuclease, grace ä TARN Polymerase liee, contient une sequence de huit nucleotides qui est centree ä -25; cette sequence est conservee entre les genes qui encodent la proteine et les genes d'ARN stable. D'apres l'attachement specifique de Tenzyme aux seuls fragments d'ADN qui contiennent ce motif, nous proposons comme signal de reconnaissance principal de TARN Polymerase de Methanococcus la sequence TTTATATA. Une comparaison de ce motif avec d'autres sequences d'ADN archaebacteriens qui ont fait Pobjet de publications revele la presence de sequences homologues ä la meme localisation en amont de 36 genes. Nous proposons donc 1'Organisation d'ensemble TTTAjATA comme un element commun aux promoteurs chez les archaebacteries. Malgre l'attachement specifique de cette enzyme, la plupart des preparations d'ARN Polymerase de Methanococcus vannielii ne reussisent pas, in vitro, ä amorcer la transcription dans les sites appropries. Nous presentons ici la premiere evidence de l'existence possible d'un facteur de transcription qui confere ä l'enzyme la capacite d'initier et de terminer la transcription, particulierement in vitro. Mots des : promoteur, empreinte, boite de TATA, transcription, ARN Polymerase. [Traduit par la revue]

Archaeal RNA polymerase and transcription regulation

Critical Reviews in Biochemistry and Molecular Biology, 2011

To elucidate the mechanism of transcription by cellular RNA polymerases (RNAPs), high resolution X-ray crystal structures together with structure-guided biochemical, biophysical and genetics studies are essential. The recently-solved X-ray crystal structures of archaeal RNA polymerase (RNAP) allow a structural comparison of the transcription machinery among all three domains of life. The archaea were once thought of closely related to bacteria, but they are now considered to be more closely related to the eukaryote at the molecular level than bacteria. According to these structures, the archaeal transcription apparatus, which includes RNAP and general transcription factors, is similar to the eukaryotic transcription machinery. Yet, the transcription regulators, activators and repressors, encoded by archaeal genomes are closely related to bacterial factors. Therefore, archaeal transcription appears to possess an intriguing hybrid of eukaryotic-type transcription apparatus and bacterial-like regulatory mechanisms. Elucidating the transcription mechanism in archaea, which possesses a combination of bacterial and eukaryotic transcription mechanisms that are commonly regarded as separate and mutually exclusive, can provide data that will bring basic transcription mechanisms across all three domains of life.

Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria

Journal of Molecular Evolution, 1991

The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogeny, as well as by the neighbor-joining method and the parsimony method, together with bootstrap analyses. It was shown that the best tree topologies predicted by the first two methods are identical, whereas the last one predicts a distinct tree. The maximum likelihood tree revealed that, after the separation from archaebacteria, the three eukaryotic RNA polymerases diverged from an ancestral precursor in the eukaryotic lineage. This result is contrasted with the published result showing multiple origins for the three eukaryotic polymerases. It was shown that eukaryotic RNA polymerase I evolved much more rapidly than RNA polymerases II and III: The N-terminal half ofRNA polymerase I shows an extraordinarily high evolutionary rate, possibly due to relaxed functional constraints. In contrast the evolutionary rate of archaebacterial RNA polymerase is remarkably limited. In addition, including the second largest subunit of the RNA polymerase, a detailed analysis for the branching pattern of the three major groups of archaebacteria was carried out by the maximum likelihood method. It was shown that the three major groups of archaebacteria are likely to form a single cluster; that is, archaebacteria are likely to be monophyletic as originally proposed by Woese and his colleagues.

Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12

Nucleic acids research, 2000

The archaeal and eukaryotic evolutionary domains diverged from each other approximately 2 billion years ago, but many of the core components of their transcriptional and translational machineries still display a readily recognizable degree of similarity in their primary structures. The F and P subunits present in archaeal RNA polymerases were only recently identified in a purified archaeal RNA polymerase preparation and, on the basis of localized sequence homologies, tentatively identified as archaeal versions of the eukaryotic RPB4 and RPB12 RNA polymerase subunits, respectively. We prepared recombinant versions of the F and P subunits from Methanococcus jannaschii and used them in in vitro and in vivo protein interaction assays to demonstrate that they interact with other archaeal subunits in a manner predicted from their eukaryotic counterparts. The overall structural conservation of the M. jannaschii F subunit, although not readily recognizable on the primary amino acid sequence...

Archaeal RNA polymerase subunits E and F are not required for transcription in vitro , but a Thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive

Molecular Microbiology, 2008

All archaeal genomes encode RNA polymerase (RNAP) subunits E and F that share a common ancestry with the eukaryotic RNAP subunits A43 and A14 (Pol I), Rpb7 and Rpb4 (Pol II), and C25 and C17 (Pol III). By gene replacement, we have isolated archaeal mutants of Thermococcus kodakarensis with the subunit F-encoding gene (rpoF) deleted, but we were unable to isolate mutants lacking the subunit E-encoding gene (rpoE). Wild-type T. kodakarensis grows at temperatures ranging from 60°C to 100°C, optimally at 85°C, and the DrpoF cells grew at the same rate as wild type at 70°C, but much slower and to lower cell densities at 85°C. The abundance of a chaperonin subunit, CpkB, was much reduced in the DrpoF strain growing at 85°C and increased expression of cpkB, rpoF or rpoE integrated at a remote site in the genome, using a nutritionally regulated promoter, improved the growth of DrpoF cells. RNAP preparations purified from DrpoF cells lacked subunit F and also subunit E and a transcription factor TFE that co-purifies with RNAP from wild-type cells, but in vitro, this mutant RNAP exhibited no discernible differences from wild-type RNAP in promoter-dependent transcription, abortive transcript synthesis, transcript elongation or termination.

The phylogeny of archaebacteria, including novel anaerobic thermoacidophiles in the light of RNA polymerase structure

Naturwissenschaften, 1982

DNA-dependent RNA polymerases of archaebacteria are distinct from those of eubacteria both in structure and in function. They show similarities to those of the eukaryotic cytoplasm. Extremely thermophilic anaerobic sulfur-respiring archaebacteria isolated from solfataric waters represent four different families, the Thermoproteaceae, the "stiff filaments", the Desulfurococcaceae and the Thermococcaceae, of a novel order, Thermoproteales. Together with the Sulfolobales, they form the second branch of the urkingdom of the archaebacteria besides that of the methanogens and extreme halophiles. Thermoplasma appears isolated.

Structural Modules of the Large Subunits of RNA Polymerase. INTRODUCING ARCHAEBACTERIAL AND CHLOROPLAST SPLIT SITES IN THE beta AND beta prime SUBUNITS OF ESCHERICHIA COLI RNA POLYMERASE

Journal of Biological Chemistry, 1996

The ␤ and ␤ subunits of Escherichia coli DNA-dependent RNA polymerase are highly conserved throughout eubacterial and eukaryotic kingdoms. However, in some archaebacteria and chloroplasts, the corresponding sequences are "split" into smaller polypeptides that are encoded by separate genes. To test if such split sites can be accommodated into E. coli RNA polymerase, subunit fragments encoded by the segments of E. coli rpoB and rpoC genes corresponding to archaebacterial and chloroplast split subunits were individually overexpressed. The purified fragments, when mixed in vitro with complementing intact RNA polymerase subunits, yielded an active enzyme capable of catalyzing the phosphodiester bond formation. Thus, the large subunits of eubacteria and eukaryotes are composed of independent structural modules corresponding to the smaller subunits of archaebacteria and chloroplasts.