On the early evolution of RNA polymerase (original) (raw)
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Origin and Evolution of RNA-Dependent RNA Polymerase
Frontiers in Genetics
RNA-dependent RNA polymerases (RdRp) are very ancient enzymes and are essential for all viruses with RNA genomes. We reconstruct the origin and evolution of this polymerase since the initial stages of the origin of life. The origin of the RdRp was traced back from tRNA ancestors. At the origin of the RdRp the most ancient part of the protein is the cofactor-binding site that had the capacity of binding to simple molecules as magnesium, calcium, and ribonucleotides. Our results suggest that RdRp originated from junctions of proto-tRNAs that worked as the first genes at the emergence of the primitive translation system, where the RNA was the informational molecule. The initial domain, worked as a building block for the emergence of the fingers and thumb domains. From the ancestral RdRp, we could establish the evolutionary stages of viral evolution from a rooted ancestor to modern viruses. It was observed that the selective pressure under the RdRp was the organization and functioning of the genome, where RNA double-stranded and RNA single-stranded virus formed a separate group. We propose an evolutionary route to the polymerases and the results suggest an ancient scenario for the origin of RNA viruses.
Structure and evolution of prokaryotic and eukaryotic RNA polymerases: a model
Journal of Theoretical Biology, 1987
A comparative overview of the subunit taxonomy and sequences of eukaryotic and prokaryotic RNA polymerases indicates the presence of a core structure conserved between both sets of enzymes. The differentiation between prokaryotic and eukaryotic polymerases is ascribed to domains and subunits peripheral to the largely conserved central structure. Possible subunit and domain functions are outlined. The core's flexible shape is largely determined by the elongated architecture of the two largest subunits, which can be oriented along the DNA axis with their bulkier amino-terminal head regions looking towards the 3' end of the gene to be transcribed and their more slender carboxyl-terminal domains at the tail end of the enzyme. The two largest prokaryotic subunits appear originally derived from a single gene.
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.
On the Evolution of the Single-Subunit RNA Polymerases
Journal of Molecular Evolution, 1997
Many eukaryotic nuclear genomes as well as mitochondrial plasmids contain genes displaying evident sequence similarity to those encoding the singlesubunit RNA polymerase (ssRNAP) of bacteriophage T7 and its relatives. We have collected and aligned these ssRNAP sequences and have constructed unrooted phylogenetic trees that demonstrate the separation of ssRNAPs into three well-defined and nonoverlapping clusters (phage-encoded, nucleus-encoded, and plasmidencoded). Our analyses indicate that these three subfamiles of T7-like RNAPs shared a common ancestor; however, the order in which the groups diverged cannot be inferred from available data. On the basis of structural similarities and mutational data, we suggest that the ancestral ssRNAP gene may have arisen via duplication and divergence of a DNA polymerase or reverse transcriptase gene. Considering the current phylogenetic distribution of ssRNAP sequences, we further suggest that the origin of the ancestral ssRNAP gene closely paralleled in time the introduction of mitochondria into eukaryotic cells through a eubacterial endosymbiosis.
Proceedings of the National Academy of Sciences, 1992
The gene encoding component H of the DNAdependent RNA polymerase (RNAP, EC 2.7.7.6) of Sulfolobus acidocalarius has been identified by comparison of the amino acid sequence with the derived amino acid sequence of an open reading frame (ORF88) in the RNAP operon. Corresponding genes were identified in Halobacterium halobium and were cloned and sequenced from Thermococcus cekr and Methanococcus vannielii. All these rpoH genes are situated between the promoters of the RNAP operons and the corresponding rpoB and rpoB2 genes. The archaeal H subunits show high sequence similarity to each other and to the C-terminal portions of the largest of four subunits shared by all three specialized nuclear RNAPs. These correlations are further evidence for the stiking similarity between archaeal and eucaryal RNAP structures and transcription systems.
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]
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.
Evolution of the RNA polymerase II C-terminal domain
Proceedings of the National Academy of Sciences, 2002
In recent years a great deal of biochemical and genetic research has focused on the C-terminal domain (CTD) of the largest subunit (RPB1) of DNA-dependent RNA polymerase II. This strongly conserved domain of tandemly repeated heptapeptides has been linked functionally to important steps in the initiation and processing of mRNA transcripts in both animals and fungi. Although they are absolutely required for viability in these organisms, C-terminal tandem repeats do not occur in RPB1 sequences from diverse eukaryotic taxa. Here we present phylogenetic analyses of RPB 1 sequences showing that canonical CTD heptads are strongly conserved in only a subset of eukaryotic groups, all apparently descended from a single common ancestor. Moreover, eukaryotic groups in which the most complex patterns of ontogenetic development occur are descended from this CTD-containing ancestor. Consistent with the results of genetic and biochemical investigations of CTD function, these analyses suggest that ...
Origins of Life and the RNA World: Evolution of RNA-Replicase Recognition
Symposium - International Astronomical Union, 2004
Central to understanding the origin of life is the elucidation of the first replication mechanism. The RNA World hypothesis suggests that the first self-replicating molecules were RNAs and that DNA later superceded RNA as the genetic material. RNA viruses were not subjected to the same evolutionary pressures as cellular organisms; consequently, they likely possess remnants of earlier replication strategies. Our laboratory investigates how members of the RNA virus family Bromoviridae can have structurally distinct 3' end tags yet are specifically recognized by conserved replication enzymes. This work addresses the idea that 3' tRNA tails were functionally replaced in some viruses by an RNA-protein complex. These viruses may serve as a timeline for the transition from the RNA world to DNA and protein based life.