Tempo and Mode in Evolution Genetics and Paleontology 50 Years After Simpson (1995) / Chapter Skim
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Phylogeny from Function: The Origin of tRNA Is in Replication, not Translation
Phylogeny from Function: The Origin of tRNA Is in Replication, not Translation
Pages 25-40
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From page 25... ...
. The challenge for those interested in biochemical evolution is to deduce, from contemporary molecules and organisms, how these pathways arose.
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From page 26... ...
Moreover, because the translation apparatus is fundamentally similar in all three contemporary kingdoms, this progenote must have been capable of templated protein synthesis substantially like our own. Here we propose a phylogeny for the origin of tRNA based on the ubiquity and conservation of tRNA-like structures in the replication of contemporary genomes, and we discuss the evidence in contemporary molecules that leads to and supports this phylogeny.
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From page 27... ...
However, just as mineralized bones, shells, or cell walls tell us about the evolution of modern cellular organisms, contemporary biological molecules provide clues regarding the evolution of the earliest forms of life. In order to discuss precellular evolution in terms that are most accessible to a wide variety of disciplines, we use the phrase "molecular fossil" to describe the molecules that are central to this analysis.
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From page 28... ...
We now consider replication in the RNA world (Gilbert, 1986) , an era that predates the evolution of either DNA or templated protein synthesis.
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From page 29... ...
The simplest such tags would have been the predecessors of the "top half" of modern tRNA, consisting of a coaxial stack of the TALC arm on the acceptor stem (see Figure 5~. The presence of such 3' terminal tRNA-like structures in two different kingdoms—contemporary bacterial viruses like Q,8 and plant viruses such as turnip yellow mosaic virus (TYMV)
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From page 30... ...
Interestingly, although eubacteria and archaea encode the 3' terminal CCA of tRNA, eukaryotes do not, and they must rely instead on tRNA nucleotidyltransferase to produce mature tRNAs (Palmer et al., 1992~. The primitive state is not yet known, but as tRNA nucleotidyltransferase is present in all cells, it seems most plausible that genomically encoded CCA was devised later to circumvent a slow or inefficient step in tRNA processing.
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From page 31... ...
In each of these instances, a genomic RNA replicates via a DNA intermediate. We call these "transitional genomes," because they can be viewed as reenacting the transition from an RNA world to the contemporary DNA world.
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From page 32... ...
The enzymology of replication of the Mauriceville retroplasmid provides further support for the transitional status of this plasmid genome (Wang and Lambowitz, 1993~. The Mauriceville reverse transcriptase
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From page 33... ...
. The terminally redundant DNA provirus is topologically equivalent to the circular CaMV genome, and transcription from the upstream promoter of the provirus to the distal polyadenylation signal generates the terminally redundant genomic RNA.
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From page 34... ...
These tRNA-like structures persisted during the evolution of DNA, and they are immortalized today in transitional genomes, RNA genomes that replicate via a DNA intermediate. In the transitional genomes, tRNAs functioned first as template and later as primer for synthesis of a cDNA copy by a reverse transcriptase encoded by the genomic RNA itself.
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From page 35... ...
Aminoacylation chemically resembles RNA polymerization, and a variant replicase could have evolved to catalyze aminoacylation, just as a group I ribozyme, which naturally catalyzes phosphoester bond transfer, can be redesigned to catalyze reactions at a carbon center (Piccirilli et al., 1992~. The specificity with which modern group I ribozymes bind ~-arginine leaves little doubt that an aminoacyl-tRNA synthetase made of RNA could charge tRNA with considerable specificity (Cornell et al., 1993~.
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From page 36... ...
This suggests that the identity of some tRNAs, and perhaps the specificity of the cognate aminoacyl-tRNA synthetases, was established before the bottom half of tRNA was incorporated into the molecule. Whether the bottom half of tRNA arose as an expansion loop within the top half or as an independent structural and functional domain that was subsequently incorporated into the top half is a question that future work may be able to resolve.
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From page 37... ...
will further support the independence of the top and bottom halves of the molecule, explain why contemporary tRNA is a cloverleaf rather than the pseudoknotted structure found in plant viruses (Mans et al., 1990) , and unlock the evolutionary history that must lie in the location and function of the (almost)
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From page 38... ...
We further suggest that the "top half" of modern tRNA a coaxial stack of the acceptor stem on the TIC arm is the ancient structural and functional domain and that the ',bottom half" of tRNA a coaxial stack of the dihydrouracil arm on the anticodon arm arose later to provide additional specificity. REFERENCES Akins, R
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From page 39... ...
1988. A novel reverse transcriptase activity associated with mitochondrial plasmids of Neurospora.
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From page 40... ...
1993. The Mauriceville plasmid reverse transcriptase can initiate cDNA synthesis de nova and may be related to reverse transcriptase and DNA polymerase progenitor.
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