Abstract:
The extreme conservation of DNA makes it difficult to trace the deep evolution of this
fundamental molecule. The precursors of DNA are produced from the constituent RNA
precursors through ribonucleotide reduction, leading to the logical conclusion that DNA
evolved after RNA. Thymine (T) is produced by further processing of deoxyuracil (dU), which
suggests that the evolution of modern DNA might have been via a uracil-containing
intermediate form of DNA. It is therefore proposed that DNA evolution proceeded in the
following order: RNA →U-DNA →T-DNA. We have previously argued that the transition
from U-DNA to T-DNA was driven by cytosine deamination (Poole et al., 2001), which would
lead to mutagenic generation of U in the genome via C to U deamination events. However, a
transition to T is an indirect fix to this problem; it enables identification of mutagenic U:G pairs
arising from cytosine deamination, but it would not enable repair. Thus T does not deal with
the issue of cytosine deamination itself. We have proposed that the U to T transition may have
been driven by inefficient repair of cytosine deamination. To do this, we attempted to generate
a modern cell containing U in place of T in its genome. While we were not able to reach the
final goal, we have made considerable progress towards it in this thesis.
In addition to this, we have also investigated whether the initial RNA to U-DNA transition
could have evolved earlier through an alternative pathway. The enzyme require for this
reaction, ribonucleotide reductase, performs complex free radical chemistry, so is believed to
have occurred late in evolution. If DNA is instead able to be produced through an alternative
and simpler pathway, it is possible that the transition could have occurred far earlier in
evolution than previously thought. We have created a strain of E. coli deficient in
ribonucleotide reduction, and have made considerable progress towards generating a strain
capable of synthesising its own deoxyribonucleotides by the alternative deoxyriboaldolase
pathway.