Exploring the origins of DNA using synthetic biology Alannah Marie

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.