Unravelling the Evolution of Us

By Emelina Glavaš

Image by Colin Lloyd on Unsplash

As biologist Kenneth R. Miller once said, "our own genomes carry the story of evolution, written in DNA, the language of molecular genetics, and the narrative is unmistakable" [1]. The emergence of DNA is arguably one of the most significant evolutionary events throughout history, leading us all to where we are now, right in this moment. Biologists are continually striving to understand our evolutionary pathway, by use of molecular evolution, biochemistry, molecular genetics, and microbial experimental evolution. It is suggested that the story of DNA began with its molecular cousin, a genetic material known as RNA. But what changes were involved in its evolution, and what selective advantage did these provide over other genetic systems? RNA and U-DNA-based relics are present in the modern world in the form of viruses. If these organisms coexist with us, can we really say DNA has provided a better basis for life?

What is DNA?

DNA, standing for deoxyribonucleic acid, has become somewhat of an icon for modern biology. It is defined as a molecule allowing for the storage and maintenance of genetic information, present in almost all living organisms.

Our understanding of DNA has increased rapidly since its discovery, beginning with its initial observation by biochemist Friedrich Miescher in 1869, where early biochemical methods were used to isolate the molecule from sperm and white blood cell samples [2]. This sparked interest from many scientists, including Phoebus Levene and Erwin Chargaff, who carried out experiments to reveal more about this mystery molecule [3].

Years later, chemist Rosalind Franklin further advanced the knowledge of DNA, discovering what is known as the B form, determining there were two states of the DNA molecule, and providing a basis for understanding the structure of the molecule [4]. These contributions led to the development of Watson and Crick’s biological breakthrough, concluding the structure of DNA to be a three-dimensional double helix, composed of a series of nucleotides containing a phosphate group, a deoxyribose sugar, and a nitrogen-containing base, known cumulatively as deoxyribonucleotides [4]. There are four bases in DNA known as adenine (A), thymine (T), cytosine (C) and guanine (G), held together in corresponding pairs by hydrogen bonds [5].

Where did DNA Come From?

The deoxyribonucleotide synthesis pathways within all cells allude to the emergence of DNA through a two-step evolutionary event, beginning with its molecular cousin RNA [5]. There are two structural differences between DNA and RNA — due to the presence of a hydrogen, DNA contains deoxyribose sugars, whereas the sugars in RNA have a hydroxyl group in its place, resulting in ribose. Secondly, RNA contains no T, but instead a different nucleotide base known as uracil (U). Thus, DNA comprises A, T, C, and G while RNA contains bases A, U, C, and G.

Before RNA fully evolved into DNA, it is hypothesised that an intermediate form known as U-DNA existed. Like both RNA and DNA, this molecule successfully stored genetic information, and therefore can provide the basis for life. Similar to a fossil, U-DNA represents a transitional form between RNA and DNA, containing the U nucleotides seen in RNA, but the deoxyribose of DNA [6]. This thinking is formally referred to as the RNA world hypothesis [7].

How did it Evolve?

Modern DNA arose through steps involving multiple key enzymes, with the functions of ribonucleotide reductase and thymidylate synthase being most notable. Ribonucleotide reductase replaced the ribose sugars of RNA with deoxyribose, creating the intermediate form, U-DNA. DNA then evolved after the replacement of U with T nucleotides via thymidylate synthase through subsequent steps [6].

For DNA to be so widely distributed among modern organisms today, common thought is that it must have provided some form of benefit. Despite few biochemical differences, DNA is often considered superior to both RNA and U-DNA, as it allowed for an increase in the storage and maintenance of genetic information when compared to other already present genetic systems. Another advantage of DNA over RNA is that the latter can carry out a function known as autolytic selfcleavage [8], simply meaning it chops itself up more. For these reasons, DNA could provide a backbone for larger, more complex genomes, without having a detrimental number of errors or mutations [9].

Is DNA Really the Best Basis for Life?

Extant relics of RNA-based genetic systems exist in the form of RNA viruses [10]. These include the now widely recognised coronaviruses, with relatively large RNA-based genomes. Extant U-DNA viruses are also present in the modern world [11]. These relics may be an example of a ‘frozen accident’ [12], where a genetic aspect has been retained not because it is an optimal state, but instead because other biological systems rely on it remaining present [13]. Alternately, these relics may not be evolutionary throwbacks, but rather represent organisms where non-DNA-based genetic systems have re-evolved. Or, perhaps modern RNA and U-DNA viruses were just successful in evolving alongside us. If this were the case, DNA — and all the organisms that have evolved to use it — should not be considered so revolutionary after all.

References

[1] Miller, K. (2009). Seals, evolution, and the real 'missing link'.

[2] Dahm, R. (2005). Friedrich Miescher and the discovery of DNA. Developmental biology, 278(2), 274-288.

[3] Pray, L. (2008) Discovery of DNA structure and function: Watson and Crick. Nature Education 1(1):100

[4] Klug, A. (1968). Rosalind Franklin and the discovery of the structure of DNA. Nature, 219(5156), 808-810.

[5] Watson, J. D., & Crick, F. H. (1953, January). The structure of DNA. Cold Spring Harbor symposia on quantitative biology (Vol. 18, pp. 123-131). Cold Spring Harbor Laboratory Press.

[6] Poole, A., Penny, D., & Sjöberg, B. M. (2001). Confounded cytosine! Tinkering and the evolution of DNA. Nature Reviews Molecular Cell Biology, 2(2), 147-151.

[7] Gilbert W. 1986. Origin of life: The RNA world. Nature, 319: 618.

[8] Sharmeen, L., Kuo, M. Y., Dinter-Gottlieb, G., & Taylor, J. (1988). Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. Journal of virology, 62(8), 2674.

[9] Lazcano, A., Guerrero, R., Margulis, L., & Oro, J. (1988). The evolutionary transition from RNA to DNA in early cells. Journal of molecular evolution, 27(4), 283-290.

[10] Wintersberger, U., & Wintersberger, E. (1987). RNA makes DNA: a speculative view of the evolution of DNA replication mechanisms. Trends in Genetics, 3, 198-202.

[11] Takahashi, I., & Marmur, J. (1963). Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis. Nature, 197(4869), 794-795.

[12] Crick, F., H., C. (1968). The origin of the genetic code. Journal of Molecular Biology, 38:367–379

[13] Jeffares, D. C., Poole, A. M., & Penny, D. (1998). Relics from the RNA world. Journal of molecular evolution, 46(1), 18-36.