On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution

Abstract

The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature "decide" upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases.

Keywords: DNA; RNA world; molecular evolution; nucleobases; prebiotic chemistry.

Figure 1

The native nucleobases of the genetic alphabet (top) and the Watson-Crick base-pairing relationship of the DNA nucleo-bases (bottom). In RNA the base uracil (U) assumes the place of thymine (T).

Figure 2

A) Selected examples of extensive RNA nucleobase modification identified in biological nucleic acids. i) Adenine is most often alkylated at its N6 amino group, but here it has also been altered at the C2 position with an alkylthio group. ii) Guanine has been heavily reworked by the replacement of its heterocyclic N7 with a carbon, which is further substituted with an amidine group. iii) Cytosine has been tautomerized and aminated at the C1 position with a lysine residue. iv) Uracil substituted at the C5 position with a secondary aminoalkyl group and a thiocarbonyl at C2. B) Selected examples of conservative base modifications that are known to occur more often in RNA. The modified pyrimidines, with the exception of s²U, are also utilized in exotic DNA genomes. Frequently, the modifications include alkylation of the purine exocyclic amino groups (as for N2 of guanine and N6 of adenine) or modifications at C5 of the pyrimidines. Also shown is the deamination of adenine leading to hypoxanthine (called inosine in RNA), an important modification used as a guanine surrogate in edited RNA transcripts.

Figure 3

Modified or alternative bases that have been shown to be capable of genetic functions. The left column shows bases that are known to be reliable surrogates for adenine or thymine either in vivo or in vitro. The middle column contains guanine or cytosine surrogates. The right column represents base-pairing relationships that are not known to occur in nature. The base pairs colored gray in this figure were among those first demonstrated to be enzymatically incorporated into RNA and DNA by Benner.^[7]

Figure 4

Periods of possible selection pressures. Evolutionary arrow from the formation of the Earth ~4.5 billion years ago and prebiotic chemistry to LUCA-based life and extant biology today, marked by major “events” that could have been crucial to hosting multiple selection pressures that shaped the composition of the genetic alphabet (LUCA = Last Universal Common Ancestor).

Figure 5

Numerous heterocycles have been identified in prebiotic chemistry simulation experiments and in meteorites. Shown here are some of the purine and pyrimidine nucleobases relevant to our discussion. The structures shown in black have been identified in both meteorites and observed in prebiotic chemistry experiments. The structures in red have only been observed in simulated prebiotic chemistry experiments. The structure in green has been recently identified in meteorites.

Figure 6

Reaction genealogy of purines and pyrimidines starting from three simple amino-substituted heterocycles. Shown are 2,6-diaminopurine (Dap), adenine (A), and 2,4-diaminopyrimidine (Dpy), all considered to be prebiotically plausible heterocycles, which can in principle give rise to many different types of nucleobases, including the native alphabet and its surrogates. The reactions shown here are all well known and occur in contemporary biochemistry.

Figure 7

The prebiotic abundance of a nucleobase (or any molecular entity) can be viewed as the net result of synthetic (input channels) and degradation (decomposition or side reactions) pathways. While decomposition removes the nucleobase from the pool, some side reactions (such as alkylation of amino groups) could actually enhance the stability of a particular base in a prebiotic environment.

Figure 8

Generation of nucleosides under prebiotic conditions using the nucleobases and D-ribose. A) Orgel and coworkers demonstrated that of all the native bases, only adenine formed the relevant glycosidic bond to produce adenosine, but still with only low yields. B) Using a concentrated solution of magnesium sulfate and magnesium chloride (mimicking seawater) and an excess of ribose, hypoxanthine has been observed to regio- and stereoselectively produce the corresponding nucleoside. C) Under similar conditions, the Hud laboratory was the first to report a successful prebiotic glycosylation reaction using an alternative pyrimidine heterocycle.

Figure 9

Genetic fidelity pressures. A) A WC-like isoG : isoC base pair that utilizes the dominant tautomer. B) A minor tautomeric form of isoG paired with U. C) Guanine can also base pair with uracil, generating a wobble pair. D) The 2-thiouracil base is highly specific for adenine since it cannot wobble pair with guanine.

Figure 10

A general mechanism for DNA strand cleavage that originates from a spontaneous deglycosylation reaction.

Figure 11

Damaged DNA bases often contain weaker glycosidic bonds (shown in red) in comparison to the native bases. Interestingly, many of these bases arise in cells as post-transcriptional RNA modifications. The greater N-glycosyl stability asssociated with ribonucleosides may have endowed the RNA world with the flexibility to utilize a wider variety of heterocycles.