Cosmologists believe that the universe began over 14 billion years ago with the Big Bang. Clouds of gas emitted by the Big Bang, condensed to form the Sun and its planets about 4.6 billion years ago. As the early Earth was covered with water, this gave rise to the first biochemical systems. Cellular life was a relatively late stage in biochemical evolution. This was preceded by self-replicating polynucleotides that were the progenitors of the first genomes. In this blog, we will explore the evolution of the genome – from the RNA world to the first DNA molecules, and how this complexity increased.
Th oxygen content of the atmosphere remained very low until photosynthesis evolved. Experiments attempting to recreate these conditions have shown that electrical discharges in a methane-ammonia mixture result in chemical synthesis of a range of amino acids. Therefore, at least some of the building blocks of biomolecules could have formed in the ancient chemosphere.
The first biochemical systems were centred on RNA. A major break-through came in the mid-1980s when it was found that RNA can have catalytic activity. In the test tube, synthetic RNA molecules have been shown to carry out other biologically relevant reactions such as synthesis of ribonucleotides and copying of RNA molecules. It is now envisaged that RNA molecules initially replicated in a slow manner by acting as templates for binding of complementary nucleotides. As this process would have been very inaccurate, a variety of RNA sequences would have emerged. It is possible that a form of natural selection occurred so that efficient replicating systems predominated. In turn, this would have provided the potential for more sophisticated catalytic properties.
The first DNA genomes
So how did the RNA world develop into the DNA world? The first major change was probably the development of protein enzymes. These enzymes supplemented and then eventually replaced most of the catalytic activities of ribozymes. There are several unanswered questions relating to this stage of biochemical evolution, including why the transition from RNA to protein occurred in the first place.
The transition to protein catalysis demanded a radical shift in the function of the RNA protogenomes. The RNA protogenomes had abandoned their roles as enzymes and took on a coding function. The transfer of coding function to the more stable DNA was inevitable. Additionally, the replacement of uracil with its methylated derivative thymine probably conferred even more stability on the DNA polynucleotide. According to this, the first DNA genomes would have been comprised of separate molecules, each specifying a single protein. The linking together of these genes into the first chromosomes would have improved the efficiency of gene distribution during cell division. DNA genomes would have given these cells a significant advantage compared with those still containing RNA protogenomes.
Acquisition of new genes
Fossil record evidence has shown that 3.5 billion years ago biochemical systems had evolved into cells similar in appearance to modern bacteria. Following the fossil record, the first evidence for eukaryotic cells appeared about 1.4 billion years ago and the first multicellular algae by 0.9 billion years ago. Multicellular animals appeared around 640 million years ago. Since then, evolution has continued rapidly and with increasing diversification. Morphological evolution was accompanied by genome evolution. There were two sudden bursts of gene numbers. The first occurred when eukaryotes appeared about 1.4 billion years ago. The second expansion is associated with vertebrates which became established soon after the Cambrian period.
There are several ways in which new genes can be acquired and genomes can evolve. These include:
- Gene duplication: A region of DNA can be duplicated via an error in recombination or through a retrotranspoisition event. A large number of mutations can accumulate in the duplicate gene, rendering the gene non-functional or in some cases, confer some benefit.
- Whole genome duplication: An organism’s entire genetic information is copied (polyploidy). This may provide an evolutionary benefit to the organism creating a greater possibility of functional and selectively favoured genes.
- Transposable elements: These elements can be inserted into the genetic code via different mechanisms – excising DNA from one place and inserting into another or copying a specific region and inserting copies elsewhere.
- Mutation: Spontaneous mutations are constantly occurring in an organism’s genome and cause either negative, positive or neutral effects.
- Pseudogenes: Functional genes can become pseudogenes via several mechanisms, including the deletion or insertion of nucleotides.
- Exon shuffling: New genes can be created via exon shuffling. This can occur by any of the following processes: transposon mediated shuffling, sexual recombination or non-homologous recombination.
- Genome reduction and gene loss: Many species exhibit genome reduction when some of their genes are no longer necessary to survive. For example, when their nutrients are supplied by a host.
- Acquiring genes from other species: Horizontal gene transfer has been a major event in the evolution of prokaryotic genomes. There are several mechanisms including transformation and conjugation.
The human genome
Although the human genome was sequenced over 10 years ago, there is still much we do not understand about the evolution of the human genome. Perhaps the most dramatic result in this field, over the past decade, has been the sequencing of ancient DNA from archaic hominins, like Neanderthals and Denisovans. These analyses have revealed the relationships between archaic genomes and present-day human genomes, identifying gene flow events. In addition, they have also established variants that became fixed in modern humans after their separation from ancestors.
Advances in DNA sequencing, functional genomics and population genetic modelling have deepened our understanding of human demographic history and natural selection. It has enabled us to probe evidence of selection. Key examples include:
- Lactose tolerance: After the domestication of cattle, human diets profoundly changed. The lactase persistence allele is common in individuals of European descent because of the increased nutrition of cow’s milk. Lactose tolerance is one of the strongest signals of selection seen anywhere in the genome.
- Malaria resistance: Researchers found that the geographical distribution of the sickle-cell mutation (Glu6Val) in the beta haemoglobin gene (HBB) was limited to Africa and correlated with malaria endemicity. Individuals with the sickle-cell trait are resistant to malaria. Many more alleles for malaria resistance have shown evidence of selection.
- Pigmentation: As modern humans migrated out of Africa, they experienced less sunlight and colder temperatures. Humans have experienced positive selection at numerous genes to alter the amount of skin pigment produced. For example, investigations identified a variant in SLC24A5 for lighter pigmentation. This variant explains roughly one-third of the variation in pigmentation between Europeans and West Africans.
During the period when life on Earth first began, fundamental components of life such as RNA, DNA and amino acids emerged. Understanding the evolution of the genome is not only important to understand how humans arose, but it also has important implications for understanding disease. Interestingly, these principles can be applied to synthetic biology and could also provide insight into life on other planets. Complexity arose from basic components and is continually evolving to adapt to the changing environments. This can be seen today as organism’s attempt to adapt to increasing global temperatures. With ongoing advances in genome sequencing and other high-throughput techniques, the amount of available data is increasing, which in turn, can provide a more in depth understanding of how our genome is evolving.
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