Genes are the building blocks of life and the fundamental units of heredity, containing the genetic instructions that determine the physical characteristics and traits of living organisms. The process by which genes are created is continual and complex, involving genetic and environmental factors.
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While it is widely understood that DNA serves as the blueprint for life, it is the genotype - the specific combination of genes present within an organism's DNA - that ultimately determines the physical characteristics and traits that the organism will display, which is referred to as the phenotype.
The expression or non-expression of various genes within an organism's DNA can lead to variations in its phenotype, which can be influenced by a variety of factors, including environmental conditions and interactions between different genes. Therefore, the interplay between genes and environmental factors contributes to alterations in the phenotype of an organism, which may, in turn, affect its genotype over time. In general, genes themselves are the products of evolution through natural selection, whereby beneficial genetic variations are favored and passed on to subsequent generations. It is through various intricate processes that govern this phenomenon of gene creation.
The Mechanisms of Forming Novel Genes
Genes are formed through a variety of mechanisms, whereby at the basic level, the formation of genes occurs through a process known as “mutation”. Mutations arise from alterations in the DNA sequence of a gene, which can happen spontaneously due to DNA replication errors or following exposure to environmental agents – such as radiation or chemicals. The impact of mutations on organisms may be harmful, neutral, or advantageous, depending on the specific mutation.
Mutations in genes may also create new alleles, i.e., versions of a gene. There is also the potential for creating new traits via mutations if such mutations result in a novel, functional protein, whereby new traits could be selected for and passed on to future generations. Over time, the accumulation of these mutations can lead to the emergence of entirely new genes with completely novel functions.
One such form of mutation by which new genes are created is called gene duplication. This form of mutation arises when a segment of DNA is replicated and integrated into the genome, leading to the emergence of two identical or almost identical copies of a gene. While one copy may retain its original function, the other copy may undergo subsequent mutations that lead to the development of a new function. With the passage of time, the two copies may diverge, giving rise to two distinct genes with different functions.
Another method in which genes can be created is lateral gene transfer (LGT), also called horizontal gene transfer. This occurs when genes are transferred between organisms of the same or different species. This is exemplified in bacteria, which can acquire new genes through the uptake of DNA from other bacteria in their environment. HGT creates an avenue for the rapid spread of new traits via a population or species, operating under multiple mechanisms; transformation, transduction, and conjugation.
Gene fusion and gene fission are also mechanisms that have the potential to generate new genes with novel functions. Gene fusion occurs when two or more genes fuse together, which were initially separate, giving rise to a novel gene. This fusion event occurs through various processes, such as translocation, retro-transposition, unequal crossing-over during meiosis, or the fusing of transcripts of differing genes. The resulting new gene may exhibit a novel function dissimilar from the original genes.
In contrast, gene fission happens when a single gene is split into two or more separate genes. This event can occur through different mechanisms, such as recombinational processes or single base events, e.g., frameshift and nonsense mutations, as well as through the breaking apart of a single transcript. The resulting genes may have unique functions distinct from the original gene.
Although both gene fusion and fission can contribute to the emergence of new genes with novel functions, they are relatively infrequent compared to gene duplication and horizontal gene transfer. Nonetheless, these mechanisms have been observed in various organisms, and their potential to generate new genes underscores the dynamic nature of genome evolution.
The de novo Gene Birth
It is worth noting that the aforementioned processes have primarily focused on creating new genes by modifying or duplicating existing genes. However, a pertinent question arises: How do new genes emerge without any pre-existing genes to build upon?
The process by which novel genes arise without the need for pre-existing genes is known as de novo gene birth. In de novo gene birth, genes are created from non-coding sequences of DNA. An example of a gene that arose from this process is the AFGP gene found in Arctic codfish, whereby it essentially codes for the antifreeze glycoprotein (AFGP), enabling the organism to withstand sub-zero temperatures by hindering the formation of lethal ice crystals in its bloodstream.
The antifreeze functionality of AFGP is chiefly attributed to the presence of multiple Thr-Ala/Pro-Ala repeats, where research has shown that the mechanism by which these repeats were generated is via duplication, specifically the repeated duplication of a single ancestral sequence.
Fundamentally, as it is currently understood at the time of writing, de novo genes are brought about by mutations in non-coding segments of DNA, and over time these mutations are subjected to selection and refinement, resulting in a novel gene that is advantageous and conducive for survival the organisms survival.
The transitional phase that lies between non-coding DNA and established genes is commonly referred to as “proto-genes”. The de novo gene birth process is currently not completely well understood and is an ongoing scientific investigation, and thus a dynamic area of research.
References and Further Reading
Chandrasekaran C, Betrán E. (2008) Origins of new genes and pseudogenes. Nature Education. 1(1), p. 181. https://www.nature.com/scitable/topicpage/origins-of-new-genes-and-pseudogenes-835/
Durrens P, Nikolski M, Sherman D. (2008) Fusion and fission of genes define a metric between fungal genomes. PLoS Comput Biol. 4(10), p. e1000200. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000200
Levy A. (2019) How evolution builds genes from scratch. Nature. 574(7778), pp. 314-316. https://pubmed.ncbi.nlm.nih.gov/31619796/
Long M, VanKuren NW, Chen S, Vibranovski MD. (2013) New gene evolution: little did we know. Annu Rev Genet. 47, pp. 307-33. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4281893/