Origin of New Genes in Eukaryotes

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Origin of New Genes in Eukaryotes

Mutation, gene flow, genetic drift, and natural selection are the four driving forces of evolution (Park, 2013). There is a scientific consensus on the processes that lead to single nucleotide polymorphisms (SNPs), that is, simple “letter” changes, insertions, and deletions. The process by which entire chromosomes can be copied due to nondisjunction is also well understood, however such large changes tend to be deleterious or at least affect fertility. “Brand new” de novo traits in a species require new genes to be added to coding regions of the genome of that species. This process is less understood, but has been elucidated in recent years. It is new genes that drive the phenotypic diversity of life and ultimately macroevolution (Chen et al., 2013).

Only germline mutations are relevant to evolution since somatic cell mutations cannot be passed to offspring. In mammals, including humans, this includes gametes (egg and sperm), gametocytes (oocytes and spermatocytes), gametogonia (oogonia and spermatogonia), or even early embryonic cells (Klug & Cummings, 2006). Many mutations are simple point mutations representing one “letter” (base) change in the nucleotide sequence of a gene. These are known as single nucleotide polymorphisms (SNPs). Some SNPs are substitutions and may or may not affect the amino acid sequence of the resultant protein, since there are 43=64 possible codons and that code for just 20 amino acids and three stop codons. Other SNPs are deletions or insertions resulting in frameshift mutations, which could be very deleterious as the entire reading frame would be disrupted, potentially producing an entirely different amino acid sequence resulting in a nonfunctional, potentially shorter (a stop codon could be introduced) protein. SNPs in genes are fairly rare and on the range of in a million per gamete per generation in humans, however the prevalence of so-called neutral mutations in the non-coding portions of DNA is considerably higher as their presence is unlikely to affect the fitness of an organism. It is also important to point out that while the occurrence of point mutations is rare, like any mutation, it can spread quickly (on an evolutionary timescale) among a population by means of sexual reproduction (Klug & Cummings, 2006). These types of mutations along with a slew of others have the capacity to create new alleles, but generally not new genes as they act on previously present genetic information. In the context of evolution, this begs the question of how new genes, and thus new structures, behaviors, and physiological pathways arise in species.

Five proposed mechanisms for new gene generation include (1) gene duplication, (2) transposable element protein domestication, (3) horizontal (lateral) gene transfer, (4) gene fusion/fission, and (5) de novo origination. New genes have two likely outcomes, fixation (100% frequency) or extinction (Chandrasekaran & Betrán, 2008). While these processes occur in prokaryotes, this paper will focus on evolution in the eukaryotic system. The process of sexual reproduction including meiosis, as with simple mutations to existing genes, allows for the random distribution of new genes to offspring in a population. SNPs, natural selection, gene flow, and genetic drift further affect the frequency of new genes among populations (Park, 2013).

Gene duplication appears to be the most common source of new genes and includes duplications of an entire genome or its portions, including exons and individual genes. Duplicated genes can then evolve along parallel lines where mutations may occur at different locations and during different evolutionary time spans. Practical mechanisms include nondisjunction and unequal crossover in meiosis as well as transpositions of transposons. The same duplication methods can affect non-coding regions of chromosomes. Rates of gene duplication exceed rates of SNPs and have been found to represent more of the differences between chimps and humans than do point mutations. Nondisjunction can result in whole-genome duplication (Chandrasekaran & Betrán, 2008). Whole genome duplication events are important in the duplication of Hox (body plan) gene clusters. Duplicated genes can undergo parallel evolution and are associated with morphological complexity and key radiation events in vertebrates. Subsequent Hox deletions may also lead to considerable morphological changes and thus radiation events (Soshnikova et al., 2013).

Transposable element (TE) protein domestication involves recruiting (being able to express) portions of the genome once thought of as junk now known to be involved in immunity, reproduction, chromosome replication, and cell cycle control. TE domestication events have occurred throughout the evolutionary history of eukaryotes and are particularly common in human and other mammalian genomes. Some TE genes have been shown to perform essential cellular functions. TEs are also involved in exon shuffling and gene duplication (Volff, 2006). It has also been suggested by studying activity regulated cytoskeletal-associated protein (Arc) genes that the process may work in reverse where host genes may be incorporated into transposable elements, which helps explain the origin and diversity of transposable elements (Abrusán et al., 2013).

Horizontal (or lateral) gene transfer (HGT) involves the transfer of genes between the genomes of two individuals of different species. This is in contrast to vertical gene transfer which is the transfer of genetic information to offspring of the same species via meiosis (in sexually reproducing species). Lateral gene transfer includes endosymbiotic gene transfer, the continuous process of transferring genes from endosymbionts such as mitochondria and plastids to the nucleus of their host cells, however the endosymbiotic origin of organelles is rare. HGT in prokaryotes is straightforward and occurs by three processes: “(1) transformation - direct uptake of fee exogenous DNA; (2) transduction - virus-mediated DNA transfer; and (3) conjugation - plasmid-mediated DNA transfer (Schönknecht et al., 2013).” Many instances of HGT have been shown from prokaryotes to eukaryotes with a few instances of the reverse. Evidence for HGT among only eukaryotes is emerging and includes transduction by viral vectors. Eukaryotes owe many of their genes to HGT, mostly from prokaryotes, some of which have enabled adaptive radiation into new niches (Schönknecht et al., 2013).

Gene fusion involves combining two transcripts to form a new gene, while conversely fission involves forming two distinct genes from one. This process works in concert with ay of the four other proposed mechanisms for new gene creation. De novo origination involves new genes arising from previously non-coding portions of DNA and necessarily involves exon suffling. Such genes do not have homologues in other lineages. Investigation of more recent de novo genes allows researchers to better postulate their genetic precursors along with the mechanics of their origin (Chandrasekaran & Betrán, 2008).

In contrast to the origination of new genes, pseudogenes epitomize the deterioration of existing genes such that they resemble paralogous or homologous genes, but can no longer translate to functional proteins. The degredation of genes due to mutation is just as much a feature of evolution as inferred improvements. Recent findings suggest that pseudogenes live on as RNA genes, now known to facilitate a host of functions beyond that of tRNA and rRNA (Chandrasekaran & Betrán, 2008).

Emerging research and further advances in bioinformatics will be able to better map the origin of new genes in clades over the course of evolutionary history as well as provide insight into the mechanics of new gene formation. New technologies, such as gene silencing, will enable researches to show exactly how identified new genes evolved new molecular functions, organs and macrostructures, behaviors, and intelligence (Chen et al., 2013). This information will continue to add to the modern evolutionary synthesis, better modeling the origins of phenotypic diversity and its relevance to adaptive radiation.

Works Cited

Abrusán,G. , Szilágyi,A. , Zhang,Y. , & Papp,B. (2013). Turning gold into 'junk': Transposable elements utilize central proteins of cellular networks. Nucleic Acids Research, 41(5), 3190-3200. Web.

Chandrasekaran ,C.&Betrán ,E.(2008)Origins of new genes and pseudogenes.Nature Education1(1):181. Web.

Chen,S. , Krinsky,B. , & Long,M. (2013). New genes as drivers of phenotypic evolution. Nature Reviews. Genetics, 14(9), 645-660. Web.

Klug, William S., and Michael R. Cummings. Concepts of Genetics. 8th ed. Upper Saddle River, NJ: Pearson/Prentice Hall, 2006. Print.

Park, Michael Alan. Biological Anthropology. 7th ed. New York: McGraw-Hill Humanities/Social Sciences/Languages, 2013. Print.

Schönknecht,G. , Weber,A. , & Lercher,M. (2014). Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. BioEssays, 36(1), 9-20. Web.

Soshnikova,N. , Dewaele,R. , Janvier,P. , Krumlauf,R. , & Duboule,D. (2013). Duplications of hox gene clusters and the emergence of vertebrates. Developmental Biology, 378(2), 194-199. Web.

Volff, Jean-Nicolas. "Turning Junk into Gold: Domestication of Transposable Elements and the Creation of New Genes in Eukaryotes." BioEssays 28.9 (2006): 913-22. Web.

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