User:Meaganbotnick/sandbox

My topic of choice is gene superfamily.

Gene Superfamily

Gene superfamilies are genes and proteins from a common ancestral origin, but differ in function, as well as expression. They will contain single genes, as well as multi-gene families. Gene families are groups of genes that have sequence homology, overlapping functions, and are typically under a common control. Some genes in a superfamily will be in clusters, while others will be dispersed individually.

Distribution in the genome
The members of the superfamily that are found in clusters tend to be gene families. They’re typically formed by unequal crossover events, resulting in tandem duplications of genes. These members will likely have similar function, and are advantageous if gene product is needed in large amounts. These genes will exhibit concerted evolution. The sequence of the repetitive gene will be maintained within a species, but will differ when compared between species.

Dispersed genes are typically a result of reverse transcription of mRNA, followed by insertion. Products of reverse transcription are easily identified because they will lack introns. If functional, they are called retrogenes, and will likely differ in function and expression from the clustered members of the same superfamily. Typically, these reverse transcription products become retropsuedogenes, which lack function.

Duplication
A new gene family member is first formed by a duplication event. This event may involve the whole genome, a single gene, or a gene region. There are three common mechanisms of duplicating a gene. Polyploidization will result in duplication of the entire genome. This can be caused by a failure to divide in mitosis, or hybridization of 2 closely related organisms.

Tandem duplication is caused by unequal crossover events in mitosis or meiosis of germline cells. This can encompass regions of different sizes, although duplication of whole genes is most common. Tandem duplication will result in gene clusters. The rate of duplication will increase as the size of the cluster increases, due to a greater likelihood of crossover events. Genes duplicated in tandem have an increased rate of homogenization, or convergence. When genes with similar sequences are in close proximity nonreciprocal gene transfer is likely to occur between the two genes. This may also result in a variant repeat being fixed into the gene family. This homogenization results in 2 or more identical copies of the gene in tandem. This may also result in a variant repeat being fixed into the gene family.

Reverse transcription will also result in gene duplication. In the human genome, Long and Short Interspersed Nuclear Elements (LINEs, and SINEs) are the most common products of reverse transcription. These regions possess a reverse transcriptase gene, and can autonomously retrotranspose themselves around the genome. The products of reverse transcription events are the source of novel genes dispersed throughout the genome. They provide the gene superfamily with diversity in expression and function.

Mutation Accumulation
As gene redundancy increases, selective pressure to repair spontaneous mutations will decrease. Mutations are permitted to accumulate, as long as one functional copy of the gene remains. Furthermore, there is positive selection pressure on genes whose mutations have resulted in a novel function. If the mutation is located within the coding region of the gene, the gene product will differ from the original. If the mutation is located within a regulatory element, the expression will differ.

Mutations will lead to functional differentiation, allowing for the growth and diversification of the gene superfamily. At a certain point, sequence divergence as a result of mutations will prevent potential gene conversion. Homogenization of genes is much slower between genes of diverse function, or between subtypes of a superfamily.

As new functions and diverse members of gene families arise, the incidence of amino acid substitution tends to increase. It is difficult to determine whether this acceleration of substitution occurs as a result of positive selection, or reduced selective constraint.