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Exon Recombination

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...

Conservative Site-specific Recombination and Phase Variation

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...

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Related Experiment Video

Updated: Jul 4, 2026

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx).

Amy J Baldwin¹, Kathy Busse, Alan M Simm

¹School of Biosciences, Cardiff University, UK.

Nucleic Acids Research

|June 19, 2008

Summary

Trinucleotide exchange (TriNEx) is a novel method for directed evolution, creating diverse protein variants by swapping DNA sequences. This technique significantly enhanced TEM-1 beta-lactamase activity and resistance, demonstrating its power in protein engineering.

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Molecular Evolution of the Tre Recombinase

Molecular Evolution of the Tre Recombinase

Published on: May 29, 2008

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Last Updated: Jul 4, 2026

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

Molecular Evolution of the Tre Recombinase

Molecular Evolution of the Tre Recombinase

Published on: May 29, 2008

Area of Science:

Molecular Biology
Protein Engineering
Biotechnology

Background:

Directed evolution aims to create novel protein variants with desired properties.
Existing methods for generating molecular diversity have limitations in scope and efficiency.

Purpose of the Study:

To introduce a new method, Trinucleotide exchange (TriNEx), for generating molecular diversity.
To demonstrate the effectiveness of TriNEx in creating functional protein variants with altered properties.

Main Methods:

TriNEx utilizes an engineered transposon (MuDel) to delete and replace trinucleotide sequences within a target gene.
A DNA cassette (SubSeq(NNN)) provides randomized trinucleotide sequences for substitution.
The bla gene encoding TEM-1 beta-lactamase was used as a model system.

Main Results:

Mutations were distributed throughout the bla gene, resulting in single, double, and triple nucleotide changes.
TriNEx generated amino acid substitutions that significantly altered TEM-1 beta-lactamase activity, increasing ceftazidime activity by up to 64-fold and clavulanate resistance by up to 8-fold.
The method enabled access to mutations not easily achievable by other techniques, such as charge-switch and aromatic substitutions.

Conclusions:

TriNEx is an effective method for generating diverse protein variants with altered functions.
The technique combines site-directed saturation mutagenesis with whole-gene mutagenesis capabilities.
TriNEx offers a powerful approach for protein engineering and directed evolution applications.