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Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

Gene Conversion

Gene Conversion

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...

Genome Copying Errors

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.

Gene Duplication and Divergence

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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...

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Related Experiment Video

Updated: Jul 3, 2026

Structure-function Studies in Mouse Embryonic Stem Cells Using Recombinase-mediated Cassette Exchange

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Published on: April 27, 2017

Retention of enzyme gene duplicates by subfunctionalization.

F N Braun¹, D A Liberles

¹Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden. chefnb@sbc.su.se

International Journal of Biological Macromolecules

|November 6, 2003

Summary

The duplication-degeneration-complementation (DDC) process allows gene duplicates to divide ancestral functions, slowing pseudogene formation. This study models DDC for enzyme function, linking sequence changes to binding affinity via amino acid composition.

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Area of Science:

Evolutionary biology
Biochemistry
Molecular genetics

Background:

Gene duplication is a major driver of evolutionary innovation.
Pleiotropic genes, with multiple functions, pose unique evolutionary challenges.
Pseudogene formation can limit the evolutionary potential of duplicated genes.

Purpose of the Study:

To model the Duplication-Degeneration-Complementation (DDC) process for enzyme-like pleiotropic functions.
To investigate how sequence divergence between gene duplicates influences functional partitioning.
To establish a link between enzyme physical-chemical properties and sequence evolution.

Main Methods:

Developed a mathematical model for DDC driven by sequence divergence.
Incorporated an idealized sequence-function mapping based on hydrophobic-polar (HP) amino acid composition.
Related enzyme-substrate binding affinity to the HP amino acid composition of the binding pocket.

Main Results:

The DDC model demonstrates how gene duplicates can subfunctionalize, dividing ancestral functions.
Sequence divergence was shown to be a key factor in driving functional partitioning.
A clear relationship was established between enzyme binding affinity and HP amino acid composition.

Conclusions:

DDC effectively frustrates pseudogene formation by enabling functional specialization of gene duplicates.
The study provides a mechanistic link between sequence evolution and the physical-chemical properties of enzyme function.
This model offers insights into the evolution of complex gene families and functional diversification.