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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Complex fate of paralogs.
Radek Szklarczyk1, Martijn A Huynen, Berend Snel
1Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands. radek@cmbi.ru.nl
BMC Evolutionary Biology
|December 20, 2008
Summary
Gene duplication drives evolutionary innovation by allowing paralogs to specialize within protein complexes, leading to new functions and adaptations, such as in yeast.
Area of Science:
- Evolutionary biology
- Molecular systems biology
- Genomics
Background:
- High-coverage mass spectrometry and protein complex reconstruction enable evolutionary studies.
- Gene duplication is a key driver of evolutionary innovation.
- Protein complexes provide a framework for studying gene duplication evolution.
Purpose of the Study:
- To investigate the roles of paralogous proteins within protein complexes.
- To understand how gene duplication contributes to functional diversification.
- To explore the evolutionary implications of paralog specialization.
Main Methods:
- Analysis of high-coverage mass spectrometry data.
- Reconstruction and examination of protein complexes.
- Comparative genomics and evolutionary analysis.
Main Results:
- Paralogs within the same complex exhibit specialized roles, including mRNA dosage increase, mutually exclusive participation forming alternative complexes, and contributions to structural growth.
- Gene duplication events led to specialization of ancestral proteins, enabling them to divide roles in multi-protein assemblies.
- One duplicate gene may exit the complex, accelerating its evolution and potentially generating new functions.
Conclusions:
- Conditionally assembled paralogous subunits likely facilitated yeast adaptation to anaerobic conditions.
- Specialized paralogs and rapidly evolving duplicate genes offer raw material for novel functions.
- Understanding paralog roles in protein complexes sheds light on evolutionary adaptation and innovation.
Related Concept Videos
01:57Gene 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...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
02:37Gene 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.
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.
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...
01:57Protein 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...
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...
01:57Protein 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...
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...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...