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Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation
Kevin Hannay1, Edward M Marcotte, Christine Vogel
1Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, 2500 Speedway, MBB 3.210, Austin, TX 78712, USA. moleculeboy24@gmail.com
BMC Genomics
|December 18, 2008
Summary
Gene duplicates offer some protection against gene loss, but their buffering effect is limited across diverse organisms. This buffering capacity is not conserved and varies, suggesting other mechanisms contribute significantly to cellular robustness.
Area of Science:
- Genomics
- Evolutionary Biology
- Systems Biology
Background:
- Gene duplication is a proposed mechanism for buffering gene loss.
- The extent and correlates of duplicate gene buffering remain debated across species.
Purpose of the Study:
- To comprehensively compare gene essentiality, duplication, and buffering by duplicates.
- To reveal general trends in duplicate gene buffering across diverse bacteria and eukaryotes.
Main Methods:
- Comparative analysis of gene essentiality and duplication.
- Examination of buffering capacity of gene duplicates across eleven model organisms.
- Case study on functional similarity and activity of buffering duplicates in yeast and worm.
Main Results:
- Gene duplicates enhance survival after gene deletion in nine of eleven organisms, but by a maximum of 13%.
- Buffering capacity is independent of gene essentiality but higher for highly expressed genes (e.g., 23% in E. coli).
- Sequence similarity and number of duplicates are weak predictors; buffering duplicates in yeast and worm show functional similarities and increased activity.
Conclusions:
- Gene essentiality and duplicate buffering are not conserved across organisms and do not correlate with complexity.
- Buffering by duplicates contributes minimally to robustness, with other processes like alternative pathways playing dominant roles.
- Observed buffering in yeast and worm may be organism-specific, potentially a byproduct of high dosage demands.
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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.
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