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Published on: December 17, 2016
Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census
1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA. Mark.Gerstein@yale.edu
Proteins
|December 16, 1998
Summary
Microbial genomes share common protein folds, with universal folds favoring mixed helix-sheet structures over all-helical ones. This analysis reveals evolutionary relationships and membrane protein preferences across diverse organisms.
Area of Science:
- Structural bioinformatics
- Comparative genomics
- Protein evolution
Background:
- Protein structure and fold usage vary across different organisms.
- The Protein Data Bank (PDB) contains approximately 340 soluble protein folds.
- Understanding shared folds can illuminate evolutionary relationships and functional constraints.
Purpose of the Study:
- To compare protein fold usage patterns across eight diverse microbial genomes.
- To identify universally shared protein folds and analyze their structural characteristics.
- To investigate the relationship between fold expression, genome duplication, and evolutionary relatedness.
Main Methods:
- Comparative analysis of protein folds present in eight microbial genomes (yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, E. coli).
- Identification of shared folds and analysis of their structural composition (all-helical vs. mixed helix-sheet).
- Ranking of folds by expression and genome duplication, and construction of a phylogenetic tree based on shared folds.
- Transmembrane-helix (TM) prediction for analyzing membrane protein fold usage.
Main Results:
- 240 out of ~340 soluble protein folds are found in at least one of the eight genomes, with 30 folds shared across all.
- Universally shared folds are enriched in mixed helix-sheet structures and superfolds, differing significantly from general PDB folds.
- Genome classification based on shared folds shows topology similar to conventional evolutionary trees.
- Membrane protein fold usage follows a 'Zipf-like' law, with no preference for specific numbers of TM-helices.
Conclusions:
- A core set of protein folds is conserved across diverse microbial life.
- Structural biases in universally shared folds reflect functional or evolutionary pressures.
- Shared fold patterns provide a robust basis for inferring microbial evolutionary relationships.
- Membrane protein architecture is governed by general principles rather than specific TM-helix counts.
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