ArticleExploiting genomic patterns to discover new supramolecular protein assemblies |
| Morgan Beeby 1, Thomas A. Bobik 2, Todd O. Yeates 1 3 4 * |
1UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, California 90095
2Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011
3Department of Chemistry and Biochemistry, University of California Los Angeles, California 90095-1569
4Molecular Biology Institute, Paul D. Boyer Hall, Los Angeles, California 90095-1570
|
| email: Todd O. Yeates (yeates@mbi.ucla.edu) |
*Correspondence to Todd O. Yeates, Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles Young Dr. East, Los Angeles, CA 90095-1569
Funded by:
BER Program, U.S. Department of Energy Office of Science
| supramolecular assembly bacterial ultrastructure paralog homolog self assembly carboxysome bacterial microcompartment |
| Bacterial microcompartments are supramolecular protein assemblies that function as bacterial organelles by compartmentalizing particular enzymes and metabolic intermediates. The outer shells of these microcompartments are assembled from multiple paralogous structural proteins. Because the paralogs are required to assemble together, their genes are often transcribed together from the same operon, giving rise to a distinctive genomic pattern: multiple, typically small, paralogous proteins encoded in close proximity on the bacterial chromosome. To investigate the generality of this pattern in supramolecular assemblies, we employed a comparative genomics approach to search for protein families that show the same kind of genomic pattern as that exhibited by bacterial microcompartments. The results indicate that a variety of large supramolecular assemblies fit the pattern, including bacterial gas vesicles, bacterial pili, and small heat-shock protein complexes. The search also retrieved several widely distributed protein families of presently unknown function. The proteins from one of these families were characterized experimentally and found to show a behavior indicative of supramolecular assembly. We conclude that cotranscribed paralogs are a common feature of diverse supramolecular assemblies, and a useful genomic signature for discovering new kinds of large protein assemblies from genomic data. |
Received: 30 July 2008; Revised: 19 September 2008; Accepted: 22 September 2008
10.1002/pro.1
About DOI
