Take our Survey

Reference: Bogumil D, et al. (2012) Chaperones divide yeast proteins into classes of expression level and evolutionary rate. Genome Biol Evol 4(5):618-25

Reference Help

Abstract


It has long been known that many proteins require folding via molecular chaperones for their function. Although it has become apparent that folding imposes constraints on protein sequence evolution, the effects exerted by different chaperone classes are so far unknown. We have analyzed data of protein interaction with the chaperones in Saccharomyces cerevisiae using network methods. The results reveal a distinct community structure within the network that was hitherto undetectable with standard statistical tools. Sixty-four yeast chaperones comprise ten distinct modules that are defined by interaction specificity for their 2,691 interacting proteins. The classes of interacting proteins that are in turn defined by their dedicated chaperone modules are distinguished by various physiochemical protein properties and are characterized by significantly different protein expression levels, codon usage, and amino acid substitution rates. Correlations between substitution rate, codon bias, and gene expression level that have long been known for yeast are apparent at the level of the chaperone-defined modules. This indicates that correlated expression, conservation, and codon bias levels for yeast genes are attributable to previously unrecognized effects of protein folding. Proteome-wide categories of chaperone-substrate specificity uncover novel hubs of functional constraint in protein evolution that are conserved across 20 fungal genomes.

Reference Type
Journal Article
Authors
Bogumil D, Landan G, Ilhan J, Dagan T
Primary Lit For
Additional Lit For
Review For

Interaction Annotations


Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.

Interactor Interactor Type Assay Annotation Action Modification Phenotype Source Reference

Gene Ontology Annotations


Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

Gene Gene Ontology Term Qualifier Aspect Method Evidence Source Assigned On Annotation Extension Reference

Phenotype Annotations


Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details.

Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

Regulation Annotations


Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, SPELL, or YeastMine.

Regulator Target Experiment Assay Construct Conditions Strain Background Reference