Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation

Abstract

BackgroundTo make sense out of gene expression profiles, such analyses must be pushed beyond the mere listing of affected genes. For example, if a group of genes persistently display similar changes in expression levels under particular experimental conditions, and the proteins encoded by these genes interact and function in the same cellular compartments, this could be taken as very strong indicators for co-regulated protein complexes. One of the key requirements is having appropriate tools to detect such regulatory patterns.ResultsWe have analyzed the global adaptations in gene expression patterns in the budding yeast when the Hsp90 molecular chaperone complex is perturbed either pharmacologically or genetically. We integrated these results with publicly accessible expression, protein-protein interaction and intracellular localization data. But most importantly, all experimental conditions were simultaneously and dynamically visualized with an animation. This critically facilitated the detection of patterns of gene expression changes that suggested underlying regulatory networks that a standard analysis by pairwise comparison and clustering could not have revealed.ConclusionsThe results of the animation-assisted detection of changes in gene regulatory patterns make predictions about the potential roles of Hsp90 and its co-chaperone p23 in regulating whole sets of genes. The simultaneous dynamic visualization of microarray experiments, represented in networks built by integrating one's own experimental with publicly accessible data, represents a powerful discovery tool that allows the generation of new interpretations and hypotheses.

Identification of an Hsp90 mutation that selectively disrupts cAMP/PKA signaling in Saccharomyces cerevisiae

“…In S. pombe, treatment with geldanamycin increased fbp1 transcription, but the overall expression was 20 % less than the hsp90 (git10) mutation (Alaamery and Hoffman 2008). In addition, there was only about 20 % overlap of targets with altered expression in cells treated with the Hsp90 inhibitor radicicol or containing a deletion in the gene encoding the Hsp90 cochaperone Sba1 (Echeverria et al 2011). It seems likely that many of these effects are due to altered Sgt1 interaction.…”

“…To gain appreciation of how our results compare with transcriptional changes that occur upon general inhibition of Hsp90, we compared the list of genes that displayed altered expression in hsc82-W296A cells with the list of genes affected by Hsp90 inhibition in yeast. A prior study (Echeverria et al 2011) identified 185 genes whose expression changed at least 1.5 log fold either when Hsp90 was inhibited by radicicol and/or when cells contained a deletion in the cochaperone SBA1. A comparison of the two lists showed that only 38, or 20 %, of the genes identified in that study were also affected by hsc82-W296A mutation (Table S3).…”

“…Sse1, an Hsp70 binding partner required for full activity of Hsp90 client proteins (Liu et al 1999), and the Sch9 kinase, which is known to regulate Hsp90 function , cooperate to regulate PKA activity (Trott et al 2005). More recently, a report demonstrated that treatment with the Hsp90 inhibitor radicicol resulted in the upregulation of 114 genes in yeast, 26 of which contain Msn2/Msn4 binding elements, known as stress-response elements (STREs) (Echeverria et al 2011). Hsp90 regulation of PKA activity also plays a key role in pathogenesis of Candida albicans.…”

The expanding proteome of the molecular chaperone HSP90

“…Interestingly, some previously identified HSP90 client proteins and interactors were found to be than 23 studies in which higher-throughput, unbiased survey approaches have been taken to detect proteins interacting directly or indirectly with HSP90. These studies have commonly involved genetic, chemical genetic and physical interaction screens performed in yeast [8][9][10][11][12][13][14] as well as large-scale analyses, commonly utilizing affinity purification of HSP90, of proteins present in HSP90 complexes. 7,[15][16][17][18][19][20] Only a few efforts have been made previously toward characterizing the global cellular effects of HSP90 inhibition in mammalian cells.…”

An interplay between the p38 MAPK pathway and AUBPs regulates c-fos mRNA stability during mitogenic stimulation

“…Integration of experimental data in protein-protein interaction (PPI) networks to build explorable maps using Cytoscape (http://www.cytoscape.org) has been previously described [29,30]. Briefly, using the human-centred PPI database built by Echeverria et al [31], it was possible to extract a network containing the PPIs between the query proteins and their interactors.…”