The Environmental Stress Response (ESR) was defined by one of the early transcriptomic studies using then-revolutionary DNA microarrays [1]. The group comprises 279 genes induced by diverse stresses (“iESR” genes), and 595 repressed genes (“rESR”) that can be subdivided into 436 PAC / RiBi genes and 159 Ribosomal Protein (RP) genes, described in more detail below.
In 2017, the ESR gene group was updated slightly:
Four iESR genes and one PAC / RiBi gene are no longer annotated as separate genes were deleted from ESR gene list. Nineteen genes originally annotated as PAC / RiBi were reassigned to the RP cluster based on updated annotations by the Saccharomyces Genome Database (SGD) as ribosomal proteins, leading to 436 PAC / RiBi genes remaining. The RP group was updated by the reassignment of 19 originally-named PAC / RiBi genes, along with the addition of 11 new genes identified as ribosomal proteins by SGD.
This file ESR_clusters_UPDATED_2017-FORPUBLICATION lists the Environmental Stress Response (ESR) genes and cluster updated from the original assignments in Gasch et al. 2000 (doi: 10.1091/mbc.11.12.4241). Clusters include the induced-ESR (iESR), PAC/RiBi , and Ribosomal Protein (RP) genes. Column C lists gene assignments as defined in Gasch et al. 2000; Column B lists updated gene assignments as used by the Gasch Lab .
Overview of the ESR
The ESR gene set was defined by hierarchical clustering of gene expression changes from hundreds of transcriptomic samples tracking temporal responses of Saccharomyces cerevisiae to different environmental conditions, including heat shocks, oxidative and reductive stress, osmotic shock, starvation conditions, and others. The response includes both induced and repressed genes, which display near mirror-image expression changes in response to diverse types of stress. An overview of the program is summarized below.
The induced ESR genes (shorthanded “iESR” genes) includes 279 genes (four from the original set are no longer considered separate genes) that are induced in response to diverse stresses. The group is enriched for genes known to play defense roles during stress, including a subset of protein-folding chaperones, oxidoreductases, carbohydrate metabolism genes (including those for trehalose and glycogen metabolism), and others. Many of the genes can be regulated by the “general stress” transcription factors, Msn2 and its paralog Msn4, in response to multiple stresses. Most genes are also regulated by other transcription factors as well, which fine tune expression during specific conditions.
The repressed ESR genes (“rESR”) can be subdivided into two groups. Ribosomal protein (RP) genes are repressed by diverse conditions in the ESR, with slightly different expression of genes enriched for functions in rRNA processing, other aspects of ribosome biogenesis, transcription and translation, and additional growth-related genes. Because this group was originally noted to be enriched for “PAC” promoter elements, the cluster was originally named the “PAC” cluster but is now more commonly referred to as the Ribosome Biogenesis (RiBi) group due to enrichment for that functional group.
Download the updated ESR gene list here: ESR_clusters_UPDATED_2017-FORPUBLICATION