Stress-free with Rpd3: a unique chromatin complex mediates the response to oxidative stress.

Eukaryotic cells are constantly bombarded with a plethora of extracellular and intracellular stresses that they must quickly respond to in order to survive (1). These stresses can come in the form of changes in temperature, nutrient availability, osmotic changes, and DNA-damaging events (extracellular), as well as oxidative stress from normal metabolism and replicative/transcriptional DNA damage (intracellular). In order to respond to a wide range of stresses, cells must be able to rapidly translate a stress response signal into a specific transcriptional program (2). While there are some common themes that underlie the general “environmental stress response” (ESR), the transcriptional programs each stressor initiates are unique and tailored to deal with each specific type of stress (3). The exact mechanisms underlying the cellular response to a particular stress are poorly defined and continue to be an exciting area of active research. A question of particular significance is how the cell is able to modulate the chromatin environment surrounding the genes necessary to respond to specific stresses encountered by the cell. This is a complex problem, as many genes may need to be quickly, and precisely, upor downregulated in response to each particular type of stress (3). In order to achieve this level of control, the cell must utilize one or more signaling cascades activated by the stressor to alter the chromatin landscape precisely at many genomic loci by recruiting a host of chromatin-modifying enzymes (4). It is likely that the posttranslational modifications (PTMs) created by these enzymes form a chromatin signature, or code, that can help to initiate the ESR through recruitment of chromatin effector proteins that dock on these histone PTMs (5–8). In this issue of Molecular and Cellular Biology, using Saccharomyces cerevisiae, Baker and colleagues (9) explore a connection between a complex containing the histone deacetylase Rpd3 and the ESR pathway, thereby increasing our understanding of how cell signaling and chromatin come together to regulate the cellular response to stress. As described below, these studies break new ground and give rise to many fascinating new questions that await future discoveries. In this report (9), Baker et al. demonstrate that the histone deacetylase Rpd3 forms a third complex, which we call herein Rpd3 “micro” (Rpd3 ), given that it is the smallest of the three Rpd3 complexes identified thus far (Fig. 1A). This result is in agreement with a previous finding (10). Rpd3 has been associated with two other complexes, Rpd3L and Rpd3S (11), each with unique functions. Rpd3L has been shown to be involved in the response to heat stress and ribosome biogenesis (12, 13), while Rpd3S functions to maintain chromatin integrity and repress cryptic transcription within gene bodies (14). Using liquid chromatography-mass spectrometry (LC-MS), the authors demonstrated that Rpd3 physically associates with Snt2 and Ecm5 to form the Rpd3 complex. Interestingly, Snt2 and Ecm5 each contain recognizable histone interaction motifs, including plant homeodomain (PHD) fingers and bromo-adjacent homology (BAH) domains (Fig. 1B), strongly implicating them in chromatin interaction. Intriguingly, Ecm5 also contains a putative histone demethylase domain (Fig. 1B)— however, whether this protein contains demethylase activity remains unknown. An initial clue that Rpd3 might be fundamental to the stress response pathway was provided by a prior study linking Snt2 to osmotic stress (15). To further investigate this possibility, the authors created strains lacking Rpd3, Snt2, and Ecm5, both singly and in pairs. Interestingly, while strains lacking Snt2 or Rpd3 showed resistance to hydrogen peroxide (H2O2), cells lacking Ecm5 were highly sensitive. This suggests that while both Ecm5 and Snt2 are present in the same complex, they may play opposing functions in the response to oxidative stress. This result was also seen when these strains were treated with rapamycin, an inhibitor of the TOR (target of rapamycin) pathway that simulates nitrogen starvation. Further arguing for opposing roles, the authors observed opposing changes in gene expression when either Snt2 or Ecm5 was deleted. Whether the opposing functions between Snt2 and Ecm5 are driven through DNA sequence recognition, the epigenetic landscape, posttranslational modification of Ecm5 or Snt2, protein-protein interactions with specific transcription factors, or yet another mechanism remains to be elucidated. To gain further insight into where Rpd3 is found across the genome, the authors performed genome-wide localization studies. All three members of Rpd3 were found to colocalize primarily at promoter regions. Strikingly, the authors discovered two distinct sets of promoters: a set that recruited Snt2 and Ecm5 only upon treatment with H2O2 and a set of “superenriched” promoters that had Snt2 and Ecm5 constitutively bound (Fig. 1C). Interestingly, Rpd3 recruitment did not require Ecm5 and Snt2 at the H2O2-responsive promoters but was necessary for Rpd3 to localize at the superenriched promoters, suggesting a fundamental difference in how Rpd3 is targeted to these genes. Whether Snt2 and Ecm5 function independently of Rpd3 at H2O2-responsive promoters remains an intriguing question. Additionally, a Pdr1/Pdr3 sequence motif was identified; this motif overlapped with the 20 most highly H2O2-enriched Snt2/Ecm5-bound promoters, whereas other Snt2/Ecm5 target genes are regulated by Rap1 and Ste12. These observations suggest a possible mechanism for the positive or negative gene expression changes observed at individ-