The stress-induced attachment of small ubiquitin-like modifier (SUMO) to a diverse collection of nuclear proteins regulating chromatin architecture, transcription, and RNA biology has been implicated in protecting plants and animals against numerous environmental challenges. In order to better understand stress-induced SUMOylation, we combined stringent purification of SUMO conjugates with isobaric tag for relative and absolute quantification mass spectrometry and an advanced method to adjust for sample-to-sample variation so as to study quantitatively the SUMOylation dynamics of intact Arabidopsis seedlings subjected to stress. Inspection of 172 SUMO substrates during and after heat shock (37°C) revealed that stress mostly increases the abundance of existing conjugates, as opposed to modifying new targets. Some of the most robustly up-regulated targets participate in RNA processing and turnover and RNA-directed DNA modification, thus implicating SUMO as a regulator of the transcriptome during stress. Many of these targets were also strongly SUMOylated during ethanol and oxidative stress, suggesting that their modification is crucial for general stress tolerance. Collectively, our quantitative data emphasize the importance of SUMO to RNA-related processes protecting plants from adverse environments. The ability of cellular organisms to cope with environmental challenges requires the detection and immediate initiation of defense responses designed to mitigate the damage inflicted and enhance the organism's ability to tolerate future insults. For sessile organisms such as plants, robust stress responses are fundamental to their survival in a wide range of adverse environments (1, 2). Genetic and biochemical studies have identified a plethora of input pathways and output responses for stress protection in both prokaryotes and eukaryotes. Universally important is the synthesis of heat shock proteins that minimize protein aggregation and stimulate protein refolding through intrinsic chaperone activities (3).The stress-induced modification of intracellular proteins by small ubiquitin-like modifier (SUMO) 1 has recently emerged as an additional line of defense in eukaryotes (4 -6). Attachment of the ϳ100-amino-acid SUMO protein is driven by an ATPdependent, three-step enzyme cascade, which in Arabidopsis thaliana involves the E1 heterodimer (SAE2 together with either of two SAE1 isoforms), a single E2 SCE1, and at least two E3s (SAP, MIZ1 (SIZ1), and MMS21/HYP2) (7-11). The end result is the isopeptide linkage of one or more SUMO moieties to accessible target lysine(s). Most commonly, a consensus ⌿KxE SUMO-binding motif is modified, where ⌿ represents a bulky hydrophobic residue (12, 13). In some cases, the bound SUMOs themselves are also substrates, which results in poly-SUMO chains decorating the target (14, 15). Once generated, SUMO conjugates can be disassembled by a family of deSUMOylating proteases that specifically cleave these isopeptide bonds, thus allowing SUMO to act reversibly (e.g. Refs. 7,[16][17][18].Imp...