Novel Proteomics Strategy Brings Insight into the Prevalence of SUMO-2 Target Sites

Blomster, Henri A.; Hietakangas, Ville; Wu, Jianmin; Kouvonen, Petri; Hautaniemi, Sampsa; Sistonen, Lea

doi:10.1074/mcp.m800551-mcp200

Cited by 78 publications

(70 citation statements)

References 50 publications

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“…Consistent with our previous proteomic analysis of Arabidopsis (41) and with analyses by others using yeast and mammalian cell cultures (14,15,20,42,64), we found that stress increases the SUMOylation state of a number of predominantly nuclear substrates that affect a wide range of nuclear events. Processes highlighted by our study as being heavily influenced by stress-induced SUMOylation center on RNA homeostasis, with some of the most dynamically upregulated targets (13 of 34 targets increased by Ͼ7-fold, Tier 1) known or predicted to be involved in RNA binding, splicing, end processing and polyadenylation, and/or turnover (65).…”

Section: Development Of a Quantitative Proteomic Strategy To Monitor supporting

confidence: 78%

Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis

Miller

Scalf

Rytz

et al. 2013

Molecular & Cellular Proteomics

126

152

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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...

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Section: Development Of a Quantitative Proteomic Strategy To Monitor supporting

confidence: 78%

Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis

Miller

Scalf

Rytz

et al. 2013

Molecular & Cellular Proteomics

126

152

View full text Add to dashboard Cite

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“…These results indicate that a substantial fraction of the sites seems to be unrelated to proteasomal-mediated degradation and suggests that Ub conjugation to SR proteins may work as a regulatory signal instead of as a degradation labeling (16,49). Likewise, proteomic approaches revealed that RNA-binding proteins are the predominant group among small Ubiquitin-like modifier (SUMO) conjugation substrates, including several hnRNPs, SR family members and spliceosome components (50,51). Furthermore, SUMO conjugation has been found to regulate different aspects of mRNA metabolism such as pre-mRNA 3 0 end processing and RNA editing, by modifying the function of poly(A) polymerase, symplekin and CPSF-73 in the former case and ADAR1 in the latter (52,53).…”

Section: Post-translational Modifications Of Sr Proteins: Above and Bmentioning

confidence: 98%

Regulating the regulators: Serine/arginine‐rich proteins under scrutiny

et al. 2012

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SummarySerine/arginine-rich (SR) proteins are among the most studied splicing regulators. They constitute a family of evolutionarily conserved proteins that, apart from their initially identified and deeply studied role in splicing regulation, have been implicated in genome stability, chromatin binding, transcription elongation, mRNA stability, mRNA export and mRNA translation. Remarkably, this list of SR protein activities seems far from complete, as unexpected functions keep being unraveled. An intriguing aspect that awaits further investigation is how the multiple tasks of SR proteins are concertedly regulated within mammalian cells. In this article, we first discuss recent findings regarding the regulation of SR protein expression, activity and accessibility. We dive into recent studies describing SR protein auto-regulatory feedback loops involving different molecular mechanisms such as unproductive splicing, microRNA-mediated regulation and translational repression. In addition, we take into account another step of regulation of SR proteins, presenting new findings about a variety of post-translational modifications by proteomics approaches and how some of these modifications can regulate SR protein sub-cellular localization or stability. Towards the end, we focus in two recently revealed functions of SR proteins beyond mRNA biogenesis and metabolism, the regulation of micro-RNA processing and the regulation of small ubiquitin-like modifier (SUMO) conjugation.

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“…The mammalian SUMO protein family includes four members, of which only SUMO-2/3 are conjugated in a stress-dependent manner. A recent report in which the authors used a proteomic approach to determine the proteins modified by SUMO-2/3 shows that most targets do not contain a consensus sumoylation site (Blomster et al, 2009). Stress-inducible chaperones might be involved in this consensus siteindependent recognition mechanism of SUMO-2/3.…”

Section: Hsp27 Facilitates Hsf1 Sumoylationmentioning

confidence: 99%

Heat shock protein 27 is involved in SUMO-2/3 modification of heat shock factor 1 and thereby modulates the transcription factor activity

et al. 2009

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Heat shock protein 27 (HSP27) accumulates in stressed cells and helps them to survive adverse conditions. We have already shown that HSP27 has a function in the ubiquitination process that is modulated by its oligomerization/phosphorylation status. Here, we show that HSP27 is also involved in protein sumoylation, a ubiquitinationrelated process. HSP27 increases the number of cell proteins modified by small ubiquitin-like modifier (SUMO)-2/3 but this effect shows some selectivity as it neither affects all proteins nor concerns SUMO-1. Moreover, no such alteration in SUMO-2/3 conjugation is achievable by another HSP, such as HSP70. Heat shock factor 1 (HSF1), a transcription factor responsible for HSP expression, is one of the targets of HSP27. In stressed cells, HSP27 enters the nucleus and, in the form of large oligomers, binds to HSF1 and induces its modification by SUMO-2/3 on lysine 298. HSP27-induced HSF1 modification by SUMO-2/3 takes place downstream of the transcription factor phosphorylation on S303 and S307 and does not affect its DNA-binding ability. In contrast, this modification blocks HSF1 transactivation capacity. These data show that HSP27 exerts a feedback inhibition of HSF1 transactivation and enlighten the strictly regulated interplay between HSPs and HSF1. As we also show that HSP27 binds to the SUMO-E2-conjugating enzyme, Ubc9, our study raises the possibility that HSP27 may act as a SUMO-E3 ligase specific for SUMO-2/3.

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Novel Proteomics Strategy Brings Insight into the Prevalence of SUMO-2 Target Sites

Cited by 78 publications

References 50 publications

Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis

Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis

Regulating the regulators: Serine/arginine‐rich proteins under scrutiny

Heat shock protein 27 is involved in SUMO-2/3 modification of heat shock factor 1 and thereby modulates the transcription factor activity

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