Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II

Cbx4 SUMOylates BRD4 to regulate the expression of inflammatory cytokines in post-traumatic osteoarthritis

Brominated domain protein 4 (BRD4) is a chromatin reader known to exacerbate the inflammatory response in post-traumatic osteoarthritis (PTOA) by controlling the expression of inflammatory cytokines. However, the extent to which this regulatory effect is altered after BRD4 translation remains largely unknown. In this study, we showed that the E3 SUMO protein ligase CBX4 (Cbx4) is involved in the SUMO modification of BRD4 to affect its ability to control the expression of the proinflammatory genes IL-1β, TNF-α, and IL-6 in synovial fibroblasts. Specifically, Cbx4-mediated SUMOylation of K1111 lysine residues prevents the degradation of BRD4, thereby activating the transcriptional activities of the IL-1β, TNF-α and IL-6 genes, which depend on BRD4. SUMOylated BRD4 also recruits the multifunctional methyltransferase subunit TRM112-like protein (TRMT112) to further promote the processing of proinflammatory gene transcripts to eventually increase their expression. In vivo, treatment of PTOA with a Cbx4 inhibitor in rats was comparable to treatment with BRD4 inhibitors, indicating the importance of SUMOylation in controlling BRD4 to alleviate PTOA. Overall, this study is the first to identify Cbx4 as the enzyme responsible for the SUMO modification of BRD4 and highlights the central role of the Cbx4-BRD4 axis in exacerbating PTOA from the perspective of inflammation.

The SUMO gene MrSmt3 is involved in SUMOylation, conidiation and stress response in Metarhizium robertsii

Smt3, as a small ubiquitin-like modifier (SUMO), play an essential role in the regulation of protein SUMOylation, and thus this process can affect various important biological functions. Here, we investigated the roles of MrSmt3 (yeast SUMO/Smt3 homologs) in the entomopathogenic fungus Metarhizium robertsii. Our results of subcellular localization assays demonstrated that MrSmt3 was present in the cytoplasm and nucleus, whereas MrSmt3 was largely localized in the nucleus during oxidative stress. Importantly, disruption of MrSmt3 significantly decreased the level of protein SUMOylation under heat stress. Deletion of MrSmt3 led to a significant decrease in conidial production, and increased sensitivity to various stresses, including heat, oxidative, and cell wall-disturbing agents. However, bioassays of direct injection and topical inoculation demonstrated that deletion of MrSmt3 did not affect fungal virulence. Furthermore, RNA-seq analysis identified 1,484 differentially expressed genes (DEGs) of the WT and ΔMrSmt3 during conidiation, including 971 down-regulated DEGs and 513 up-regulated DEGs, and further analysis showed that the expression level of several classical conidiation-associated genes, such as transcription factor AbaA (MAA_00694), transcription factor bZIP (MAA_00888) and transcription factor Ste12 (MAA_10450), was down-regulated in the ΔMrSmt3 mutant. Specifically, the major downregulated DEGs were mainly associated with a variety of metabolic regulatory processes including metabolic process, organic substance metabolic process and primary metabolic process. Collectively, our findings highlight the important roles of the SUMO gene MrSmt3 in modulating SUMOylation, conidiation and stress response in M. robertsii.

1,10-phenanthroline inhibits sumoylation and reveals that yeast SUMO modifications are highly transient

The steady-state levels of protein sumoylation depend on relative rates of conjugation and desumoylation. Whether SUMO modifications are generally long-lasting or short-lived is unknown. Here we show that treating budding yeast cultures with 1,10-phenanthroline abolishes most SUMO conjugations within one minute, without impacting ubiquitination, an analogous post-translational modification. 1,10-phenanthroline inhibits the formation of the E1~SUMO thioester intermediate, demonstrating that it targets the first step in the sumoylation pathway. SUMO conjugations are retained after treatment with 1,10-phenanthroline in yeast that express a defective form of the desumoylase Ulp1, indicating that Ulp1 is responsible for eliminating existing SUMO modifications almost instantly when de novo sumoylation is inhibited. This reveals that SUMO modifications are normally extremely transient because of continuous desumoylation by Ulp1. Supporting our findings, we demonstrate that sumoylation of two specific targets, Sko1 and Tfg1, virtually disappears within one minute of impairing de novo sumoylation. Altogether, we have identified an extremely rapid and potent inhibitor of sumoylation, and our work reveals that SUMO modifications are remarkably short-lived.

DeSUMOylation of chromatin-bound proteins limits the rapid transcriptional reprogramming induced by daunorubicin in acute myeloid leukemias

Genotoxicants have been used for decades as front-line therapies against cancer on the basis of their DNA-damaging actions. However, some of their non-DNA-damaging effects are also instrumental for killing dividing cells. We report here that the anthracycline Daunorubicin (DNR), one of the main drugs used to treat Acute Myeloid Leukemia (AML), induces rapid (3 h) and broad transcriptional changes in AML cells. The regulated genes are particularly enriched in genes controlling cell proliferation and death, as well as inflammation and immunity. These transcriptional changes are preceded by DNR-dependent deSUMOylation of chromatin proteins, in particular at active promoters and enhancers. Surprisingly, inhibition of SUMOylation with ML-792 (SUMO E1 inhibitor), dampens DNR-induced transcriptional reprogramming. Quantitative proteomics shows that the proteins deSUMOylated in response to DNR are mostly transcription factors, transcriptional co-regulators and chromatin organizers. Among them, the CCCTC-binding factor CTCF is highly enriched at SUMO-binding sites found in cis-regulatory regions. This is notably the case at the promoter of the DNR-induced NFKB2 gene. DNR leads to a reconfiguration of chromatin loops engaging CTCF- and SUMO-bound NFKB2 promoter with a distal cis-regulatory region and inhibition of SUMOylation with ML-792 prevents these changes.

SUMOylation of PDGF receptor α affects signaling via PLCγ and STAT3, and cell proliferation

BACKGROUND

The platelet-derived growth factor (PDGF) family of ligands exerts their cellular effects by binding to α- and β-tyrosine kinase receptors (PDGFRα and PDGFRβ, respectively). SUMOylation is an important posttranslational modification (PTM) which regulates protein stability, localization, activation and protein interactions. A mass spectrometry screen has demonstrated SUMOylation of PDGFRα. However, the functional role of SUMOylation of PDGFRα has remained unknown.

RESULTS

In the present study, we validated that PDGFRα is SUMOylated on lysine residue 917 as was previously reported using a mass spectrometry approach. Mutation of lysine residue 917 to arginine (K917R) in PDGFRα substantially decreased SUMOylation, indicating that this amino acid residue is a major SUMOylation site. Whereas no difference in the stability of wild-type and mutant receptor was observed, the K917R mutant PDGFRα was less ubiquitinated than wild-type PDGFRα. The internalization and trafficking of the receptor to early and late endosomes were not affected by the mutation, neither was the localization of the PDGFRα to Golgi. However, the K917R mutant PDGFRα showed delayed activation of PLC-γ and enhanced activation of STAT3. Functional assays showed that the mutation of K917 of PDGFRα decreased cell proliferation in response to PDGF-BB stimulation.

CONCLUSIONS

SUMOylation of PDGFRα decreases ubiquitination of the receptor and affects ligand-induced signaling and cell proliferation.

A functional intact SUMOylation machinery in Aspergillus flavus contributes to fungal and aflatoxin contamination of food

SUMO adducts occur in Aspergillus flavus, and are implicated in fungal biology, while the underlying mechanism and the SUMOylation apparatus components in this saprophytic food spoilage mould, remain undefined. Herein, genes encoding SUMOylation cascade enzymes in A. flavus, including two heterodimeric SUMO E1 activating enzymes, a unique SUMO E2 conjugating enzyme, and one of SUMO E3 ligases, were identified and functionally analyzed. Global SUMO adducts immunoassay, multiple morphological comparison, aflatoxin attributes test, fungal infection and transcriptomic analyses collectively revealed that: E1 and E2 were essential for intracellular SUMOylation, and contributed to both stress response and fungal virulence-related events, including sporulation, colonization, aflatoxins biosynthesis; the primary E3 in this fungus, AfSizA, might serve as the molecular linkage of SUMOylation pathway to fungal virulence rather than SUMOylation-mediated stress adaptation. These findings demonstrated that SUMOylation machinery in A. flavus was functionally intact and contributed to multiple pathobiological processes, hence offering ideas and targets to control food contamination by this mycotoxigenic fungus.

The Ubiquitin-like Proteins of Saccharomyces cerevisiae

In this review, we present a comprehensive list of the ubiquitin-like modifiers (Ubls) of Saccharomyces cerevisiae, a common model organism used to study fundamental cellular processes that are conserved in complex multicellular organisms, such as humans. Ubls are a family of proteins that share structural relationships with ubiquitin, and which modify target proteins and lipids. These modifiers are processed, activated and conjugated to substrates by cognate enzymatic cascades. The attachment of substrates to Ubls alters the various properties of these substrates, such as function, interaction with the environment or turnover, and accordingly regulate key cellular processes, including DNA damage, cell cycle progression, metabolism, stress response, cellular differentiation, and protein homeostasis. Thus, it is not surprising that Ubls serve as tools to study the underlying mechanism involved in cellular health. We summarize current knowledge on the activity and mechanism of action of the S. cerevisiae Rub1, Smt3, Atg8, Atg12, Urm1 and Hub1 modifiers, all of which are highly conserved in organisms from yeast to humans.

Sumoylation is Largely Dispensable for Normal Growth but Facilitates Heat Tolerance in Yeast

Numerous proteins are sumoylated in normally growing yeast and SUMO conjugation levels rise upon exposure to several stress conditions. We observe high levels of sumoylation also during early exponential growth and when nutrient-rich medium is used. However, we find that reduced sumoylation (∼75% less than normal) is remarkably well-tolerated, with no apparent growth defects under nonstress conditions or under osmotic, oxidative, or ethanol stresses. In contrast, strains with reduced activity of Ubc9, the sole SUMO conjugase, are temperature-sensitive, implicating sumoylation in the heat stress response, specifically. Aligned with this, a mild heat shock triggers increased sumoylation which requires functional levels of Ubc9, but likely also depends on decreased desumoylation, since heat shock reduces protein levels of Ulp1, the major SUMO protease. Furthermore, we find that a ubc9 mutant strain with only ∼5% of normal sumoylation levels shows a modest growth defect, has abnormal genomic distribution of RNA polymerase II (RNAPII), and displays a greatly expanded redistribution of RNAPII after heat shock. Together, our data implies that SUMO conjugations are largely dispensable under normal conditions, but a threshold level of Ubc9 activity is needed to maintain transcriptional control and to modulate the redistribution of RNAPII and promote survival when temperatures rise.

SUMOylation of SYNJ2BP-COX16 promotes breast cancer progression through DRP1-mediated mitochondrial fission

Treatments targeting oncogenic fusion proteins are notable examples of successful drug development. Abnormal splicing of genes resulting in fusion proteins is a critical driver of various tumors, but the underlying mechanism remains poorly understood. Here, we show that SUMOylation of the fusion protein Synaptojanin 2 binding protein-Cytochrome-c oxidase 16 (SYNJ2BP-COX16) at K107 induces mitochondrial fission in breast cancer and that the K107 site regulates SYNJ2BP-COX16 mitochondrial subcellular localization. Compared with a non-SUMOylated K107R mutant, wild-type SYNJ2BP-COX16 contributed to breast cancer cell proliferation and metastasis in vivo and in vitro by increasing adenosine triphosphate (ATP) production and cytochrome-c oxidase (COX) activity. SUMOylated SYNJ2BP-COX16 recruits dynamin-related protein 1 (DRP1) to the mitochondria to promote ubiquitin-conjugating enzyme 9 (UBC9) binding to DRP1, enhance SUMOylation of DRP1 and phosphorylation of DRP1 at S616, and then induce mitochondrial fission. Moreover, Mdivi-1, an inhibitor of DRP1 phosphorylation, decreased the localization of DRP1 in mitochondria, and prevents SYNJ2BP-COX16 induced mitochondrial fission, cell proliferation and metastasis. Based on these data, SYNJ2BP-COX16 promotes breast cancer progression through the phosphorylation of DRP1 and subsequent induction of mitochondrial fission, indicating that SUMOylation at the K107 residue of SYNJ2BP-COX16 is a novel potential treatment target for breast cancer.

OUP accepted manuscript

Tight control of gene expression networks required for adipose tissue formation and plasticity is essential for adaptation to energy needs and environmental cues. However, the mechanisms that orchestrate the global and dramatic transcriptional changes leading to adipocyte differentiation remain to be fully unraveled. We investigated the regulation of nascent transcription by the sumoylation pathway during adipocyte differentiation using SLAMseq and ChIPseq. We discovered that the sumoylation pathway has a dual function in differentiation; it supports the initial downregulation of pre-adipocyte-specific genes, while it promotes the establishment of the mature adipocyte transcriptional program. By characterizing endogenous sumoylome dynamics in differentiating adipocytes by mass spectrometry, we found that sumoylation of specific transcription factors like PPARγ/RXR and their co-factors are associated with the transcription of adipogenic genes. Finally, using RXR as a model, we found that sumoylation may regulate adipogenic transcription by supporting the chromatin occurrence of transcription factors. Our data demonstrate that the sumoylation pathway supports the rewiring of transcriptional networks required for formation of functional adipocytes. This study also provides the scientists in the field of cellular differentiation and development with an in-depth resource of the dynamics of the SUMO-chromatin landscape, SUMO-regulated transcription and endogenous sumoylation sites during adipocyte differentiation.