Protein SUMOylation is a dynamic post-translational modification that regulates numerous cellular processes, including DNA repair, transcription, and proteostasis. SUMO modifiers are conjugated to lysine residues on substrate proteins via a conserved enzymatic cascade and can form diverse chain architectures that encode specific cellular outcomes. The identification of SUMOylated proteins and their modification sites has historically been challenging due to the low abundance of SUMOylation and the complexity of SUMO remnants after proteolysis. Recent advances in proteomics have led to the development of enrichment strategies and mass spectrometry (MS)-based methods that now enable the site-specific mapping of SUMO modifications. This chapter provides an overview of the biological roles and structural diversity of SUMOylation, and presents an MS-based workflow designed to identify SUMOylation sites with high specificity and depth. These tools offer new opportunities to dissect the SUMO-modified proteome in health and disease.

SUMOylation is a post-translational modification regulating protein localization, stability, and activity, with effects varying depending on the conjugated SUMO protein and type of SUMOylation. To determine how enhanced SUMOylation affects protein localization, we fused ZNF, a SUMOylation tag derived from SUMO E3 ligase ZNF451 that biases substrates toward SUMO2/3, to the GFP-binding nanobody vhhGFP4 (VHH), creating VHH-ZNF to drive SUMOylation of GFP-tagged substrates in trans. In vitro, VHH-ZNF increased SUMO2/3 modification of p53-GFP, preferentially generating polySUMO2 chains at the canonical K386 site. In HEK293 cells co-expressing p53-GFP and VHH-ZNF, immunoblotting and proteomics confirmed increased SUMO2/3 conjugation of p53 at K386. Fluorescence microscopy analyses revealed that SUMOylated p53 transitions from a diffuse nuclear distribution to SUMO-positive nuclear foci that partially overlap with promyelocytic leukemia (PML) and, less so, to 53BP1 nuclear bodies. Overall, we developed a method to increase the SUMOylation of GFP-tagged proteins and to visualize SUMOylation-dependent re-localization in cells.

Altered iron homeostasis has long been implicated in Parkinson's disease (PD), although the mechanisms have not been clear. Given the critical role of PD-related activating variants in leucine-rich repeat protein kinase 2 (LRRK2) within membrane trafficking pathways, we examined the impact of the homozygous variant LRRK2G2019S on iron homeostasis within the RAW264.7 mouse macrophage cell line with high iron capacity. Proteomics analysis revealed a dysregulation of iron-related proteins in steady state, with highly elevated levels of ferritin light chain (FTL1) and a reduction of ferritin heavy chain (FTH1). LRRK2G2019S mutant cells showed efficient ferritinophagy upon iron chelation, but upon iron overload, there was a near-complete block in the degradation of the ferritinophagy adaptor NCOA4. These conditions led to an accumulation of phosphorylated Rab8 (RAB8A) at the plasma membrane, which is selectively inhibited by LRRK type II kinase inhibitors. Iron overload then led to increased oxidative stress and ferroptotic cell death. These data implicate LRRK2 as a key regulator of iron homeostasis and point to the need for an increased focus on the mechanisms of iron dysregulation in PD.

SUMOylation is a posttranslational modification that regulates multiple aspects of protein biology, including the activity of transcription factors such as p53. Although strategies exist to decrease protein SUMOylation in a targeted manner, options are limited to increase SUMOylation in a protein-specific manner. Here, we developed a strategy to induce SUMOylation of a target protein relying on its genetic fusion to a 32-residue tag termed ZNF and composed of the SUMO E3 module of ZNF451. Through in vitro and cell-based assays, we establish that this SUMOylation tag promotes robust poly/multi-SUMOylation of p53, used as a model substrate, with a strong preference for SUMO2/3 as compared to SUMO1. Mass spectrometry experiments performed on transfected HEK293 cells stably expressing a modified form of SUMO3 indicate that lysine 386, the main SUMOylation acceptor site of p53, is the primary target of ZNF-mediated SUMOylation. Increased SUMOylation represses p53 transcriptional activity in luciferase reporter assays, a result compatible with the general repressive effects of SUMOylation on transcription factor activity. Finally, fusion of ZNF to HSF1 and DNMT3A also increase their SUMOylation level, showcasing that ZNF could potentially be used to promote the SUMOylation of a broad range of proteins implicated in DNA metabolism. Overall, this strategy will facilitate the investigation of the impact of increased SUMOylation on specific protein substrates.

The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity, and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often requiring exogenous gene expression in cells and immunoaffinity purification of SUMO-remnant peptides following tryptic digestion. Previously, an antibody was developed to enrich tryptic peptides containing the remnant NQTGG on the receptor lysine, although the specifics of the structural interaction motif remained unclear. This study integrates de novo sequencing, intact mass spectrometry, cross-linking mass spectrometry, and molecular docking to elucidate the structural interaction motifs of a SUMO-remnant antibody. Additional cross-linking experiments were performed using SUMOylated peptides and high-field asymmetric waveform ion mobility spectrometry (FAIMS) to enhance the sensitivity and confirm interactions at the paratope interface. This study establishes a robust framework for characterizing antibody-antigen interactions, offering valuable insights into the structural basis of SUMO-remnant peptide recognition.

Protein inhibitor of activated STAT (PIAS) proteins are E3 SUMO ligases playing important roles in protein stability and signaling transduction pathways. PIAS proteins are overexpressed in the triple-negative breast cancer cell line MDA-MB-231, and PIAS knockout (KO) results in a reduction in cell proliferation and cell arrest in the S phase. However, the molecular mechanisms underlying PIAS functions in cell proliferation and cell cycle remain largely unknown. Here, we used quantitative SUMO proteomics to explore the regulatory role of PIAS SUMO E3 ligases upon CRISPR/Cas9 KO of individual PIAS. A total of 1422 sites were identified, and around 10% of SUMO sites were regulated following KO of one or more PIAS genes. We identified protein substrates that were either specific to individual PIAS ligase or regulated by several PIAS ligases. Ki-67 and TOP2A, which are involved in cell proliferation and epithelial-to-mesenchymal transition, are SUMOylated at several lysine residues by all PIAS ligases, suggesting a level of redundancy between these proteins. Confocal microscopy and biochemical experiments revealed that SUMOylation regulated TOP2A protein stability, while this modification is involved in the recruitment of Ki-67 nucleolar proteins containing the SUMO interacting motif. These results provide novel insights into both the redundant and specific regulatory mechanisms of cell proliferation and cell cycle mediated by PIAS SUMO E3 ligases.

The modification of proteins by the addition of ubiquitin and other ubiquitin-like proteins (UBLs) is involved in a wide range of cellular processes including cell cycle progression, the DNA damage response, endocytosis, cell signalling, autophagy and protein quality control. The UBL family comprises more than a dozen structurally related members, with ubiquitin, small ubiquitin-like modifier (SUMO) proteins, NEDD8, ISG15 and FAT10 being the most commonly known. Each UBL is associated with a distinct set of enzymes that alter the architecture and fate of their cognate proteins. UBL-conjugating enzymes add one or more UBLs to lysine and non-lysine acceptor sites on their target proteins, forming a complex distribution of monomeric and polymeric modifications. Different approaches and strategies are available to identify the sites of UBL modification, the types of modification and their dynamics upon various cellular stimuli; these techniques can decipher the complex architecture of UBL substrates and expand our understanding of UBL functions and their importance in cellular homeostasis and human diseases. This Primer covers the current methods for identifying UBL substrates, their modification sites and UBL chain linkages, and describes where the application of these methods can be used to gain biological insights into UBL functions.

The protein inhibitor of activated STAT1 (PIAS1) is an E3 SUMO ligase that plays important roles in various cellular pathways. Increasing evidence shows that PIAS1 is overexpressed in various human malignancies, including prostate and lung cancers. Here we used quantitative SUMO proteomics to identify potential substrates of PIAS1 in a system-wide manner. We identified 983 SUMO sites on 544 proteins, of which 62 proteins were assigned as putative PIAS1 substrates. In particular, vimentin (VIM), a type III intermediate filament protein involved in cytoskeleton organization and cell motility, was SUMOylated by PIAS1 at Lys-439 and Lys-445 residues. VIM SUMOylation was necessary for its dynamic disassembly and cells expressing a non-SUMOylatable VIM mutant showed a reduced level of migration. Our approach not only enables the identification of E3 SUMO ligase substrates but also yields valuable biological insights into the unsuspected role of PIAS1 and VIM SUMOylation on cell motility.

Cyanobacteria are the oldest known life form inhabiting Earth and the only prokaryotes capable of performing oxygenic photosynthesis. Synechocystis sp. PCC 6803 (Synechocystis) is a model cyanobacterium used extensively in research on photosynthesis and environmental adaptation. Posttranslational protein modification by lysine acetylation plays a critical regulatory role in both eukaryotes and prokaryotes; however, its extent and function in cyanobacteria remain unexplored. Herein, we performed a global acetylome analysis on Synechocystis through peptide prefractionation, antibody enrichment, and high accuracy LC-MS/MS analysis; identified 776 acetylation sites on 513 acetylated proteins; and functionally categorized them into an interaction map showing their involvement in various biological processes. Consistent with previous reports, a large fraction of the acetylation sites are present on proteins involved in cellular metabolism. Interestingly, for the first time, many proteins involved in photosynthesis, including the subunits of phycocyanin (CpcA, CpcB, CpcC, and CpcG) and allophycocyanin (ApcA, ApcB, ApcD, ApcE, and ApcF), were found to be lysine acetylated, suggesting that lysine acetylation may play regulatory roles in the photosynthesis process. Six identified acetylated proteins associated with photosynthesis and carbon metabolism were further validated by immunoprecipitation and Western blotting. Our data provide the first global survey of lysine acetylation in cyanobacteria and reveal previously unappreciated roles of lysine acetylation in the regulation of photosynthesis. The provided data set may serve as an important resource for the functional analysis of lysine acetylation in cyanobacteria and facilitate the elucidation of the entire metabolic networks and photosynthesis process in this model cyanobacterium.

Protein phosphorylation on serine, threonine, and tyrosine (Ser/Thr/Tyr) is well established as a key regulatory posttranslational modification used in signal transduction to control cell growth, proliferation, and stress responses. However, little is known about its extent and function in diatoms. Phaeodactylum tricornutum is a unicellular marine diatom that has been used as a model organism for research on diatom molecular biology. Although more than 1000 protein kinases and phosphatases with specificity for Ser/Thr/Tyr residues have been predicted in P. tricornutum, no phosphorylation event has so far been revealed by classical biochemical approaches. Here, we performed a global phosphoproteomic analysis combining protein/peptide fractionation, TiO(2) enrichment, and LC-MS/MS analyses. In total, we identified 264 unique phosphopeptides, including 434 in vivo phosphorylated sites on 245 phosphoproteins. The phosphorylated proteins were implicated in the regulation of diverse biological processes, including signaling, metabolic pathways, and stress responses. Six identified phosphoproteins were further validated by Western blotting using phospho-specific antibodies. The functions of these proteins are discussed in the context of signal transduction networks in P. tricornutum. Our results advance the current understanding of diatom biology and will be useful for elucidating the phosphor-relay signaling networks in this model diatom.

Bcl2-associated athanogene 3 (BAG3), a member of the BAG family of co-chaperones, plays a critical role in regulating apoptosis, development, cell motility, autophagy, and tumor metastasis and in mediating cell adaptive responses to stressful stimuli. BAG3 carries a BAG domain, a WW domain, and a proline-rich repeat (PXXP), all of which mediate binding to different partners. To elucidate BAG3's interaction network at the molecular level, we employed quantitative immunoprecipitation combined with knockdown and human proteome microarrays to comprehensively profile the BAG3 interactome in humans. We identified a total of 382 BAG3-interacting proteins with diverse functions, including transferase activity, nucleic acid binding, transcription factors, proteases, and chaperones, suggesting that BAG3 is a critical regulator of diverse cellular functions. In addition, we characterized interactions between BAG3 and some of its newly identified partners in greater detail. In particular, bioinformatic analysis revealed that the BAG3 interactome is strongly enriched in proteins functioning within the proteasome-ubiquitination process and that compose the proteasome complex itself, suggesting that a critical biological function of BAG3 is associated with the proteasome. Functional studies demonstrated that BAG3 indeed interacts with the proteasome and modulates its activity, sustaining cell survival and underlying resistance to therapy through the down-modulation of apoptosis. Taken as a whole, this study expands our knowledge of the BAG3 interactome, provides a valuable resource for understanding how BAG3 affects different cellular functions, and demonstrates that biologically relevant data can be harvested using this kind of integrated approach.

MicroRNAs (miRNAs) are small noncoding RNAs, approximately 22 nucleotides in length, found in diverse organisms. They have emerged in recent years as key regulators of a broad spectrum of cellular functions. miRNAs regulate biological processes by inducing translational inhibition and degradation of their target mRNAs through base pairing to partially or fully complementary sites. In the field of miRNA research, the identification of the targets of individual miRNAs is of utmost importance. Our understanding of the molecular mechanisms by which individual miRNAs modulate cellular functions will remain incomplete until a full set of miRNA targets is identified and validated. Since a miRNA may regulate many of its targets at the translational level without affecting mRNA abundance, proteomic methods are best suited for revealing the full spectrum of miRNA targets. Quantitative proteomics is emerging as a powerful toolbox for identifying miRNA targets and for quantifying the contribution of translational repression by miRNAs. In this review, the authors summarize the quantitative proteomic approaches that have been employed for identification of miRNA targets and discuss current challenges as well as possible ways of overcoming them.

Signal transducers and activators of transcription 3 (Stat3) has been reported to be involved in the pathogenesis of various human diseases and is constitutively active in human multiple myeloma (MM) U266 cells. The Stat3-regulated mechanisms involved in these processes, however, are not fully defined. To further understand the regulation of Stat3 activity, we performed a systematic proteomic analysis of Stat3 interacting proteins in U266 cells. This analysis, termed quantitative immunoprecipitation combined with knockdown (QUICK), combines RNAi, stable isotope labeling with amino acids in cell culture (SILAC), immunoprecipitation, and quantitative MS. As a result, quantitative mass spectrometry analysis allowed us to distinguish specific Stat3 interacting proteins from background proteins and led to the identification of a total of 38 proteins. Three Stat3 interacting proteins - 14-3-3ζ, PRKCB and Hsp90 - were further confirmed by reciprocal co-immunoprecipitations and surface plasmon resonance (SPR) analysis. Our results therefore not only uncover a number of Stat3 interacting proteins that possess a variety of cellular functions, but also provide new insight into the mechanisms that regulate Stat3 activity and function in MM cells.

Substantial evidence indicates that microRNA-21 (miR-21) is a key oncomiR in carcinogenesis and is significantly elevated in multiple myeloma (MM). In this study, we explored the role of miR-21 in human MM cells and searched for miR-21 targets. By knocking down the expression of endogenous miR-21 in U266 myeloma cells, we observed reduced growth, an arrested cell cycle, and increased apoptosis. To further understand its molecular mechanism in the pathogenesis of MM, we employed a SILAC (stable isotope labeling by amino acids in cell culture)-based quantitative proteomic strategy to systematically identify potential targets of miR-21. In total, we found that the expression of 178 proteins was up-regulated significantly by miR-21 inhibition, implying that they could be potential targets of miR-21. Among these, the protein inhibitor of activated STAT3 (PIAS3) was confirmed as a direct miR-21 target by Western blotting and reporter gene assays. We further demonstrated that miR-21 enhances the STAT3-dependent signal pathway by inhibiting the function of PIAS3 and that down-regulation of PIAS3 contributes to the oncogenic function of miR-21. This elucidation of the role of PIAS3 in the miR-21-STAT3 positive regulatory loop not only may shed light on the molecular basis of the biological effects of miR-21 observed in MM cells but also has direct implications for the development of novel anti-MM therapeutic strategies.

The 14-3-3 proteins are a family of regulatory signaling molecules that interact with other proteins in a phosphorylation-dependent manner and function as adapter or scaffold proteins in signal transduction pathways. One family member, 14-3-3ζ, is believed to function in cell signaling, cycle control, and apoptotic death. A systematic proteomic analysis done in our laboratory has identified signal transducers and activators of transcription 3 (Stat3) as a novel 14-3-3ζ interacting protein. Following our initial finding, in this study, we provide evidence that 14-3-3ζ interacts physically with Stat3. We further demonstrate that phosphorylation of Stat3 at Ser727 is vital for 14-3-3ζ interaction and mutation of Ser727 to Alanine abolished 14-3-3ζ/Stat3 association. Inhibition of 14-3-3ζ protein expression in U266 cells inhibited Stat3 Ser727 phosphorylation and nuclear translocation, and decreased both Stat3 DNA binding and transcriptional activity. Moreover, 14-3-3ζ is involved in the regulation of protein kinase C (PKC) activity and 14-3-3ζ binding to Stat3 protects Ser727 dephosphorylation from protein phosphatase 2A (PP2A). Taken together, our findings support the model that multiple signaling events impinge on Stat3 and that 14-3-3ζ serves as an essential coordinator for different pathways to regulate Stat3 activation and function in MM cells.