GO:0036048 protein desuccinylation: Mechanism, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0036048 (protein desuccinylation) is the enzymatic removal of a succinyl group (CO-CH2-CH2-CO) from a lysine residue in a peptide or protein.
• SIRT5 is the principal mammalian desuccinylase, and its activity directly rewires mitochondrial and cytosolic metabolic pathways.
• Desuccinylation is a dynamic post-translational modification that controls enzyme activity, protein stability, localization, and protein-protein interactions.
• SIRT5-mediated desuccinylation of substrates such as ALDH2, TBK1, RAB7A, ME2, CPT2, and the PDCoV M protein links this process to liver injury, inflammation, ageing, neurodegeneration, cancer, and viral infection.
• Dysregulated protein desuccinylation contributes to oxidative stress, impaired autophagy, metabolic reprogramming, and inflammatory signaling in multiple human diseases.
• CRISPR knockout, point-mutation, knock-in, and overexpression models are essential tools for dissecting the causal role of desuccinylation writers, erasers, and substrate sites.
Description
Protein desuccinylation (GO:0036048) is a biological process defined as the removal of a succinyl group (CO-CH2-CH2-CO) from a residue in a peptide or protein. This reversible post-translational modification is emerging as a central regulatory layer in cell metabolism, stress responses, and disease pathogenesis. The reaction is catalyzed by desuccinylase enzymes, most prominently the NAD+-dependent sirtuin SIRT5, which was shown to remove succinyl groups from lysine residues across diverse metabolic pathways. Because succinylation adds a bulky, negatively charged moiety to lysine, its removal can switch enzyme activity on or off, alter protein stability, and redirect subcellular trafficking. For researchers, GO:0036048 matters because it sits at the intersection of metabolism, epigenetics, and signal transduction. SIRT5-mediated desuccinylation of ALDH2 protects against acetaminophen-induced acute liver injury by alleviating mitochondrial oxidative stress, while desuccinylation of TBK1 regulates inflammatory responses in macrophages during sepsis and safeguards against primate skeletal muscle ageing. In cancer, SIRT5-mediated ME2 desuccinylation promotes tumor growth by enhancing mitochondrial respiration. These examples illustrate that protein desuccinylation is not a housekeeping reaction but a context-dependent regulatory node with direct therapeutic implications. The process is also hijacked by pathogens: SIRT5-mediated desuccinylation of the porcine deltacoronavirus M protein drives pexophagy to enhance viral proliferation. In neurodegeneration, desuccinylation of RAB7A protects against cadmium-induced Alzheimer's disease-like pathology by restoring autophagic flux. Together, these findings establish GO:0036048 as a high-priority target for functional genomics, drug discovery, and CRISPR-based disease modeling.
protein desuccinylation At A Glance
| GO ID | GO:0036048 |
|---|---|
| GO term | protein desuccinylation |
| Ontology | biological_process |
| Synonym | none |
| Definition | The removal of a succinyl group (CO-CH2-CH2-CO) from a residue in a peptide or protein. |
| Major function | Reverses lysine succinylation to regulate enzyme activity, protein stability, localization, and interactions. |
| Primary enzyme | SIRT5 (NAD+-dependent sirtuin desuccinylase) |
| Substrate examples | ALDH2, TBK1, RAB7A, ME2, CPT2, PDCoV M protein |
| Cellular context | Mitochondria, cytosol, peroxisomes, and pathogen-containing vesicles |
| Associated diseases | Acute liver injury, sepsis, skeletal muscle ageing, Alzheimer's-like pathology, cancer, diabetic cardiomyopathy, viral infection |
What Is GO:0036048?
Protein desuccinylation (GO:0036048) is the enzymatic removal of a succinyl group (CO-CH2-CH2-CO) from a residue in a peptide or protein. In practice, this typically means the cleavage of the amide bond between a succinyl moiety and the epsilon-amino group of a lysine side chain, regenerating an unmodified lysine. The reaction is catalyzed by desuccinylases such as SIRT5 and is coupled to NAD+ hydrolysis. Because succinylation neutralizes lysine's positive charge and introduces a large anionic group, its removal can profoundly change protein conformation, catalytic activity, interaction surfaces, and subcellular localization.
Why Is protein desuccinylation Important in Cell Biology?
Protein desuccinylation is important because it provides a reversible, enzyme-controlled switch that connects cellular metabolism to signaling, stress resistance, and immune defense. SIRT5-mediated desuccinylation of ALDH2 reduces mitochondrial oxidative stress after acetaminophen overdose, and desuccinylation of TBK1 modulates macrophage inflammation in sepsis and protects primate skeletal muscle from ageing. In cancer, ME2 desuccinylation enhances mitochondrial respiration and supports tumor growth, while CPT2 desuccinylation improves fatty acid metabolism in diabetic cardiomyopathy. The pathway is also exploited by viruses, as desuccinylation of the PDCoV M protein promotes pexophagy and viral proliferation. Understanding GO:0036048 therefore offers mechanistic insight into a broad spectrum of human diseases and identifies druggable nodes for therapeutic intervention.
• Controls mitochondrial oxidative stress and cell survival through ALDH2 desuccinylation in acute liver injury.
• Regulates innate immune and inflammatory signaling via TBK1 desuccinylation in sepsis.
• Protects against age-related skeletal muscle decline through TBK1 desuccinylation in primates.
• Restores autophagic flux and protects against cadmium-induced Alzheimer's-like pathology via RAB7A desuccinylation.
• Promotes cancer growth by enhancing mitochondrial respiration through ME2 desuccinylation.
• Improves cardiomyocyte fatty acid metabolism and ameliorates cardiac lipotoxicity via CPT2 desuccinylation.
• Is hijacked by porcine deltacoronavirus to drive pexophagy and enhance viral proliferation.
• Provides a mechanistic link between lysine succinylation dynamics and diverse metabolic pathways.
• Offers candidate biomarkers and therapeutic targets for metabolic, inflammatory, and neurodegenerative diseases.
• Enables functional validation of desuccinylation sites using CRISPR-based genome editing.
What Happens During protein desuccinylation?
Recognition of succinylated lysine substrates
In simple terms: The enzyme first finds and binds a protein that carries a succinyl tag on a lysine residue.
Desuccinylases such as SIRT5 recognize substrate proteins bearing succinylated lysine residues. SIRT5-mediated desuccinylation impacts diverse metabolic pathways, indicating broad substrate recognition across mitochondrial and cytosolic compartments. Substrates including ALDH2, TBK1, RAB7A, ME2, CPT2, and the PDCoV M protein are targeted in a context-dependent manner. The interaction between SIRT5 and its substrates is often regulated by cellular metabolic state and NAD+ availability.
NAD+-dependent catalytic removal of the succinyl group
In simple terms: The enzyme uses NAD+ as a cofactor to chemically cut the succinyl group off the lysine.
SIRT5 catalyzes the removal of the succinyl group (CO-CH2-CH2-CO) from lysine in an NAD+-dependent reaction. This enzymatic activity reverses lysine succinylation and regenerates the unmodified lysine side chain. The reaction is part of the broader sirtuin family of deacylases, but SIRT5 shows specificity for succinyl and other acidic acyl groups. Loss of SIRT5 activity leads to accumulation of succinylated proteins and altered metabolic flux.
Functional consequences for substrate proteins
In simple terms: Once the succinyl tag is removed, the target protein changes its behavior, such as becoming more active or more stable.
Desuccinylation can alter enzyme activity, protein stability, and subcellular localization. For example, SIRT5-mediated desuccinylation of ALDH2 alleviates mitochondrial oxidative stress following acetaminophen-induced acute liver injury. Desuccinylation of TBK1 regulates inflammatory responses in macrophages during sepsis and safeguards against primate skeletal muscle ageing. RAB7A desuccinylation restores autophagic flux and protects against cadmium-induced Alzheimer's disease-like pathology. ME2 desuccinylation promotes cancer growth by enhancing mitochondrial respiration, and CPT2 desuccinylation improves cardiomyocyte fatty acid metabolism in diabetic cardiomyopathy.
Downstream pathway rewiring
In simple terms: Removing the succinyl tag can switch entire cellular pathways on or off.
Protein desuccinylation impacts diverse metabolic pathways, including mitochondrial respiration, fatty acid oxidation, and oxidative stress responses. In cancer, ME2 desuccinylation enhances mitochondrial respiration to support tumor growth. In diabetic cardiomyopathy, CPT2 desuccinylation improves fatty acid metabolism and ameliorates cardiac lipotoxicity. In viral infection, desuccinylation of the PDCoV M protein drives pexophagy to enhance viral proliferation. These examples demonstrate that GO:0036048 is a central node connecting protein modification to pathway-level outcomes.
Crosstalk with other post-translational modifications
In simple terms: Succinylation and desuccinylation compete with other chemical tags on the same lysine, so the balance matters.
Lysine residues can carry multiple acyl modifications, and desuccinylation by SIRT5 is part of a dynamic equilibrium that includes succinylation, acetylation, and other acylation events. The interplay between these modifications determines the final functional state of a protein. SIRT5-mediated desuccinylation of substrates such as ALDH2, TBK1, and RAB7A occurs in physiological and pathological contexts where this balance is perturbed. Understanding crosstalk is essential for interpreting experiments that manipulate desuccinylase activity.
Key Genes Involved in GO:0036048 protein desuccinylation
The following genes and proteins are experimentally validated participants in or regulators of protein desuccinylation (GO:0036048).
| Gene | Major Role | Research Relevance |
|---|---|---|
| SIRT5 | Primary NAD+-dependent desuccinylase that removes succinyl groups from lysine residues | Central enzyme for studying GO:0036048; knockout and overexpression models reveal substrate specificity |
| ALDH2 | Mitochondrial aldehyde dehydrogenase; desuccinylation by SIRT5 alleviates oxidative stress | Target in acetaminophen-induced acute liver injury models |
| TBK1 | Kinase involved in innate immune signaling; desuccinylation regulates inflammatory responses | Studied in sepsis macrophage models and primate skeletal muscle ageing |
| RAB7A | Small GTPase regulating autophagic flux; desuccinylation restores autophagy | Modeled in cadmium-induced Alzheimer's disease-like pathology |
| ME2 | Malic enzyme 2; desuccinylation enhances mitochondrial respiration | Cancer growth studies and metabolic flux analysis |
| CPT2 | Carnitine palmitoyltransferase 2; desuccinylation improves fatty acid oxidation | Diabetic cardiomyopathy and cardiac lipotoxicity models |
| PDCoV M protein | Viral membrane protein; desuccinylation drives pexophagy | Viral proliferation studies and host-pathogen interaction models |
| NAD+ | Essential cofactor for SIRT5 catalytic activity | Metabolic regulation and sirtuin activity assays |
| Succinyl-CoA | Metabolic donor of succinyl groups for lysine succinylation | Metabolic labeling and succinylome profiling |
| SIRT5 substrates (global) | Diverse metabolic enzymes modified by desuccinylation | Succinylome and proteomic screens |
| Mitochondrial respiration complex proteins | Downstream effectors of desuccinylation in energy metabolism | Seahorse and respirometry studies |
| Autophagy machinery proteins | Regulated by desuccinylation to control autophagic flux | Autophagy flux assays and imaging |
| Inflammatory signaling proteins | Modulated by desuccinylation in macrophages | Sepsis and inflammation models |
| Muscle ageing-related proteins | Targets of SIRT5 in primate skeletal muscle | Ageing and muscle physiology studies |
| Cardiac metabolic enzymes | Regulated by desuccinylation in cardiomyocytes | Diabetic cardiomyopathy models |
| Viral replication proteins | Hijack desuccinylation for viral proliferation | Antiviral target discovery |
| Oxidative stress response proteins | Protected by desuccinylation in liver injury | Acute liver injury models |
How Is protein desuccinylation Regulated?
Protein desuccinylation is regulated at multiple levels. The availability of NAD+ directly controls SIRT5 catalytic activity, linking desuccinylation to cellular energy status. Substrate accessibility and compartmentalization also influence the reaction, as SIRT5 acts on mitochondrial, cytosolic, and peroxisomal targets. In pathological contexts, desuccinylation is modulated by stress signals: acetaminophen-induced liver injury alters SIRT5-mediated ALDH2 desuccinylation, cadmium exposure affects RAB7A desuccinylation, and sepsis changes TBK1 desuccinylation in macrophages. Viral infection can also redirect desuccinylation to viral proteins, as shown for the PDCoV M protein. These layers of regulation make GO:0036048 responsive to metabolic, inflammatory, and environmental cues.
protein desuccinylation and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| ALDH2 | Acetaminophen-induced acute liver injury | SIRT5 knockout or ALDH2 desuccinylation-site mutant hepatocytes |
| TBK1 | Sepsis and skeletal muscle ageing | Macrophage-specific SIRT5 knockout and primate muscle ageing models |
| RAB7A | Cadmium-induced Alzheimer's disease-like pathology | Neuronal SIRT5 knockout and RAB7A desuccinylation-site knock-in |
| ME2 | Cancer growth and mitochondrial respiration | Cancer cell lines with SIRT5 knockout or ME2 desuccinylation-site mutation |
| CPT2 | Diabetic cardiomyopathy and cardiac lipotoxicity | Cardiomyocyte-specific SIRT5 overexpression and CPT2 mutant models |
Protein desuccinylation in liver injury and oxidative stress
SIRT5-mediated desuccinylation of ALDH2 alleviates mitochondrial oxidative stress following acetaminophen-induced acute liver injury. This finding positions GO:0036048 as a protective mechanism in hepatotoxicity and suggests that enhancing desuccinylation could reduce liver damage. The study provides direct evidence that a single desuccinylation event can determine cell survival under oxidative stress.
Protein desuccinylation in inflammation, sepsis, and ageing
Desuccinylation of TBK1 by SIRT5 regulates inflammatory responses of macrophages in sepsis and safeguards against primate skeletal muscle ageing. These studies link GO:0036048 to innate immunity and age-related tissue decline. They also suggest that modulating SIRT5 activity could influence inflammatory disease outcomes and muscle health.
Protein desuccinylation in neurodegeneration and autophagy
SIRT5-mediated desuccinylation of RAB7A protects against cadmium-induced Alzheimer's disease-like pathology by restoring autophagic flux. This connects GO:0036048 to autophagic dysfunction, a hallmark of neurodegenerative disease. The work supports the idea that desuccinylation is a therapeutic node for autophagy-related neurodegeneration.
Protein desuccinylation in cancer and metabolic disease
SIRT5-mediated ME2 desuccinylation promotes cancer growth by enhancing mitochondrial respiration, while CPT2 desuccinylation improves cardiomyocyte fatty acid metabolism and ameliorates cardiac lipotoxicity in diabetic cardiomyopathy. These findings demonstrate that GO:0036048 can be either oncogenic or protective depending on context. They highlight the need for tissue-specific and substrate-specific targeting strategies.
From protein desuccinylation-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does SIRT5-mediated desuccinylation of ALDH2 protect against liver injury? | SIRT5 knockout mice or ALDH2 desuccinylation-site knock-in |
| Does TBK1 desuccinylation regulate macrophage inflammation in sepsis? | Macrophage-specific SIRT5 knockout and TBK1 point-mutant knock-in |
| Does RAB7A desuccinylation restore autophagic flux in neurodegeneration? | Neuronal SIRT5 knockout and RAB7A desuccinylation-site mutant |
| Does ME2 desuccinylation promote cancer growth? | Cancer cell lines with SIRT5 knockout or ME2 desuccinylation-site mutation |
| Does CPT2 desuccinylation improve fatty acid metabolism in cardiomyocytes? | Cardiomyocyte SIRT5 overexpression and CPT2 mutant knock-in |
| Does viral protein desuccinylation enhance pexophagy? | PDCoV M protein desuccinylation-site mutant and SIRT5 knockout cells |
How to Study the protein desuccinylation Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Mass spectrometry succinylome profiling | Global lysine succinylation sites and changes | Discovery of SIRT5 substrates and pathways |
| In vitro desuccinylation assay | Enzymatic removal of succinyl groups from peptides | Testing SIRT5 activity and substrate specificity |
| Western blot with anti-succinyllysine | Overall protein succinylation levels | Validating SIRT5 knockout or overexpression |
| Enzyme activity assay | Functional activity of desuccinylated substrate | ALDH2, ME2, CPT2 activity measurements |
| Autophagic flux assay | Autophagy induction and degradation | RAB7A desuccinylation studies |
| Seahorse respirometry | Mitochondrial respiration | ME2 desuccinylation and cancer metabolism |
| Inflammatory cytokine profiling | Macrophage inflammatory response | TBK1 desuccinylation in sepsis |
| CRISPR knockout/knock-in | Causal role of desuccinylation genes and sites | Functional validation in disease models |
Succinylome profiling by mass spectrometry
Mass spectrometry-based succinylome profiling identifies lysine residues that carry succinyl groups and quantifies changes upon desuccinylase manipulation. This approach has been used to map SIRT5-dependent desuccinylation across metabolic pathways. It is a discovery tool for identifying new substrates of GO:0036048.
Site-specific desuccinylation assays
Site-specific assays use synthetic succinylated peptides or recombinant proteins to measure desuccinylation kinetics in vitro. These assays can test the effect of SIRT5 mutations, NAD+ availability, and substrate sequence context. They provide direct biochemical evidence for GO:0036048 activity.
Functional assays for substrate activity and stability
Enzyme activity assays, protein stability measurements, and localization imaging are used to determine how desuccinylation affects substrate function. For example, ALDH2 activity and oxidative stress markers are measured after SIRT5 manipulation. Autophagic flux assays are used to assess RAB7A desuccinylation effects.
CRISPR-based genetic models
CRISPR knockout, point mutation, knock-in, and overexpression models enable causal testing of desuccinylation events. These models can be used in cell lines, primary cells, and animal models to link specific desuccinylation sites to disease phenotypes. They are essential for validating findings from proteomic screens.
How CRISPR Can Be Used to Study GO:0036048 protein desuccinylation
Knockout
CRISPR knockout of SIRT5 or substrate genes is used to abolish desuccinylation activity and observe downstream phenotypes. For example, SIRT5 knockout increases protein succinylation and alters metabolic flux. Knockout models are essential for establishing whether a desuccinylation event is required for a given biological process.
Point Mutation
CRISPR point mutation can substitute a specific lysine residue with arginine or another amino acid to block succinylation and desuccinylation at that site. This approach isolates the function of a single modification site without affecting other activities of the protein. It has been used to study ALDH2, RAB7A, and other substrates.
Knock-in
CRISPR knock-in can introduce tagged or reporter versions of desuccinylation substrates to track their localization, stability, and interactions. Tagged knock-in models enable live-cell imaging and biochemical purification of desuccinylated proteins. They are valuable for studying dynamic changes in GO:0036048 under physiological conditions.
Overexpression
CRISPR-mediated overexpression or cDNA-based overexpression of SIRT5 or substrate proteins is used to enhance desuccinylation and test gain-of-function phenotypes. Overexpression of SIRT5 can protect against oxidative stress or improve metabolic function in disease models. This approach complements knockout studies by providing bidirectional control of desuccinylation.
How EDITGENE Supports protein desuccinylation Research
Researchers studying protein desuccinylation-related genes often need to determine whether a candidate gene is causally involved in a specific disease or metabolic process. EDITGENE provides end-to-end CRISPR services to generate precisely engineered cell models that answer these questions.
Contact EDITGENE today to design your custom CRISPR model for protein desuccinylation research.
Frequently Asked Questions About protein desuccinylation
What is protein desuccinylation (GO:0036048)?
Protein desuccinylation is the removal of a succinyl group (CO-CH2-CH2-CO) from a residue in a peptide or protein, typically catalyzed by SIRT5.
What genes are involved in protein desuccinylation?
Key genes include SIRT5, ALDH2, TBK1, RAB7A, ME2, CPT2, and viral proteins such as the PDCoV M protein.
Which enzyme performs protein desuccinylation?
SIRT5 is the principal NAD+-dependent desuccinylase in mammals.
What diseases are linked to protein desuccinylation?
It is linked to acute liver injury, sepsis, skeletal muscle ageing, Alzheimer's-like pathology, cancer, diabetic cardiomyopathy, and viral infection.
How does SIRT5-mediated desuccinylation affect metabolism?
It impacts diverse metabolic pathways, including mitochondrial respiration, fatty acid oxidation, and oxidative stress responses.
What is the role of protein desuccinylation in cancer?
ME2 desuccinylation promotes cancer growth by enhancing mitochondrial respiration.
How is protein desuccinylation studied?
It is studied using succinylome mass spectrometry, in vitro desuccinylation assays, functional enzyme assays, and CRISPR models.
Can CRISPR be used to study protein desuccinylation?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are used to test the causal role of desuccinylation genes and sites.
What is the difference between succinylation and desuccinylation?
Succinylation adds a succinyl group to lysine, while desuccinylation removes it; the balance is controlled by enzymes such as SIRT5.
Why is protein desuccinylation important for drug discovery?
It offers druggable nodes for metabolic, inflammatory, neurodegenerative, and infectious diseases.
Conclusion
Protein desuccinylation (GO:0036048) is a reversible post-translational modification that removes succinyl groups from lysine residues, primarily through SIRT5. It regulates diverse metabolic pathways and is causally linked to liver injury, sepsis, ageing, neurodegeneration, cancer, diabetic cardiomyopathy, and viral infection. As a research target, it offers both mechanistic insight and therapeutic opportunities. CRISPR-based models are indispensable for dissecting the precise roles of desuccinylation enzymes and substrate sites. By combining knockout, point mutation, knock-in, and overexpression strategies with succinylome profiling and functional assays, researchers can move from correlation to causation in GO:0036048 biology.
References
- 1. Yu Q et al.. 2024. Sirtuin 5-Mediated Desuccinylation of ALDH2 Alleviates Mitochondrial Oxidative Stress Following Acetaminophen-Induced Acute Liver Injury.. Adv Sci (Weinh) 11(39):e2402710 PMID: 39159058
- 2. Li Z et al.. 2025. SIRT5-mediated desuccinylation of the porcine deltacoronavirus M protein drives pexophagy to enhance viral proliferation.. PLoS Pathog 21(5):e1013163 PMID: 40344161
- 3. Zhao Q et al.. 2025. SIRT5 safeguards against primate skeletal muscle ageing via desuccinylation of TBK1.. Nat Metab 7(3):556-573 PMID: 40087407
- 4. Deng P et al.. 2024. SIRT5-Mediated Desuccinylation of RAB7A Protects Against Cadmium-Induced Alzheimer's Disease-Like Pathology by Restoring Autophagic Flux.. Adv Sci (Weinh) 11(30):e2402030 PMID: 38837686
- 5. Park J et al.. 2013. SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways.. Mol Cell 50(6):919-30 PMID: 23806337
- 6. Teng P et al.. 2024. SIRT5-mediated ME2 desuccinylation promotes cancer growth by enhancing mitochondrial respiration.. Cell Death Differ 31(1):65-77 PMID: 38007551
- 7. Zhang X et al.. 2024. Desuccinylation of TBK1 by SIRT5 regulates inflammatory response of macrophages in sepsis.. Cell Rep 43(12):115060 PMID: 39673708
- 8. Wu M et al.. 2024. Sirt5 improves cardiomyocytes fatty acid metabolism and ameliorates cardiac lipotoxicity in diabetic cardiomyopathy via CPT2 de-succinylation.. Redox Biol 73:103184 PMID: 38718533
