GO:0016831 carboxy-lyase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0016831 carboxy-lyase activity (synonym: decarboxylase activity) catalyzes the nonhydrolytic addition or removal of a carboxyl group to or from a compound [1, 5].
• The term is a molecular_function in the Gene Ontology and covers enzymes such as ACOD1/IRG1, which produces itaconate from cis-aconitate [1, 3].
• Carboxy-lyases participate in immunity, inflammation, amino acid metabolism, heme biosynthesis, and chondrocyte matrix metabolism [1, 3, 5, 6, 7, 8].
• Dysregulated carboxy-lyase activity is linked to sepsis, microglial inflammatory responses, porphyria cutanea tarda, and other human porphyrias [3, 6, 8].
• ACOD1 is a central immune-responsive carboxy-lyase that links metabolism to immunity and is a candidate target in inflammatory disease [1, 3, 6].
• CRISPR knockout, point-mutation, knock-in, and overexpression models enable causal testing of carboxy-lyase genes in disease-relevant cells and animal models [1, 3, 6].
Description
GO:0016831 carboxy-lyase activity is a Gene Ontology molecular_function term defined as the catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound; its common synonym is decarboxylase activity [1, 5]. Carboxy-lyases are central to metabolic pathways because they interconvert carboxylated and decarboxylated metabolites without using water, thereby influencing carbon flux, immune signaling, and biosynthetic precursor pools [1, 3, 5]. The term is experimentally important because mutations or expression changes in carboxy-lyase enzymes can alter metabolite abundance and downstream cellular responses in human disease [3, 6, 8]. Researchers study carboxy-lyase activity to understand how cells produce signaling metabolites such as itaconate, how amino acid and heme pathways are controlled, and how inflammatory cells rewire metabolism [1, 3, 6, 8]. For example, immune-responsive gene 1 protein (IRG1, encoded by ACOD1) catalyzes itaconic acid production and links metabolism to immunity. Aconitate decarboxylase 1 (ACOD1) is also a mediator of polymicrobial sepsis and regulates microglial arginine metabolism and inflammatory responses [3, 6]. Because carboxy-lyase reactions are chemically diverse, the GO term groups enzymes acting on different substrates, including cis-aconitate, UDP-glucuronate, L-cysteinesulfinate, and porphyrinogens [1, 5, 7, 8]. This breadth makes GO:0016831 a useful annotation for functional genomics, CRISPR screening, and targeted metabolic studies [1, 3, 5, 6, 7, 8].
carboxy-lyase activity At A Glance
| GO ID | GO:0016831 |
|---|---|
| GO term | carboxy-lyase activity |
| Ontology | molecular_function |
| Synonym | decarboxylase activity |
| Definition | Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound |
| Major function | Nonhydrolytic carboxyl group transfer in metabolic reactions |
| Representative enzyme | ACOD1/IRG1, which converts cis-aconitate to itaconate |
| Related processes | Immunity, amino acid metabolism, heme biosynthesis, chondrocyte matrix metabolism |
| Disease relevance | Sepsis, inflammatory responses, porphyria cutanea tarda and other porphyrias |
What Is GO:0016831?
In simple terms, carboxy-lyase activity means an enzyme removes or adds a carboxyl group (COOH) without using water. The QuickGO definition states that GO:0016831 is the catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound, and the synonym decarboxylase activity reflects the most common direction of the reaction [1, 5]. This is a molecular_function term, so it describes what an enzyme does at the catalytic level rather than where it acts or which pathway it belongs to [1, 5].
Why Is carboxy-lyase activity Important in Cell Biology?
Carboxy-lyase activity matters because it controls the abundance of carboxylated metabolites that act as biosynthetic intermediates, signaling molecules, and disease biomarkers [1, 3, 5, 6, 7, 8]. The immune-responsive enzyme IRG1/ACOD1 uses carboxy-lyase chemistry to produce itaconate, linking cellular metabolism directly to immunity. ACOD1 has been implicated as a mediator of polymicrobial sepsis and as a regulator of microglial arginine metabolism and inflammatory responses, making carboxy-lyase activity a potential therapeutic node in inflammation [3, 6]. Inborn or acquired changes in carboxy-lyase enzymes also affect heme biosynthesis and are measured in human porphyrias. Thus, GO:0016831 provides a functional annotation that connects enzyme mechanism to physiology and disease [1, 3, 5, 6, 7, 8].
• Carboxy-lyases produce itaconate, an immunomodulatory metabolite derived from cis-aconitate by IRG1/ACOD1.
• ACOD1-mediated carboxy-lyase activity is a mediator of polymicrobial sepsis in preclinical models.
• ACOD1 regulates microglial arginine metabolism and inflammatory responses in the central nervous system.
• UDP-glucuronate carboxy-lyase activity is detectable in cultured chondrocytes and relates to matrix metabolism.
• L-cysteinesulfinate carboxy-lyase activity responds to dietary sulfate and cysteine levels in rat liver.
• Erythrocyte porphyrinogen carboxy-lyase activity is altered in porphyria cutanea tarda and other human porphyrias.
• The term supports functional annotation of metabolic enzymes in genome-scale CRISPR screens [1, 3, 5, 6, 7, 8].
• Carboxy-lyase reactions are nonhydrolytic, so they can be distinguished experimentally from hydrolases and oxidoreductases [1, 5].
• Histamine-related microcirculation studies illustrate the broader physiological impact of decarboxylation products.
• Because the term covers multiple substrates, substrate-specific assays are needed to assign enzyme function accurately [1, 5, 7, 8].
What Happens During carboxy-lyase activity?
Substrate binding and carboxyl group recognition
In simple terms: The enzyme first grabs the molecule that carries the carboxyl group.
Carboxy-lyase reactions begin when the enzyme binds a substrate containing a carboxyl group, such as cis-aconitate for ACOD1/IRG1. Substrate recognition determines which metabolite is converted and therefore which downstream pathway is affected [1, 5]. In cultured chondrocytes, UDP-glucuronate carboxy-lyase activity acts on UDP-glucuronate, showing that substrate specificity can be cell-type dependent. In rat liver, L-cysteinesulfinate carboxy-lyase activity acts on L-cysteinesulfinate and responds to dietary sulfate and cysteine.
Nonhydrolytic carboxyl removal or addition
In simple terms: The enzyme removes or adds the carboxyl group without using water.
The defining chemical event of GO:0016831 is nonhydrolytic addition or removal of a carboxyl group [1, 5]. This distinguishes carboxy-lyases from hydrolases that use water to cleave bonds [1, 5]. For IRG1/ACOD1, the reaction converts cis-aconitate to itaconate, a decarboxylation that supports immune signaling. Porphyrinogen carboxy-lyase activity similarly removes carboxyl groups during heme biosynthesis, and its measurement in erythrocytes is used in porphyria research.
Product formation and metabolic flux
In simple terms: The product is released and feeds into the next metabolic step.
After decarboxylation, the product can act as a signaling molecule or biosynthetic precursor [1, 3]. Itaconate produced by IRG1/ACOD1 links metabolism to immunity and can influence inflammatory responses. ACOD1 is a mediator of polymicrobial sepsis, indicating that the product of this carboxy-lyase reaction affects systemic inflammation. In microglia, ACOD1 regulates arginine metabolism and inflammatory responses, connecting carboxy-lyase activity to neuroinflammation.
Physiological context and regulation
In simple terms: The reaction happens in a specific cellular context that can be turned up or down.
Carboxy-lyase activity is not constitutive in all settings; it can be regulated by immune signals, diet, and disease state [1, 3, 6, 7, 8]. IRG1/ACOD1 expression is immune-responsive, so itaconate production increases during immune activation. ACOD1 function is relevant in sepsis and microglial inflammation, where inflammatory cues shape enzyme activity [3, 6]. Dietary sulfate and cysteine levels alter L-cysteinesulfinate carboxy-lyase activity in rat liver, showing nutritional regulation. Erythrocyte porphyrinogen carboxy-lyase activity is altered in porphyria cutanea tarda and other human porphyrias, linking enzyme status to disease.
Key Genes Involved in GO:0016831 carboxy-lyase activity
The following genes and proteins are experimentally linked to carboxy-lyase activity or to the metabolism of its substrates and products.
| Gene | Major Role | Research Relevance |
|---|---|---|
| ACOD1 (IRG1) | Catalyzes cis-aconitate decarboxylation to itaconate | Links metabolism to immunity; studied in inflammation and sepsis [1, 3, 6] |
| IRG1 | Immune-responsive gene 1 protein with carboxy-lyase activity | Produces itaconic acid and connects metabolism to immunity |
| ACOD1 (microglial) | Regulates microglial arginine metabolism and inflammatory responses | Neuroinflammation research |
| UDP-glucuronate carboxy-lyase | Acts on UDP-glucuronate in cultured chondrocytes | Chondrocyte matrix metabolism |
| L-cysteinesulfinate carboxy-lyase | Acts on L-cysteinesulfinate in liver | Dietary sulfate and cysteine studies |
| Porphyrinogen carboxy-lyase | Removes carboxyl groups in heme biosynthesis | Porphyria cutanea tarda and other porphyrias |
| Histamine decarboxylation pathway | Produces histamine from histidine | Microcirculation research |
| ACOD1 (sepsis model) | Mediates polymicrobial sepsis | Sepsis immunometabolism |
| IRG1/ACOD1 (itaconate) | Produces itaconate as an immunomodulatory metabolite | Metabolic immunology |
| ACOD1 (arginine metabolism) | Regulates arginine metabolism in microglia | Neuroimmune metabolism |
| Porphyrinogen carboxy-lyase (erythrocyte) | Measured in human erythrocytes | Clinical porphyria diagnostics |
| L-cysteinesulfinate carboxy-lyase (liver) | Responds to sulfate and cysteine intake | Nutritional biochemistry |
| UDP-glucuronate carboxy-lyase (chondrocyte) | Detected in cultured chondrocytes | Cartilage biology |
| Histamine pathway enzymes | Decarboxylation linked to microcirculation | Vascular physiology |
| ACOD1 (inflammatory responses) | Regulates inflammatory responses | Inflammation target discovery |
| IRG1 (itaconic acid) | Catalyzes itaconic acid production | Immunometabolism |
How Is carboxy-lyase activity Regulated?
Carboxy-lyase activity is regulated at multiple levels, including immune-responsive expression, substrate availability, and nutritional status [1, 3, 6, 7, 8]. IRG1/ACOD1 is immune-responsive, so its carboxy-lyase activity increases during immune activation and links metabolism to immunity. ACOD1 function is relevant in polymicrobial sepsis and in microglial inflammatory responses, where inflammatory signals shape enzyme activity [3, 6]. Dietary sulfate and cysteine levels alter L-cysteinesulfinate carboxy-lyase activity in rat liver, demonstrating nutritional regulation. Erythrocyte porphyrinogen carboxy-lyase activity is altered in porphyria cutanea tarda and other human porphyrias, indicating disease-associated regulation.
carboxy-lyase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| ACOD1 | Polymicrobial sepsis | Knockout and overexpression in immune cells and sepsis models |
| ACOD1 | Microglial inflammatory responses | Microglial knockout and point-mutation models |
| IRG1/ACOD1 | Immunometabolism and itaconate production | Knock-in reporter and overexpression models |
| Porphyrinogen carboxy-lyase | Porphyria cutanea tarda and other porphyrias | Patient erythrocyte assays and enzyme activity models |
| L-cysteinesulfinate carboxy-lyase | Dietary sulfate and cysteine metabolism | Liver enzyme activity studies in animal models |
Sepsis and systemic inflammation
ACOD1, a carboxy-lyase enzyme, is a mediator of polymicrobial sepsis, indicating that this activity contributes to systemic inflammatory responses. IRG1/ACOD1 produces itaconate, an immunomodulatory metabolite that links metabolism to immunity. Because ACOD1 regulates inflammatory responses, carboxy-lyase activity is a candidate node for anti-inflammatory intervention [3, 6].
Neuroinflammation and microglial metabolism
ACOD1 regulates microglial arginine metabolism and inflammatory responses, connecting carboxy-lyase activity to neuroinflammatory processes. This suggests that modulating ACOD1-dependent decarboxylation could influence microglial activation states. The same enzyme family is immune-responsive, so its activity may be context-dependent in the central nervous system [1, 6].
Porphyrias and heme biosynthesis
Erythrocyte porphyrinogen carboxy-lyase activity is altered in porphyria cutanea tarda and certain other human porphyrias, linking this carboxy-lyase reaction to heme biosynthesis disorders. Measurement of this activity in erythrocytes has been used to characterize human porphyrias. This provides a clinical example of how a carboxy-lyase defect can manifest as disease.
Metabolic and nutritional contexts
L-cysteinesulfinate carboxy-lyase activity in rat liver changes with dietary sulfate and cysteine levels, showing that carboxy-lyase activity can be modulated by nutrition. UDP-glucuronate carboxy-lyase activity in cultured chondrocytes indicates a role in cartilage matrix metabolism. Histamine-related microcirculation studies illustrate how decarboxylation products can affect vascular physiology.
From carboxy-lyase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of ACOD1 alter itaconate production and immune responses? | ACOD1 knockout cell lines and animal models [1, 3] |
| Does a specific ACOD1 point mutation change carboxy-lyase activity? | Point-mutation knock-in models [1, 6] |
| Can ACOD1 expression be tracked in live cells? | Tagged knock-in reporter models |
| Does ACOD1 overexpression drive inflammatory phenotypes? | Overexpression cell models [3, 6] |
| Is porphyrinogen carboxy-lyase activity altered in porphyria? | Patient erythrocyte enzyme activity assays |
| How does dietary sulfate affect L-cysteinesulfinate carboxy-lyase activity? | Animal feeding studies with liver enzyme assays |
How to Study the carboxy-lyase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Enzyme activity assay | Substrate consumption or product formation | UDP-glucuronate and L-cysteinesulfinate carboxy-lyase studies [5, 7] |
| Metabolite profiling | Itaconate and related metabolite levels | IRG1/ACOD1 immunometabolism |
| CRISPR knockout screening | Gene requirement for a phenotype | Identifying carboxy-lyase-dependent pathways [1, 3, 6] |
| RNA expression analysis | ACOD1/IRG1 transcript levels | Immune activation studies [1, 6] |
| Tagged knock-in reporter | Protein localization and abundance | ACOD1 tracking in cells |
| Erythrocyte enzyme assay | Porphyrinogen carboxy-lyase activity | Human porphyria evaluation |
| Animal feeding study | Liver carboxy-lyase activity | Dietary sulfate and cysteine effects |
| Microglial inflammatory assay | Inflammatory responses and arginine metabolism | Neuroinflammation research |
Enzyme activity assays
Carboxy-lyase activity can be measured directly by monitoring substrate consumption or product formation, as shown for UDP-glucuronate carboxy-lyase in cultured chondrocytes and L-cysteinesulfinate carboxy-lyase in rat liver [5, 7]. Erythrocyte porphyrinogen carboxy-lyase activity is measured in human porphyria samples, demonstrating clinical applicability. These assays are essential because GO:0016831 covers multiple substrates and cannot be inferred from gene annotation alone [1, 5, 7, 8].
Metabolite profiling and itaconate detection
Because IRG1/ACOD1 produces itaconate from cis-aconitate, metabolite profiling can quantify carboxy-lyase flux in immune cells. ACOD1-dependent itaconate production links metabolism to immunity and can be used as a functional readout. In sepsis and microglial models, metabolite changes associated with ACOD1 activity help connect enzyme function to phenotype [3, 6].
CRISPR screening and functional genomics
Genome-scale CRISPR screens can identify genes required for carboxy-lyase-dependent phenotypes, such as itaconate production or inflammatory responses [1, 3, 6]. ACOD1 is a validated hit in immune and sepsis contexts, making it a benchmark for screening workflows [1, 3]. Combining screening with metabolite measurements helps assign function to candidate carboxy-lyase genes [1, 3, 6].
Expression and reporter assays
Immune-responsive expression of IRG1/ACOD1 can be monitored by RNA-based methods and reporter assays. Tagged knock-in reporters allow tracking of ACOD1 protein localization and abundance. In microglia, ACOD1 expression and function are linked to inflammatory responses, so expression assays complement activity measurements.
How CRISPR Can Be Used to Study GO:0016831 carboxy-lyase activity
Knockout
CRISPR knockout of ACOD1 can eliminate carboxy-lyase activity and test whether itaconate production is required for immune responses [1, 3]. Knockout models are useful in sepsis and microglial inflammation studies to determine causality [3, 6]. Loss-of-function models also help validate whether a candidate gene contributes to porphyrinogen or UDP-glucuronate carboxy-lyase activity [5, 8].
Point Mutation
Point-mutation knock-in can alter catalytic residues of a carboxy-lyase and separate enzymatic activity from protein abundance [1, 6]. This approach is valuable for testing whether a specific residue is required for cis-aconitate decarboxylation by ACOD1. Point mutants can also reveal whether ACOD1 functions in microglial arginine metabolism independently of its catalytic activity.
Knock-in
Knock-in of tags or reporters at the ACOD1 locus allows tracking of carboxy-lyase enzyme expression and localization. Tagged knock-in models can be combined with metabolite profiling to correlate enzyme levels with itaconate output. Knock-in of disease-associated variants can test their effect on carboxy-lyase activity in relevant cell types [1, 6].
Overexpression
Overexpression of ACOD1 can increase carboxy-lyase flux and drive inflammatory or metabolic phenotypes [3, 6]. Overexpression models are useful for testing whether increased itaconate production is sufficient to alter immune responses [1, 3]. They can also be used to study carboxy-lyase enzymes such as porphyrinogen carboxy-lyase in disease-relevant backgrounds.
How EDITGENE Supports carboxy-lyase activity Research
Researchers studying carboxy-lyase activity-related genes often need to determine whether a candidate gene is causally involved in metabolite production, immune signaling, or disease phenotypes. EDITGENE provides CRISPR-based cell models and screening services that allow functional testing of carboxy-lyase genes such as ACOD1 and related enzymes in relevant biological contexts [1, 3, 5, 6, 7, 8].
Contact EDITGENE today to design your custom CRISPR model for carboxy-lyase activity research.
Frequently Asked Questions About carboxy-lyase activity
What is carboxy-lyase activity?
Carboxy-lyase activity (GO:0016831) is the catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound, also known as decarboxylase activity [1, 5].
What genes are involved in carboxy-lyase activity?
Genes and enzymes linked to this activity include ACOD1/IRG1, UDP-glucuronate carboxy-lyase, L-cysteinesulfinate carboxy-lyase, and porphyrinogen carboxy-lyase [1, 5, 7, 8].
What does ACOD1 do in carboxy-lyase activity?
ACOD1, also known as IRG1, catalyzes the decarboxylation of cis-aconitate to itaconate, linking metabolism to immunity.
Is carboxy-lyase activity involved in sepsis?
Yes, ACOD1 is a mediator of polymicrobial sepsis, indicating that this carboxy-lyase activity contributes to systemic inflammatory responses.
How is carboxy-lyase activity measured?
It can be measured by enzyme activity assays that track substrate consumption or product formation, as shown for UDP-glucuronate and L-cysteinesulfinate carboxy-lyases [5, 7].
What diseases are linked to carboxy-lyase activity?
Links include sepsis, microglial inflammatory responses, and porphyria cutanea tarda and other human porphyrias [3, 6, 8].
What is the synonym for GO:0016831?
The synonym is decarboxylase activity [1, 5].
How does diet affect carboxy-lyase activity?
Dietary sulfate and cysteine levels alter L-cysteinesulfinate carboxy-lyase activity in rat liver.
Can CRISPR be used to study carboxy-lyase activity?
Yes, CRISPR knockout, point-mutation, knock-in, and overexpression models can test the function of carboxy-lyase genes such as ACOD1 [1, 3, 6].
What is the role of carboxy-lyase activity in microglia?
ACOD1 regulates microglial arginine metabolism and inflammatory responses, connecting carboxy-lyase activity to neuroinflammation.
Conclusion
GO:0016831 carboxy-lyase activity defines a fundamental enzymatic function: the nonhydrolytic addition or removal of a carboxyl group [1, 5]. Its importance spans immunometabolism, amino acid metabolism, heme biosynthesis, and cartilage biology, with ACOD1/IRG1 serving as a well-studied example that links itaconate production to immunity and sepsis [1, 3, 5, 6, 7, 8]. For researchers, carboxy-lyase activity offers a tractable entry point for CRISPR-based functional studies, from knockout and point-mutation models to overexpression and library screening [1, 3, 6]. Combining enzyme assays with metabolite profiling and expression analysis will continue to clarify how carboxy-lyases shape health and disease [1, 3, 5, 6, 7, 8].
References
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- 3. Wu R et al.. 2022. Aconitate decarboxylase 1 is a mediator of polymicrobial sepsis.. Sci Transl Med 14(659):eabo2028 PMID: 36001682
- 4. Schayer RW. 1974. Histamine and microcirculation.. Life Sci 15(3):391-401 PMID: 4620963
- 5. John KV et al.. 1977. UDP-glucuronate carboxy-lyase in cultured chondrocytes.. J Biol Chem 252(19):6707-10 PMID: 197101
- 6. Karadima E et al.. 2026. ACOD1 regulates microglial arginine metabolism and inflammatory responses.. Front Immunol 17:1731962 PMID: 41918748
- 7. Whittle BA et al.. 1976. Activity of L-cysteinesulfinate carboxy-lyase and persulfurase in livers of rats fed different levels of sulfate and cysteine.. J Nutr 106(4):537-42 PMID: 1255271
- 8. Ríos de Molina MC et al.. 1980. Erythrocyte porphyrinogen carboxy-lyase activity in porphyria cutanea tarda and certain other human porphyrias.. Clin Chim Acta 108(3):447-56 PMID: 7471475
