GO:1901787 benzoyl-CoA metabolic process: Anaerobic Aromatic Degradation Pathway, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:1901787 benzoyl-CoA metabolic process describes the chemical reactions and pathways involving benzoyl-CoA, the central intermediate in anaerobic aromatic compound degradation.
• Benzoyl-CoA is formed by the reductive dearomatization of benzoyl-CoA, a reaction catalyzed by benzoyl-CoA reductase, a key enzyme in anaerobic bacteria.
• In plants, benzoyl-CoA is a precursor for salicylic acid biosynthesis via a three-step pathway involving benzoyl-CoA ligase and benzoyl-CoA hydroxylase.
• Benzoyl-CoA metabolism is a universal biomarker for anaerobic degradation of aromatic compounds and is studied in model organisms such as Aromatoleum aromaticum EbN1.
• Dysregulation of benzoyl-CoA metabolism can influence host physiology, as shown by sodium benzoate (a benzoyl-CoA precursor) affecting histone benzoylation and social behavior in a maternal immune activation model.
• Research on this pathway employs gene knockout, knock-in, and overexpression models, along with CRISPR library screening and bioinformatics to dissect gene function.
Description
Benzoyl-CoA metabolic process (GO:1901787) is a biological process defined as the chemical reactions and pathways involving benzoyl-CoA. Benzoyl-CoA is a key intermediate in the anaerobic degradation of aromatic compounds, where it serves as the central hub for the breakdown of diverse aromatic substrates such as benzoate, toluene, and phenol. This pathway is essential for the global carbon cycle, as it allows anaerobic microorganisms to utilize aromatic compounds as carbon and energy sources. The importance of benzoyl-CoA extends beyond microbial metabolism; in plants, benzoyl-CoA is an intermediate in the biosynthesis of salicylic acid, a critical defense hormone. Recent studies have also linked benzoyl-CoA metabolism to host-microbe interactions and epigenetic regulation through histone benzoylation. Understanding the enzymes, genes, and regulatory mechanisms of benzoyl-CoA metabolism is therefore crucial for microbiology, plant biology, and biomedical research.
benzoyl-CoA metabolic process At A Glance
| GO ID | GO:1901787 |
|---|---|
| GO term | benzoyl-CoA metabolic process |
| Ontology | biological_process |
| Synonym | benzoyl-CoA metabolism |
| Major function | Chemical reactions and pathways involving benzoyl-CoA, including its formation, reduction, and conversion to other metabolites. |
| Key enzymes | Benzoyl-CoA reductase, benzoyl-CoA ligase, benzoyl-CoA hydroxylase, and other radical enzymes. |
| Model organisms | Aromatoleum aromaticum EbN1, Thauera aromatica, and other anaerobic bacteria. |
| Related pathways | Anaerobic aromatic degradation, salicylic acid biosynthesis, and histone benzoylation. |
What Is GO:1901787?
According to the Gene Ontology, GO:1901787 benzoyl-CoA metabolic process is defined as the chemical reactions and pathways involving benzoyl-CoA. This includes the synthesis, modification, and degradation of benzoyl-CoA, as well as its conversion to other metabolites. The process is central to anaerobic aromatic degradation and also plays a role in plant salicylic acid biosynthesis.
Why Is benzoyl-CoA metabolic process Important in Cell Biology?
Benzoyl-CoA metabolic process is important because it is a central node in the anaerobic degradation of aromatic compounds, which are widespread environmental pollutants and key components of the carbon cycle. This pathway enables microorganisms to break down recalcitrant aromatic compounds, contributing to bioremediation and global carbon cycling. In plants, benzoyl-CoA is a precursor for salicylic acid, a hormone critical for defense against pathogens. Furthermore, benzoyl-CoA metabolism can influence host physiology through the production of metabolites like sodium benzoate, which affects epigenetic marks and behavior. Thus, studying this process has implications for environmental microbiology, plant biology, and human health.
• Central to anaerobic degradation of aromatic compounds, a key process in the global carbon cycle.
• Enables bioremediation of aromatic pollutants in anaerobic environments.
• Provides a universal biomarker for anaerobic aromatic degradation.
• Involved in plant salicylic acid biosynthesis, a defense hormone.
• Links microbial metabolism to host epigenetic regulation via histone benzoylation.
• Model system for studying radical enzymes and oxygen-sensitive catalysis.
• Relevant to understanding microbial community dynamics in anaerobic habitats.
• Potential target for engineering improved biodegradation pathways.
• Implications for neurological and behavioral research through gut-brain axis.
• Offers insights into evolution of metabolic pathways for aromatic compound utilization.
What Happens During benzoyl-CoA metabolic process?
Benzoyl-CoA Formation
In simple terms: First, benzoyl-CoA is made from benzoate or other aromatic precursors.
Benzoyl-CoA is formed by the activation of benzoate with coenzyme A, catalyzed by benzoyl-CoA ligase. In anaerobic bacteria, this step is essential for channeling aromatic compounds into the degradation pathway. In plants, benzoyl-CoA is synthesized from cinnamic acid derivatives as part of salicylic acid biosynthesis.
Reductive Dearomatization
In simple terms: Then, the stable aromatic ring of benzoyl-CoA is broken by adding electrons.
Benzoyl-CoA reductase catalyzes the reductive dearomatization of benzoyl-CoA, a key step in anaerobic aromatic degradation. This enzyme uses ATP and reduced ferredoxin to overcome the high activation energy of ring reduction. The product is a cyclic diene, which is further processed to central intermediates.
Ring Cleavage and Beta-Oxidation
In simple terms: After the ring is opened, the molecule is broken down into smaller pieces.
Following dearomatization, the ring is cleaved by hydrolases to yield 3-hydroxypimelyl-CoA, which is further degraded via beta-oxidation to acetyl-CoA and succinyl-CoA. These central metabolites enter the tricarboxylic acid cycle.
Salicylic Acid Biosynthesis in Plants
In simple terms: In plants, benzoyl-CoA is converted to salicylic acid, a defense hormone.
In plants, benzoyl-CoA is hydroxylated by benzoyl-CoA hydroxylase to form salicyloyl-CoA, which is then hydrolyzed to salicylic acid. This three-step pathway from phenylalanine via benzoyl-CoA is critical for plant immunity.
Histone Benzoylation
In simple terms: Benzoyl-CoA can also modify histones, affecting gene expression.
Benzoyl-CoA serves as a substrate for histone lysine benzoylation, a post-translational modification that regulates gene expression. Sodium benzoate, a precursor, can increase histone benzoylation in astrocytes, influencing social behavior in a maternal immune activation model.
Key Genes Involved in GO:1901787 benzoyl-CoA metabolic process
The following genes and proteins are key players in benzoyl-CoA metabolic process, as identified in model organisms and plants.
| Gene | Major Role | Research Relevance |
|---|---|---|
| bcrA | Benzoyl-CoA reductase subunit | Catalyzes reductive dearomatization in anaerobic bacteria |
| bcrB | Benzoyl-CoA reductase subunit | Essential for electron transfer during ring reduction |
| bcrC | Benzoyl-CoA reductase subunit | ATP-binding subunit of the reductase complex |
| bcrD | Benzoyl-CoA reductase subunit | Ferredoxin-binding subunit |
| badA | Benzoyl-CoA ligase | Activates benzoate to benzoyl-CoA in Aromatoleum aromaticum |
| badB | Benzoyl-CoA reductase | Reductive dearomatization in Aromatoleum aromaticum |
| badC | Benzoyl-CoA hydrolase | Ring cleavage after reduction |
| badD | Benzoyl-CoA dehydrogenase | Oxidation of benzoyl-CoA in some pathways |
| bamA | Benzoyl-CoA mutase | Catalyzes carbon skeleton rearrangement |
| bamB | Benzoyl-CoA mutase subunit | Radical enzyme involved in benzoyl-CoA metabolism |
| bamC | Benzoyl-CoA mutase subunit | Essential for catalytic activity |
| bamD | Benzoyl-CoA mutase subunit | ATP-binding subunit |
| bamE | Benzoyl-CoA mutase subunit | Ferredoxin-binding subunit |
| bamF | Benzoyl-CoA mutase subunit | Small subunit of the mutase |
| bamG | Benzoyl-CoA mutase subunit | Accessory protein for maturation |
| bamH | Benzoyl-CoA mutase subunit | Involved in radical generation |
| bamI | Benzoyl-CoA mutase subunit | Chaperone-like function |
| bamJ | Benzoyl-CoA mutase subunit | Essential for enzyme assembly |
How Is benzoyl-CoA metabolic process Regulated?
Benzoyl-CoA metabolic process is regulated at multiple levels. In anaerobic bacteria, the expression of benzoyl-CoA degradation genes is induced by aromatic substrates and controlled by specific transcriptional regulators. For example, in Aromatoleum aromaticum EbN1, the bad genes are upregulated in the presence of benzoate. In plants, salicylic acid biosynthesis via benzoyl-CoA is regulated by developmental and defense signals. Additionally, benzoyl-CoA levels can influence histone benzoylation, which in turn affects gene expression.
benzoyl-CoA metabolic process and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| bcrA | Anaerobic aromatic degradation | Knockout in Aromatoleum aromaticum EbN1 |
| badA | Benzoate metabolism | Overexpression in E. coli |
| bamA | Radical enzyme catalysis | Point mutation in Thauera aromatica |
| PAL | Salicylic acid biosynthesis | Knockout in Arabidopsis thaliana |
| BSH | Histone benzoylation | Knock-in in mouse astrocytes |
Neurological and Behavioral Disorders
Sodium benzoate, a metabolite linked to benzoyl-CoA metabolism, has been shown to improve social behavior in offspring exposed to maternal immune activation by regulating histone lysine benzoylation in astrocytes. This suggests that benzoyl-CoA metabolism may influence neurodevelopmental and behavioral outcomes through epigenetic mechanisms.
Plant Immunity and Disease Resistance
In plants, benzoyl-CoA is a precursor for salicylic acid, a key defense hormone. Disruption of the benzoyl-CoA pathway leads to reduced salicylic acid levels and increased susceptibility to pathogens. Thus, genes in this pathway are potential targets for engineering disease-resistant crops.
Environmental Bioremediation
Anaerobic bacteria that degrade aromatic pollutants via benzoyl-CoA metabolism are crucial for bioremediation. Understanding this pathway can inform strategies to enhance the breakdown of toxic aromatic compounds in contaminated sites.
From benzoyl-CoA metabolic process-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| What is the role of bcrA in benzoyl-CoA reduction? | Knockout of bcrA in Aromatoleum aromaticum EbN1 |
| How does benzoyl-CoA affect histone benzoylation? | Overexpression of benzoyl-CoA ligase in astrocytes |
| What is the catalytic mechanism of benzoyl-CoA reductase? | Point mutation of active site residues in bcrB |
| How is salicylic acid biosynthesis regulated? | Knock-in of tagged PAL in Arabidopsis |
| What genes are essential for anaerobic benzoate degradation? | CRISPR library screening in Aromatoleum aromaticum |
| Can benzoyl-CoA metabolism be engineered for bioremediation? | Overexpression of bad genes in Pseudomonas putida |
How to Study the benzoyl-CoA metabolic process Process
| Method | What It Measures | Typical Application |
|---|---|---|
| RNA-seq | Gene expression changes | Identify genes upregulated during benzoyl-CoA metabolism |
| Proteomics | Protein abundance | Map enzymes involved in aromatic degradation |
| Metabolomics | Metabolite levels | Quantify benzoyl-CoA and intermediates |
| Enzyme assays | Catalytic activity | Characterize benzoyl-CoA reductase |
| CRISPR knockout | Gene function | Test essentiality of bcr genes |
| CRISPR knock-in | Tagged protein localization | Study protein interactions |
| ChIP-seq | Histone modifications | Assess histone benzoylation |
| Bioinformatics | Pathway reconstruction | Predict metabolic networks |
Genomic and Transcriptomic Analysis
RNA-seq and microarray analysis can identify genes differentially expressed during benzoyl-CoA metabolism. For example, in Aromatoleum aromaticum EbN1, transcriptomics revealed the bad gene cluster is upregulated in the presence of benzoate.
Proteomics and Metabolomics
Proteomic profiling of benzoyl-CoA degrading bacteria can identify key enzymes, while metabolomics can quantify benzoyl-CoA and its derivatives. These methods have been used to map the catabolic network of Aromatoleum aromaticum.
Enzymatic Assays
In vitro assays with purified enzymes, such as benzoyl-CoA reductase, can measure catalytic activity and substrate specificity. These assays are essential for understanding the mechanism of radical enzymes.
CRISPR-Cas9 Genome Editing
CRISPR-Cas9 knockout and knock-in models allow functional dissection of genes involved in benzoyl-CoA metabolism. For instance, knockout of bcrA in Aromatoleum aromaticum can confirm its essential role in anaerobic benzoate degradation.
How CRISPR Can Be Used to Study GO:1901787 benzoyl-CoA metabolic process
Knockout
CRISPR knockout of genes such as bcrA or badA can abolish benzoyl-CoA metabolism, confirming their essential roles. For example, knockout of bcrA in Aromatoleum aromaticum EbN1 results in loss of anaerobic growth on benzoate.
Point Mutation
Point mutations can be introduced to study catalytic residues. For instance, mutating the ATP-binding site of bcrC can reveal its role in benzoyl-CoA reduction.
Knock-in
Knock-in of epitope tags allows visualization and immunoprecipitation of benzoyl-CoA enzymes. Tagging bcrA with FLAG can facilitate protein interaction studies.
Overexpression
Overexpression of benzoyl-CoA ligase or other pathway enzymes can increase flux through the pathway. In plants, overexpression of PAL enhances salicylic acid production.
How EDITGENE Supports benzoyl-CoA metabolic process Research
Researchers studying benzoyl-CoA metabolic process-related genes often need to determine whether a candidate gene is causally involved in the pathway or merely correlated with its activity. EDITGENE provides comprehensive CRISPR gene editing services to enable precise functional studies.
Contact EDITGENE today to design your custom CRISPR model for benzoyl-CoA metabolic process research.
Frequently Asked Questions About benzoyl-CoA metabolic process
What is benzoyl-CoA metabolic process?
Benzoyl-CoA metabolic process (GO:1901787) is the set of chemical reactions and pathways involving benzoyl-CoA, a key intermediate in anaerobic aromatic degradation and plant salicylic acid biosynthesis.
What genes are involved in benzoyl-CoA metabolic process?
Key genes include bcrA, bcrB, bcrC, bcrD (benzoyl-CoA reductase subunits), badA (benzoyl-CoA ligase), and bamA (benzoyl-CoA mutase).
What is the role of benzoyl-CoA in anaerobic bacteria?
In anaerobic bacteria, benzoyl-CoA is the central intermediate for degrading aromatic compounds, allowing them to use these compounds as carbon and energy sources.
How is benzoyl-CoA involved in plant salicylic acid biosynthesis?
In plants, benzoyl-CoA is converted to salicylic acid via a three-step pathway involving benzoyl-CoA ligase and benzoyl-CoA hydroxylase.
What enzymes catalyze benzoyl-CoA metabolism?
Key enzymes include benzoyl-CoA reductase, benzoyl-CoA ligase, benzoyl-CoA hydrolase, and benzoyl-CoA mutase, many of which are radical enzymes.
What is the significance of benzoyl-CoA as a biomarker?
Benzoyl-CoA is a universal biomarker for anaerobic degradation of aromatic compounds, indicating microbial activity in anoxic environments.
How does sodium benzoate affect histone benzoylation?
Sodium benzoate, a precursor of benzoyl-CoA, can increase histone lysine benzoylation, influencing gene expression and behavior in animal models.
What model organisms are used to study benzoyl-CoA metabolism?
Aromatoleum aromaticum EbN1 and Thauera aromatica are common model organisms for anaerobic benzoyl-CoA metabolism.
What research methods are used to study benzoyl-CoA metabolic process?
Methods include RNA-seq, proteomics, metabolomics, enzyme assays, and CRISPR-Cas9 genome editing.
How can CRISPR be used to study benzoyl-CoA metabolism?
CRISPR knockout, knock-in, and overexpression models allow functional dissection of genes involved in benzoyl-CoA metabolism.
Conclusion
Benzoyl-CoA metabolic process (GO:1901787) is a fundamental biological process with wide-ranging implications, from anaerobic bioremediation to plant immunity and host epigenetic regulation. The pathway's central intermediate, benzoyl-CoA, serves as a hub for diverse metabolic routes, and its study continues to reveal new connections to human health and disease. Leveraging CRISPR-based tools and multi-omics approaches will further illuminate the genes and mechanisms governing this process.
References
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- 3. Zhu B et al.. 2025. Complete biosynthesis of salicylic acid from phenylalanine in plants.. Nature 645(8079):218-227 PMID: 40702181
- 4. Porter AW et al.. 2014. Benzoyl-CoA, a universal biomarker for anaerobic degradation of aromatic compounds.. Adv Appl Microbiol 88:167-203 PMID: 24767428
- 5. Li T et al.. 2025. Probiotics derived sodium benzoate improves social behavior of offspring exposed in the maternal immune activation through regulation of histone lysine benzoylation in astrocytes.. Mol Psychiatry 30(12):5849-5864 PMID: 40855005
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