Coxiella burnetii is a Gram-negative bacterium that causes Q fever, a zoonotic disease affecting humans and animals worldwide . It is known for its ability to survive within host cells by manipulating the host's immune response .
3-Oxoacyl-[acyl-carrier-protein] synthase is an enzyme involved in fatty acid biosynthesis. In bacteria, this process is crucial for cell membrane formation and energy storage. The enzyme catalyzes the condensation of acyl-ACP with malonyl-ACP to form 3-oxoacyl-ACP, a key step in elongating fatty acid chains .
While there is no direct research on recombinant Coxiella burnetii fabF, studying such enzymes could provide insights into bacterial metabolism and potentially reveal targets for therapeutic interventions. The development of recombinant enzymes in other bacteria has helped elucidate metabolic pathways and identify potential drug targets .
| Enzyme | Function | Relevance in Bacteria |
|---|---|---|
| 3-Oxoacyl-ACP Synthase | Condenses acyl-ACP with malonyl-ACP | Essential for fatty acid biosynthesis |
| FabF (3-Oxoacyl-ACP Synthase II) | Specific to unsaturated fatty acid synthesis | Important in certain bacterial species |
- Coxiella burnetii immunogenic proteins as a basis for new Q fever vaccines.
- Exploratory Study on Th1 Epitope-Induced Protective Immunity against Coxiella burnetii.
- Reaction mechanism of recombinant 3-oxoacyl-(acyl-carrier-protein) synthase III.
- Characterization of recombinant Ybgf protein for the detection of Coxiella burnetii antibodies.
Expression and Purification: Express recombinant Coxiella burnetii fabF in a suitable host like E. coli and purify it for biochemical studies.
Enzymatic Activity Assays: Investigate the enzyme's activity and specificity using various substrates.
Structural Analysis: Perform structural studies to understand the enzyme's mechanism and potential binding sites for inhibitors.
Metabolic Pathway Analysis: Study the role of fabF in Coxiella burnetii's fatty acid biosynthesis pathway and its impact on bacterial survival and virulence.
This protein is involved in the type II fatty acid elongation cycle. It catalyzes the elongation of various acyl-ACPs by adding two carbons from malonyl-ACP to an acyl acceptor. Specifically, it efficiently catalyzes the conversion of palmitoleoyl-ACP (cis-hexadec-9-enoyl-ACP) to cis-vaccenoyl-ACP (cis-octadec-11-enoyl-ACP), a crucial step in the thermal regulation of fatty acid composition.
KEGG: cbu:CBU_0497
STRING: 227377.CBU_0497
Coxiella burnetii 3-oxoacyl-[acyl-carrier-protein] synthase 2 (fabF) is a key enzyme involved in the fatty acid biosynthesis pathway of this obligate intracellular pathogen. FabF catalyzes the addition of two-carbon units to the growing acyl chain during the elongation phase of fatty acid synthesis . As C. burnetii is the causative agent of Q fever and classified as a category B bio-weapon, understanding its metabolic enzymes is crucial .
The biological significance of fabF in C. burnetii stems from its central role in membrane lipid biosynthesis, which is essential for the pathogen's survival and adaptation within the harsh environment of the Coxiella-containing vacuole (CCV). Given that C. burnetii replicates in an acidic phagolysosomal vacuole, specialized membrane fatty acids likely play critical roles in pH resistance and intracellular survival .
While specific structural information for C. burnetii fabF is limited in the provided search results, we can draw comparisons with related bacterial enzymes. 3-Oxoacyl-ACP synthase II enzymes typically have molecular weights around 43 kDa, as seen in the Thermus thermophilus enzyme (43.2 kDa with 408 amino acid residues) .
C. burnetii possesses a highly diverse metabolic network that utilizes multiple substrates . Recent isotopolog profiling studies have revealed that C. burnetii can assimilate various carbon sources, which feed into its bipartite metabolic network .
The fatty acid biosynthesis pathway, in which fabF plays a crucial role, is likely essential for the pathogen's ability to establish and maintain its replicative niche. The fabrication of specialized membrane lipids through this pathway may contribute to the stability and functionality of the CCV, which occupies a significant portion of the host cell's volume during infection . Understanding how fabF contributes to membrane composition could provide insights into how C. burnetii maintains the integrity of its massive CCV during intracellular replication.
For recombinant expression of C. burnetii fabF, several expression systems can be considered:
E. coli-based expression system:
Recommended strain: BL21(DE3) or Rosetta 2(DE3) for rare codon optimization
Vector options: pET-28a(+) with N-terminal His-tag for efficient purification
Induction conditions: 0.5-1.0 mM IPTG at reduced temperature (16-18°C) for 16-20 hours to enhance soluble protein yield
Media: Terrific Broth supplemented with appropriate antibiotics
Cell-free expression system:
Particularly useful if the protein forms inclusion bodies in conventional systems
Allows incorporation of detergents or lipids to stabilize membrane-associated domains
The decision between these systems should be based on preliminary solubility testing. For C. burnetii proteins, which may have adapted to an acidic intracellular environment, expression conditions may need optimization to maintain proper folding and function.
A multi-step purification protocol is recommended:
| Step | Method | Buffer Composition | Expected Outcome |
|---|---|---|---|
| 1 | Immobilized Metal Affinity Chromatography (IMAC) | 50 mM Tris-HCl pH 8.0, 300 mM NaCl, 10-250 mM imidazole gradient | >80% purity |
| 2 | Size Exclusion Chromatography | 25 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol | >95% purity, removal of aggregates |
| 3 | Ion Exchange Chromatography (optional) | 20 mM Tris-HCl pH 8.0, 0-500 mM NaCl gradient | >98% purity |
Critical considerations:
Include protease inhibitors in all buffers to prevent degradation
Add 1-5 mM DTT or 0.5-2 mM TCEP to maintain cysteine residues in reduced state
Consider including 10% glycerol in final storage buffer to maintain stability
Aliquot and flash-freeze in liquid nitrogen for long-term storage at -80°C
This protocol should be optimized based on preliminary characterization of protein behavior. Activity assays should be performed after each purification step to ensure the protein remains functional.
Multiple complementary approaches should be used:
Structural integrity assessment:
Circular dichroism (CD) spectroscopy to analyze secondary structure content
Thermal shift assays to determine protein stability and identify stabilizing buffer conditions
Dynamic light scattering to assess monodispersity and detect aggregation
Functional assays:
Spectrophotometric assay measuring the condensation reaction with malonyl-ACP and acyl-ACP substrates
Radio-labeled substrate incorporation assays for direct quantification of enzymatic activity
HPLC-based assays to monitor product formation
Activity validation parameters:
Determine Km and Vmax values for key substrates
Assess temperature and pH optima (particularly important for C. burnetii proteins which function in acidic environments)
Evaluate the effects of potential inhibitors on enzyme activity
Comparing the kinetic parameters with those of fabF from other bacteria can provide insights into C. burnetii-specific adaptations related to its intracellular lifestyle.
While specific structural data for C. burnetii fabF is not provided in the search results, we can predict distinguishing features based on the organism's unique lifestyle:
Acid stability adaptations: As C. burnetii thrives in acidic phagolysosomal vacuoles, its fabF likely possesses structural modifications that enhance stability under acidic conditions. These may include:
Increased surface negative charge distribution to repel protons
Reduced number of acid-labile bonds
Strategic distribution of histidine residues with altered pKa values
Substrate binding pocket variations: The substrate specificity of C. burnetii fabF may differ from that of other bacteria, reflecting adaptations to the intracellular environment and substrate availability within the CCV.
Potential regulatory domains: Given C. burnetii's complex metabolic network that utilizes multiple substrates , its fabF might contain unique regulatory regions that respond to intracellular environmental cues.
Comparative structural analysis with other bacterial fabF enzymes, such as the T. thermophilus enzyme mentioned in the search results , would be valuable for identifying these distinguishing features.
Based on successful crystallization of related 3-oxoacyl-ACP synthases, including the one from T. thermophilus , the following screening approach is recommended:
Initial screening conditions:
Temperature: 18°C and 4°C in parallel
Protein concentration: 5-15 mg/ml range
Buffer systems: 100 mM HEPES (pH 7.0-7.5) or 100 mM MES (pH 6.0-6.5) to mimic physiological pH ranges
Precipitants: PEG series (PEG 3350, PEG 4000, PEG 8000) at 10-25% concentrations
Salt additives: 200 mM lithium sulfate, ammonium sulfate, or sodium chloride
Optimization strategies:
Microseeding to improve crystal quality and size
Hanging-drop and sitting-drop vapor diffusion in parallel
Consider inclusion of substrate analogs or inhibitors to stabilize the protein
Addition of 10-15% glycerol or similar cryoprotectants directly in crystallization condition
Co-crystallization considerations:
Including catalytically inactive substrate analogs
Testing with ACP substrate or mimics to capture physiologically relevant states
Success in crystallization will likely require extensive screening and optimization, particularly given the potential adaptations of C. burnetii fabF to acidic environments.
Computational approaches offer valuable insights when experimental structural data is limited:
Homology modeling:
Molecular dynamics simulations:
Assess protein stability under various pH conditions to investigate acid adaptation
Evaluate substrate binding dynamics and identify key interaction residues
Simulate conformational changes during catalytic cycles
Virtual screening for inhibitors:
Generate pharmacophore models based on known β-ketoacyl-ACP synthase inhibitors
Perform structure-based virtual screening to identify potential antimicrobial compounds
Predict binding modes and affinities of candidate inhibitors
Integration with experimental data:
Refine models based on limited experimental data (CD spectroscopy, HDX-MS)
Guide mutagenesis experiments by identifying functionally important residues
Predict the impact of amino acid substitutions on enzyme activity and stability
This integrated computational-experimental approach is particularly valuable for difficult-to-crystallize proteins from pathogens like C. burnetii.
Multiple complementary assays can be employed to characterize C. burnetii fabF activity:
Spectrophotometric coupled assays:
Monitor the release of CoA via reaction with 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB) at 412 nm
Couple the reaction to ACP consumption through fluorescently labeled ACP
Radioactive assays:
Use [14C]-malonyl-CoA to monitor incorporation into growing fatty acid chains
Quantify radiolabeled products via TLC separation followed by autoradiography
LC-MS based assays:
Direct detection of acyl-ACP products with different chain lengths
Identification of specific fatty acid profiles produced under various conditions
| Assay Type | Sensitivity | Throughput | Equipment Requirements | Key Advantages |
|---|---|---|---|---|
| DTNB-coupled | Medium | High | Standard spectrophotometer | Real-time monitoring, economical |
| Radioactive | Very high | Low | Scintillation counter, TLC equipment | Highly sensitive, detects all products |
| LC-MS | High | Medium | LC-MS system | Identifies product spectrum, no radioactivity |
| Fluorescent ACP | High | Medium-high | Fluorescence plate reader | Good for inhibitor screening |
When characterizing C. burnetii fabF, it's particularly important to assess activity under acidic conditions (pH 4.5-5.5) that mimic its native phagolysosomal environment, in addition to standard conditions.
While specific comparative data is not provided in the search results, we can outline an experimental approach to address this question:
pH profile determination:
Test enzymatic activity across pH range 4.0-9.0 using appropriate buffer systems
Compare with E. coli and other bacterial fabF enzymes under identical conditions
Hypothesize: C. burnetii fabF likely maintains higher relative activity at acidic pH (4.5-5.5) compared to homologs from neutralophilic bacteria
Temperature profile analysis:
Assess activity at temperatures ranging from 25°C to 50°C
Determine thermal stability through inactivation kinetics studies
Compare thermostability with the T. thermophilus enzyme (which likely has high thermostability)
Expected differences:
C. burnetii fabF likely exhibits adaptive features for function in acidic environments
The enzyme may show altered substrate specificity reflecting the intracellular availability of precursors
Regulatory mechanisms may differ from those of free-living bacteria
These comparative studies would provide insights into how C. burnetii has adapted its fatty acid biosynthesis machinery to its unique intracellular lifestyle and the acidic environment of the CCV.
While direct experimental evidence on C. burnetii fabF's role in pathogenesis is not detailed in the search results, we can propose the following based on general bacterial physiology and specific information about C. burnetii:
Membrane lipid composition adaptation:
Survival in acidic environment:
Specialized membrane fatty acids synthesized through the fabF pathway may contribute to acid resistance
The composition of membrane lipids directly impacts proton permeability and cellular pH homeostasis
Interface with host cell metabolism:
Potential coordination with T4SS:
Experimental approaches to verify these proposed roles could include:
Creating conditional fabF mutants and assessing CCV formation
Lipidomic analysis comparing wild-type and fabF-depleted C. burnetii
Examining membrane properties and acidic resistance in strains with altered fabF expression
Based on understanding bacterial pathogenesis and fatty acid metabolism, we can propose several mechanisms by which fabF may contribute to C. burnetii's virulence:
Membrane integrity and stress resistance:
Lipid-based immune modulation:
Energy storage and metabolic flexibility:
FabF contributes to the synthesis of fatty acids that serve as energy reserves
This supports C. burnetii's ability to persist in various environments and transition between developmental forms
Interface with T4SS function:
Experimental approaches to validate these hypotheses could include comparing the virulence of wild-type C. burnetii with strains having altered fabF expression in cellular and animal models of Q fever.
The ability of C. burnetii to not just survive but thrive within the acidic phagolysosomal environment is central to its pathogenesis. FabF likely plays several key roles in this adaptation:
Acid-resistant membrane composition:
FabF-dependent fatty acid synthesis contributes to a membrane lipid composition that maintains integrity under acidic stress
The specific fatty acid profile may reduce proton permeability and help maintain cellular pH homeostasis
Support for CCV expansion:
Metabolic adaptation to available nutrients:
Coordination with structural support systems:
Research approaches to investigate these relationships could include proteomic and transcriptomic analyses comparing C. burnetii grown in axenic media versus intracellular conditions, focusing on changes in fabF expression and fatty acid biosynthesis pathways.
The search results indicate that β-ketoacyl-ACP synthases like fabF are "promising targets for the development of new antibacterial agents" . Several factors support fabF as a potential drug target against C. burnetii:
Advantages of targeting fabF:
Essential metabolic function: Fatty acid biosynthesis is likely essential for C. burnetii survival and replication
Structural targetability: As an enzyme, fabF offers defined active sites for inhibitor binding
Reduced resistance potential: Target-based resistance might incur significant fitness costs for an intracellular pathogen
Selectivity potential: Differences between bacterial and human fatty acid synthesis pathways enable selective targeting
Strategic considerations:
Delivery challenges: Inhibitors must penetrate host cells and the CCV to reach the target
Synergy potential: Combining fabF inhibitors with current Q fever treatments (doxycycline, hydroxychloroquine) might enhance efficacy
Repurposing opportunity: Existing antimicrobial compounds targeting fabF in other bacteria could be evaluated against C. burnetii
| Advantages | Challenges | Mitigation Strategies |
|---|---|---|
| Essential target | Intracellular delivery | Liposomal formulations |
| Defined binding sites | Potential host toxicity | Structure-based design for selectivity |
| Low resistance potential | Redundant pathways | Target multiple fatty acid synthesis enzymes |
| Different from current targets | Slow growth complicates testing | Develop specialized screening assays |
Testing this strategy would require developing cell-based assays that can distinguish between host toxicity and specific anti-C. burnetii activity of potential fabF inhibitors.
Methodological approach:
Vector design considerations:
Create shuttle vectors containing Cas9 under control of the C. burnetii promoter
Design sgRNAs targeting fabF with minimal off-target effects
Include homology-directed repair templates for precise gene editing
Delivery methods:
Verification strategies:
PCR-based genotyping and sequencing to confirm intended modifications
Phenotypic characterization using fatty acid profiling
Monitoring growth curves in ACCM-2 medium and within host cells
Research applications:
Generate conditional knockdowns to assess essentiality
Introduce point mutations to study structure-function relationships
Create reporter fusions to monitor fabF expression and regulation
The development of clean deletion mutants, as described for the AnkF effector protein in the search results , could serve as a methodological template for fabF manipulation.
Metabolomics offers powerful approaches to understand fabF's role in C. burnetii's complex metabolic network:
Experimental design for metabolomic studies:
Sample preparation approaches:
Compare wild-type C. burnetii with fabF-modified strains (knockdown or overexpression)
Analyze samples from both axenic cultures and intracellular bacteria
Include time-course sampling to capture dynamic metabolic shifts
Analytical techniques:
Expected insights:
Identification of fabF-dependent fatty acid profiles specific to C. burnetii
Elucidation of metabolic rerouting mechanisms when fabF activity is compromised
Discovery of connections between fatty acid metabolism and other pathways
Integration with other omics data:
Correlate metabolomic changes with transcriptomic responses
Identify regulatory networks controlling fabF expression
Map protein-protein interactions involving fabF in the metabolic network
The isotopolog profiling approach mentioned in search result would be particularly valuable for tracing carbon flow through fabF-catalyzed reactions in C. burnetii's "bipartite metabolic network."
Understanding host-pathogen interactions involving fabF requires investigating several potential mechanisms:
Host fatty acid availability effects:
Design experiments to alter host cell fatty acid composition and monitor impacts on C. burnetii replication
Use stable isotope labeling to track incorporation of host-derived fatty acids into bacterial lipids
Compare fatty acid uptake versus de novo synthesis via fabF under various conditions
Interaction with host cytoskeletal elements:
The search results indicate that vimentin and other cytoskeletal components are recruited to the CCV
Investigate whether membrane composition, influenced by fabF activity, affects these interactions
Utilize super-resolution microscopy techniques like STED (mentioned in search result ) to visualize these interactions
Response to host defense mechanisms:
Examine how fabF activity is modulated in response to host-induced stresses
Investigate potential interactions between fabF-dependent membrane composition and host antimicrobial factors
Analyze fatty acid profiles in response to host immune signaling molecules
Temporal dynamics during infection:
Monitor fabF expression and activity throughout the C. burnetii infection cycle
Correlate with CCV maturation stages and bacterial developmental transitions
Identify key transition points where fabF activity becomes critical for pathogen success
These investigations would benefit from the application of techniques like those used to study the AnkF effector protein's interactions with host cell components, as described in search result .
Comparative analysis provides insights into pathogen-specific adaptations:
Methodological approach for comparative studies:
Sequence and structural comparisons:
Perform phylogenetic analysis of fabF across diverse intracellular pathogens
Identify conserved catalytic residues versus variable regions
Conduct homology modeling to predict structural differences
Heterologous expression studies:
Express fabF genes from different intracellular pathogens in a common host
Compare enzymatic parameters and substrate preferences
Assess complementation efficiency in fabF-deficient bacterial strains
Expected differences among intracellular pathogens:
Mycobacterium tuberculosis fabF likely shows adaptations for long-term persistence
Chlamydia trachomatis may have evolved fabF to function with limited substrate availability
Legionella pneumophila fabF might share features with C. burnetii given their phylogenetic relationship mentioned in search result
Relevance to pathogenesis:
Correlate fabF differences with pathogen-specific growth rates and persistence mechanisms
Identify unique features that might explain tissue tropism or disease manifestations
Evaluate potential as universal versus pathogen-specific drug targets
This comparative approach would help identify which features of C. burnetii fabF represent general adaptations to intracellular life versus specific adaptations to the unique phagolysosomal niche.
Evolutionary analysis of fabF provides insights into adaptation mechanisms:
Methodological approaches:
Phylogenetic analysis:
Construct maximum likelihood trees using fabF sequences from diverse Coxiella isolates
Calculate selection pressures (dN/dS ratios) to identify regions under positive selection
Perform ancestral sequence reconstruction to trace evolutionary trajectories
Comparative genomics:
Analyze synteny and genome context of fabF across Coxiella species
Identify horizontal gene transfer events that might have influenced fabF evolution
Compare with environmental Coxiella-like organisms to understand pre-adaptation
Structural biology integration:
Map evolutionary changes onto protein structural models
Identify co-evolving residues that maintain protein function
Predict how sequence variations influence catalytic efficiency and substrate specificity
Experimental validation:
Express ancestral and variant fabF proteins to compare enzymatic properties
Test complementation efficiency in heterologous systems
Correlate genetic variations with fatty acid profiles and virulence traits
Such evolutionary studies could reveal how C. burnetii fabF has adapted to the unique challenges of obligate intracellular growth and the acidic environment of the CCV.
Understanding structural and functional diversity of fabF has important implications for drug development:
Key considerations for structure-based drug design:
Conservation analysis:
Identify highly conserved regions across fabF from diverse pathogens
Target these regions for broad-spectrum inhibitor development
Map species-specific variations that could affect inhibitor binding
Active site comparison:
Analyze substrate binding pocket differences that might enable selective targeting
Design inhibitors exploiting unique features of C. burnetii fabF
Consider the impact of the acidic CCV environment on inhibitor binding kinetics
Resistance mechanism prediction:
Identify potential resistance-conferring mutations based on natural fabF variants
Design inhibitor scaffolds less susceptible to resistance development
Target multiple sites simultaneously to create higher genetic barriers to resistance
Experimental validation approaches:
Test candidate inhibitors against recombinant fabF enzymes from multiple species
Utilize thermal shift assays to compare binding affinities across orthologs
Employ structure-activity relationship studies to optimize selectivity profiles
| Targeting Strategy | Advantages | Challenges | Bacterial Species Considerations |
|---|---|---|---|
| Conserved catalytic site | Broad-spectrum activity | Higher host toxicity risk | Similar across most bacteria |
| Species-specific pockets | Reduced side effects | Narrower activity spectrum | Requires detailed structural data |
| Allosteric sites | Novel mechanism of action | More difficult to identify | Highly variable across species |
| Covalent inhibitors | Higher potency, longer effect | Potential immunogenicity | Depends on presence of reactive residues |
This comparative analysis would help develop antimicrobials that effectively target C. burnetii while minimizing impacts on beneficial bacteria or host enzymes.
Several cutting-edge approaches could advance our understanding of C. burnetii fabF:
CRISPRi-based conditional knockdown systems:
Develop inducible fabF repression to study essentiality at different life cycle stages
Create partial inhibition models to identify threshold levels needed for survival
Combine with transcriptomics to identify compensatory mechanisms
Advanced microscopy techniques:
Single-cell analysis approaches:
Develop methods to isolate and analyze individual bacteria from the CCV
Apply single-cell transcriptomics to identify population heterogeneity in fabF expression
Correlate with bacterial developmental forms and replication states
In vivo infection models:
Utilize animal models of Q fever to study fabF expression during actual infection
Develop tissue-specific sampling and analysis methods
Correlate fabF activity with disease progression and persistence
These approaches would build upon the methodological foundations described in the search results, particularly the techniques used to study C. burnetii's intracellular niche and the role of effector proteins like AnkF .
Several knowledge gaps represent opportunities for groundbreaking research:
Regulatory networks controlling fabF expression:
Identify transcription factors and small RNAs regulating fabF
Elucidate environmental signals that modulate fatty acid synthesis
Map the integration of fabF regulation with the broader metabolic network
Temporal dynamics during developmental transitions:
C. burnetii undergoes morphological transitions between small cell variant (SCV) and large cell variant (LCV) forms
The role of fabF in these transitions remains poorly understood
Changes in membrane composition may be critical for these developmental shifts
Connections with virulence mechanisms:
Metabolic interactions with the host:
Competition for or scavenging of fatty acid precursors
Incorporation of host-derived fatty acids into bacterial membranes
Influence on host lipid metabolism and signaling
These investigations would complement the existing work on C. burnetii's "bipartite metabolic network" mentioned in search result and could reveal new therapeutic targets.
Systems biology offers powerful frameworks for integrating diverse data types: