KEGG: bba:Bd3847
STRING: 264462.Bd3847
Bdellovibrio bacteriovorus is a small Deltaproteobacterium (0.3-0.4 μm wide, 0.8-1.2 μm long) distinguished by its unique ability to prey on other Gram-negative bacteria . The Obg protein from B. bacteriovorus is an essential GTPase belonging to the TRAFAC class OBG-HflX-like GTPase superfamily . It has garnered scientific interest because it plays critical roles in cell cycle control, stress response, ribosome biogenesis, and morphogenesis control, particularly in bacteria that undergo differentiation . Given B. bacteriovorus' predatory lifestyle and unique biphasic life cycle (consisting of a free-living attack phase and an intraperiplasmic growth phase), its Obg GTPase may have specialized functions related to predation and intraperiplasmic growth regulation .
The Obg protein from B. bacteriovorus, like other Obg proteins, consists of three main domains:
N-terminal glycine-rich domain (Obg fold): A conserved domain characteristic of Obg proteins
Central G domain: Contains five conserved motifs (G1-G5) responsible for nucleotide binding and hydrolysis
C-terminal domain: Less conserved, likely involved in protein-specific functions
The G domain shows Ras-like folds with five α-helices and six-stranded β-sheets. Each G motif has specific functions:
G1: Responsible for alpha and beta interactions for guanine nucleotide binding
G2: Binding and coordinating Mg²⁺
G3 and G4: Performs canonical hydrolytic activity
The complete sequence of B. bacteriovorus Obg consists of 343 amino acids with a molecular mass of approximately 37.3 kDa .
B. bacteriovorus Obg is characterized by:
Moderate affinity binding of GTP, GDP, and possibly (p)ppGpp
High nucleotide exchange rates
Relatively low GTP hydrolysis rate compared to other GTPases
Cycling between GTP-bound "on" state and GDP-bound "off" state to control various cellular processes
These properties make it distinct from many other bacterial GTPases and suggest a role in signaling or regulatory functions rather than primarily catalytic ones.
To investigate Obg's role in B. bacteriovorus predation, researchers can employ several approaches:
Site-directed mutagenesis: Create specific mutations in the Obg gene (similar to those described for MglA in search result ) to identify key residues essential for function. Focus on conserved residues in G domains that correspond to known activating mutations in Ras-like GTPases (e.g., G21V, L22V equivalents) .
Predation efficiency assays: Compare wild-type and Obg-mutant strains for their ability to prey on Gram-negative bacteria using:
Gene expression analysis: Examine Obg expression during different stages of the predatory cycle using:
qRT-PCR
RNA-Seq comparing attack phase vs. growth phase expression
Proteomics to monitor Obg protein levels
Protein localization studies: Use fluorescent protein fusions or immunofluorescence microscopy to track Obg localization during predation, similar to approaches used for studying MglA localization .
GTPase activity assays: Measure GTP hydrolysis rates of purified recombinant Obg under various conditions to understand its biochemical regulation.
Expression and purification of functional B. bacteriovorus Obg can be achieved through the following protocol:
Cloning:
Amplify the obg gene (WP_011166147.1) from B. bacteriovorus genomic DNA
Clone into an appropriate expression vector with a histidine or other affinity tag
Verify sequence integrity
Expression system selection:
E. coli BL21(DE3) or similar strain is commonly used
Consider codon optimization for improved expression
Use autoinduction media or IPTG-inducible systems
Expression conditions optimization:
Test different temperatures (16-30°C)
Vary induction times (3-16 hours)
Test different inducer concentrations
Purification steps:
Lyse cells in appropriate buffer (typically 50 mM Tris-HCl pH 8.0, 300 mM NaCl, 10% glycerol)
Perform affinity chromatography (Ni-NTA for His-tagged protein)
Consider ion exchange chromatography as a second purification step
Perform size exclusion chromatography for highest purity
Protein activity verification:
Assess GTP binding using fluorescent GTP analogs
Measure GTPase activity using colorimetric phosphate release assays
Verify proper folding using circular dichroism spectroscopy
Commercially available recombinant B. bacteriovorus Obg can be obtained from vendors for controls or when in-house expression is challenging .
Mutations in conserved GTPase domains can significantly alter Obg function, as demonstrated by studies on related GTPases. The effects vary depending on the specific domain and residue affected:
G1 domain (P-loop) mutations:
Mutations equivalent to G21V in Ras (G12V) typically decrease GTP hydrolysis rates 7-fold or more
These mutations create a constitutively active form that remains GTP-bound longer
In B. bacteriovorus, such mutations may affect predation efficiency by disrupting normal cycling between active/inactive states
Switch region mutations:
Mutations in switch I and II regions (equivalent to those in the G2/G3 region) can render the protein insensitive to GAP proteins
This affects the rate of GTP hydrolysis in vivo by disrupting interaction with regulatory proteins
Studies on related GTPases show that these mutations can be dominant to wild-type protein
Nucleotide binding pocket mutations:
Surface residue mutations:
The study of these mutations provides insights into Obg's role in controlling B. bacteriovorus predatory cycle and stress responses.
The relationship between Obg's GTPase activity and B. bacteriovorus' predatory behavior likely involves several aspects:
Cell cycle coordination:
Obg likely helps coordinate the transition between the free-living attack phase and intraperiplasmic growth phase
Its GTPase activity may serve as a molecular switch that responds to prey encounter signals
Stress response during predation:
Ribosome biogenesis regulation:
Nutrient sensing:
Obg may sense nucleotide levels (GTP/GDP ratios) which reflect the metabolic state
This sensing could help regulate predation based on available resources
Studies of bacterial adaptation to starvation conditions show that evolved B. bacteriovorus populations develop enhanced starvation survival rather than improved killing efficiency
Understanding these relationships requires further research, including specific studies examining Obg activity during different predatory phases.
B. bacteriovorus Obg shares core functional domains with Obg proteins from non-predatory bacteria but may have evolved specialized features related to its predatory lifestyle:
Sequence conservation:
Functional divergence:
While all Obg proteins participate in stress response and ribosome biogenesis, B. bacteriovorus Obg likely has additional functions
These may include regulation of the biphasic lifecycle transitions and adaptation to intraperiplasmic growth
The predatory nature of B. bacteriovorus suggests its Obg protein may integrate signals related to prey detection or consumption
Structural adaptations:
Regulatory network differences:
The regulatory networks controlling Obg expression and activity likely differ between predatory and non-predatory bacteria
In non-predatory bacteria like E. coli, Obg concentration correlates with growth rate
In B. bacteriovorus, Obg regulation may be tied to predation cycle phases rather than simple growth rate
Comparative studies between B. bacteriovorus Obg and those from well-studied model organisms would provide valuable insights into predation-specific adaptations.
Several functional parallels exist between Obg and other GTPases involved in bacterial predation or motility:
Comparison with MglA GTPase:
MglA, a 22kDa Ras-related GTPase, controls motility in Myxococcus xanthus, another predatory bacterium
Like Obg, MglA functions as a molecular switch cycling between GTP-bound "on" and GDP-bound "off" states
Both proteins likely coordinate complex cellular behaviors in response to environmental cues
Mutations in conserved residues of MglA affect localization and function, providing a model for studying Obg
Role in coordinating cellular processes:
Both Obg and predatory-specific GTPases coordinate multiple cellular systems
While Obg primarily regulates ribosome biogenesis and stress responses, it may also influence cytoskeletal dynamics during predation
The spatial and temporal regulation seen in MglA may have parallels in Obg function during B. bacteriovorus predation cycle
Interaction with regulatory proteins:
Response to starvation conditions:
Both Obg and predatory movement-associated GTPases help bacteria respond to nutrient limitation
In evolved B. bacteriovorus populations, improved starvation survival was observed rather than enhanced predation efficiency
This suggests GTPases like Obg may prioritize survival under stress over predation efficiency
Studying these parallels provides a framework for understanding the specialized functions of GTPases in predatory bacteria.
Targeting Obg to modify B. bacteriovorus predation efficiency for biocontrol applications could be approached through several strategies:
Genetic engineering of obg expression levels:
Overexpression of wild-type obg may enhance metabolic rates and stress tolerance
Controlled expression using inducible promoters could create "tunable" predators
Expression timing could be optimized for different target bacteria or environments
Introduction of activity-enhancing mutations:
Creation of specialized Obg variants:
Chimeric proteins combining domains from different bacterial Obg proteins
Domain swapping experiments to identify regions responsible for specific functions
Directed evolution approaches to select for enhanced predation under specific conditions
System-level modifications:
Co-engineering of Obg and its interaction partners
Modification of regulatory pathways controlling Obg activity
Integration with other predation enhancement strategies
Application-specific optimization:
For biofilm targeting: Engineer Obg variants that enhance B. bacteriovorus survival in biofilm environments
For clinical applications: Develop strains with enhanced predation against specific pathogens
For environmental applications: Create variants optimized for different temperature, pH, or oxygen conditions
The natural resistance of B. bacteriovorus to β-lactam antibiotics also allows for potential combination therapies where both the predatory bacterium and conventional antibiotics are used together .
Obg likely plays significant roles in the evolution of B. bacteriovorus predation strategies:
Adaptation to selective pressures:
Studies on parallel evolution in B. bacteriovorus during long-term coculture showed mutations in several genes, potentially including those in regulatory networks involving Obg
Instead of evolving improved killing efficiency, B. bacteriovorus adapted to better withstand nutrient limitation
This suggests Obg's stress response function may be more critical for evolutionary fitness than its role in predation optimization
Balancing predation efficiency with survival:
Obg's dual role in stress response and cellular processes creates evolutionary trade-offs
Enhanced predation might come at the cost of reduced stress tolerance
Evolutionary pressures likely shape Obg function to balance these competing needs
Host range determination:
Resistance to counter-predation mechanisms:
Lifecycle variations:
Research on experimental evolution of B. bacteriovorus in different conditions could reveal how Obg functions have been shaped by selective pressures.
When studying B. bacteriovorus Obg function in predation assays, comprehensive controls should include:
Strain controls:
Wild-type B. bacteriovorus (positive control for normal predation)
Complemented Obg mutant strains (to verify phenotype rescue)
Non-predatory bacteria (negative predation control)
Host bacteria without predator (prey survival control)
Obg protein variant controls:
Catalytically inactive Obg mutant (e.g., mutations in G1 domain)
Constitutively active Obg variant (e.g., G21V equivalent)
Tagged Obg protein control (to verify tag doesn't affect function)
Environmental condition controls:
Predator-prey ratio controls:
Technical controls:
Microscopy: Fixed cells for comparison with live imaging
Plaque assays: Phage contamination controls
Gene expression: No reverse transcriptase controls for RT-PCR
Protein purification: Tag-only protein expression control
Specificity controls:
The experimental data from predation assays should be analyzed using appropriate statistical methods, with multiple biological and technical replicates to ensure reliability.
When working with recombinant B. bacteriovorus Obg protein, several physiological parameters should be optimized:
Buffer composition:
pH: Typically 7.0-8.0 to match the optimal pH range for B. bacteriovorus
Salt concentration: 150-300 mM NaCl is common for GTPases
Divalent cations: 5-10 mM MgCl₂ is essential for GTPase activity
Reducing agents: 1-5 mM DTT or β-mercaptoethanol to maintain cysteine residues
Stabilizers: 5-10% glycerol to improve protein stability
Nucleotide binding conditions:
GTP/GDP concentration: Typically 0.1-1 mM
Incubation time: Allow sufficient time for nucleotide binding (15-30 minutes)
Temperature: 25-30°C is optimal for most GTPase binding assays
GTPase activity measurement conditions:
Reaction time: Time course experiments to determine linear range
Temperature: Assay at physiologically relevant temperatures (30-35°C)
Enzyme concentration: Determine appropriate concentration for linear kinetics
Detection method: Colorimetric phosphate detection, HPLC, or coupled enzymatic assays
Protein stability factors:
Storage temperature: Typically -80°C for long-term, -20°C with glycerol for short-term
Freeze-thaw cycles: Minimize these as they can affect activity
Protein concentration: Higher concentrations often improve stability
Interaction studies parameters:
Partner proteins: Consider co-purification with known binding partners
Detergents: Low concentrations may be needed if membrane interactions are involved
Crowding agents: PEG or BSA can mimic cellular conditions
Structural analysis conditions:
For circular dichroism: Low salt buffers and appropriate protein concentration
For crystallization: Screen various precipitants, pH values, and temperatures
For NMR studies: Isotopic labeling and appropriate buffer conditions
These parameters should be systematically optimized for each specific application of the recombinant protein.
When facing contradictory results in Obg functional studies, researchers should implement the following reconciliation strategy:
Methodological differences analysis:
Compare experimental conditions between studies (buffer composition, temperature, pH)
Assess differences in protein preparation methods (expression system, purification protocol, tag position)
Evaluate assay methodologies (in vitro vs. in vivo, detection methods, time scales)
Strain-specific variations consideration:
Experimental design evaluation:
Sample size and statistical power analysis
Biological vs. technical replication strategies
Controls used and their appropriateness
Blinding and randomization procedures
Multi-method confirmation approach:
Validate key findings using orthogonal methods
For example, complement biochemical assays with genetic approaches
Consider in vivo, in vitro, and in silico methods to build a complete picture
Data integration framework:
Create models that can accommodate seemingly contradictory data
Consider that Obg may function differently under various conditions
Use mathematical modeling to test whether contradictions can be explained by different parameters
Common confounding factors:
Collaborative resolution:
Direct collaboration between labs with contradictory results
Exchange of materials (strains, proteins, reagents) to identify source of variation
Joint design of experiments to resolve discrepancies
By systematically addressing these aspects, apparently contradictory results can often be reconciled within a more comprehensive understanding of Obg function.
Common pitfalls in analyzing B. bacteriovorus Obg mutant phenotypes and their solutions include:
Suppressor mutations development:
Pitfall: Obg is essential, so mutants may develop compensatory mutations
Solution: Sequence verify strains before and after experiments; use freshly prepared cultures; implement conditional expression systems rather than complete knockouts
Pleiotropic effects misinterpretation:
Pitfall: Attributing all phenotypic changes directly to Obg when they may be downstream effects
Solution: Use multiple mutant types (point mutations vs. expression level changes); perform complementation with wild-type and mutant variants; examine effects on known Obg interaction partners
Growth phase variability:
Host-independent (HI) variant interference:
Pitfall: HI variants can arise spontaneously and confound predation assays
Solution: Regular checking for HI growth; plaque purification; prey-dependent cultivation methods
Predator-prey ratio inconsistencies:
Inadequate phenotypic assessment:
Pitfall: Focusing on a single aspect of predation while missing others
Solution: Comprehensive phenotyping including: predation efficiency, motility, prey range, bdelloplast formation, progeny release timing, and stress survival
Environmental condition variations:
Technical artifact misinterpretation:
Pitfall: Assay-specific artifacts being attributed to biological differences
Solution: Use multiple assay methods to confirm findings; include appropriate technical controls; blind analysis when possible
By anticipating these pitfalls and implementing the suggested solutions, researchers can generate more reliable and interpretable data from B. bacteriovorus Obg studies.
Several emerging technologies hold promise for advancing our understanding of Obg's role in bacterial predation:
Advanced microscopy techniques:
Super-resolution microscopy to track Obg localization during predation with nanometer precision
Correlative light and electron microscopy (CLEM) to connect Obg localization with ultrastructural features
Light sheet microscopy for long-term live imaging of predation with minimal phototoxicity
Single-cell technologies:
Single-cell RNA-seq to profile transcriptional changes in individual predatory cells
Single-cell proteomics to measure protein-level changes during predation
Microfluidic devices for tracking individual predator-prey interactions
Protein interaction mapping:
Proximity labeling techniques (BioID, APEX) to identify proteins near Obg during different predation phases
Hydrogen-deuterium exchange mass spectrometry to map conformational changes upon nucleotide binding
Single-molecule FRET to measure Obg conformational dynamics in real-time
Genetic engineering advances:
CRISPR-Cas9 genome editing for precise manipulation of obg and related genes
Optogenetic control of Obg activity to precisely time activation/inactivation during predation
Synthetic biology approaches to create B. bacteriovorus with engineered Obg variants for enhanced function
Computational approaches:
Molecular dynamics simulations of Obg-nucleotide interactions
Machine learning analysis of predation phenotypes to identify subtle effects of mutations
Systems biology modeling of the predation cycle including Obg regulation networks
Structural biology techniques:
Cryo-electron microscopy to solve structures of Obg in different nucleotide-bound states
In-cell NMR to observe Obg conformational changes inside living predatory cells
AlphaFold2 and other AI-based structure prediction to model Obg interactions with partners
These technologies, used in combination, could provide unprecedented insights into the dynamic functions of Obg during the complex process of bacterial predation.
Understanding B. bacteriovorus Obg function could contribute to developing novel antimicrobial strategies in several ways:
Enhanced predatory bacteria engineering:
B. bacteriovorus-antibiotic combination therapies:
Novel drug target identification:
Comparative analysis between predator and prey Obg could reveal unique vulnerabilities
Inhibitors targeting pathogen Obg but sparing predator Obg could create selective antimicrobials
The essential nature of Obg in bacteria makes it an attractive target
Biofilm eradication strategies:
Host-microbiome interaction optimization:
Resistance management strategies:
This research direction represents a promising alternative to conventional antibiotics, particularly for addressing multidrug-resistant infections.
| Data Type | Analytical Method | Application | Statistical Approach | Visualization |
|---|---|---|---|---|
| Enzyme Kinetics | Michaelis-Menten Analysis | Determining kcat and Km for GTP hydrolysis | Non-linear regression | Michaelis-Menten and Lineweaver-Burk plots |
| Binding Affinity | Isothermal Titration Calorimetry | Measuring thermodynamic parameters of nucleotide binding | Binding isotherms analysis | Thermogram and binding isotherm plots |
| Protein Localization | Image Analysis Software (ImageJ/Fiji) | Quantifying distribution patterns in cells | Intensity profile analysis | Heatmaps and intensity distribution plots |
| Predation Dynamics | Growth Curve Analysis | Comparing predation efficiency between strains | Two-way ANOVA with time as factor | Time-course curves with error bands |
| Gene Expression | ΔΔCt Method (qRT-PCR) | Comparing obg expression during different phases | t-test or ANOVA with post-hoc tests | Bar charts with fold-change |
| Evolutionary Genomics | Mutation Frequency Analysis | Identifying parallel evolution in obg | Fisher's exact test for enrichment | Manhattan plots of mutation frequency |
| Structural Comparisons | Protein Structure Alignment | Comparing Obg with other GTPases | RMSD calculations | Superimposed structure ribbon diagrams |
| Multi-omics Integration | Network Analysis | Connecting Obg function to global cellular processes | Enrichment analysis; network centrality | Interaction networks with highlighted modules |
| Sequence Conservation | Phylogenetic Analysis | Tracing Obg evolution across bacterial species | Maximum likelihood methods | Phylogenetic trees with bootstrap values |
| Phenotypic Data | Principal Component Analysis | Identifying patterns in mutant phenotypes | PERMANOVA for significance | Biplot of PC1 vs PC2 with vectors |