ATP synthase subunit c (atpE) is a membrane-embedded component of the F₀ sector of ATP synthase, facilitating proton translocation during ATP production. In Prochlorococcus marinus subsp. pastoris, a marine cyanobacterium, this subunit is encoded by the atpE gene (UniProt ID: Q7V033) and consists of 81 amino acids . The recombinant version is fused with an N-terminal His tag for purification and detection .
Hydropathy Profile: Highly hydrophobic, consistent with its role in membrane proton channel formation .
Stability: Requires storage at -20°C/-80°C in Tris/PBS buffer with 6% trehalose to prevent aggregation .
Lysis: Sonication in Tris/PBS buffer.
Buffer Exchange: Lyophilized into powder form for long-term storage .
Enzyme Activity Assays: Study of ATP synthase proton translocation efficiency .
Structural Studies: NMR/X-ray crystallography to resolve membrane protein dynamics .
Antibody Production: Immunogen for raising anti-atpE antibodies .
Genomic Context: The atpE gene is part of a conserved operon in Prochlorococcus spp., reflecting adaptation to oligotrophic marine environments .
Ecotype Variation: LL-adapted Prochlorococcus strains (e.g., MIT9303) show larger genomes but retain atpE sequence homology .
Species | Prochlorococcus marinus subsp. pastoris | Bacillus caldotenax |
---|---|---|
UniProt ID | Q7V033 | P41015 |
Sequence Length | 81 aa | 72 aa |
Key Residues | GAVEGIARQPEAEGKIRGTLLLSFAFM | GLGALGAGIGNGLIVSR |
Expression Host | E. coli | E. coli |
KEGG: pmm:PMM1455
STRING: 59919.PMM1455
ATP synthase subunit c (atpE) in Prochlorococcus marinus is a critical component of the organism's ATP synthesis machinery. The significance stems from Prochlorococcus being potentially the most abundant photosynthetic organism on the planet, responsible for a substantial fraction of global photosynthesis . The c-subunit forms an oligomeric ring embedded in the thylakoid membrane, where its rotation—driven by proton translocation across the membrane—mechanically couples to ATP synthesis . This coupling mechanism is central to understanding photosynthetic energy conversion in marine ecosystems. Studying atpE from Prochlorococcus provides insights into how this abundant organism has evolutionarily optimized its energy metabolism for survival in oligotrophic ocean environments.
The c-ring stoichiometry in ATP synthases varies considerably across different organisms, which directly affects the bioenergetic efficiency of ATP production. The ratio of protons translocated to ATP synthesized depends on the number of c-subunits (n) in the oligomeric c-ring (c₍ₙ₎), which is organism-dependent . While the exact c-ring stoichiometry for Prochlorococcus marinus has not been definitively established in the provided literature, this variability is inherently related to the organism's metabolism. The factors that contribute to this stoichiometric variation remain incompletely understood . Comparative analyses between Prochlorococcus and other cyanobacteria, as well as chloroplasts from higher plants (such as spinach with 14 c-subunits), can provide evolutionary insights into how different photosynthetic organisms optimize their ATP production based on their ecological niches.
For hydrophobic membrane proteins like ATP synthase subunit c, several expression systems have proven effective. The most successful approach documented involves using a fusion protein strategy in E. coli. Specifically, the hydrophobic c₁ subunit can be expressed as a soluble MBP-c₁ fusion protein (maltose binding protein fusion), then cleaved from MBP and purified on a reversed phase column . This strategy enables the soluble expression of eukaryotic membrane proteins in BL21 derivative E. coli cells. For cyanobacterial proteins specifically, various promoter systems have been tested with different efficacies. The Ptrc promoter has shown high expression levels for heterologous proteins in cyanobacteria, although it sometimes lacks tight regulation . Metal-inducible promoters like PpetE, Pcoa, and Psmt offer tighter repression but may yield lower expression levels even when induced .
For optimal recombinant expression of ATP synthase subunit c from Prochlorococcus marinus in E. coli, a carefully designed experimental protocol is essential. Based on successful approaches with similar proteins, the recommended procedure includes:
Codon optimization: The atpE gene should be codon-optimized for E. coli expression to enhance translation efficiency, as has been demonstrated with similar membrane proteins .
Fusion protein design: Express the hydrophobic c-subunit as a fusion with maltose binding protein (MBP) to increase solubility. This approach has successfully produced significant quantities of purified c₁ subunit with correct α-helical secondary structure .
Expression vector selection: Use a vector with an inducible promoter system that provides tight regulation and high expression. The IPTG-inducible system (Ptrc or optimized variants) has shown up to 360-fold induction in some cyanobacterial systems and may work effectively for expressing cyanobacterial proteins in E. coli .
Expression conditions: Transform the construct into BL21 derivative E. coli cells, which have been successfully used for similar membrane proteins . Culture at lower temperatures (18-25°C) after induction to allow proper protein folding and reduce inclusion body formation.
Induction protocol: For IPTG-inducible systems, titrate IPTG concentration between 1 μM and 10,000 μM to determine optimal expression levels, as this range has been effective for cyanobacterial promoters .
The optimal purification strategy for recombinant ATP synthase subunit c (atpE) from Prochlorococcus marinus combines several techniques to achieve high yield and purity:
Initial purification of fusion protein: Affinity chromatography using an amylose resin for MBP-fusion proteins allows selective binding of the fusion construct while leaving most bacterial proteins in the flow-through .
Proteolytic cleavage: After initial purification, cleave the fusion tag using a specific protease (such as TEV or Factor Xa) with optimized buffer conditions to maintain protein solubility during cleavage .
Reversed-phase chromatography: The cleaved atpE protein can be purified to high homogeneity using reversed-phase column chromatography, which has proven effective for hydrophobic membrane proteins like the c-subunit .
Quality control steps: Confirm the correct α-helical secondary structure of the purified protein using circular dichroism spectroscopy, as has been done with spinach chloroplast ATP synthase c-subunit .
This multi-step approach has yielded significant quantities of highly purified c₁ subunit with verified secondary structure in previous studies with similar proteins .
Optimizing the ribosome binding site (RBS) for efficient translation of atpE in cyanobacterial expression systems requires careful consideration of several factors:
RBS sequence compatibility: Cyanobacteria (including PCC 7942, PCC 7120, and PCC 6301) have a 16S rRNA sequence of ACCTCCTTT that pairs with mRNA, suggesting that an optimal RBS would contain AGGAGG in the central region, similar to the consensus prokaryotic sequence .
Computational prediction tools: Utilize thermodynamic models such as the RBS Calculator, RBS Designer, or UTR Designer to predict translation efficiency. These tools calculate free energies for interactions between mRNA and rRNA and utilize RNA folding software to predict mRNA secondary structure .
Empirical validation: While computational tools show good correlation with expression levels in E. coli (R² values of 0.84-0.87), they are not perfect for cyanobacteria. Therefore, construct and test a small library of RBS variants to empirically determine the optimal sequence for atpE expression .
Consideration of mRNA secondary structure: Ensure that the mRNA region around the start codon lacks strong secondary structures that could impede ribosome binding. Software tools can predict these structures and their impact on translation initiation .
Translation coupling: If appropriate, consider placing atpE downstream of a well-translated gene with optimal spacing to leverage translation coupling effects .
This combined computational and empirical approach can significantly improve translation efficiency for atpE expression in cyanobacterial systems.
Studying the oligomerization properties of recombinant ATP synthase subunit c (atpE) requires specialized techniques for membrane protein analysis:
Detergent-based reconstitution: Purified atpE can be reconstituted into detergent micelles (using mild detergents like DDM or CHAPS) to maintain protein solubility while allowing oligomerization. The choice of detergent is critical, as it must maintain the native-like environment for proper c-ring assembly.
Cross-linking studies: Chemical cross-linking followed by SDS-PAGE or mass spectrometry can identify interacting residues and provide insights into the oligomeric structure. This approach can verify the formation of c-subunit rings and potentially determine the number of subunits per ring.
Analytical ultracentrifugation: This technique can determine the molecular mass of the oligomeric complex in detergent solution, helping to establish the stoichiometry of c-subunits in the assembled ring.
Cryo-electron microscopy: Single-particle cryo-EM has emerged as a powerful tool for structural analysis of membrane protein complexes. For the c-ring, this technique can reveal the number of subunits and their arrangement within the oligomeric complex.
Native mass spectrometry: Native MS can determine the intact mass of the c-ring complex, providing direct evidence of the oligomeric state when the complex is transferred from a detergent or amphipol environment into the gas phase.
These techniques, often used in combination, can provide comprehensive information about the stoichiometry and structure of the oligomeric c-ring formed by recombinant atpE protein.
CRISPR interference (CRISPRi) offers a powerful approach for studying atpE function through targeted gene repression in Prochlorococcus marinus:
Inducible CRISPRi system design: Develop an inducible CRISPRi system using anhydrotetracycline (aTc) as the inducer, which has been successfully implemented in other cyanobacteria with up to 32-fold induction in PCC 7002 and >1,200-fold induction in PCC 7120 .
sgRNA design for atpE targeting: Design single guide RNAs (sgRNAs) targeting the promoter region or early coding sequence of atpE. Multiple sgRNAs should be tested to identify those providing optimal repression efficiency.
dCas9 expression optimization: Express catalytically inactive Cas9 (dCas9) under a promoter that provides appropriate expression levels. Low-level expression is crucial, as high dCas9 levels can cause maximal repression even without inducer presence .
Titration of repression: Use varying concentrations of aTc (between 0-2,000 ng/mL) to achieve different levels of atpE repression, enabling the study of phenotypic effects across a spectrum of ATP synthase activity levels .
Phenotypic analysis: Monitor changes in growth rate, photosynthetic efficiency, ATP production, and membrane potential in response to atpE repression. This approach can reveal the physiological consequences of reduced ATP synthase activity.
Compensatory mechanisms: Analyze transcriptomic and proteomic changes following atpE repression to identify potential compensatory mechanisms that Prochlorococcus employs to maintain energy homeostasis.
Determining the c-ring stoichiometry in Prochlorococcus marinus presents several technical challenges with potential solutions:
Challenge: Membrane protein crystallization
Traditional crystallography is difficult with hydrophobic membrane proteins
Solution: Utilize lipidic cubic phase crystallization or cryo-electron microscopy, which has recently yielded high-resolution structures of c-rings from other organisms
Challenge: Low natural abundance
Challenge: Assembly verification
Ensuring that recombinantly expressed c-subunits assemble into the native oligomeric state
Solution: Combine cross-linking mass spectrometry with native mass spectrometry to verify correct assembly and stoichiometry
Challenge: Environmental adaptation
c-ring stoichiometry might vary with environmental conditions
Solution: Culture Prochlorococcus under different light, temperature, and nutrient conditions to assess potential stoichiometric plasticity
Challenge: Genetic intractability
The exact cause of c-ring stoichiometric variation across organisms remains incompletely understood . Novel integrative approaches combining structural biology, molecular dynamics simulations, and evolutionary analysis may help elucidate the factors driving c-ring stoichiometry determination in Prochlorococcus and its ecological significance.
The ATP synthase subunit c (atpE) from Prochlorococcus marinus shows interesting evolutionary features when compared to other photosynthetic organisms:
Sequence conservation patterns:
The transmembrane helices show higher conservation than loop regions
The essential proton-binding glutamate residue is universally conserved across species
Prochlorococcus, as the smallest known photosynthetic organism with a highly streamlined genome, may show sequence adaptations reflecting its specialized marine lifestyle
Structural considerations:
The α-helical secondary structure is maintained across species, reflecting the functional importance of this structural feature
The c-ring size (number of c-subunits) varies between organisms, affecting the bioenergetic efficiency of ATP production
This stoichiometric variation is inherently related to the metabolism of each organism
Evolutionary implications:
Prochlorococcus has undergone genome reduction during evolution, potentially affecting components of its ATP synthase
Analysis of its atpE sequence may provide insights into adaptations for survival in low-nutrient, high-light marine environments
The c-ring stoichiometry variability likely represents different evolutionary solutions to balancing ATP synthesis efficiency with cellular energy demands
Comparative genomic and structural studies of atpE across diverse photosynthetic organisms can illuminate how evolutionary pressures have shaped this critical component of the cellular energy production machinery.
Expression strategies for atpE differ significantly between heterotrophic E. coli and photosynthetic Prochlorococcus systems:
While E. coli systems offer higher biomass and potentially higher protein yields, expression in Prochlorococcus or related cyanobacteria may provide advantages for proper folding, assembly, and function of atpE in its native context.
Optimization strategies for heterologous expression of ATP synthase subunit c vary based on specific research objectives:
For structural studies:
Focus on high protein yield and purity
Use fusion tags that can be completely removed without leaving additional residues
Express in E. coli with MBP fusion for solubility, followed by reversed-phase chromatography purification
Consider adding stabilizing mutations if the protein shows instability
Optimize detergent selection for maintaining native-like structure
For functional reconstitution:
Express in systems that maintain proper folding and assembly
Optimize the lipid environment for reconstitution experiments
Consider co-expression with other ATP synthase subunits to facilitate proper assembly
Use milder purification conditions to preserve protein-protein interactions
Implement quality control steps to verify correct α-helical secondary structure
For evolutionary studies:
Express c-subunits from multiple species under identical conditions
Standardize expression and purification protocols across all variants
Include positive controls (e.g., well-characterized c-subunits) for comparison
Design chimeric constructs to identify determinants of c-ring stoichiometry
Develop assays to quantify oligomerization properties
For in vivo studies in cyanobacteria:
Develop inducible expression systems with tight regulation
Optimize promoter strength based on experimental needs
For high expression, modified heterologous promoters like Ptrc may be preferable
For tight regulation, aTc-inducible systems can provide up to 1,200-fold induction
Consider genetic stability issues and monitor for mutations during long-term expression
Each research objective requires specific optimization strategies, and researchers should carefully select the expression system based on their experimental requirements.
Recombinant expression of ATP synthase subunit c presents several challenges that researchers commonly encounter:
Protein aggregation and inclusion body formation
Low expression levels
Genetic instability
Improper folding
Inefficient fusion tag cleavage
Problem: Protease accessibility to cleavage sites may be limited
Solution: Design constructs with extended linkers between the fusion and target protein; optimize cleavage conditions including detergent selection; test multiple proteases
Poor yield after final purification
Problem: Significant loss during purification steps
Solution: Optimize each step of the purification protocol; consider alternative chromatography methods; minimize sample handling and transfers
Promoter leakiness in inducible systems
Addressing these challenges requires systematic optimization and careful monitoring throughout the expression and purification process.
Troubleshooting c-ring assembly issues in reconstitution experiments requires a systematic approach to identify and address specific problems:
Issue: No detectable oligomerization
Diagnostic approach: Use size-exclusion chromatography or native PAGE to assess oligomeric state
Potential solutions:
Optimize detergent type and concentration
Test different lipid compositions in reconstitution mixtures
Verify protein integrity using mass spectrometry
Adjust pH and ionic conditions to promote assembly
Consider adding ATP synthase a-subunit, which may stabilize c-ring assembly
Issue: Incorrect stoichiometry or heterogeneous assemblies
Diagnostic approach: Analyze using native mass spectrometry or analytical ultracentrifugation
Potential solutions:
Modify reconstitution protocol to allow equilibration over longer periods
Test reconstitution at different protein-to-lipid ratios
Use gentle detergent removal techniques (dialysis or Bio-Beads)
Try different pH conditions, as protonation state of key residues may affect assembly
Issue: Aggregation during reconstitution
Diagnostic approach: Monitor using dynamic light scattering or turbidity measurements
Potential solutions:
Decrease protein concentration during reconstitution
Implement step-wise detergent removal
Add stabilizing agents like glycerol or specific lipids
Use more gentle detergents for initial solubilization
Issue: Non-functional assembled rings
Diagnostic approach: Assess proton translocation activity in liposomes
Potential solutions:
Verify correct orientation in liposomes using protease protection assays
Optimize lipid composition to match native environment
Check for post-translational modifications that might be required for function
Consider co-reconstitution with other ATP synthase subunits
Issue: Poor reproducibility
Diagnostic approach: Carefully control all variables and document conditions
Potential solutions:
Standardize protein preparation methods
Use consistent detergent and lipid lots
Control temperature throughout the reconstitution process
Develop quantitative assays to measure assembly efficiency
These troubleshooting approaches address the complex challenges of membrane protein reconstitution and can significantly improve success rates in c-ring assembly experiments.
Genetic instability is a significant challenge when expressing heterologous proteins in cyanobacteria, but several strategies can mitigate this issue:
Codon optimization
Inducible expression systems
Promoter selection
Neutral genomic integration sites
Problem: Integration into sensitive genomic regions can disrupt essential functions
Solution: Target neutral integration sites that minimize disruption to the host metabolism
Toxicity reduction
Problem: Protein products or intermediates may be toxic
Solution: Include efflux pumps or sequestration mechanisms; co-express chaperones to improve folding; target protein to appropriate subcellular locations
HIP1 sequence avoidance
Regular verification
Problem: Mutations can accumulate silently
Solution: Implement regular PCR screening and sequencing of transgenes; monitor protein expression/activity; use antibiotic selection carefully
Strain engineering
Problem: Wild-type DNA repair mechanisms may promote recombination
Solution: Consider engineering strains with modified recombination pathways to enhance genetic stability
By implementing these strategies, researchers can significantly improve the genetic stability of heterologous protein expression in cyanobacterial systems, enabling more robust and reproducible experiments with recombinant ATP synthase components.
Several cutting-edge technologies are poised to revolutionize our understanding of ATP synthase c-subunit structure and function in Prochlorococcus marinus:
Cryo-electron tomography (cryo-ET)
This technique allows visualization of ATP synthase complexes in their native membrane environment
Recent advances in sub-tomogram averaging could reveal the c-ring stoichiometry and arrangement in situ
The application to Prochlorococcus cells could provide insights into the native conformation without artificial reconstitution
Single-molecule biophysics
Single-molecule FRET can measure conformational changes during c-ring rotation
Magnetic tweezers or optical traps could directly measure the mechanical properties of the c-ring
These approaches could reveal how the c-ring's unique properties in Prochlorococcus contribute to its ecological adaptation
Integrative structural biology
Combining multiple structural techniques (X-ray crystallography, cryo-EM, NMR, and mass spectrometry)
Computational integration of data from different methods can generate more complete structural models
This could reveal subtle structural features unique to Prochlorococcus ATP synthase
Advanced genetic tools
Artificial intelligence for protein design
Machine learning approaches can predict the impact of mutations on c-ring assembly and function
AI-guided protein engineering could help design variants with altered properties for mechanistic studies
These computational approaches could guide experimental design more efficiently
Improved membrane mimetics
Novel nanodiscs or lipid cubic phase systems that better mimic the native thylakoid membrane
Customized lipid compositions matching the unique membrane environment of Prochlorococcus
These systems could provide more physiologically relevant reconstitution conditions
High-resolution native mass spectrometry
Direct measurement of intact c-rings with bound lipids and interacting proteins
Determination of precise stoichiometry and detection of post-translational modifications
This could resolve questions about c-ring size variability under different conditions
These emerging technologies, particularly when used in combination, hold tremendous promise for elucidating the unique adaptations of ATP synthase in this ecologically critical marine cyanobacterium.
Comparative studies of ATP synthase c-subunits across different Prochlorococcus ecotypes offer valuable insights into evolutionary adaptation:
These comparative approaches would significantly enhance our understanding of how this crucial enzyme has been fine-tuned during the evolution and diversification of Prochlorococcus across different ocean environments.
Engineered ATP synthase c-subunits offer several promising applications for fundamental bioenergetics research:
Designer c-rings with altered stoichiometry
Engineering c-subunits that assemble into rings with specific numbers of subunits
Studying how c-ring size affects proton-to-ATP ratio and bioenergetic efficiency
This approach could resolve longstanding questions about the relationship between structure and function in ATP synthases
Fluorescent protein fusions for real-time visualization
Creating functional fluorescent fusions to monitor c-ring dynamics
Visualizing ATP synthase distribution, movement, and turnover in living cells
These tools could provide unprecedented insights into ATP synthase behavior in vivo
Site-specific probes for mechanistic studies
Introducing unnatural amino acids at specific positions for spectroscopic studies
Using click chemistry to attach probes for monitoring conformational changes
These approaches could reveal details of the proton translocation and rotary mechanisms
Chimeric c-subunits
Synthetic ATP synthases with novel properties
Engineering c-subunits that respond to alternative energy sources
Creating systems with altered ion specificities (e.g., Na⁺ instead of H⁺)
These synthetic systems could expand our understanding of energy conversion mechanisms
Minimal ATP synthase models
Designing simplified c-rings to identify essential structural requirements
Creating minimal functional systems for detailed mechanistic studies
This reductionist approach could clarify fundamental principles of rotary motors
Inducible systems for in vivo regulation
Developing precisely controlled expression systems using optimized inducible promoters
Creating conditional mutants for studying ATP synthase function
These systems could enable temporal control of ATP synthase activity for studying cellular responses
Cross-species complementation
Expressing engineered Prochlorococcus atpE in other organisms
Assessing functional compatibility across evolutionary distances
This approach could reveal constraints and flexibilities in the evolution of this essential enzyme
These engineering approaches, facilitated by advances in recombinant expression systems and regulatory tools , promise to significantly advance our fundamental understanding of ATP synthase function and evolution.