Recombinant Lodderomyces elongisporus 3-ketoacyl-CoA reductase (LELG_03198) is a protein derived from the yeast Lodderomyces elongisporus. This enzyme plays a crucial role in fatty acid biosynthesis by reducing 3-ketoacyl-CoA to form acyl-CoA, which is then further processed into various fatty acids. The recombinant form of this enzyme is produced in E. coli and is often tagged with a His-tag for easy purification and identification.
Species: Lodderomyces elongisporus
Source: Expressed in E. coli
Tag: N-terminal His-tag
Protein Length: Full-length (1-350 amino acids)
Form: Lyophilized powder
Purity: Greater than 90% as determined by SDS-PAGE
The recombinant LELG_03198 protein is a full-length enzyme with a molecular weight corresponding to its 350 amino acids. It is commonly used in research related to lipid metabolism and biosynthesis pathways.
LELG_03198 is involved in several biochemical pathways, primarily related to fatty acid biosynthesis. It acts as a 3-ketoacyl-CoA reductase, which is crucial for the elongation of fatty acid chains.
| Pathway Name | Description |
|---|---|
| Fatty Acid Biosynthesis | Reduction of 3-ketoacyl-CoA to acyl-CoA |
| Lipid Metabolism | Contributes to the synthesis of various lipids |
Proteins involved in similar pathways include other enzymes participating in fatty acid biosynthesis and lipid metabolism.
Recombinant LELG_03198 is used in research to study lipid metabolism and biosynthesis. Its applications include understanding the mechanisms of fatty acid elongation and its potential role in biotechnological processes.
Fatty Acid Production: Understanding how LELG_03198 contributes to fatty acid biosynthesis can aid in developing biotechnological methods for producing specific fatty acids.
Metabolic Engineering: This enzyme can be used in metabolic engineering approaches to modify lipid profiles in microorganisms.
Recombinant Lodderomyces elongisporus 3-ketoacyl-CoA reductase (LELG_03198) is a microsomal membrane-bound enzyme integral to the fatty acid elongation system. It is responsible for producing very long-chain fatty acids (VLCFAs), specifically 26-carbon VLCFAs, from palmitate. The enzyme catalyzes the reduction of the 3-ketoacyl-CoA intermediate in each cycle of fatty acid elongation. These VLCFAs serve as precursors for ceramide and sphingolipids.
KEGG: lel:LELG_03198
STRING: 379508.XP_001525270.1
Lodderomyces elongisporus 3-ketoacyl-CoA reductase is an enzyme that catalyzes the second step in the very long-chain fatty acid (VLCFA) elongation process. Within the microsomal fatty acid elongation (FAE) complex, this enzyme specifically reduces the 3-ketoacyl-CoA intermediate generated by 3-ketoacyl-CoA synthase (KCS). The reaction involves the reduction of a carbonyl group in the 3-ketoacyl-CoA to produce a 3-hydroxyacyl-CoA intermediate. This step is crucial in the four-enzyme cycle of fatty acid elongation, which also includes subsequent dehydration and final reduction steps to yield a fatty acyl-CoA extended by two carbon atoms .
Lodderomyces elongisporus is distinguished from other yeast species by several key characteristics. Microscopically, it exhibits a significantly higher proportion of elongated budding yeast cells compared to other species, with conidia typically measuring approximately 2–6 × 4–7 μm . L. elongisporus can be identified using chromogenic agar, where it displays a distinctive blue-turquoise coloration, contrasting with the green color of Candida albicans and the metallic dark blue of Candida tropicalis .
A defining metabolic characteristic is its inability to utilize L-arabinose and D-xylose as carbon sources, which forms the basis of the specialized Loddy test for identification . This yeast also demonstrates significant bioreduction activity on various ketones, showing optimal activity in the pH range of 7-10 with conversions of 60-80% for certain substrates . These unique properties make L. elongisporus valuable for recombinant protein studies, particularly for enzymes involved in redox reactions.
While specific structural information about L. elongisporus 3-ketoacyl-CoA reductase is not detailed in the provided search results, we can draw some inferences from related enzymes. Based on homology with other 3-ketoacyl reductases, it likely adopts a structure with a Rossmann fold typical of short-chain dehydrogenase/reductase family proteins, containing a nucleotide-binding domain for the cofactor (typically NADPH) and a substrate-binding domain.
Similar enzymes in the fatty acid elongation pathway, such as those in the Type III PKS family, display a characteristic five-layer ⍺β⍺β⍺ fold that is conserved across related enzymes . The active site would contain a catalytic triad essential for the reduction reaction. Substrate specificity would be determined by the shape and properties of the binding pocket, similar to how the binding tunnel in KCS enzymes influences their substrate preferences .
The optimal expression conditions for recombinant L. elongisporus 3-ketoacyl-CoA reductase should consider several key parameters based on enzymatic characteristics. First, select an expression system capable of proper protein folding and post-translational modifications. While E. coli might offer high yields, yeast expression systems like Pichia pastoris or Saccharomyces cerevisiae often provide better functionality for eukaryotic enzymes.
For expression in yeast systems, use strong inducible promoters (such as AOX1 for P. pastoris or GAL1 for S. cerevisiae) with temperatures between 25-30°C to minimize protein aggregation. Maintain pH between 7-10, as L. elongisporus demonstrates optimal enzymatic activity in this range . Include a histidine or similar tag for purification, positioned to avoid interfering with the active site.
Expression should be monitored through time-course sampling at 24, 48, and 72 hours post-induction. Supplement the media with zinc ions, as ketoreductases often require metal cofactors for proper folding. Following expression, perform purification under mild conditions (pH 7.5, 4°C) to preserve enzyme activity.
The enzymatic activity of recombinant L. elongisporus 3-ketoacyl-CoA reductase can be accurately measured through several complementary approaches:
Spectrophotometric Assay: Monitor the oxidation of NADPH to NADP+ at 340 nm, as the reduction of 3-ketoacyl-CoA consumes NADPH. The reaction mixture should contain:
Purified enzyme (0.1-1 μg)
3-ketoacyl-CoA substrate (50-200 μM)
NADPH (100-200 μM)
Buffer (typically 50-100 mM phosphate or Tris at pH 7.0-8.0)
HPLC Analysis: Measure the conversion of substrate to product directly using reverse-phase HPLC, which allows quantification of reaction kinetics.
Gas Chromatography: For volatile substrates like phenylacetone, use GC to measure substrate depletion and product formation.
Activity should be expressed as μmol substrate converted per gram of enzyme per minute. As demonstrated with various yeast strains, productivity can vary significantly based on substrate concentration, with L. elongisporus showing productivity of up to 40 μmol g⁻¹ min⁻¹ for certain substrates .
Based on successful approaches with L. elongisporus, sol-gel matrix immobilization has proven particularly effective for enhancing enzyme stability and reusability . The following protocol is recommended:
Sol-gel Matrix Preparation:
Mix tetramethoxysilane (TMOS) or tetraethoxysilane (TEOS) with water
Add the enzyme solution (0.5-2 mg/mL) in phosphate buffer (pH 7.5)
Allow gelation at 4°C for 24 hours
Wash with buffer to remove unbound enzyme
Cross-linked Enzyme Aggregates (CLEAs):
Precipitate the enzyme using ammonium sulfate (60-80% saturation)
Cross-link with glutaraldehyde (0.5-2% v/v)
Wash and recover the CLEAs
Enzyme Performance Analysis:
Evaluate activity retention after immobilization (typically 60-80%)
Test reusability through multiple reaction cycles (minimum 10 cycles)
Assess thermal stability at 30-50°C
Determine pH stability across the range of 5-10
L. elongisporus immobilized in sol-gel matrices has demonstrated excellent stability, maintaining over 70% of initial activity after 5 cycles of use. Additionally, immobilization expands the operational pH range and enhances resistance to substrate inhibition, allowing higher substrate concentrations (up to 10 mM) before observing productivity decline .
Directed evolution of L. elongisporus 3-ketoacyl-CoA reductase requires a systematic approach to generate and select improved variants:
Library Generation Methods:
Error-prone PCR: Use skewed dNTP ratios (0.2-0.7 mM) and MnCl₂ (0.05-0.5 mM) to introduce random mutations with a target mutation rate of 2-5 nucleotides per gene
Site-saturation mutagenesis: Focus on residues lining the substrate binding pocket and those involved in cofactor binding
DNA shuffling: Recombine gene fragments from related ketoreductases from various yeast species
Screening Strategy:
Develop a high-throughput colorimetric assay using redox indicators (such as tetrazolium salts) that change color upon NADPH oxidation
Implement microplate-based screening for initial rounds, examining 10³-10⁴ variants
Screen for multiple parameters simultaneously: activity, thermostability, pH tolerance, and substrate specificity
Iterative Improvement:
Combine beneficial mutations through site-directed mutagenesis
Validate improvements through detailed kinetic analysis (k<sub>cat</sub>, K<sub>M</sub>)
Compare enzyme performance under conditions mimicking the fatty acid elongation pathway
The mutations targeting residues in the hydrophobic substrate binding tunnel would be particularly valuable, as these regions determine substrate specificity in related enzymes . Focus especially on residues equivalent to those in the kinked regions of substrate binding tunnels, which influence preference for saturated versus unsaturated substrates.
Cofactor engineering can significantly alter the catalytic properties of L. elongisporus 3-ketoacyl-CoA reductase through several strategic modifications:
| Cofactor Modification | Implementation Strategy | Expected Effect | Measurement Method |
|---|---|---|---|
| NADH vs. NADPH preference | Modify the conserved Asp/Glu residue in the cofactor binding site | Shift cofactor preference from NADPH to NADH | Measure activity ratios with each cofactor |
| Regeneration system coupling | Co-express glucose dehydrogenase or formate dehydrogenase | Enhance reaction efficiency through continuous cofactor regeneration | Monitor reaction progress over extended periods |
| Binding site engineering | Modify residues that interact with the adenine ribose moiety | Increase cofactor binding affinity | Determine K<sub>d</sub> values through isothermal titration calorimetry |
Integration of L. elongisporus 3-ketoacyl-CoA reductase into synthetic metabolic pathways requires careful pathway design and optimization:
Pathway Design Considerations:
Ensure balanced expression of all pathway enzymes using promoters of appropriate strength
Co-localize enzymes through scaffolding proteins or fusion constructs to enhance substrate channeling
Include regulatory elements responsive to product accumulation or substrate depletion
Implementation Strategies:
Build a modular pathway with standardized genetic parts for easy optimization
Express the complete fatty acid elongation complex (KCS, KCR, HCD, ECR) rather than KCR alone
Balance NADPH availability through concurrent expression of NADPH-generating enzymes
Performance Optimization:
Use adaptive laboratory evolution to enhance pathway flux
Implement dynamic regulation to respond to changing cellular conditions
Knock out competing pathways that might divert intermediates
The integration would be particularly effective for producing specialized fatty acid derivatives like hydroxylated fatty acids or α,ω-dicarboxylic acids. Since L. elongisporus demonstrates high productivity in the bioreduction of various ketones (up to 40 μmol g⁻¹ min⁻¹) , it could be effectively coupled with KCS enzymes with different substrate specificities to produce diverse elongated products.
Monitor pathway performance through metabolite profiling using LC-MS/MS, analyze flux distribution with ¹³C metabolic flux analysis, and use biosensors to provide real-time feedback on pathway intermediates.
Substrate inhibition has been observed with L. elongisporus at substrate concentrations above 10 mM, showing significant productivity decline . Several approaches can effectively address this challenge:
Fed-batch Substrate Addition:
Maintain substrate concentration below inhibitory levels (4-8 mM) through controlled feeding
Implement an automated system that adds substrate based on consumption rates
Optimize feeding profile through design of experiments methodology
Biphasic Reaction Systems:
Create a two-phase system using an organic solvent (e.g., n-hexane, toluene, or MTBE)
The organic phase serves as a substrate reservoir, releasing substrate into the aqueous phase gradually
Test multiple solvent systems to identify optimal partition coefficients
Protein Engineering Approaches:
Target residues in the substrate binding pocket that influence substrate affinity
Introduce mutations that reduce binding affinity slightly but improve turnover rate
Screen for variants with higher K<sub>i</sub> values for substrate inhibition
Enzyme Immobilization Benefits:
Immobilize the enzyme in sol-gel matrix to create a microenvironment that buffers against high substrate concentrations
Use porous materials that control substrate diffusion rates
Combine immobilization with protein engineering for additive improvements
Process Optimization:
Implement in situ product removal strategies to shift reaction equilibrium
Optimize reaction parameters (temperature, pH, ionic strength) to minimize inhibition effects
Use mathematical modeling to predict optimal operational conditions
The implementation of these strategies has shown that with proper immobilization techniques and process design, L. elongisporus biocatalysts can maintain high productivity (>60% of maximum) even at elevated substrate concentrations .
Improving stability of recombinant L. elongisporus 3-ketoacyl-CoA reductase requires a multi-faceted approach:
Protein Engineering for Enhanced Stability:
Introduce disulfide bridges at positions identified through computational analysis
Replace surface-exposed hydrophobic residues with polar residues
Identify and mutate residues in flexible regions to reduce unfolding
Use consensus design approaches based on alignment with thermostable homologs
Formulation Strategies:
Immobilization Techniques:
Storage and Operational Stability:
Lyophilization with appropriate cryoprotectants
Immobilization in hydrophobic supports for operation in organic solvents
Controlled dehydration to enhance thermostability
Co-immobilization with stabilizing proteins or cofactors
Implementation of these strategies has shown significant improvements in enzyme stability. For example, lyophilized forms of related yeast enzymes have demonstrated efficient biocatalytic activity in the production of enantiopure alcohols on preparative scale , indicating that properly stabilized L. elongisporus 3-ketoacyl-CoA reductase could achieve similar industrial performance.
Researchers face several analytical challenges when studying L. elongisporus 3-ketoacyl-CoA reductase:
Challenge: Distinguishing Enzyme Activity from Background Cell Metabolism
Solution:
Use cell-free extract controls from non-expressing host cells
Implement specific inhibitors for related enzymes
Develop selective assays using structurally unique substrates
Employ isotope-labeled substrates to track specific conversions
Challenge: Accurately Quantifying Cofactor Consumption in Complex Mixtures
Solution:
Implement HPLC methods for direct NADPH/NADP⁺ quantification
Use coupled enzyme assays with specific detection systems
Develop fluorescence-based assays for enhanced sensitivity
Account for non-enzymatic NADPH oxidation through proper controls
Challenge: Measuring Kinetics with Hydrophobic Substrates
Solution:
Use co-solvents (5-10% DMSO, ethanol) that don't impact enzyme activity
Employ cyclodextrins to improve substrate solubility
Develop biphasic reaction systems with proper mixing
Use substrate analogs with improved water solubility for initial characterization
Challenge: Determining True Substrate Specificity Profiles
Solution:
Create a standardized substrate panel with diverse chain lengths and functional groups
Normalize activity data to account for differences in substrate solubility
Use competition assays to determine relative substrate preferences
Implement LC-MS/MS methods to detect all potential products
Challenge: Correlating In Vitro Activity with In Vivo Function
Solution:
Develop cell-based assays measuring fatty acid profile changes
Use metabolic labeling with stable isotopes
Implement liposome-based systems mimicking natural membrane environment
Correlate enzyme kinetics with physiological substrate concentrations
Implementing these solutions allows for more accurate characterization of enzyme activity. For example, researchers have successfully used standardized testing conditions to characterize the pH profiles and substrate specificity of various yeast strains, revealing that L. elongisporus exhibits optimal bioreduction activity between pH 7-10 with conversions in the 60-80% range for specific substrates .
The genetic diversity among natural L. elongisporus isolates can significantly influence the functional properties of their 3-ketoacyl-CoA reductases. Research in this area should address:
Population Genetics Analysis:
Sequence the 3-ketoacyl-CoA reductase gene from geographically diverse L. elongisporus isolates
Identify natural variants and polymorphic sites through comparative genomics
Analyze selection pressure on different domains of the enzyme
Correlate genetic variation with ecological niches of the isolates
Functional Characterization of Natural Variants:
Express and purify enzymes from diverse isolates
Compare kinetic parameters (k<sub>cat</sub>, K<sub>M</sub>) across substrates
Assess thermal stability and pH optima variations
Evaluate cofactor preference and efficiency
Structure-Function Relationship Analysis:
Model the structural differences between variants
Identify key residues responsible for functional differences
Use site-directed mutagenesis to confirm the role of specific variations
Develop predictive models relating sequence variations to functional properties
These analyses would provide valuable insights into evolutionary adaptations of L. elongisporus 3-ketoacyl-CoA reductase and identify naturally optimized variants for specific applications. The approach is similar to how researchers have analyzed different yeast strains for their bioreduction capabilities, revealing significant variations in productivity (ranging from 10-60 μmol g⁻¹ min⁻¹) and substrate preferences .
The potential for L. elongisporus 3-ketoacyl-CoA reductase in novel fatty acid-derived compound biosynthesis is substantial and can be explored through several approaches:
Designer Fatty Acid Production:
Engineer pathways incorporating the reductase for omega-3/omega-6 fatty acid production
Create branched-chain fatty acids through modified elongation cycles
Produce fatty acids with precisely positioned functional groups
Generate cyclopropane or cyclopropene fatty acids with unique properties
Therapeutic Compound Development:
Synthesize fatty acid-derived signaling molecules like prostaglandins
Produce specialized hydroxy fatty acids with anti-inflammatory properties
Generate precursors for lipid-based drug delivery systems
Create fatty acid-peptide conjugates with enhanced bioavailability
Biofuel and Biomaterial Applications:
Engineer pathways for medium-chain fatty acid production optimized for biofuels
Create precursors for bioplastics with tailored properties
Produce wax esters with specific melting points for industrial applications
Generate fatty alcohols and aldehydes for fragrance and cosmetic applications
Proof-of-Concept Studies:
Reconstruct complete fatty acid elongation systems with L. elongisporus 3-ketoacyl-CoA reductase
Test compatibility with various 3-ketoacyl-CoA synthases for diverse substrate incorporation
Evaluate the reductase's ability to process non-natural substrates
Optimize systems for the production of commercially valuable compounds
The high efficiency of L. elongisporus in bioreduction reactions (with productivity of up to 40 μmol g⁻¹ min⁻¹ for certain substrates) suggests strong potential for applications requiring stereoselective reduction steps in complex biosynthetic pathways.
Systems biology approaches can provide comprehensive insights into L. elongisporus 3-ketoacyl-CoA reductase function within cellular metabolism:
Multi-omics Integration:
Combine transcriptomics, proteomics, and metabolomics data from L. elongisporus under various growth conditions
Identify co-regulated genes and proteins associated with 3-ketoacyl-CoA reductase
Map metabolite changes associated with altered reductase expression
Develop regulatory network models for fatty acid metabolism
Flux Analysis and Modeling:
Perform ¹³C metabolic flux analysis to quantify carbon flow through fatty acid elongation
Develop genome-scale metabolic models of L. elongisporus
Simulate the effects of reductase overexpression or knockout
Identify limiting steps and bottlenecks in fatty acid elongation
Comparative Systems Analysis:
Compare metabolic networks across yeast species with different fatty acid profiles
Identify unique regulatory features of L. elongisporus fatty acid metabolism
Evaluate the impact of different growth conditions on pathway regulation
Assess the integration of reductase function with cellular redox balance
Advanced Visualization and Analysis:
Develop interactive metabolic maps highlighting reductase activity
Implement machine learning to identify non-obvious relationships in multi-omics data
Use time-resolved analysis to capture dynamic responses
Create predictive models for metabolic engineering applications
This systems-level understanding would complement the existing knowledge about L. elongisporus enzymatic capabilities, which has already revealed significant bioreduction activity across various pH ranges (optimal between pH 7-10) and substrate types .
Optimizing gene expression systems for high-yield production of recombinant L. elongisporus 3-ketoacyl-CoA reductase requires attention to multiple factors:
Codon Optimization Strategy:
Analyze the codon usage bias of the expression host
Optimize the coding sequence while preserving mRNA secondary structure
Consider harmonization rather than maximization of codon adaptation index
Validate optimization through predictive algorithms before synthesis
Expression Vector Design:
Select appropriate promoter strength based on protein solubility concerns
Include optimal ribosome binding sites or Kozak sequences
Consider adding introns for enhanced expression in eukaryotic hosts
Include appropriate secretion signals if extracellular production is desired
Host Cell Engineering:
Select hosts with appropriate post-translational modification capabilities
Consider chaperone co-expression for improved folding
Engineer redox environment for optimal disulfide bond formation
Modify central carbon metabolism to enhance precursor and energy supply
Fermentation Process Development:
Experimental Design Approach:
Use factorial design to identify critical parameters
Implement response surface methodology for optimization
Apply statistical process control during production
Develop scale-down models for process characterization
The successful implementation of these practices can significantly improve yield and quality of the recombinant enzyme, similar to how optimization enabled efficient biocatalyst production for various yeast strains used in preparative-scale bioreduction reactions .
Elucidating the catalytic mechanism of L. elongisporus 3-ketoacyl-CoA reductase through crystallography and structural biology requires a systematic approach:
Protein Crystallization Strategy:
Screen various construct designs with different N/C-terminal truncations
Test multiple crystallization conditions (>1000) using sparse matrix screens
Optimize promising conditions through fine gradient screening
Consider surface entropy reduction mutations to promote crystal contacts
Explore co-crystallization with substrates, products, and cofactors
Use microseeding techniques to improve crystal quality
Structural Determination Methods:
Collect high-resolution X-ray diffraction data (aiming for <2.0 Å)
Use molecular replacement with related structures as search models
Consider selenomethionine labeling for experimental phasing if necessary
Perform careful model building and refinement
Mechanistic Studies:
Obtain structures with bound substrate analogs and cofactors
Capture reaction intermediates through cryo-trapping techniques
Perform time-resolved crystallography when possible
Generate structures of catalytically important mutants
Complementary Techniques:
Use hydrogen-deuterium exchange mass spectrometry to map dynamics
Apply nuclear magnetic resonance for solution-state analysis
Implement molecular dynamics simulations to model catalytic steps
Perform quantum mechanics/molecular mechanics calculations to model transition states
These approaches would provide insights similar to those obtained for related enzymes, where structural analysis revealed binding tunnels with distinct shapes influencing substrate specificity . Understanding these structural features would explain L. elongisporus 3-ketoacyl-CoA reductase's performance in the bioreduction of various ketones, including its optimal pH range (7-10) and substrate preferences .
Effective high-throughput screening for improved L. elongisporus 3-ketoacyl-CoA reductase variants requires specialized methods tailored to the enzyme's characteristics:
Colorimetric Activity Assays:
Develop NAD(P)H-coupled assays using tetrazolium salts (NBT, INT)
Implement pH indicators for proton-consuming/producing reactions
Use chromogenic substrate analogs that change color upon conversion
Optimize signal-to-noise ratio through reaction condition tuning
Fluorescence-Based Methods:
Develop assays using fluorogenic substrate analogs
Implement FRET-based sensors for conformational changes
Use fluorescence polarization to detect product formation
Apply flow cytometry for single-cell analysis with cell-surface displayed variants
Microfluidic Approaches:
Develop droplet microfluidics for ultrahigh-throughput screening (10⁶-10⁸ variants)
Create gradient microfluidic devices for simultaneous condition optimization
Implement microarray-based screening for immobilized enzyme variants
Use microchamber arrays for parallel reaction monitoring
Automation and Data Analysis:
Implement robotic systems for assay miniaturization to 384 or 1536-well formats
Develop image analysis algorithms for colony-based screens
Use machine learning to identify patterns in screening data
Implement design of experiments for efficient parameter optimization
The effectiveness of these screening methods can be evaluated by comparing the improvement factors achieved. For reference, optimization studies of different yeast strains have demonstrated productivity variations ranging from 10 to 60 μmol g⁻¹ min⁻¹ for bioreduction reactions , suggesting significant potential for improvement through directed evolution and high-throughput screening.