Recombinant Blochmannia pennsylvanicus Probable ubiquinone biosynthesis protein UbiB (ubiB)

What is Blochmannia pennsylvanicus and what is the significance of studying its UbiB protein?

Blochmannia pennsylvanicus is an obligate endosymbiont that lives within the carpenter ant Camponotus pennsylvanicus. Its significance lies in its unique evolutionary adaptations as a long-term bacterial mutualist. The UbiB protein specifically plays a crucial role in ubiquinone biosynthesis, a process essential for cellular respiration and energy production. Studying this protein provides insights into how endosymbionts maintain critical metabolic functions despite genome reduction, and offers valuable perspective on the evolution of host-symbiont relationships .

The protein's significance extends to understanding bacterial adaptation mechanisms in restricted environments and the maintenance of essential biochemical pathways in obligate endosymbionts. Research approaches should include comparative genomics and functional studies that examine the protein's role in the context of the endosymbiont's reduced genome and specialized ecological niche.

What is the molecular structure and primary function of UbiB in Blochmannia pennsylvanicus?

UbiB in Blochmannia pennsylvanicus is a 546-amino acid protein involved in ubiquinone biosynthesis. The complete amino acid sequence begins with mLVDELCRLYSIIKTILNY and continues through to the C-terminal sequence ending with WTIGWKRIIQ . Structurally, UbiB is predicted to contain conserved domains typical of ubiquinone biosynthesis proteins, and functions primarily as an ATPase in the ubiquinone biosynthetic pathway .

Experimental approaches to study UbiB structure typically include X-ray crystallography, NMR spectroscopy, or cryo-EM analysis of the purified recombinant protein. Functional characterization involves enzymatic assays measuring ATPase activity, complementation studies in bacterial strains lacking UbiB, and interaction studies with other components of the ubiquinone biosynthesis pathway.

How does the genomic context of ubiB in B. pennsylvanicus compare to other bacterial species?

The ubiB gene in B. pennsylvanicus (locus name BPEN_648) exists within a significantly reduced genome of 792 kb. Unlike many free-living bacteria with larger genomes, B. pennsylvanicus has experienced genome reduction while maintaining essential metabolic pathways. Comparative genomic analysis reveals that B. pennsylvanicus retains the complete pathway for isoprenoid biosynthesis, which provides essential substrates for ubiquinone synthesis .

When compared to its close relative B. floridanus, there is complete conservation in gene order and strand orientation, suggesting extreme stasis in genome architecture—a characteristic of long-term bacterial mutualists of insects. This stability constrains evolutionary potential but ensures maintenance of vital functions. Research methodologies should include synteny analysis, phylogenetic reconstruction of the ubiB gene across bacterial species, and analysis of selection pressures using dN/dS ratios to understand evolutionary constraints on the gene.

What are the optimal conditions for expression and purification of recombinant B. pennsylvanicus UbiB protein?

Expression and purification of recombinant B. pennsylvanicus UbiB requires careful optimization due to its membrane-associated nature and potential toxicity when overexpressed. The recommended protocol includes:

Expression System Selection:

• E. coli BL21(DE3) with pET or pBAD vectors containing rare codon optimization

• Induction at lower temperatures (16-18°C) to reduce inclusion body formation

• IPTG concentration: 0.1-0.3 mM for pET systems; 0.002-0.02% L-arabinose for pBAD

Purification Strategy:

• Cell lysis in buffer containing 50 mM Tris-HCl pH 8.0, 300 mM NaCl, 10% glycerol, and protease inhibitors

• Membrane fraction isolation via ultracentrifugation (100,000 × g, 1 hour)

• Solubilization using 1% n-dodecyl β-D-maltoside or 1% Triton X-100

• IMAC purification using Ni-NTA resin for His-tagged protein

• Size exclusion chromatography for final polishing

The purified protein should be stored in a Tris-based buffer with 50% glycerol at -20°C for short-term or -80°C for extended storage. Repeated freeze-thaw cycles should be avoided, and working aliquots should be stored at 4°C for up to one week .

How can researchers design experiments to investigate UbiB's ATPase activity and its role in ubiquinone biosynthesis?

To investigate UbiB's ATPase activity and its role in ubiquinone biosynthesis, researchers should implement a multi-faceted experimental design:

ATPase Activity Assay:

• Malachite green phosphate detection assay to quantify released inorganic phosphate

• Radiolabeled ATP hydrolysis assay using [γ-32P]ATP

• Coupled enzyme assay with pyruvate kinase and lactate dehydrogenase

Ubiquinone Biosynthesis Assessment:

• Complementation studies in E. coli ΔubiB strains

• HPLC or LC-MS analysis of ubiquinone levels in wild-type vs. mutant strains

• Isotope labeling with 13C-labeled precursors to trace carbon flow through the pathway

Structure-Function Analysis:

• Site-directed mutagenesis of conserved residues suspected to be involved in ATP binding or catalysis

• In vitro reconstitution of ubiquinone biosynthesis using purified components

Interaction Studies:

• Pull-down assays to identify protein interaction partners

• Blue native PAGE to characterize potential multiprotein complexes

• Bacterial two-hybrid or FRET analysis to confirm specific interactions

Researchers should employ an ABAB experimental design for functional studies, where:
A1 - Baseline measurements of ubiquinone production or ATPase activity
B1 - Introduction of recombinant UbiB protein
A2 - Removal of the protein/inhibition of activity
B2 - Reintroduction of protein or activity

This design strengthens causal inferences by demonstrating reversibility of effects and providing internal experimental controls.

What methods can be used to investigate the potential interaction between UbiB and other proteins in the ubiquinone biosynthesis pathway?

To investigate protein-protein interactions involving UbiB in the ubiquinone biosynthesis pathway, researchers should employ multiple complementary approaches:

In vitro Interaction Studies:

• Co-immunoprecipitation using anti-UbiB antibodies or epitope tags

• Surface plasmon resonance to measure binding kinetics between UbiB and potential partners

• Isothermal titration calorimetry to determine thermodynamic parameters of interactions

• Analytical ultracentrifugation to characterize complex formation

In vivo Interaction Studies:

• Bacterial two-hybrid system optimized for membrane proteins

• Bimolecular fluorescence complementation (BiFC) in bacterial systems

• Protein-fragment complementation assays (PCA)

• Chemical cross-linking followed by mass spectrometry identification

Structural Approaches:

• Cryo-EM analysis of purified complexes

• X-ray crystallography of co-purified proteins

• Hydrogen-deuterium exchange mass spectrometry to map interaction interfaces

Recent studies indicate that UbiB may function within a multiprotein complex similar to UbiJ and UbiK in the ubiquinone biosynthesis pathway . Particular attention should be paid to potential interactions with UbiT, UbiU, and UbiV proteins, which are involved in the O2-independent pathway for ubiquinone biosynthesis, as these interactions could reveal functional redundancy or complementarity between O2-dependent and O2-independent pathways.

What are the main challenges in working with recombinant B. pennsylvanicus UbiB and how can they be addressed?

Working with recombinant B. pennsylvanicus UbiB presents several challenges that require specific approaches to overcome:

Challenge 1: Protein Solubility and Stability

• Problem: UbiB may form inclusion bodies when overexpressed

• Solution: Express at lower temperatures (16°C) with reduced inducer concentration; use fusion tags (MBP, SUMO); solubilize using mild detergents like n-dodecyl β-D-maltoside

Challenge 2: Maintaining Native Structure and Function

• Problem: Detergents may disrupt protein folding and activity

• Solution: Screen multiple detergents (DDM, LMNG, GDN); consider nanodisc or styrene-maleic acid copolymer (SMA) reconstitution for a more native-like membrane environment

Challenge 3: Low Expression Yields

• Problem: Endosymbiont proteins often express poorly in heterologous systems

• Solution: Optimize codon usage for expression host; use strong promoters with tight regulation; consider cell-free expression systems

Challenge 4: Protein Degradation

• Problem: Protease sensitivity during expression and purification

• Solution: Add protease inhibitor cocktails; include glycerol (10-20%) in all buffers; minimize time between purification steps; maintain samples at 4°C throughout

Challenge 5: Assessing Enzymatic Activity

• Problem: Complex membrane-associated enzymatic reaction is difficult to monitor

• Solution: Develop sensitive coupled assays; use radiolabeled substrates; consider whole-cell assays or reconstituted systems

A systematic approach to optimization using factorial experimental design is recommended to efficiently identify optimal conditions for expression and purification.

How can researchers differentiate between UbiB's role in O2-dependent versus O2-independent ubiquinone biosynthesis pathways?

Differentiating UbiB's role in O2-dependent versus O2-independent ubiquinone biosynthesis pathways requires specialized experimental approaches:

Experimental Design Matrix:

Methodological Approaches:

• Create conditional knockout strains where UbiB expression can be controlled while simultaneously manipulating oxygen availability

• Utilize oxygen-sensitive fluorescent probes to correlate local O2 concentration with UbiB activity

• Apply ABAB experimental design with A phases representing anaerobic conditions and B phases representing aerobic conditions

• Employ quantitative proteomics to measure changes in UbiB abundance and post-translational modifications under varying oxygen conditions

• Investigate potential interactions between UbiB and proteins specific to the O2-independent pathway (UbiT, UbiU, UbiV) using co-immunoprecipitation or bacterial two-hybrid systems

The data should be analyzed using multivariate statistical methods to distinguish direct effects of UbiB from secondary metabolic adaptations to oxygen limitation.

What are the key considerations for designing site-directed mutagenesis experiments to identify critical functional residues in UbiB?

Designing effective site-directed mutagenesis experiments for UbiB requires strategic selection of target residues and appropriate functional assays:

Target Residue Selection Criteria:

• Conserved residues identified through multiple sequence alignment across bacterial species

• Predicted functional domains (ATP-binding motifs, catalytic sites)

• Regions with low dN/dS ratios indicating strong purifying selection

• Residues within poly(A) tracts, which are common in Blochmannia ORFs and may affect protein function

Mutation Strategy Table:

Experimental Design Considerations:

• Generate a library of single-point mutants for comprehensive functional mapping

• Create double mutants to identify synergistic or compensatory effects

• Implement parallel phenotypic screens in both aerobic and anaerobic conditions

• Utilize complementation assays in ΔubiB strains to assess in vivo functionality

• Perform in vitro biochemical characterization of purified mutant proteins

Controls and Validation:

• Include synonymous mutations as negative controls

• Create positive controls with mutations in known essential domains

• Verify protein expression levels by Western blotting to distinguish between expression and functional effects

• Confirm structural integrity through circular dichroism or limited proteolysis

This systematic approach will help identify critical functional residues and domains in UbiB, providing insights into its mechanism of action in ubiquinone biosynthesis.

How does the evolutionary conservation of UbiB in B. pennsylvanicus compare to its homologs in other bacteria, and what does this reveal about selective pressures?

The evolutionary conservation pattern of UbiB in B. pennsylvanicus provides significant insights into selective pressures operating on this endosymbiont:

Genomic analyses reveal that UbiB is maintained in B. pennsylvanicus despite significant genome reduction, indicating strong purifying selection for ubiquinone biosynthesis. Comparison with B. floridanus shows that while many genes have been lost during evolution, the ubiquinone biosynthetic pathway remains largely intact . This selective retention suggests that ubiquinone production provides essential fitness benefits to both the endosymbiont and its ant host.

Phylogenetic analysis should examine:

• Conservation of specific domains across diverse bacterial lineages

• Identification of lineage-specific adaptations in the UbiB sequence

• Comparison of evolutionary rates between different functional domains

• Correlation between host ecology and UbiB sequence divergence

An interesting finding is that despite the accelerated protein evolution, B. pennsylvanicus and B. floridanus show complete conservation in gene order and strand orientation, suggesting extreme genomic architectural stasis . This pattern constrains the evolutionary potential of endosymbionts but may ensure the maintenance of essential metabolic pathways like ubiquinone biosynthesis.

What is the relationship between UbiB function and the unique metabolic adaptations of Blochmannia as an ant endosymbiont?

The function of UbiB in B. pennsylvanicus is intricately linked to the specialized metabolic adaptations of this bacterium as an ant endosymbiont:

Blochmannia pennsylvanicus maintains complete pathways for the biosynthesis of isoprenoids, which are essential substrates for the synthesis of peptidoglycan and several organic compounds including the side chains of ubiquinone . This retention indicates that ubiquinone biosynthesis is a critical function that connects cellular energetics to cell wall integrity.

The metabolic context of UbiB function can be understood through several key adaptations:

• Energy metabolism: Ubiquinone is essential for aerobic respiration, suggesting that B. pennsylvanicus maintains aerobic metabolism despite its intracellular lifestyle. This contrasts with some other endosymbionts that have lost respiratory capacity.

• Membrane integrity: B. pennsylvanicus retains genes for peptidoglycan synthesis and the sec-dependent secretory pathway , indicating that membrane and cell wall functions remain important. UbiB's role in ubiquinone production may therefore be linked to maintaining proper membrane function.

• Stress response: B. pennsylvanicus encodes membrane-bound heat-induced protease HtpX and periplasmic chaperonins , suggesting that cellular stress responses remain important. Ubiquinone's antioxidant properties may contribute to stress tolerance.

• Host interaction: The retention of UbiB may reflect the need to maintain energy production to support nutrient exchange with the ant host. Carpenter ants derive essential amino acids from their Blochmannia endosymbionts, creating selective pressure to maintain metabolic capacity.

To fully understand this relationship, researchers should utilize co-culture systems or specialized ant tissue cultures that maintain the natural host environment to study how UbiB function responds to host-derived signals.

What are the implications of studying B. pennsylvanicus UbiB for understanding O2-independent ubiquinone biosynthesis in other bacterial pathogens?

Studying UbiB in B. pennsylvanicus has significant implications for understanding O2-independent ubiquinone biosynthesis in bacterial pathogens, particularly those that encounter oxygen-limited environments during infection:

Recent research has identified an O2-independent pathway for ubiquinone biosynthesis involving proteins UbiT, UbiU, and UbiV . Understanding how UbiB functions in relation to this pathway could reveal how bacteria maintain energy metabolism under variable oxygen conditions—a critical adaptation for many pathogens that transition between aerobic and anaerobic environments during infection.

Implications for Pathogen Research:

• Therapeutic target identification: UbiB and related proteins may represent novel antibacterial targets for pathogens that rely on ubiquinone biosynthesis during infection. The O2-independent pathway is particularly relevant for targeting bacteria in anaerobic infection sites.

• Metabolic flexibility: Understanding how pathogens switch between O2-dependent and O2-independent ubiquinone biosynthesis could reveal mechanisms of metabolic adaptation during host colonization.

• Evolutionary insights: The O2-independent pathway proteins (UbiT, UbiU, UbiV) are found in alpha-, beta-, and gammaproteobacterial clades, including several human pathogens . Comparative genomic analyses should examine how pathogens and non-pathogens differ in their ubiquinone biosynthesis pathways.

• Biofilm relevance: Many pathogens form biofilms with steep oxygen gradients. Understanding how ubiquinone biosynthesis operates across these gradients could inform anti-biofilm strategies.

Research Applications:

• Development of high-throughput screening assays for inhibitors targeting UbiB or the O2-independent pathway components

• Creation of attenuated pathogen strains through manipulation of ubiquinone biosynthesis pathways

• Metabolic modeling of energy production in pathogens under varying oxygen conditions

This research could ultimately contribute to new therapeutic approaches targeting bacterial energy metabolism in a context-dependent manner, potentially overcoming limitations of current antibiotics in anaerobic or microaerobic infection sites.

What emerging technologies and methodologies could advance our understanding of B. pennsylvanicus UbiB function and regulation?

Several cutting-edge technologies and methodologies show promise for advancing our understanding of B. pennsylvanicus UbiB:

CryoEM and AlphaFold Integration:
Combining cryo-electron microscopy with AlphaFold structural predictions could reveal UbiB's structural details and conformational changes during catalysis. This approach is particularly valuable for membrane-associated proteins that are challenging for traditional structural biology methods.

Single-Molecule Techniques:

• Single-molecule FRET to monitor conformational changes during ATP binding and hydrolysis

• Optical tweezers to measure force generation during potential conformational changes

• High-speed AFM to visualize UbiB dynamics in membrane environments

Advanced Genetic Methods:

• CRISPR interference for precise temporal control of ubiB expression

• Multiplex genome engineering to introduce comprehensive mutant libraries

• Single-cell transcriptomics to identify condition-specific regulation

Systems Biology Approaches:

• Metabolic flux analysis using 13C-labeled intermediates to quantify pathway contributions

• Multi-omics integration of transcriptomics, proteomics, and metabolomics data

• Machine learning algorithms to identify regulatory patterns from large datasets

Microfluidic Systems:

• Oxygen gradient devices to study UbiB function under precisely controlled O2 concentrations

• Microfluidic co-culture systems to investigate host-endosymbiont interactions

• Droplet-based high-throughput screening for UbiB modulators

In Situ Techniques:

• Proximity labeling (BioID, APEX) to map the UbiB interactome in living cells

• Super-resolution microscopy to visualize UbiB localization and dynamics

• In-cell NMR to monitor structural changes under physiological conditions

These advanced technologies could reveal how UbiB integrates into the complex cellular networks controlling energy metabolism and how its function adapts to the specialized endosymbiotic lifestyle of B. pennsylvanicus.

How might research on B. pennsylvanicus UbiB contribute to our understanding of host-symbiont co-evolution?

Research on B. pennsylvanicus UbiB offers a unique window into host-symbiont co-evolution through several conceptual frameworks:

1. Metabolic Integration and Complementarity:
UbiB's role in ubiquinone biosynthesis represents a critical metabolic function that may have shaped the evolutionary trajectory of the host-symbiont relationship. By studying how this pathway has been maintained despite genome reduction, researchers can gain insights into metabolic dependencies between ants and their bacterial endosymbionts.

2. Molecular Clock Applications:
The accelerated evolutionary rates observed in Blochmannia proteins (10-50 fold faster than free-living relatives) provide an opportunity to calibrate molecular clocks for symbiont evolution. Comparative analysis of UbiB across Blochmannia strains from different ant species could reveal co-diversification patterns and timing of host-symbiont speciation events.

3. Experimental Evolution Approaches:

• Experimental evolution of ant colonies with their endosymbionts under varying selective pressures

• Monitoring genetic changes in UbiB and related genes over multiple generations

• Testing how metabolic demands of the host influence symbiont gene retention

4. Comparative Genomics Framework:
The extreme genome architectural stasis in Blochmannia species despite protein sequence divergence suggests unique evolutionary constraints. This pattern differs from that observed in other endosymbionts and merits investigation as a possible signature of ant-specific symbiotic associations.

5. Ecological Context Analysis:
Carpenter ants occupy diverse ecological niches, from temperate to tropical environments. Studying UbiB adaptations across Blochmannia from different ant species could reveal how environmental factors shape symbiont metabolism.

This research could ultimately contribute to broader theoretical models of symbiosis, particularly regarding how essential metabolic pathways are maintained and adapted in the face of reductive genome evolution, and how these adaptations influence host ecology and evolution.

What potential applications exist for exploiting the UbiB protein and the O2-independent ubiquinone biosynthesis pathway in biotechnology and medicine?

The UbiB protein and O2-independent ubiquinone biosynthesis pathway offer several promising applications in biotechnology and medicine:

Therapeutic Applications:

• Novel Antimicrobial Development:

  • Target-based screening for inhibitors of UbiB and the O2-independent pathway

  • Development of narrow-spectrum antibiotics effective under anaerobic conditions

  • Design of combination therapies targeting both O2-dependent and O2-independent pathways to prevent resistance development

• Anaerobic Infection Treatment:

  • Specific targeting of pathogens in oxygen-limited infection sites (abscesses, biofilms)

  • Creation of prodrugs activated under anaerobic conditions that target ubiquinone biosynthesis

Biotechnological Applications:

• Biofuel and Bioproduct Engineering:

  • Enhancement of microbial ubiquinone production for commercial applications

  • Engineering microbes with robust energy metabolism for industrial fermentations under microaerobic conditions

  • Development of bacterial strains capable of maintaining ATP production across oxygen gradients

• Biosensor Development:

  • Creation of whole-cell biosensors using UbiB pathway components to detect specific environmental conditions

  • Design of reporter systems for monitoring bacterial metabolic state in complex environments

Research Tools:

• Metabolic Probe Development:

  • Creation of chemical probes to study ubiquinone biosynthesis in live cells

  • Development of tools to map O2 gradients in bacterial communities

• Synthetic Biology Applications:

  • Design of synthetic bacterial consortia with complementary ubiquinone biosynthesis capabilities

  • Creation of minimal cells with streamlined but robust energy metabolism

The recent discovery of the O2-independent pathway for ubiquinone biosynthesis opens particularly exciting possibilities for applications in microaerobic and anaerobic biotechnology processes, potentially enabling more efficient industrial fermentations under oxygen-limited conditions. Biomedical applications could address the significant challenge of treating infections in anaerobic environments, where many conventional antibiotics show reduced efficacy.

How should researchers interpret contradictory findings regarding UbiB function in different experimental systems?

When facing contradictory findings regarding UbiB function across different experimental systems, researchers should implement a systematic approach to resolve discrepancies:

Analytical Framework for Resolving Contradictions:

• Experimental Context Evaluation:

  • Examine differences in expression systems (E. coli vs. native host)

  • Compare in vitro vs. in vivo experimental conditions

  • Assess oxygen availability during experiments

  • Consider effects of fusion tags or detection methods

• Biological Variable Analysis:

  • Evaluate strain-specific genetic backgrounds

  • Consider post-translational modifications or protein processing

  • Examine protein partners present in different systems

  • Assess metabolic state and growth conditions

• Technical Rigor Assessment:

  • Compare sensitivity and specificity of different assay methods

  • Evaluate statistical power and experimental replication

  • Consider time-dependent effects and kinetic parameters

  • Review reagent quality and validation

Experimental Reconciliation Strategy:

• Direct Comparison Experiments:

  • Design experiments that directly compare UbiB function under identical conditions

  • Use ABAB design methodology to test reversibility of effects

  • Include appropriate positive and negative controls

• Integrative Analysis:

  • Combine multiple orthogonal techniques to study the same aspect of UbiB function

  • Apply computational modeling to reconcile apparently contradictory data

  • Develop unifying hypotheses that explain context-dependent function

• Collaborative Resolution:

  • Establish collaborations between labs reporting contradictory findings

  • Exchange materials and protocols to identify sources of variation

  • Perform cross-validation experiments in different laboratories

When interpreting contradictory findings, researchers should consider that UbiB may have context-dependent functions, particularly given the evidence for both O2-dependent and O2-independent pathways for ubiquinone biosynthesis . The unique metabolic context of an endosymbiont like B. pennsylvanicus may also result in functional adaptations not observed in model systems.

What statistical approaches are most appropriate for analyzing UbiB activity data in different oxygen conditions?

When analyzing UbiB activity across different oxygen conditions, researchers should employ robust statistical approaches tailored to the experimental design:

Statistical Analysis Framework for Oxygen-Dependent Studies:

Advanced Statistical Considerations:

• Multivariate Analysis:

  • Principal Component Analysis (PCA) to identify patterns across multiple parameters

  • Partial Least Squares Regression to correlate oxygen levels with multiple dependent variables

  • MANOVA for simultaneous analysis of multiple outcome measures

• Bayesian Approaches:

  • Bayesian hierarchical modeling to account for biological variability

  • Bayesian network analysis to infer causal relationships between oxygen, UbiB activity, and downstream effects

• Machine Learning Methods:

  • Random forest regression for complex, non-linear relationships

  • Support vector machines for classification of oxygen-dependent states

Practical Implementation Guidelines:

• Conduct power analysis before experiments to ensure sufficient sample size

• Include appropriate technical and biological replicates

• Apply data transformation (log, square root) when necessary to meet statistical assumptions

• Use robust methods resistant to outliers

• Include sensitivity analyses to assess the impact of analytical choices

When reporting results, researchers should clearly state the statistical methods used, justification for their selection, and provide measures of effect size in addition to p-values. This comprehensive statistical approach will enhance the reliability and interpretability of UbiB activity data across oxygen conditions.

How can researchers effectively integrate data from genomic, transcriptomic, and proteomic studies to build a comprehensive model of UbiB function in B. pennsylvanicus?

Building a comprehensive model of UbiB function in B. pennsylvanicus requires sophisticated integration of multi-omics data:

Multi-omics Integration Framework:

• Data Acquisition and Preprocessing:

  • Genomic data: Complete genome sequencing with focus on ubiB locus and flanking regions

  • Transcriptomic data: RNA-seq under various conditions (oxygen levels, growth phases, host tissues)

  • Proteomic data: Global and targeted proteomics, post-translational modification analysis

  • Metabolomic data: Targeted analysis of ubiquinone and intermediates

• Individual Omics Analysis:

  • Genomic: Comparative analysis with other Blochmannia species, identification of regulatory elements

  • Transcriptomic: Differential expression analysis, co-expression network construction

  • Proteomic: Protein abundance quantification, modification site mapping, interaction network analysis

  • Metabolomic: Pathway flux analysis, correlation of metabolite levels with UbiB expression

• Integration Approaches: