While the exact function and characteristics of the Bacillus licheniformis UPF0477 protein BLi01284/BL02661 are not detailed in the provided references, Bacillus licheniformis itself is a well-documented bacterium with diverse applications. Bacillus licheniformis is a Gram-positive, endospore-forming bacterium commonly found in soil and plant environments . It is closely related to Bacillus subtilis and is known for its ability to grow under both aerobic and anaerobic conditions .
Bacillus licheniformis is industrially significant due to its production of extracellular enzymes, biochemicals, antibiotics, and aminopeptidases . This bacterium synthesizes various proteases, including α-amylase, penicillinase, and pectinolytic enzymes, which are used in industries such as detergent manufacturing, starch hydrolysis, and textile processing . Certain strains also produce peptide antibiotics, specialty chemicals, and poly-γ-glutamic acid .
Enzyme Production: Bacillus licheniformis strains can produce a range of enzymes, including phytase, protease, cellulase, and xylanase . These enzymes facilitate the degradation of various compounds, enhancing the nutritional value of substrates .
Probiotic Potential: Certain strains of Bacillus licheniformis exhibit probiotic properties, tolerating low pH and high bile salt concentrations, which are crucial for survival in the gastrointestinal tract . For example, Bacillus licheniformis (B4) has shown the ability to survive at pH 3.0 and in 1.0% bile salts for 5 hours and demonstrates high proliferative activity at 50°C .
Protein Hydrolysis: Bacillus licheniformis can degrade proteins like glycinin and β-conglycinin, increasing the degree of protein hydrolysis and crude protein content in fermented products .
Antimicrobial Activity: Bacillus licheniformis produces antimicrobial substances, including bacteriocins, which inhibit the growth of other bacteria, fungi, and viruses . These bacteriocins have various mechanisms of action, such as disrupting cell membranes and inhibiting cell wall biosynthesis .
Genomic analysis of Bacillus licheniformis strains reveals shared and unique genes that contribute to their specific traits. For instance, comparative genomics has identified unique genes in certain strains related to metabolic pathways and stress response . The development of genetic tools, such as multiple ribosomal binding sites (RBS), enhances protein production in Bacillus licheniformis, making it a robust host for industrial applications .
Fermentation with Bacillus licheniformis can significantly improve the quality of feed by reducing phytic acid, neutral detergent fiber (NDF), and acid detergent fiber (ADF) content . This leads to better nutrient availability and digestibility .
Bacillus licheniformis synthesizes a variety of antimicrobial compounds, including:
Lichenin: A bacteriocin-like component active against Streptococcus bovis and other anaerobic bacteria .
Licheniformins: Antibacterial agents with bacteriostatic activity against Mycobacterium tuberculosis and other organisms .
Sublichenin: An antimicrobial compound that acts on cell wall synthesis .
Multiple expression systems have been successfully utilized for the recombinant production of BLi01284/BL02661, each with specific advantages depending on research objectives :
| Expression System | Characteristics | Typical Applications |
|---|---|---|
| E. coli | High yield, cost-effective, rapid expression | Structural studies, antibody production, preliminary functional assays |
| Baculovirus | Post-translational modifications, higher solubility | Enzyme activity studies, protein-protein interaction analyses |
| Yeast | Glycosylation patterns, secretion capability | Functional studies requiring eukaryotic processing |
| Mammalian cell | Complex folding, authentic post-translational modifications | Detailed functional characterization, interaction studies |
For studies focusing on basic biochemical characterization, E. coli systems typically provide sufficient quantity and quality of the recombinant protein. For more complex analyses requiring native-like post-translational modifications, the baculovirus or mammalian systems are recommended despite their higher cost and technical complexity .
Purification of recombinant BLi01284/BL02661 can be achieved through a multi-step process tailored to the expression system used. A methodological approach includes:
Cell lysis: For E. coli systems, sonication or high-pressure homogenization in a buffer containing 50 mM Tris-HCl (pH 8.0), 300 mM NaCl, and 1 mM PMSF is recommended .
Initial purification: Affinity chromatography using the appropriate tag (typically His-tag or Avi-tag as mentioned in the product descriptions) with imidazole gradient elution .
Secondary purification: Size exclusion chromatography using Superdex 75 or 200 columns to remove aggregates and achieve >90% purity.
Quality control: SDS-PAGE analysis to confirm >85% purity as indicated in product specifications , followed by Western blotting and mass spectrometry to verify protein identity.
For proteins expressed with the Avi-tag biotinylation system, streptavidin-based affinity purification can provide excellent purity in a single step. In cases where inclusion bodies form, particularly in E. coli systems, additional refolding steps using gradual dialysis against decreasing concentrations of urea or guanidine hydrochloride are necessary to obtain active protein .
The selection of appropriate promoters significantly impacts the expression efficiency of BLi01284/BL02661 in Bacillus licheniformis host systems. Recent studies have characterized several promoter options with varying strengths and induction characteristics :
| Promoter Type | Characteristics | Expression Efficiency | Optimal Application |
|---|---|---|---|
| P43 constitutive | Strong, constitutive expression | High continuous production | When constant protein expression is desired regardless of growth phase |
| PbacA (from bacitracin synthase operon) | Strong endogenous promoter | High yield, native to B. licheniformis | When compatibility with the host's transcriptional machinery is crucial |
| Prha (rhamnose-inducible) | Induced by rhamnose (0-20 g/L), not by glucose | Tunable expression | When tight regulation of expression timing is required |
| Pman (mannose-inducible) | Induced by mannose addition | Moderate to high | When gradual induction is preferred |
For optimal expression of BLi01284/BL02661 in B. licheniformis, the PbacA promoter has demonstrated superior performance for constitutive expression, while the Prha system offers excellent control for inducible expression . When using the rhamnose-inducible system, it's important to note that B. licheniformis requires approximately 36 hours to deplete 20 g/L of rhamnose, compared to just 9 hours for glucose .
Advanced promoter engineering approaches such as hybrid promoter construction and RBS (ribosome binding site) engineering can further enhance expression by 2-5 fold compared to standard promoters .
To elucidate the biochemical function of BLi01284/BL02661 as a putative phosphoesterase, a comprehensive methodological workflow should include:
Substrate screening assay: Test activity against a panel of phosphorylated substrates including:
p-nitrophenyl phosphate (general phosphatase activity)
Various phosphorylated nucleotides (AMP, ADP, ATP)
Phosphorylated proteins/peptides
Phospholipids
Enzyme kinetics characterization:
Determine optimal pH and temperature conditions (based on B. licheniformis native environment)
Measure Km, Vmax, and kcat values for identified substrates
Evaluate the effects of potential inhibitors and activators
Metal ion dependency analysis: As many phosphoesterases require metal cofactors, systematically test activity in the presence of various metal ions (Mg²⁺, Mn²⁺, Zn²⁺, Ca²⁺) and with EDTA to establish cofactor requirements.
Structural biology approaches:
X-ray crystallography or cryo-EM to determine three-dimensional structure
Site-directed mutagenesis of predicted catalytic residues based on structural data
Molecular docking of potential substrates
In vivo functional validation:
Generate knockout strains of BLi01284 in B. licheniformis
Perform comparative metabolomics and phenotype analysis
Conduct complementation studies with wild-type and mutant versions
This multi-faceted approach has successfully elucidated the function of previously uncharacterized proteins in related Bacillus species and would be appropriate for determining the specific role of BLi01284/BL02661 .
Recent breakthrough research has demonstrated that incorporating multiple ribosomal binding sites (RBSs) within a single mRNA leader sequence can dramatically enhance protein expression in Bacillus licheniformis . When applied to BLi01284/BL02661 expression, this methodology could provide significant advantages:
The mechanism involves the construction of expression plasmids carrying the BLi01284/BL02661 gene with varying numbers of RBSs within the mRNA leader region. Research has shown that protein expression levels increased proportionally with the number of RBSs, with dramatic improvements observed when increasing from one to four RBSs .
Quantitative data from similar experiments with GFP showed:
Six RBSs increased fluorescence intensity 5-fold compared to a single RBS
Protein with six RBSs constituted >50% of total intracellular protein
The translation efficiency of six RBSs was approximately 100 times higher than previously strong promoters coupled with native 5'-UTRs
To implement this methodology for BLi01284/BL02661:
Design and construction: Use the one-step method for ligation of tandem repeat sequences as described by researchers to create expression constructs with multiple RBSs (1, 3, 5, and 6 RBSs).
Expression optimization: Clone these constructs into pHY300-PLK compatible plasmid with the P43 promoter.
Quantification methodology: Measure protein production through SDS-PAGE densitometry, Western blotting, and phosphoesterase activity assays if functional assays are available.
This approach is particularly valuable for difficult-to-express proteins or when high yields are required for structural or biochemical studies. The technique has been proven effective for both intracellular and secreted proteins in B. licheniformis .
Expression of BLi01284/BL02661 in E. coli frequently results in inclusion body formation, creating significant challenges for obtaining soluble, functional protein . Addressing these insolubility issues requires a systematic approach:
Challenges and Solutions for BLi01284/BL02661 Insolubility:
Expression conditions optimization:
Temperature reduction: Lowering expression temperature to 16-20°C can significantly improve folding
Induction modulation: Using lower IPTG concentrations (0.1-0.5 mM instead of 1 mM) and extending expression time
Media formulation: Supplementing with osmolytes like sorbitol (0.5 M) and betaine (2.5 mM) that act as chemical chaperones
Fusion tag selection:
Solubility-enhancing tags: MBP (maltose-binding protein) and SUMO tags have shown superior performance over His-tags for similar Bacillus proteins
Tag position effects: N-terminal vs. C-terminal tag placement can significantly affect folding dynamics
Co-expression strategies:
Chaperone co-expression: GroEL/GroES, DnaK/DnaJ/GrpE systems can assist proper folding
Rare codon supplementation: Co-expression of rare tRNAs for codons frequently used in Bacillus but rare in E. coli
Refolding methodologies (when inclusion bodies are unavoidable):
Step-wise dialysis: Gradually reducing denaturant concentration over 24-48 hours
On-column refolding: Immobilizing denatured protein on affinity resin before refolding
Pulsatile refolding: Introducing protein into refolding buffer in pulses to prevent aggregation
Buffer optimization:
Addition of low concentrations of non-ionic detergents (0.05% Triton X-100)
Inclusion of stabilizing agents like L-arginine (0.4-0.8 M)
Testing various pH conditions (pH 6.0-9.0) to identify optimal stability range
For phosphoesterases like BLi01284/BL02661, inclusion of potential cofactors (Mg²⁺, Mn²⁺) in the lysis and purification buffers often enhances stability and solubility by promoting proper folding through metal ion coordination .
Genomic analysis of UPF0477 protein BLi01284/BL02661 across Bacillus species reveals important evolutionary patterns that provide insights into its potential function. Comparative genomic approaches have shown:
Orthologous genes to BLi01284/BL02661 are present in several closely related Bacillus species with varying degrees of sequence conservation :
| Species | Sequence Identity (%) | Synteny Conservation | Predicted Function |
|---|---|---|---|
| B. subtilis | 78-82% | High | Putative phosphoesterase |
| B. pumilus | 75-78% | High | Putative phosphoesterase |
| B. megaterium | 68-72% | Moderate | Putative phosphoesterase |
| B. cereus group | 55-60% | Low | Hypothetical protein |
| Other Firmicutes | 40-50% | Very low | Uncharacterized |
The high conservation of this protein among soil-dwelling and industrially relevant Bacillus species suggests it may play a role in core metabolic functions rather than specialized adaptations. Amino acid residues predicted to be involved in catalytic activity show particularly high conservation (>95% identity), supporting the phosphoesterase functional annotation .
Genomic context analysis indicates that BLi01284/BL02661 is often located in proximity to genes involved in nucleotide metabolism and stress response pathways in most Bacillus species. This syntenic arrangement provides additional evidence that the protein may function in phosphate-related metabolic processes or stress signaling pathways .
Pan-genome analysis comparing B. licheniformis CBA7126 with closely related strains identified BLi01284/BL02661 as part of the core genome shared among all analyzed B. licheniformis strains, further supporting its importance in fundamental cellular processes .
Investigation of BLi01284/BL02661's potential role in B. licheniformis stress responses requires a multi-faceted methodological approach:
Transcriptomic analysis under stress conditions:
RNA-Seq analysis of B. licheniformis exposed to various stressors (osmotic stress, oxidative stress, heat shock)
qRT-PCR validation of BLi01284/BL02661 expression patterns during stress response
Promoter-reporter fusion constructs (using GFP or luciferase) to visualize temporal expression patterns
Gene knockout and complementation studies:
Protein-protein interaction network mapping:
Bacterial two-hybrid screening to identify interaction partners
Co-immunoprecipitation followed by mass spectrometry
Proximity-dependent biotin labeling (BioID) to identify transient interactions
Phosphoproteome analysis:
Comparative phosphoproteomics between wild-type and ΔBLi01284 strains
Identification of differentially phosphorylated proteins during stress response
In vitro validation of potential substrate proteins
This methodological approach is supported by previous studies on B. licheniformis stress responses, which have shown that osmotic stress triggers complex transcriptional changes involving multiple systems, including SigB-controlled general stress response genes . The osmostress response in B. licheniformis involves synthesis and import of compatible solutes along with secondary oxidative stress responses , providing a framework for investigating potential roles of BLi01284/BL02661 in these pathways.
Based on research on osmotic stress in B. licheniformis, methodologies using 1M NaCl shock treatments followed by time-resolved transcriptional profiling would be particularly relevant for studying this protein's potential stress-related functions .
Comparative genomics offers powerful approaches to predict the biochemical function of uncharacterized proteins like UPF0477 protein BLi01284/BL02661:
Phylogenetic profiling methodology:
Construct a presence/absence matrix of BLi01284/BL02661 homologs across diverse bacterial species
Identify co-evolving genes that show similar phylogenetic distribution patterns
Apply statistical methods (mutual information, Pearson correlation) to quantify co-evolution strength
Functional prediction based on characterized co-evolving genes
Gene neighborhood analysis:
Examine the genomic context of BLi01284/BL02661 across multiple Bacillus genomes
Identify conserved gene clusters and operonic structures
Apply the "guilt by association" principle to infer function based on neighboring genes with known functions
Structural bioinformatics approaches:
Predict three-dimensional structure using homology modeling or AlphaFold2
Identify structural homologs using fold recognition algorithms
Analyze conserved domains and potential active sites
Predict binding pockets and potential substrates through molecular docking
Integrated functional networks:
Combine multiple genomic features (co-expression, protein-protein interactions, genomic proximity)
Use machine learning algorithms to weight and integrate diverse evidence types
Validate predictions through targeted experimental approaches
Application of these methodologies to related Bacillus proteins has successfully predicted functions later confirmed experimentally. For example, OrthoANI (Orthologous Average Nucleotide Identity) analysis has been used to classify B. licheniformis strains and identify strain-specific functions . The genome structure comparison between B. licheniformis CBA7126 and related strains using MAUVE alignment has revealed important functional elements that could inform the analysis of BLi01284/BL02661 .
Published research indicates that B. licheniformis CBA7126 possesses 19 unique genes compared to closely related strains, with functions related to carbon metabolism and prophage elements . Similar comparative approaches could reveal the specialized role of BLi01284/BL02661 within B. licheniformis metabolic networks.
Recent research has established B. licheniformis as an effective platform for ergothioneine (EGT) production . To investigate whether BLi01284/BL02661 plays a role in this biosynthetic pathway, the following experimental approaches are recommended:
Gene expression correlation analysis:
Quantify BLi01284/BL02661 expression levels during different phases of EGT production using RT-qPCR
Compare expression patterns with known EGT biosynthetic genes (EanA, EanB, EanAN, EanBN)
Analyze RNA-Seq data from EGT-producing strains to identify co-expressed gene clusters
Gene disruption and overexpression studies:
Create a BLi01284 knockout strain using CRISPR/Cas9 gene editing
Measure EGT production in the knockout strain versus wild-type (using HPLC analysis as described in )
Overexpress BLi01284/BL02661 in EGT-producing strains and quantify impact on production
Perform complementation studies with mutant variants to identify essential domains
Metabolomic analysis:
Compare metabolite profiles between wild-type and BLi01284-modified strains
Focus on intermediates in the EGT pathway (hercynine, hercynylcysteine sulfoxide)
Use LC-MS/MS to quantify changes in metabolic flux through the pathway
Protein-protein interaction studies:
Perform co-immunoprecipitation experiments with BLi01284/BL02661 and known EGT biosynthetic enzymes
Use bacterial two-hybrid assays to screen for interactions
Employ in vitro reconstitution of the EGT pathway with and without BLi01284/BL02661
Based on the methodologies used in successful EGT production studies, experiments should be conducted under optimal conditions for EGT synthesis: 37°C incubation, 250 rpm shaking, with appropriate substrate amino acids (particularly cysteine, which was shown to be rapidly utilized in EGT production) .
If BLi01284/BL02661 functions as a phosphoesterase in nucleotide metabolism, it might indirectly affect EGT biosynthesis through modulation of energy metabolism or regulation of biosynthetic gene expression, making these connections important to investigate.
B. licheniformis is known for producing various antimicrobial substances, including bacteriocins, bacitracins, and licheniformins with significant antimycobacterial activity . To investigate whether BLi01284/BL02661 contributes to these antimicrobial properties:
Genetic manipulation and bioactivity testing:
Generate BLi01284 knockout and overexpression strains
Compare antimicrobial activity using agar diffusion assays against indicator strains (particularly Mycobacterium species)
Quantify production of known antimicrobials (bacitracin, licheniformins) using HPLC and bioassays
Perform complementation studies with site-directed mutants targeting predicted catalytic residues
Secretome analysis:
Compare protein profiles in culture supernatants from wild-type and BLi01284-modified strains
Employ LC-MS/MS to identify differentially abundant antimicrobial peptides
Investigate post-translational modifications of secreted antimicrobials that might require phosphoester processing
Transcriptional regulation studies:
Analyze expression of antimicrobial biosynthetic gene clusters in BLi01284 knockout versus wild-type
Investigate whether BLi01284/BL02661 affects quorum sensing systems that regulate antimicrobial production
Use chromatin immunoprecipitation sequencing (ChIP-seq) to identify potential regulatory interactions
Phosphorylation state analysis:
If BLi01284/BL02661 functions as a phosphoesterase, investigate the phosphorylation status of regulatory proteins involved in antimicrobial synthesis
Employ phosphoproteomic analysis to identify potential substrates
Perform in vitro dephosphorylation assays with purified BLi01284/BL02661 and candidate substrates
Current research indicates that B. licheniformis has unique capabilities in synthesizing and producing a range of antibacterial compounds . If BLi01284/BL02661 is involved in regulatory phosphorylation/dephosphorylation events, it could potentially impact the expression or activation of these antimicrobial systems, particularly through interaction with transcriptional regulators like DegU, AbrB, or CcpA that are known to be involved in B. licheniformis' regulatory networks .
Advanced promoter engineering strategies provide powerful tools for studying BLi01284/BL02661 function through precisely controlled expression. Recent developments in B. licheniformis promoter technology enable sophisticated experimental approaches:
Inducible expression systems optimization:
Implement rhamnose-inducible (Prha) promoter systems for titratable expression of BLi01284/BL02661
Utilize mannose-inducible promoters (Pman) for gradual induction
Employ hybrid promoters combining the strength of constitutive promoters with regulatory elements from inducible systems
Optimize induction conditions based on documented response curves (e.g., rhamnose concentration 0-20 g/L)
Transcription factor-based promoter engineering:
Incorporate recognition sites for key transcription factors (DegU, AbrB, CcpA, GlnR) to create synthetic promoters with custom regulation profiles
Design promoters responding to specific environmental conditions relevant to BLi01284/BL02661's hypothesized function
Use characterized transcription factor binding sites to build promoters with desired expression dynamics
Multiple ribosome binding site (RBS) integration:
Apply the multi-RBS technology demonstrated in recent research to achieve ultra-high expression levels when needed
Construct expression cassettes with 1-6 RBSs to create an expression gradient for dose-response studies
Implement the one-step ligation method for tandem repeat sequences to efficiently generate multi-RBS constructs
Combine with secretion signals if export of BLi01284/BL02661 is desired
Experimental application methodology:
Create a series of strains with BLi01284/BL02661 under different promoter controls
Monitor phenotypic effects across a spectrum of expression levels
Correlate expression level with specific cellular functions using transcriptomics and metabolomics
Identify minimum expression level required for function and toxic threshold
These strategies can be particularly powerful when combined with reporter systems (such as GFP fusion) to monitor expression levels in real-time. The documented 5-fold increase in protein production achieved with six RBSs compared to single RBS constructs provides a quantifiable range for expression tuning experiments.
For studying potential stress-response roles, combining stress-responsive promoters with BLi01284/BL02661 expression could reveal important functional relationships and regulatory mechanisms that would be difficult to elucidate with constitutive expression systems.
Characterizing potential post-translational modifications (PTMs) of BLi01284/BL02661 requires sophisticated mass spectrometry approaches tailored to phosphoesterase proteins:
Sample preparation methodology:
Parallel purification from multiple expression systems (E. coli, B. licheniformis native)
Phosphatase inhibitor inclusion during extraction (sodium orthovanadate, sodium fluoride, β-glycerophosphate)
Dual proteolytic digestion approach (trypsin followed by Glu-C) to enhance sequence coverage
Enrichment strategies for phosphopeptides (TiO2, IMAC) if phosphorylation is suspected
MS instrumentation and methodology:
High-resolution MS/MS using Orbitrap or Q-TOF systems for accurate mass determination
Electron transfer dissociation (ETD) or electron capture dissociation (ECD) for labile PTM preservation
Parallel reaction monitoring (PRM) for targeted analysis of predicted modification sites
Data-independent acquisition (DIA) for comprehensive PTM landscape analysis
Data analysis workflow:
Open search algorithms to identify unexpected modifications
Site localization scoring (Ascore, ptmRS) for precise PTM position assignment
Quantitative analysis using label-free or TMT-based approaches to determine stoichiometry
Integration of MS data with structural models to evaluate functional implications
Validation strategies:
Site-directed mutagenesis of identified PTM sites
Functional assays comparing wild-type and PTM-deficient variants
Temporal PTM profiling under different growth or stress conditions
In vitro enzymatic assays with purified proteins to confirm PTM effects on activity
For potential phosphoesterases like BLi01284/BL02661, particular attention should be paid to serine, threonine, and tyrosine phosphorylation, which could represent either regulatory modifications or enzyme-substrate intermediates. Additionally, given B. licheniformis' propensity for protein secretion , signal peptide processing and other N-terminal modifications should be carefully analyzed.
Cross-linking mass spectrometry (XL-MS) can also provide valuable insights into protein-protein interactions that might regulate BLi01284/BL02661 function or localize it within specific protein complexes, offering functional context beyond simple PTM identification.
Structural biology approaches provide essential insights into the catalytic mechanism of putative phosphoesterases like BLi01284/BL02661. A comprehensive structural biology workflow would include:
Protein crystallography methodology:
Optimization of recombinant protein production with minimal flexible regions
High-throughput crystallization screening (sitting-drop vapor diffusion)
Co-crystallization with potential substrates, product analogs, and inhibitors
Heavy atom derivatization for phase determination if molecular replacement fails
High-resolution data collection at synchrotron radiation facilities
Cryo-electron microscopy approach:
Sample preparation optimization for single-particle analysis
Collection of large datasets (>5000 micrographs) on high-end cryo-EM systems
2D and 3D classification to identify conformational states
High-resolution refinement targeting sub-3Å resolution
Model building and refinement against the EM density
NMR spectroscopy for dynamics:
¹⁵N/¹³C-labeled protein production for backbone and sidechain assignment
Chemical shift perturbation experiments with ligands to identify binding sites
Relaxation dispersion experiments to characterize millisecond timescale dynamics
Hydrogen-deuterium exchange to identify protected regions
Computational structure analysis:
Molecular dynamics simulations to sample conformational space
QM/MM calculations to model transition states during catalysis
Docking studies with potential substrates to predict binding modes
Evolutionary coupling analysis to identify co-evolving residue networks
Structure-guided functional studies:
Alanine scanning of predicted catalytic and substrate-binding residues
Activity assays with structure-based mutants to validate mechanistic hypotheses
Engineering of substrate specificity based on structural insights
Design of specific inhibitors targeting the active site
The integration of these approaches allows for comprehensive characterization of the catalytic mechanism. For a putative phosphoesterase like BLi01284/BL02661, particular attention should be paid to identifying the catalytic triad or metal-coordinating residues typical of phosphoesterase enzymes, as well as substrate-binding pockets that determine specificity.
Recent advances in AlphaFold2 and RoseTTAFold can complement experimental approaches by providing initial structural models that can guide experimental design and interpretation, particularly useful if experimental structure determination proves challenging.
Systems biology approaches provide powerful frameworks for integrating BLi01284/BL02661 into the broader metabolic and regulatory networks of B. licheniformis:
Multi-omics integration methodology:
Combine transcriptomics, proteomics, metabolomics, and fluxomics data from wild-type and BLi01284 knockout strains
Implement temporal profiling under various conditions (stress, different carbon sources)
Apply network inference algorithms to identify regulatory relationships
Develop mathematical models representing the integrated data
Genome-scale metabolic modeling:
Update existing B. licheniformis metabolic models to include BLi01284/BL02661 function
Perform flux balance analysis (FBA) to predict metabolic consequences of BLi01284 perturbation
Conduct in silico gene knockout simulations to generate testable hypotheses
Validate model predictions with experimental measurements of growth and metabolite production
Protein-protein interaction network mapping:
Perform affinity purification coupled with mass spectrometry (AP-MS) to identify interaction partners
Utilize bacterial two-hybrid or split-protein complementation assays for binary interaction detection
Construct temporal interaction networks under different conditions
Map interactions onto known regulatory pathways
Regulatory network reconstruction:
Implement ChIP-seq to identify transcription factor binding sites genome-wide
Perform RNA-seq following BLi01284 perturbation to identify affected genes
Utilize clustered regularly interspaced short palindromic repeats interference (CRISPRi) for targeted gene repression
Construct causal network models from perturbation data
Integration with industrial bioprocess data:
Correlate BLi01284/BL02661 expression with production metrics in industrial strains
Develop predictive models for optimizing expression in biomanufacturing contexts
Design synthetic regulatory circuits incorporating BLi01284/BL02661 for enhanced control
Recent research has highlighted B. licheniformis' complex stress response systems and sophisticated gene regulation mechanisms , providing context for integrating BLi01284/BL02661 into these networks. The established osmotic stress response pathways, which include SigB-controlled genes and compatible solute synthesis, offer a framework for investigating potential regulatory roles of this putative phosphoesterase .