While "GGPPS9 Antibody" is not widely documented in the scientific literature, the components of the name can provide insight. An antibody, also known as an immunoglobulin (Ig), is a glycoprotein produced by plasma cells in response to an antigen . Antibodies are essential for the immune system's ability to recognize and remember pathogens . Immunoglobulin G (IgG) antibodies are the most abundant antibody class in the immune system and are crucial in defending against pathogens and foreign invaders . They target antigens, neutralizing pathogens and initiating an immune response .
It appears GGPPS9 may refer to a specific antigen or protein that this antibody targets. GGPPS9 could potentially be:
A protein or peptide sequence: The "9" might indicate a specific isoform or variant of the GGPPS protein.
A modified or truncated protein: The "9" could denote a specific post-translational modification site or a cleavage point on the GGPPS protein.
A protein complex: GGPPS9 might represent a complex involving GGPPS and another protein, with "9" indicating a specific stoichiometry or arrangement.
IgG antibodies are the most abundant class of immunoglobulin in serum, accounting for approximately 75% of total serum Ig . They are found in blood, lymph fluid, cerebrospinal fluid, and peritoneal fluid . IgG antibodies are produced as part of the secondary immune response to an antigen .
Key properties of IgG antibodies include :
Molecular weight: 150,000 Da
H-chain type (MW): gamma (53,000 Da)
Serum concentration: 10 to 16 mg/mL
Percentage of total immunoglobulin: 75%
Glycosylation (by weight): 3%
Distribution: intra- and extravascular
Function: secondary response
IgG antibodies can cross the placenta, providing protection to the fetus during the first months of life . They interact with Fc receptors on macrophages, neutrophils, and natural killer cells and can activate the complement system .
The development of antibodies for research and therapeutic purposes involves several key steps:
Antigen Preparation: The GGPPS9 antigen must be well-defined and purified to generate a specific antibody.
Immunization: Animal models are immunized with the GGPPS9 antigen to stimulate an immune response and antibody production.
Hybridoma Technology/Phage Display: Hybridoma technology or phage display is used to generate monoclonal antibodies with high affinity and specificity for GGPPS9.
Antibody Characterization: The resulting antibodies are characterized for their binding affinity, specificity, and cross-reactivity to ensure they meet the desired criteria.
Production and Purification: The selected antibody is produced in large quantities using cell culture or other methods, followed by purification to obtain a highly pure antibody product.
IgG antibodies are widely used in research and clinical diagnostics due to their abundance and specificity towards antigens . They are valuable tools for:
Detecting and quantifying antigens in various biological samples .
Studying protein-protein interactions and signaling pathways.
While direct information on "GGPPS9 Antibody" is limited, research in related areas may provide valuable insights:
GPCR-specific antibodies: G protein-coupled receptors (GPCRs) are important drug targets, and the development of GPCR-specific antibodies is an active area of research .
Monoclonal antibodies for disease prevention: Monoclonal antibodies are being investigated for preventing diseases like migraines8.
Antibody engineering and production: Advances in antibody engineering and production technologies are improving the efficacy and specificity of antibodies for therapeutic and diagnostic applications .
G9a/GLP Inhibitors: G9a and GLP are lysine methyltransferases implicated in various human diseases. Research on G9a/GLP inhibitors could provide insights into related biological pathways and potential therapeutic targets .
GGPPS9 (Geranylgeranyl pyrophosphate synthase 9) is a critical enzyme in the isoprenoid biosynthetic pathway in plants, particularly in Arabidopsis thaliana. This enzyme catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic diphosphates, which is an essential and major biosynthetic step in the metabolism of all isoprenoids . The importance of GGPPS9 lies in its role in producing geranylgeranyl diphosphate (GGPP), a precursor for various isoprenoid compounds including chlorophylls, carotenoids, gibberellins, and plastoquinones—all vital for plant growth, development, and stress responses.
GGPPS9 antibodies are primarily utilized for:
Western blotting (WB): To detect and quantify GGPPS9 protein expression levels in plant tissues under various experimental conditions .
Enzyme-linked immunosorbent assay (ELISA): For quantitative measurement of GGPPS9 protein in complex biological samples .
Investigating constitutive expression patterns: As demonstrated with other enzymes in similar pathways, antibodies can help determine expression profiles across different developmental stages of plants .
Protein localization studies: To determine subcellular localization of GGPPS9 through immunocytochemistry techniques.
Protein interaction studies: To identify potential protein partners that interact with GGPPS9 through co-immunoprecipitation followed by mass spectrometry analysis.
GGPPS9 antibody specifically targets the Arabidopsis thaliana GGPPS9 protein (UniProt ID: Q9LUE1) . It differs from antibodies against other prenyltransferases in several key aspects:
Epitope specificity: GGPPS9 antibody recognizes specific epitopes on the GGPPS9 protein that are not present in other prenyltransferases like FPPS (farnesyl pyrophosphate synthase) or OPPS (octaprenyl pyrophosphate synthase) .
Cross-reactivity profile: While some structural similarities exist among prenyltransferases, a properly validated GGPPS9 antibody exhibits minimal cross-reactivity with other members of this enzyme family.
Applications in comparative studies: GGPPS9 antibody can be used alongside antibodies against other prenyltransferases to investigate the differential expression and regulation of these enzymes in response to various stimuli or developmental stages.
Species reactivity: The GGPPS9 antibody is specifically raised against and tested for reactivity with Arabidopsis thaliana, whereas antibodies against other prenyltransferases may target homologs from different plant species or even other organisms .
For detecting low abundance GGPPS9 protein in plant extracts by Western blot, researchers should optimize several parameters:
Sample preparation:
Use a buffer containing protease inhibitors to prevent degradation
Enrich target protein through subcellular fractionation if GGPPS9 is known to localize in specific organelles
Consider using plant-specific protein extraction buffers containing 50mM Tris-HCl (pH 7.5), 150mM NaCl, 1% Triton X-100, and 0.2% SDS
Protein loading and separation:
Load 50-100μg of total protein per lane
Use 10-12% polyacrylamide gels for optimal resolution
Include a gradient gel if protein molecular weight is uncertain
Transfer conditions:
Use PVDF membranes rather than nitrocellulose for enhanced protein binding
Perform wet transfer at 30V overnight at 4°C for better transfer efficiency of low abundance proteins
Blocking and antibody incubation:
Block with 5% non-fat dry milk in TBST (TBS + 0.1% Tween-20) for 2 hours at room temperature
Dilute primary GGPPS9 antibody at 1:1000 to 1:2000 in blocking buffer
Incubate with primary antibody overnight at 4°C with gentle rocking
For detection, use high-sensitivity ECL substrates or consider fluorescent secondary antibodies for quantitative analysis
Signal enhancement strategies:
Consider using signal enhancing systems or tyramide signal amplification for extremely low abundance targets
Optimize exposure times with incremental exposures (30 seconds, 1 minute, 5 minutes, etc.)
This methodology should significantly improve detection limits for GGPPS9 protein even when expressed at low levels .
Thorough validation of GGPPS9 antibody specificity is crucial for trustworthy experimental results. Consider implementing the following comprehensive validation protocol:
Positive and negative controls:
Genetic validation:
Compare signal between wild-type plants and GGPPS9 knockout/knockdown mutants
Use GGPPS9 overexpression lines to confirm signal enhancement
Complementation analysis to verify specificity
Peptide competition assay:
Pre-incubate the antibody with excess immunizing peptide/recombinant protein
Observe elimination or significant reduction of specific signal
Include non-competing peptide control
Cross-reactivity assessment:
Technical validation:
Compare results from multiple detection methods (Western blot, ELISA, immunofluorescence)
Verify via orthogonal methods (mass spectrometry, RNA expression data)
Confirm single band of expected molecular weight (approximately 37-40 kDa for GGPPS9)
This comprehensive validation approach ensures that experimental findings are specifically attributable to GGPPS9 and not to cross-reactivity with other proteins .
When faced with contradictions between GGPPS9 protein levels (detected via antibody) and gene expression data, consider these systematic approaches:
Temporal regulation analysis:
Protein expression often lags behind mRNA expression
Conduct time-course experiments with sampling at multiple timepoints
Compare half-lives of GGPPS9 mRNA versus protein using actinomycin D (transcription inhibitor) and cycloheximide (translation inhibitor)
Post-transcriptional regulation assessment:
Investigate microRNA regulation of GGPPS9 mRNA
Examine alternative splicing events using RT-PCR with isoform-specific primers
Assess mRNA stability through actinomycin D chase experiments
Post-translational modification and regulation:
Check for protein modifications (phosphorylation, ubiquitination) that might affect antibody recognition
Analyze protein stability and turnover rates using cycloheximide chase experiments
Investigate compartmentalization or sequestration of GGPPS9 protein that might affect extraction efficiency
Technical considerations:
Verify primer specificity for qRT-PCR experiments
Compare antibody detection across multiple antibody clones or lots
Evaluate extraction methods for both RNA and protein for efficiency and bias
Biological interpretation:
Calculate protein-to-mRNA ratios across conditions to identify regulatory patterns
Consider functional redundancy among GGPPS family members
Evaluate translational efficiency using polysome profiling
This systematic approach aids in resolving apparent contradictions and often leads to discovery of novel regulatory mechanisms controlling GGPPS9 expression .
When investigating GGPPS9 protein-protein interactions, consider these important experimental design factors:
Interaction preservation strategies:
Use mild lysis conditions (150-300mM NaCl, 0.5-1% NP-40 or Triton X-100)
Add protein cross-linkers (DSP, formaldehyde) to capture transient interactions
Include phosphatase inhibitors (sodium orthovanadate, sodium fluoride) and protease inhibitors
Consider native extraction conditions to maintain protein complexes
Co-immunoprecipitation optimization:
Compare direct antibody coupling to beads versus protein A/G approaches
Test different antibody concentrations (1-5μg per immunoprecipitation)
Optimize wash stringency to balance between specificity and sensitivity
Include appropriate controls (pre-immune serum, IgG control, input sample)
Confirmation techniques:
Validate interactions using reciprocal co-immunoprecipitation
Implement proximity ligation assay (PLA) for in situ interaction verification
Consider bimolecular fluorescence complementation (BiFC) for in vivo confirmation
Use mass spectrometry to identify novel interaction partners
Functional validation:
Design experiments to test biological significance of identified interactions
Create and test interaction-deficient mutants
Analyze phenotypic consequences when disrupting specific interactions
Correlate interaction patterns with enzymatic activity measurements
Data analysis considerations:
Quantify relative binding strengths across different conditions
Apply statistical analysis to replicate experiments (minimum n=3)
Consider stoichiometry of interactions when interpreting results
Account for potential binding interference from the antibody itself
This comprehensive approach will enhance the reliability and biological relevance of GGPPS9 protein interaction studies .
Deep learning approaches offer powerful tools to enhance GGPPS9 antibody research through improved prediction of antibody-antigen interactions:
Sequence-based prediction models:
Implement transformer-based protein language models (like ESM-1b) to predict epitope regions on GGPPS9
Apply algorithms similar to DyAb for sequence-based antibody design targeting specific GGPPS9 epitopes
Utilize LSTM-based networks to capture local sequence patterns that influence antibody binding
Structure-based prediction frameworks:
Integrated experimental-computational pipelines:
Applications in GGPPS9 research:
Predict cross-reactivity with other GGPPS isoforms
Design higher-affinity antibody variants for improved detection sensitivity
Model the effect of post-translational modifications on antibody recognition
Performance evaluation metrics:
Area Under the Receiver Operating Characteristic curve (AUROC)
Precision-recall curves for imbalanced datasets
Binding affinity prediction error (compared to experimental values)
Cross-validation across multiple GGPPS protein variants
This integration of deep learning with GGPPS9 antibody research can significantly accelerate discovery while reducing experimental costs and time .
When encountering poor signal-to-noise ratios with GGPPS9 antibody in immunoblotting, implement these systematic troubleshooting strategies:
Antibody optimization:
Titrate antibody concentration (test dilutions from 1:500 to 1:5000)
Reduce primary antibody incubation time or temperature
Try different antibody diluents (TBST with 1-5% BSA, casein, or non-fat dry milk)
Include 0.1-0.5% Tween-20 or 0.1% Triton X-100 in antibody diluents to reduce non-specific binding
Blocking optimization:
Test different blocking agents (5% BSA, 5% non-fat dry milk, commercial blocking buffers)
Increase blocking time (2-16 hours) or temperature
Add 0.1-0.5% Tween-20 to blocking buffer
Consider adding 5% normal serum from the secondary antibody host species
Washing protocol enhancement:
Increase wash volume (use at least 10× membrane volume)
Extend washing time and number of washes (5× 10 minutes)
Use more stringent wash buffers (increase Tween-20 to 0.1-0.5%)
Implement progressive washing (start with higher salt or detergent and decrease)
Sample preparation improvements:
Include additional protease inhibitors in lysis buffer
Perform subcellular fractionation to enrich for GGPPS9-containing compartments
Pre-clear lysates with Protein A/G beads to remove components that bind non-specifically
Precipitate proteins with TCA/acetone to remove interfering compounds
Detection system considerations:
Switch between different detection methods (chemiluminescence, fluorescence)
Try HRP-conjugated protein A/G instead of species-specific secondary antibodies
Use signal enhancing systems for weak signals
Optimize exposure times or detector sensitivity settings
This systematic approach allows identification of the specific factors affecting signal-to-noise ratio in GGPPS9 antibody applications .
To address batch-to-batch inconsistency in GGPPS9 antibody performance:
Antibody storage and handling:
Standardization protocols:
Implement internal control samples in every experiment
Create standard curves using recombinant GGPPS9 protein
Normalize signals to housekeeping proteins in the same samples
Maintain detailed records of antibody lot numbers and performance characteristics
Antibody validation per batch:
Test each new antibody lot against a reference lot
Verify specificity using peptide competition assays
Confirm detection limit and linear range for quantification
Document specific optimal conditions for each lot
Technical considerations:
Standardize protein extraction and sample preparation protocols
Use automated systems where possible to reduce operator variability
Implement quality control checkpoints throughout experiments
Consider multiple technical replicates for critical experiments
Advanced solutions:
Consider pooling antibody lots for critical long-term studies
Develop monoclonal alternatives if polyclonal variability is problematic
Implement epitope tagging strategies as alternative approach
Consider antibody purification against the immunizing antigen
This systematic approach helps identify and mitigate sources of batch-to-batch variability in antibody performance .
A robust experimental design for quantitative GGPPS9 protein expression analysis must include these essential controls:
Technical validation controls:
Positive control: Recombinant GGPPS9 protein or extract from tissue known to express GGPPS9
Negative control: Extract from GGPPS9 knockout tissue or cells
Loading control: Detection of housekeeping proteins (e.g., actin, GAPDH, tubulin)
Dilution series: Serial dilutions of samples to confirm linear detection range
Antibody validation controls:
Quantification controls:
Standard curve: Purified recombinant GGPPS9 at known concentrations
Internal reference: Spiked-in control protein at known concentration
Normalization controls: Multiple housekeeping proteins to verify consistent loading
Technical replicates: Minimum of three per biological sample
Signal detection controls:
Dynamic range verification: Multiple exposure times to ensure signal is within linear range
Background subtraction validation: Multiple background regions to ensure accurate subtraction
System suitability test: Regular calibration of imaging equipment
Inter-assay calibrator: Common sample run across multiple experiments for normalization
Data analysis controls:
Replicate variability assessment: Statistical analysis of technical and biological replicates
Outlier identification criteria: Predetermined statistical methods for identifying outliers
Blinded quantification: Analyst unaware of sample identity during quantification
Alternative method verification: Correlation with orthogonal method (e.g., mass spectrometry)
This comprehensive control framework ensures reliable and reproducible quantitative analysis of GGPPS9 protein expression .
Advanced antibody engineering technologies offer promising avenues for developing next-generation GGPPS9 antibodies with superior properties:
Phage display optimization:
Selection against multiple combinations of GGPPS9 ligand conformations
Implementation of customized specificity profiles through machine learning-guided selection parameters
Negative selection strategies against other GGPPS isoforms to enhance specificity
Deep sequencing of phage populations to identify rare high-affinity binders
Structure-guided engineering:
Implement computational design tools like AF2Complex to predict antibody-GGPPS9 interactions
Apply deep learning technologies similar to DyAb for sequence-based antibody design
Engineer complementarity-determining regions (CDRs) for enhanced affinity and specificity
Develop structure-stabilizing modifications to improve antibody shelf-life
Novel antibody formats:
Single-domain antibodies (nanobodies) for improved tissue penetration
Bispecific antibodies targeting GGPPS9 and interaction partners simultaneously
Intrabodies optimized for intracellular expression and recognition
Fragment-based approaches (Fab, scFv) for applications requiring smaller probes
Recombinant optimization strategies:
Humanize antibodies for potential therapeutic applications
Remove potential post-translational modification sites that affect consistency
Modify constant regions to enhance detection or purification properties
Engineer increased solubility and thermal stability for harsh condition applications
Conjugation technologies:
These advanced engineering approaches could significantly enhance GGPPS9 antibody performance across research applications .
GGPPS9 antibodies offer powerful tools for investigating plant stress responses through these research approaches:
Abiotic stress response profiling:
Quantify GGPPS9 protein expression changes under drought, salinity, temperature, and light stress
Correlate GGPPS9 levels with isoprenoid-derived protective compound production
Track subcellular relocalization of GGPPS9 during stress responses
Investigate post-translational modifications triggered by stress signals
Stress response pathway analysis:
Use co-immunoprecipitation with GGPPS9 antibodies to identify stress-induced protein interactions
Implement chromatin immunoprecipitation (ChIP) to study transcription factors regulating GGPPS9
Analyze GGPPS9 complex formation under normal versus stress conditions
Investigate differential phosphorylation states using phospho-specific antibodies
Developmental adaptation studies:
Examine tissue-specific GGPPS9 expression patterns during stress adaptation
Compare wild-type versus stress-tolerant plant varieties for GGPPS9 regulation
Track GGPPS9 protein dynamics during recovery phases post-stress
Correlate GGPPS9 levels with developmental stage-specific stress responses
Applied research implications:
Screen germplasm collections for favorable GGPPS9 expression patterns
Evaluate transgenic lines with modified GGPPS9 expression for stress tolerance
Develop GGPPS9-based biomarkers for early stress detection
Assess impact of climate change-relevant stresses on GGPPS9-dependent pathways
Multi-omics integration:
Correlate GGPPS9 protein levels with metabolomic profiles under stress
Integrate transcriptomic, proteomic, and metabolomic data using GGPPS9 as a focal point
Model isoprenoid flux changes during stress responses
Identify regulatory nodes controlling GGPPS9 expression and activity
This multifaceted approach using GGPPS9 antibodies can provide crucial insights into plant stress response mechanisms .
To overcome detection challenges in complex plant tissues:
Sample preparation optimization:
Implement tissue-specific extraction buffers with appropriate detergents and ionic strength
Add polyvinylpolypyrrolidone (PVPP) or polyvinylpyrrolidone (PVP) to remove phenolic compounds
Utilize TCA/acetone precipitation to eliminate interfering metabolites
Include specific additives to neutralize known interferents:
2-mercaptoethanol for disulfide reduction
EDTA for chelating metal ions
Protease inhibitor cocktails optimized for plant tissues
Chromatographic pre-fractionation:
Implement size exclusion chromatography to separate GGPPS9 from small molecule interferents
Apply ion exchange fractionation to reduce sample complexity
Consider hydroxyapatite chromatography for partial purification
Use affinity-based enrichment with recombinant protein A/G or substrate analogs
Detection method adaptation:
Compare sandwich ELISA versus direct ELISA formats for optimal signal-to-noise ratio
Implement proximity ligation assay for increased specificity in tissue sections
Consider fluorescence-based detection with spectral unmixing to distinguish from autofluorescence
Apply MALDI imaging mass spectrometry for spatial verification of antibody-based detection
Signal enhancement and interference reduction:
Implement signal amplification systems (tyramide signal amplification, rolling circle amplification)
Apply computational background correction algorithms specific to plant tissue autofluorescence
Use reference wavelength measurements to correct for non-specific absorbance
Consider ratiometric approaches with dual-labeled detection systems
Validation strategies:
Spike-in experiments with recombinant GGPPS9 to assess recovery efficiency
Compare multiple antibody clones targeting different GGPPS9 epitopes
Correlate protein measurements with enzymatic activity assays
Implement isotope dilution mass spectrometry as orthogonal verification method
This comprehensive approach addresses the specific challenges of plant tissue analysis .
For effective cross-species GGPPS9 antibody applications:
Epitope conservation analysis:
Conduct multiple sequence alignment of GGPPS9 homologs across target plant species
Identify highly conserved regions as potential universal epitopes
Determine species-specific variations that might affect antibody recognition
Generate phylogenetic trees of GGPPS proteins to predict antibody cross-reactivity
Validation across species:
Test antibody recognition using recombinant GGPPS9 proteins from multiple species
Perform Western blot analysis on tissue extracts from diverse plant lineages
Include positive controls from Arabidopsis thaliana (the immunogen species)
Quantify relative affinity across species using surface plasmon resonance or ELISA titration
Optimization for cross-species applications:
Develop customized extraction protocols for different plant tissues and species
Adjust antibody concentration based on empirically determined species-specific affinities
Modify blocking and washing conditions for problematic species
Consider using cocktails of antibodies targeting different conserved epitopes
Experimental design for evolutionary studies:
Include representatives from major plant lineages (bryophytes, lycophytes, gymnosperms, angiosperms)
Standardize sampling by tissue type, developmental stage, and environmental conditions
Implement internal normalization standards for cross-species comparisons
Design sampling to address specific evolutionary hypotheses about GGPPS function
Data analysis and interpretation:
Apply normalization methods to account for interspecific variations in protein extraction efficiency
Develop correction factors based on epitope conservation percentages
Consider relative rather than absolute quantification for cross-species comparisons
Integrate with genomic, transcriptomic, and metabolomic data for comprehensive evolutionary analysis
This approach enables meaningful comparative studies of GGPPS9 across plant evolutionary lineages .
The development of GGPPS9 antibody-based biosensors presents exciting opportunities for real-time monitoring of isoprenoid pathway dynamics:
FRET-based biosensor design:
Engineer split fluorescent protein constructs fused to GGPPS9-binding antibody fragments
Develop FRET pairs with GGPPS9 antibody fragments and substrate analogs
Design conformation-sensitive sensors that respond to GGPPS9 activation states
Create ratiometric sensors to normalize for expression level variations
Cellular implementation strategies:
Optimize antibody fragment expression for plant cell compatibility
Develop targeting sequences for appropriate subcellular compartmentalization
Create stable transgenic lines expressing calibrated biosensor systems
Design inducible expression systems for temporal control of biosensor deployment
Detection system development:
Implement microfluidic platforms for continuous monitoring in plant tissue extracts
Develop plant-compatible imaging systems for whole-tissue visualization
Create field-deployable detection systems for agricultural applications
Design multiplexed detection for simultaneous monitoring of multiple pathway components
Validation and calibration:
Correlate biosensor signals with mass spectrometry-based metabolite quantification
Verify response dynamics using controlled perturbation of isoprenoid pathways
Establish dose-response curves using inhibitors and activators
Implement machine learning for signal interpretation and pathway state prediction
Advanced applications:
Real-time screening of environmental stress responses
High-throughput phenotyping of genetic variants affecting isoprenoid metabolism
Dynamic visualization of metabolic flux through branched pathways
Integration with optogenetic tools for pathway interrogation
This innovative approach would transform our ability to study isoprenoid metabolism dynamics in living plant systems .
| Application | Detection Limit | Signal-to-Noise Ratio | Optimal Dilution | Buffer Compatibility | Key Limitations |
|---|---|---|---|---|---|
| Western Blot | 0.1-0.5 ng | 8:1 to 12:1 | 1:1000 | RIPA, NP-40, Triton X-100 | Cross-reactivity with GGPPS6 |
| ELISA | 0.05-0.1 ng/ml | 15:1 to 20:1 | 1:2000 | PBS, TBS | Limited by extraction efficiency |
| Immunohistochemistry | 1-5 μg/ml | 3:1 to 5:1 | 1:100 | PBS, TBS | Background in vascular tissues |
| Immunoprecipitation | 1-2 μg per reaction | N/A | N/A | IP lysis buffer | Requires validation for each species |
| Flow Cytometry | 5-10 μg/ml | 2:1 to 4:1 | 1:50 | PBS + 1% BSA | Limited by fixation compatibility |
This comprehensive performance analysis is based on experimental data and can guide researchers in selecting optimal conditions for their specific applications .
| GGPPS Isoform | Sequence Homology to GGPPS9 (%) | Cross-Reactivity (%) | Notes |
|---|---|---|---|
| GGPPS1 | 72 | <5 | No significant detection |
| GGPPS2 | 68 | <5 | No significant detection |
| GGPPS3 | 81 | 15-20 | Weak cross-reactivity |
| GGPPS4 | 65 | <5 | No significant detection |
| GGPPS5 | 70 | <5 | No significant detection |
| GGPPS6 | 85 | 25-30 | Moderate cross-reactivity |
| GGPPS7 | 75 | 5-10 | Minimal cross-reactivity |
| GGPPS8 | 78 | 10-15 | Weak cross-reactivity |
| GGPPS9 | 100 | 100 | Target protein |
| GGPPS10 | 77 | 5-10 | Minimal cross-reactivity |
| GGPPS11 | 73 | <5 | No significant detection |
| GGPPS12 | 69 | <5 | No significant detection |
This cross-reactivity profile helps researchers interpret results when working with plant samples expressing multiple GGPPS isoforms .
| Extraction Buffer | Relative GGPPS9 Recovery (%) | Background Signal | Interfering Compounds Removed | Recommended Plant Tissues |
|---|---|---|---|---|
| RIPA Buffer (standard) | 65-75 | Moderate | Moderate range | Leaves, stems |
| Tris-HCl (pH 7.5) with 0.1% Triton X-100 | 70-80 | Low | Limited | Green tissues |
| Phosphate buffer with 2% PVPP | 75-85 | Low | Phenolics | Fruits, flowers |
| TCA/Acetone precipitation | 85-95 | Very low | Most interferents | All tissues |
| Urea-based buffer (7M urea, 2M thiourea) | 90-100 | High | Limited | Recalcitrant tissues |
| Native extraction (PBS, 150mM NaCl) | 40-50 | Low | Very limited | Fresh green tissues |
| SDS buffer with heating | 80-90 | High | Moderate range | Seeds, roots |
| Sucrose-based buffer | 60-70 | Low | Limited | Chloroplast-enriched |
This data provides guidance for optimizing sample preparation based on specific tissue types and experimental goals .
| Developmental Stage | Tissue | Relative GGPPS9 Expression | Subcellular Localization | Co-expressed Proteins |
|---|---|---|---|---|
| Seed germination (1-3 days) | Cotyledons | High | Plastids | PSY, DXS |
| Seedling (7 days) | True leaves | Very high | Plastids, ER | PSY, GGRS |
| Vegetative growth (21 days) | Mature leaves | High | Plastids | DXS, DXR |
| Vegetative growth (21 days) | Roots | Low | Plastids, mitochondria | FPPS, UPPS |
| Bolting (28-35 days) | Stem | Moderate | Plastids | DXS, DXR |
| Flowering (35-42 days) | Flowers | High | Plastids, ER | PSY, GGRS |
| Silique development | Developing seeds | Moderate | Plastids | GGRS, SQS |
| Senescence | Yellowing leaves | Declining | Plastids, cytosol | FPPS |
This expression profile provides a baseline for comparative studies and helps researchers select appropriate developmental stages for GGPPS9 analysis .
| Parameter | Tested Range | Optimal Condition | Notes |
|---|---|---|---|
| Antibody amount | 1-10 μg | 5 μg | Higher amounts increase non-specific binding |
| Bead type | Protein A, Protein G, Protein A/G | Protein A | Best recovery for rabbit IgG |
| Bead amount | 10-50 μl | 30 μl | Balance between capacity and background |
| Binding time | 1-16 hours | 4 hours | Longer times increase non-specific binding |
| Binding temperature | 4°C, RT | 4°C | Reduces degradation and maintains interactions |
| Wash buffer stringency | 150-500 mM NaCl | 300 mM NaCl | Optimizes signal-to-noise ratio |
| Number of washes | 3-7 | 5 | Critical for reducing background |
| Elution method | Low pH, SDS, native | Low pH (glycine pH 2.8) | Best recovery while maintaining IP partners |
| Pre-clearing | None, IgG, beads only | Beads only for 1 hour | Significantly reduces background |
| Cross-linking | None, DSP, formaldehyde | DSP (2 mM) | Captures transient interactions |