CLE45 Antibody

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Product Specs

Buffer
Preservative: 0.03% Proclin 300
Constituents: 50% Glycerol, 0.01M PBS, pH 7.4
Form
Liquid
Lead Time
Made-to-order (14-16 weeks)
Synonyms
CLE45 antibody; At1g69588 antibody; F24J1CLAVATA3/ESR antibody; CLE)-related protein 45 [Cleaved into: CLE45p] antibody
Target Names
CLE45
Uniprot No.

Target Background

Function
CLE45 is an extracellular signal peptide that plays a crucial role in regulating cell fate. It exhibits several regulatory functions, including:

* **Repressing root apical meristem maintenance:** CLE45 acts to suppress the maintenance of the root apical meristem.
* **Repressing protophloem differentiation:** CLE45, in conjunction with BAM3, represses the differentiation of protophloem cells.
* **Regulating the transition of protophloem cells:** CLE45, along with BRX, BAM3, and CLE45, collectively regulate the transition of protophloem cells from proliferation to differentiation, impacting the postembryonic growth capacity of the root meristem. This signaling pathway is dependent on CRN and CLV2 and involves MAKR5 for transduction/amplification.
* **Triggering MAKR5 accumulation:** CLE45 triggers the accumulation of MAKR5 in developing sieve elements, a process mediated by BAM3.
* **Preventing auxin response:** CLE45, in a dose-dependent manner, prevents auxin response in the root meristem, leading to the repression of protophloem differentiation and periclinal sieve element precursor cell division.
* **Promoting pollen tube growth:** CLE45 promotes the elongation of pollen tube growth in a SKM1 and SKM2-dependent manner, particularly under relatively high temperatures (30 degrees Celsius). This enhancement of pollen tube growth under high temperatures suggests a role in conferring tolerance against heat stress, potentially through the maintenance of mitochondrial activity.
* **Alleviating mitochondrial decay:** CLE45 alleviates mitochondrial decay in pollen tube in vitro culture.
Gene References Into Functions
  1. A study identified BAM3 as the CLE45 receptor in the root and mapped its peptide binding surface biochemically. The study also revealed that CRN stabilizes BAM3 expression, which is essential for BAM3-mediated CLE45 signaling. PMID: 28607033
  2. Research findings strongly suggest that the interaction between pollen and pistil through the CLE45-SKM1/SKM2 signaling pathway sustains pollen performance at higher temperatures, leading to successful seed production. PMID: 23910659
Database Links

KEGG: ath:AT1G69588

STRING: 3702.AT1G69588.1

UniGene: At.69448

Protein Families
CLV3/ESR signal peptide family
Subcellular Location
[CLE45p]: Secreted, extracellular space.
Tissue Specificity
Expressed at low levels in flowers, especially in pistils. Present in vascular tissues. In roots, confined to protophloem and sieve element precursor cells.

Q&A

What is CLE45 and why are antibodies against it important for plant developmental research?

CLE45 is a 12-amino acid peptide (H-Arg-Arg-Val-Arg-Arg-Gly-Ser-Asp-Pro-Ile-His-Asn-OH) belonging to the CLAVATA3/EMBRYO SURROUNDING REGION family of signaling peptides. It plays a critical role in regulating protophloem differentiation and root development in plants . CLE45 is genuinely expressed in developing protophloem sieve elements (PPSEs) and functions through an autocrine signaling mechanism via the BAM3 receptor .

Antibodies against CLE45 enable researchers to:

  • Precisely localize CLE45 peptide expression in tissue sections

  • Monitor spatial and temporal changes in CLE45 distribution during developmental processes

  • Assess receptor-ligand interactions with potential binding partners like BAM3 and RPK2

  • Validate gene expression studies with protein-level detection

  • Perform immunoprecipitation to identify novel interaction partners

The significance of these antibodies lies in their ability to bridge molecular and cellular approaches in understanding plant vascular development regulation, particularly regarding the maintenance of stem cell populations and differentiation patterns in root meristems.

How does CLE45 antibody specificity compare to antibodies against related CLE peptides?

Developing highly specific antibodies against CLE45 presents unique challenges due to sequence similarities with other CLE family members. CLE45 differs structurally from related peptides CLE25 and CLE26, with notable variations at positions 4 and 7 compared to CLE26, and multiple position differences from CLE25 . These distinct residues provide potential epitope targets for antibody specificity.

When evaluating CLE45 antibody specificity:

CLE PeptideKey Differentiating ResiduesCommon Cross-ReactivityRecommended Validation
CLE45R4, G6, S7, P9CLE26Peptide competition assay, KO controls
CLE26K4, T7CLE45Parallel immunodetection
CLE25Multiple positionsLess commonWestern blot comparison

Rigorous validation protocols should include:

  • Immunoblotting against synthetic peptide arrays containing various CLE family members

  • Testing on tissues from CLE45 knockout/knockdown plants versus wild-type

  • Peptide competition assays using purified CLE45 and closely related peptides

  • Side-by-side comparison with orthogonal detection methods (e.g., RNA probes)

What are the optimal sample preparation methods for CLE45 immunodetection in plant tissues?

Effective immunodetection of CLE45 in plant tissues requires careful consideration of fixation and extraction protocols to preserve peptide integrity while maintaining tissue architecture. CLE45's small size (12 amino acids, 1462.61 Da) and potential post-translational modifications demand specialized approaches.

Recommended fixation protocols include:

  • Paraformaldehyde (4%) in phosphate buffer at neutral to slightly alkaline pH (7.2-7.4) for 2-4 hours

  • Ethanol:acetic acid fixation (3:1) for improved peptide epitope preservation

  • Low-temperature embedding in LR White resin for immunogold electron microscopy

For protein extraction and immunoblotting:

  • Trichloroacetic acid precipitation followed by acetone washes effectively concentrates small peptides

  • Modified Tris-Tricine SDS-PAGE systems with 16-18% acrylamide gels better resolve small peptides

  • Immediate protease inhibitor addition (including metalloproteases) is critical to prevent rapid degradation

  • Membrane transfers benefit from glutaraldehyde-assisted fixation for improved retention of small peptides

When considering pH dependence of CLE45 activity:

  • Buffer system selection is crucial, as CLE45 perception is pH-dependent, specifically requiring the R4 residue

  • Extraction buffers should maintain neutral to slightly acidic pH (6.5-7.0) to preserve biological activity

  • Structured comparative controls across pH gradients may be necessary when analyzing binding interactions

These specialized preparation techniques help overcome the inherent challenges in detecting small signaling peptides in complex plant tissue matrices.

How can CLE45 antibodies be used to investigate pH-dependent peptide perception mechanisms?

Recent research has revealed that CLE45 peptide perception exhibits striking pH dependency, with wild-type Arabidopsis becoming insensitive to CLE45 treatment on neutral to alkaline pH media . This pH-dependent perception specifically requires the CLE45 R4 residue and is not observed with related peptides CLE25 and CLE26. Antibody-based approaches offer powerful tools to dissect these mechanisms.

Methodological approach for investigating pH-dependent CLE45 perception:

  • Differential epitope accessibility assays:

    • Prepare plant tissue samples maintained at varying pH conditions (5.5, 6.5, 7.5)

    • Apply CLE45-specific antibodies targeting distinct epitopes including and excluding the R4 residue

    • Compare antibody binding patterns through immunofluorescence or immunogold labeling

    • Quantify signal intensity differences across pH gradients using confocal microscopy

  • Receptor-ligand interaction visualization:

    • Employ proximity ligation assays (PLA) using antibodies against CLE45 and BAM3/RPK2 receptors

    • Perform assays across pH gradients to visualize pH-dependent interaction dynamics

    • Quantify PLA signals to determine optimal pH ranges for receptor-ligand interactions

    • Compare wild-type CLE45 with synthetic variants where R4 is substituted

  • Combined physiological and immunohistochemical analyses:

    • Track root growth inhibition potency alongside antibody-based CLE45 localization

    • Establish correlation matrices between:

      • pH conditions

      • Protophloem differentiation status

      • CLE45 localization patterns

      • Receptor distribution changes

This methodological framework enables researchers to connect CLE45's pH-dependent perception with its functional consequences for protophloem differentiation, potentially revealing mechanisms by which plants integrate environmental pH sensing with developmental signaling pathways.

What are the techniques for using CLE45 antibodies to study the interplay between CLE45 signaling and RLCK-VII-5 kinases?

Research has identified RECEPTOR-LIKE CYTOPLASMIC KINASE VII-5 (RLCK-VII-5) family members, particularly PBL34, as critical components of CLE peptide signaling pathways . Antibody-based approaches can elucidate the spatiotemporal dynamics of CLE45-triggered signaling cascades involving these kinases.

Advanced methodological approaches include:

  • Co-immunoprecipitation with phosphorylation state analysis:

    • Immunoprecipitate CLE45-receptor complexes using CLE45 antibodies

    • Probe for associated RLCK-VII-5 family kinases (especially PBL34)

    • Analyze phosphorylation patterns of precipitated proteins before and after CLE45 treatment

    • Perform time-course experiments to capture signaling dynamics

  • Multiplexed immunofluorescence with phospho-specific antibodies:

    • Generate or source phospho-specific antibodies against activated forms of PBL34

    • Perform dual or triple labeling with antibodies against:

      • CLE45 peptide

      • Total PBL34 protein

      • Phosphorylated PBL34

    • Analyze colocalization patterns using super-resolution microscopy

    • Quantify signal ratios across developmental zones and treatment conditions

  • In situ proximity-dependent labeling:

    • Develop antibody-enzyme conjugates (e.g., CLE45 antibody-HRP conjugates)

    • Apply proximity-dependent labeling in tissue sections to identify proteins in close proximity

    • Compare labeling patterns in wild-type versus pbl34 mutant backgrounds

    • Identify additional pathway components through mass spectrometry analysis

This integrated approach reveals how CLE45 signaling activates downstream RLCK-VII-5 kinases while distinguishing their roles from related kinases involved in immune responses, such as those in the RLCK-VII-8 clade that respond normally to CLE45 treatment .

How can dual immunodetection of CLE45 and its receptors address questions about autocrine versus paracrine signaling?

CLE45 functions through dual signaling modes: autocrine signaling via BAM3 in developing protophloem sieve elements (PPSEs) and paracrine signaling to neighboring cell files through RPK2 to maintain pluripotency . Sophisticated antibody-based approaches can differentiate these distinct signaling modes.

Methodological framework:

  • High-resolution dual-receptor localization:

    • Apply multi-epitope imaging using antibodies against:

      • CLE45 peptide

      • BAM3 receptor

      • RPK2 receptor

    • Employ spectral unmixing to resolve closely spaced epitopes

    • Analyze receptor distributions across cell boundaries using 3D reconstruction

    • Quantify signal colocalization coefficients between CLE45 and each receptor

  • Cell-specific signaling activation mapping:

    • Combine CLE45 antibody detection with phospho-specific antibodies against activated signaling components

    • Track phosphorylation cascades from source cells (autocrine) to neighboring cells (paracrine)

    • Evaluate signaling gradients through computational image analysis

    • Compare patterns in wild-type versus receptor mutant backgrounds

  • Genetic mosaic analysis with antibody validation:

    • Generate plants with cell-type specific knockout/knockdown of CLE45 production

    • Apply antibodies to track CLE45 distribution despite its absence in source cells

    • Measure signaling responses in neighboring cells through phospho-specific antibodies

    • Quantify minimum effective distance for paracrine signaling effects

This comprehensive approach enables researchers to dissect the dual signaling mechanisms of CLE45, addressing fundamental questions about how concentration gradients and receptor specificity contribute to distinct developmental outcomes in adjacent cell populations.

What strategies can be employed to investigate CLE45 antibody binding characteristics in the context of synthetic peptide variants?

Synthetic CLE45 variant peptides with specific amino acid substitutions represent valuable tools for dissecting structure-function relationships. Antibody binding studies with these variants can reveal critical epitope determinants and correlate binding properties with biological activity.

Advanced methodological approaches include:

  • Epitope mapping with alanine scanning libraries:

    • Generate a comprehensive library of CLE45 variants with single alanine substitutions

    • Perform parallel antibody binding assays using various anti-CLE45 antibodies

    • Create binding affinity heat maps correlating sequence positions with recognition strength

    • Compare antibody binding profiles with functional activity in root growth inhibition assays

  • Competition binding analysis with structure-activity correlations:

    • Implement competitive ELISA assays using wild-type CLE45 and variant peptides

    • Calculate IC50 values for each variant's ability to compete with wild-type

    • Correlate competition efficiency with:

      • Biological activity in planta

      • pH-dependent behavior alterations

      • Receptor binding preferences

  • Surface plasmon resonance (SPR) characterization:

    • Immobilize anti-CLE45 antibodies on sensor chips

    • Measure binding kinetics (kon, koff) for wild-type and variant CLE45 peptides

    • Determine equilibrium dissociation constants (KD) across different buffer conditions

    • Create structure-binding relationship models

CLE45 VariantAntibody Binding (% of WT)Root Inhibition ActivitypH DependencyPredominant Receptor
Wild-type100%StrongHighBAM3 > RPK2
R4AVaries by antibodyReducedMinimalAltered specificity
G6ATypically preservedModeratePreservedSimilar to WT
S7ATypically preservedModeratePreservedSimilar to WT
P9AOften reducedMinimalVariableReduced recognition

This strategic approach enables researchers to establish clear connections between CLE45's structural features, antibody recognition properties, and biological functions, potentially revealing new insights into structure-based peptide engineering for agricultural applications.

What are the recommended protocols for producing and validating custom CLE45 antibodies?

Generating high-quality, specific antibodies against the small CLE45 peptide requires careful consideration of antigen design, immunization strategies, and rigorous validation. This methodological framework outlines the optimal approach for researchers developing custom CLE45 antibodies.

Antigen design and production strategy:

  • Synthesize full-length CLE45 peptide (H-RRVRRGSDPIHN-OH) with >95% purity

  • Consider using a carrier protein conjugation approach:

    • KLH (keyhole limpet hemocyanin) for maximizing immunogenicity

    • BSA (bovine serum albumin) for screening assays

  • Carefully select conjugation chemistry:

    • MBS (m-maleimidobenzoyl-N-hydroxysuccinimide ester) for N-terminal conjugation

    • EDC (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide) for side-chain conjugation

  • Maintain native peptide structure by using appropriate spacers between carrier and peptide

Immunization and antibody production:

  • Employ multiple-host strategy (rabbit, guinea pig, goat) for diverse epitope recognition

  • Implement extended immunization schedule (12-16 weeks) with at least 5 boosts

  • Monitor antibody titers via ELISA using both conjugated and free peptide

  • Consider hybridoma development for monoclonal antibodies targeting specific epitopes

Comprehensive validation protocol:

  • Specificity testing:

    • ELISA against CLE45 and related peptides (CLE25, CLE26)

    • Peptide array screening with systematic amino acid substitutions

    • Western blot using synthetic peptides and plant extracts

    • Testing on CLE45-deficient plant tissues (genetic knockout/knockdown)

  • Application-specific validation:

    • Immunohistochemistry with appropriate negative controls

    • Pre-absorption controls with excess peptide antigen

    • Concentration gradient testing to determine optimal working dilutions

    • Cross-species reactivity assessment if studying CLE45 in multiple plant species

  • Functionality verification:

    • Neutralization assays to determine if antibodies block CLE45-receptor interactions

    • Co-immunoprecipitation validation with known interacting proteins

    • Verification that antibody recognition is maintained across relevant pH ranges

This comprehensive approach ensures development of highly specific antibodies suitable for multiple research applications while minimizing cross-reactivity with related CLE family peptides.

How should researchers optimize immunohistochemical protocols for detecting endogenous CLE45 in different plant tissues?

Detecting endogenous CLE45 in plant tissues presents unique challenges due to its low abundance, small size, and the complex matrix of plant cell walls and vacuoles. This methodological framework provides a systematic approach to optimize immunohistochemical detection of CLE45.

Tissue preparation optimization:

  • Fixation parameter assessment:

    • Compare aldehyde-based fixatives at varying concentrations:

      • Paraformaldehyde (2-4%)

      • Glutaraldehyde (0.1-0.5%)

      • Combined formulations (Modified FAA: formalin-acetic acid-alcohol)

    • Optimize fixation duration (1-24 hours) and temperature (4°C vs. room temperature)

    • Evaluate the impact of vacuum infiltration cycles (3-5 cycles of 5 minutes)

  • Embedding and sectioning considerations:

    • For light microscopy: Paraffin embedding with extended infiltration for complete penetration

    • For electron microscopy: LR White or Lowicryl resins with low-temperature polymerization

    • Section thickness optimization: 4-7 μm for light microscopy, 70-90 nm for TEM

    • Mount sections on adhesive-coated slides to prevent loss during processing

Antigen retrieval and signal enhancement:

  • Epitope unmasking strategies:

    • Heat-induced epitope retrieval (HIER) using citrate buffer (pH 6.0)

    • Enzymatic recovery using proteinase K at carefully titrated concentrations

    • Detergent-assisted permeabilization with Triton X-100 (0.1-0.5%)

    • Combined approaches based on empirical optimization

  • Signal amplification methods:

    • Tyramide signal amplification (TSA) for chromogenic and fluorescent detection

    • Polymer-based detection systems with minimal background

    • Sequential antibody layering with species-specific secondary antibodies

    • Quantum dot conjugation for improved signal stability and sensitivity

Protocol optimization matrix:

Tissue TypeRecommended FixationOptimal Antigen RetrievalBackground Reduction Strategy
Root meristem4% PFA, 4 hours, 4°CCitrate pH 6.0, 95°C, 20 min5% milk, 1% BSA blocking
Vascular cambiumFAA, overnight, 4°CProteinase K (1 μg/ml), 10 minAvidin/biotin blocking
Shoot apex3% PFA + 0.1% GA, 2 hoursTris-EDTA pH 9.0, 95°C, 15 min0.1% Sudan Black B in 70% ethanol
Mature phloemEthanol:acetic acid (3:1)1% SDS, 5 minMouse IgG blocking for endogenous IgG

This systematic approach allows researchers to develop tissue-specific protocols that maximize CLE45 detection sensitivity while minimizing background interference, enabling accurate localization of this important developmental signaling peptide.

What are the best practices for quantifying CLE45 peptide levels using antibody-based techniques?

Accurately quantifying endogenous CLE45 peptide levels in plant tissues requires specialized antibody-based approaches that address the challenges of detecting small signaling peptides. This methodological framework provides comprehensive strategies for reliable CLE45 quantification.

Sample preparation for quantitative analysis:

  • Extraction optimization:

    • Implement rapid tissue harvesting with flash-freezing in liquid nitrogen

    • Utilize acidified methanol extraction (methanol:water:acetic acid, 90:9:1) for peptide stability

    • Incorporate internal standard peptides (isotopically labeled CLE45) for recovery normalization

    • Consider solid-phase extraction (SPE) with C18 cartridges for sample concentration

  • Pre-analytical considerations:

    • Standardize tissue collection timing to account for diurnal fluctuations

    • Normalize sampling to specific developmental stages rather than chronological age

    • Implement consistent tissue-to-extraction buffer ratios (100 mg tissue/ml buffer)

    • Perform parallel protein content determination for standardization

Quantitative immunoassay approaches:

  • Competitive ELISA development:

    • Optimize coating conditions using synthetic CLE45 peptide

    • Develop standard curves spanning 0.1-100 ng/ml concentration range

    • Implement four-parameter logistic curve fitting for accurate interpolation

    • Validate using spike recovery experiments with known quantities of synthetic peptide

  • Multiplex immunoassay platforms:

    • Develop bead-based multiplex assays for simultaneous detection of multiple CLE peptides

    • Implement internal quality controls at low, medium, and high concentrations

    • Perform cross-reactivity assessments with related CLE peptides

    • Validate against orthogonal quantification methods (e.g., mass spectrometry)

Validation and quality control framework:

Performance ParameterAcceptance CriteriaVerification Method
Lower limit of detection (LLOD)≤0.1 ng/mlSignal-to-noise ratio >3:1
Lower limit of quantification (LLOQ)≤0.5 ng/mlCV <20%, recovery 80-120%
Intra-assay precisionCV <10%10 replicates at 3 concentrations
Inter-assay precisionCV <15%3 assays on different days
Recovery80-120%Spike recovery at 3 concentrations
LinearityR² >0.98Dilution series of high concentration sample
SpecificityCross-reactivity <5%Testing with CLE25, CLE26, and other CLE peptides

This comprehensive approach ensures reliable quantification of CLE45 peptide levels across different tissue types and experimental conditions, enabling meaningful comparative analyses in developmental studies.

How can researchers troubleshoot inconsistent CLE45 immunodetection results across different plant tissues?

Inconsistent immunodetection of CLE45 across different plant tissues can arise from multiple factors including tissue-specific matrix effects, expression level variations, and technical challenges. This systematic troubleshooting framework addresses common issues and provides methodological solutions.

Tissue-specific matrix interference assessment:

  • Identify potential interfering compounds:

    • Perform parallel extractions with and without polyvinylpolypyrrolidone (PVPP) to remove phenolics

    • Test for cell wall component interference using pre-treatment with cell wall degrading enzymes

    • Evaluate protease activity by adding protease inhibitor cocktails of increasing strength

    • Assess oxidative environment effects by incorporating antioxidants (ascorbate, DTT)

  • Tissue-specific protocol modifications:

    • Adjust tissue:buffer ratios based on water content of different tissues

    • Implement tissue-specific permeabilization protocols (longer for tissues with thick cell walls)

    • Modify blocking solutions to address tissue-specific background issues

    • Optimize antigen retrieval conditions for each tissue type

Technical parameter optimization matrix:

IssuePotential CausesInvestigation ApproachSolution Strategies
No signal in specific tissuesEpitope maskingTest multiple antigen retrieval methodsOptimize unmasking protocol for tissue type
Low expression levelsCompare with RT-qPCR dataImplement signal amplification systems
Tissue-specific post-translational modificationsTest alternative antibodies targeting different epitopesDevelop modification-specific antibodies
High backgroundEndogenous peroxidase activityPre-block with H₂O₂ treatmentUse alternative detection systems (e.g., alkaline phosphatase)
Endogenous biotinIncorporate avidin/biotin blocking stepSwitch to non-biotin detection systems
Non-specific antibody bindingIncrease blocking strength and durationAdd normal serum matching secondary antibody species
Inconsistent resultsFixation variabilityStandardize fixation protocolsImplement internal control markers for processing quality
Antibody batch variationTest new lots against reference standardsPrepare large batches of working dilutions
Section thickness differencesUse calibrated microtomesInclude thickness measurement in protocols

Validation with complementary approaches:

  • Confirm expression patterns with in situ hybridization for CLE45 mRNA

  • Utilize fluorescent protein fusions in transgenic plants as reference patterns

  • Perform side-by-side comparisons with multiple antibodies targeting different CLE45 epitopes

  • Implement robust negative controls (peptide competition, genetic knockouts)

This comprehensive troubleshooting framework allows researchers to systematically identify and address the causes of inconsistent CLE45 immunodetection, leading to more reliable and reproducible results across diverse plant tissues.

What approaches can resolve cross-reactivity issues between CLE45 antibodies and other CLE family members?

Cross-reactivity between antibodies targeting CLE45 and other CLE family members represents a significant challenge for specific detection. This methodological framework provides systematic approaches to identify, characterize, and resolve such cross-reactivity issues.

Cross-reactivity assessment and characterization:

  • Comprehensive cross-reactivity profiling:

    • Perform dot blot or ELISA screening against all known CLE peptides

    • Generate quantitative cross-reactivity percentages for each peptide

    • Create epitope maps using peptide arrays with overlapping sequences

    • Identify specific amino acid positions contributing to cross-reactivity

  • Structural analysis of cross-reactive epitopes:

    • Compare sequence alignments of cross-reactive CLE peptides

    • Identify conserved motifs versus CLE45-specific residues

    • Model potential structural similarities using computational approaches

    • Design synthetic variant peptides to confirm key residues involved

Resolution strategies for cross-reactivity issues:

  • Antibody purification approaches:

    • Implement negative affinity purification using cross-reactive peptides

    • Perform sequential affinity chromatography to remove cross-reactive antibodies

    • Use epitope-specific chromatography with synthetic peptides containing CLE45-unique regions

    • Validate purified fractions for improved specificity

  • Experimental design modifications:

    • Include appropriate genetic controls (knockout/knockdown lines)

    • Perform parallel detection with antibodies targeting different epitopes

    • Implement competing peptide controls at optimized concentrations

    • Design dual-labeling approaches that can differentiate between family members

  • Advanced specificity enhancement techniques:

    • Develop subtraction protocols using pre-absorption with cross-reactive peptides

    • Implement two-antibody sandwich assays requiring dual epitope recognition

    • Design ratio-based detection approaches comparing signals from different antibodies

    • Employ bioinformatic filtering of imaging data based on expected distribution patterns

Decision matrix for cross-reactivity resolution:

Cross-reactivity LevelPrimary Resolution ApproachSecondary ApproachValidation Method
Minor (<10%)Titer optimizationBlocking with competing peptidesKnockout control comparison
Moderate (10-30%)Negative affinity purificationDual antibody approachesPeptide array verification
Severe (>30%)New antibody developmentComplementary detection methodsOrthogonal technology validation

How can researchers address challenges in detecting phosphorylation changes in CLE45 signaling pathways?

Detecting phosphorylation changes in components of the CLE45 signaling pathway presents significant technical challenges due to the transient nature of these modifications, their subcellular localization, and the complexity of plant tissues. This methodological framework provides strategies to overcome these challenges.

Optimized phosphoprotein extraction and preservation:

  • Rapid phosphorylation state preservation:

    • Implement flash-freezing of tissues in liquid nitrogen within seconds of treatment

    • Include phosphatase inhibitor cocktails at elevated concentrations (2-3× standard)

    • Maintain cold chain throughout extraction process (4°C or lower)

    • Consider protein crosslinking approaches for extremely labile phosphorylation sites

  • Extraction protocol modifications:

    • Utilize phenol-based extraction methods for maximum protein recovery

    • Implement TUBE (Tandem Ubiquitin Binding Entity) technology for enrichment

    • Perform fractionation to concentrate membrane-associated signaling components

    • Incorporate dephosphorylation controls to establish baseline signals

Advanced phosphorylation detection strategies:

  • Phospho-specific antibody approaches:

    • Develop antibodies against phosphorylated motifs in key signaling components (BAM3, RPK2, PBL34)

    • Implement parallel detection with total protein antibodies for normalization

    • Perform time-course experiments to capture transient phosphorylation events

    • Utilize proximity ligation assays to detect protein-protein interactions dependent on phosphorylation

  • Mass spectrometry-based approaches:

    • Implement phosphopeptide enrichment using TiO₂ or IMAC (Immobilized Metal Affinity Chromatography)

    • Develop targeted MRM (Multiple Reaction Monitoring) assays for key phosphopeptides

    • Perform label-free quantification with internal standard peptides

    • Create spectral libraries of CLE45-induced phosphorylation events

Experimental design considerations:

Signaling ComponentTypical Phosphorylation KineticsRecommended Detection WindowSample Preparation Strategy
Receptor kinases (BAM3/RPK2)Rapid (30s-5min)0-30 min with 30s intervalsDirect tissue freezing, membrane enrichment
Cytoplasmic kinases (PBL34)Intermediate (2-15min)0-60 min with 5 min intervalsCytosolic fraction isolation
Transcription factorsDelayed (15-60min)0-120 min with 15 min intervalsNuclear isolation protocol

Validation framework:

  • Use phosphomimic and phospho-dead mutants to confirm antibody specificity

  • Perform parallel analyses with genetic pathway mutants (bam3, rpk2, pbl34)

  • Correlate phosphorylation patterns with downstream transcriptional changes

  • Validate key findings using orthogonal approaches (in-gel kinase assays, genetic complementation)

This comprehensive methodological framework enables researchers to capture and analyze the dynamic phosphorylation events triggered by CLE45 signaling, providing insights into the molecular mechanisms underlying its developmental effects in plants.

How might antibody-based approaches contribute to understanding the evolutionary conservation of CLE45 signaling across plant species?

CLE peptide signaling represents an ancient regulatory mechanism in plants, but the evolutionary conservation and divergence of CLE45-specific functions across different plant lineages remain poorly understood. Antibody-based approaches offer unique opportunities to investigate these evolutionary aspects across diverse plant species.

Comparative immunodetection methodologies:

  • Cross-species epitope mapping:

    • Generate antibodies against conserved epitopes of CLE45 using sequence alignments

    • Perform systematic immunodetection across evolutionarily diverse plant species

    • Create distribution maps of CLE45-like epitopes in primitive versus advanced plants

    • Correlate immunodetection patterns with vascular complexity development

  • Receptor-ligand conservation analysis:

    • Develop co-immunoprecipitation protocols adaptable across species

    • Compare CLE45-receptor interactions in bryophytes, lycophytes, gymnosperms, and angiosperms

    • Identify conserved versus species-specific interaction partners

    • Relate binding properties to evolutionary changes in vascular development

Functional conservation assessment framework:

  • Heterologous expression studies with antibody validation:

    • Express CLE45 orthologs from different species in Arabidopsis

    • Use antibodies to confirm expression and localization patterns

    • Assess cross-species functionality through phenotypic rescue experiments

    • Correlate structural conservation with functional conservation

  • Comparative phosphoproteomics approach:

    • Develop phospho-specific antibodies against conserved signaling components

    • Compare phosphorylation patterns triggered by native versus heterologous CLE45 peptides

    • Identify conserved phosphorylation cascades versus species-specific responses

    • Create evolutionary models of CLE45 signaling pathway development

Evolutionary trajectory mapping:

Plant GroupExpected CLE45 ConservationAnticipated Receptor SystemKey Research Questions
BryophytesPartial - ancestral CLE-like peptidesProto-LRR receptor systemDo moss CLE peptides influence cell differentiation?
LycophytesModerate - specialized for primitive vasculatureSimplified receptor repertoireCan lycophyte CLE45-like peptides inhibit Arabidopsis root growth?
GymnospermsHigh - conserved vascular regulationExpanded receptor familyDo conifer CLE45 orthologs maintain pH sensitivity?
AngiospermsVery high - specialized phloem regulationComplex receptor-coreceptor systemsHow has CLE45 signaling specificity evolved in monocots versus dicots?

This evolutionary research framework using antibody-based approaches will provide critical insights into how CLE45 signaling has evolved from primitive plant forms to complex vascular plants, potentially revealing fundamental principles of developmental regulation conserved across hundreds of millions of years of plant evolution.

What are promising strategies for developing CLE45 antibody-based tools to manipulate plant development for agricultural applications?

Antibody-based technologies targeting CLE45 offer intriguing possibilities for agricultural innovation through precise manipulation of root architecture and vascular development. This forward-looking framework outlines promising research directions for translating CLE45 signaling knowledge into practical agricultural applications.

Antibody-based manipulation technologies:

  • Neutralizing antibody approaches:

    • Develop high-affinity antibodies that specifically block CLE45-receptor interactions

    • Create stabilized antibody formulations for soil application or seed treatment

    • Engineer antibody fragments optimized for plant tissue penetration

    • Establish delivery systems using nanoparticle carriers for sustained release

  • Receptor-targeted immunomodulation:

    • Design bispecific antibodies linking CLE45 receptors to specific coreceptors

    • Create antibody-based artificial scaffolds to enhance or inhibit specific signaling outputs

    • Develop conformation-specific antibodies that lock receptors in active or inactive states

    • Engineer antibody-peptide fusions with tailored signaling properties

Agricultural application development pathway:

  • Proof-of-concept studies:

    • Demonstrate root architecture modification through localized antibody application

    • Establish dose-response relationships for growth enhancement effects

    • Quantify impacts on drought tolerance, nutrient acquisition, and yield components

    • Validate specificity against off-target developmental processes

  • Delivery system optimization:

    • Develop seed coating technologies with controlled antibody release properties

    • Engineer soil amendment formulations protecting antibody activity in rhizosphere

    • Create transgenic approaches for in planta antibody production with tissue specificity

    • Establish nanobody expression systems driven by stress-responsive promoters

Potential agricultural applications matrix:

Crop TypeTarget PhenotypeCLE45 Manipulation ApproachExpected Agricultural Benefit
CerealsEnhanced root depthLocalized CLE45 neutralization in root apexImproved drought tolerance and subsoil nutrient access
LegumesIncreased lateral root densityPeriodic CLE45 signaling modulationEnhanced symbiotic nodulation and phosphorus acquisition
Fruit treesControlled scion-rootstock interactionsGraft junction treatment with signaling modulatorsImproved compatibility and stress adaptation
Tuber cropsModified storage organ developmentTissue-specific manipulation of CLE peptide gradientsOptimized tuber size distribution and quality

Regulatory and implementation considerations:

  • Develop non-GMO approaches using externally applied antibody-based biostimulants

  • Establish safety assessment protocols specific to protein-based agricultural inputs

  • Create detection methods for antibody persistence in harvested products

  • Design economically viable production systems for agricultural-scale antibody manufacturing

This forward-looking research framework provides a roadmap for translating fundamental knowledge about CLE45 signaling into innovative agricultural technologies that could contribute to sustainable crop improvement in the face of climate change and resource limitations.

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