Recombinant Vitis vinifera Photosystem II reaction center protein Z (psbZ)

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Description

Overview of Recombinant Vitis vinifera psbZ

PsbZ is a core subunit of PSII, embedded in the thylakoid membrane of chloroplasts. The recombinant form (UniProt ID: Q0ZJ23) retains the full-length sequence (1–62 amino acids) of the native protein from Vitis vinifera (grapevine) . Key specifications include:

PropertyDetails
SourceVitis vinifera (Grape)
Expression HostEscherichia coli
TagN-terminal His-tag
Molecular Weight~7.2 kDa (theoretical)
Amino Acid SequenceMTIAFQLAVFALIATSSILLISVPVVFASPDGWSSNKNIVFSGTSLWIGLVFLVGILNSLIS
Purity>90% (SDS-PAGE verified)
StorageLyophilized powder at -20°C/-80°C; reconstituted in Tris/PBS buffer

Production and Biochemical Characterization

3.1. Expression and Purification

  • Expressed in E. coli BL21(DE3) using codon-optimized vectors .

  • Purified via immobilized metal affinity chromatography (IMAC) due to the His-tag .

4.1. Mechanistic Studies

  • Used to dissect PSII assembly and repair pathways, particularly interactions with D1/D2 proteins .

  • Serves as a template for mutagenesis to probe residues critical for PSII stability .

4.2. Biotechnological Relevance

  • Insights into psbZ’s role in stress adaptation inform strategies to enhance crop resilience .

  • Potential tool for engineering photosynthesis in synthetic biology platforms .

Future Perspectives

Further studies could explore:

  • PsbZ’s interaction with viral proteins (e.g., Grapevine leafroll-associated virus 3) to mitigate pathogen impacts .

  • Structural resolution via cryo-EM to map PSII-Z binding sites within supercomplexes .

Product Specs

Form
Lyophilized powder
Please note: We prioritize shipping the format currently in stock. However, if you have specific requirements for the format, please indicate them in your order. We will prepare the product according to your request.
Lead Time
Delivery time may vary depending on the purchase method and location. For specific delivery timeframes, please consult your local distributor.
Note: All proteins are shipped with standard blue ice packs. If you require dry ice shipping, please inform us in advance as additional fees will apply.
Notes
Repeated freezing and thawing is not recommended. Store working aliquots at 4°C for up to one week.
Reconstitution
We recommend briefly centrifuging the vial prior to opening to ensure the contents settle at the bottom. Reconstitute the protein in deionized sterile water to a concentration of 0.1-1.0 mg/mL. For long-term storage, we recommend adding 5-50% glycerol (final concentration) and aliquoting at -20°C/-80°C. Our standard glycerol concentration is 50%, which can be used as a reference.
Shelf Life
The shelf life is influenced by various factors, including storage conditions, buffer composition, temperature, and the intrinsic stability of the protein.
Generally, the shelf life for liquid form is 6 months at -20°C/-80°C. Lyophilized form has a shelf life of 12 months at -20°C/-80°C.
Storage Condition
Store at -20°C/-80°C upon receipt. Aliquoting is necessary for multiple uses. Avoid repeated freeze-thaw cycles.
Tag Info
Tag type is determined during the manufacturing process.
The tag type will be determined during the production process. If you have a specific tag type in mind, please inform us, and we will prioritize developing it based on your request.
Synonyms
psbZ; Photosystem II reaction center protein Z; PSII-Z
Buffer Before Lyophilization
Tris/PBS-based buffer, 6% Trehalose.
Datasheet
Please contact us to get it.
Expression Region
1-62
Protein Length
full length protein
Species
Vitis vinifera (Grape)
Target Names
psbZ
Target Protein Sequence
MTIAFQLAVFALIATSSILLISVPVVFASPDGWSSNKNIVFSGTSLWIGLVFLVGILNSL IS
Uniprot No.

Target Background

Function
This protein regulates the interaction between photosystem II (PSII) cores and the light-harvesting antenna.
Database Links

KEGG: vvi:4025086

Protein Families
PsbZ family
Subcellular Location
Plastid, chloroplast thylakoid membrane; Multi-pass membrane protein.

Q&A

What is the function of psbZ in the photosystem II complex of Vitis vinifera?

The psbZ protein is a small but essential component of the photosystem II (PSII) reaction center in Vitis vinifera. It plays a crucial role in the organization and stability of PSII supercomplexes. In grapevines, psbZ contributes to maintaining optimal photochemical efficiency, particularly under varying light conditions. The protein helps regulate electron transport and energy transfer within the PSII complex.

Methodologically, researchers can determine psbZ function through:

  • Chlorophyll fluorescence measurements to assess PSII activity (Fv/Fm ratio)

  • Electron transport rate determination in isolated thylakoids

  • Protein association studies using crosslinking and immunoprecipitation

  • Analysis of photosynthetic activity in psbZ-deficient mutants compared to wild type

In Vitis vinifera, the photochemical efficiency of PSII (measured as Fv/Fm) typically ranges from 0.792 to 0.795 under normal conditions, but declines significantly under high irradiance stress, pointing to the potential protective role of proteins like psbZ .

How is psbZ expression regulated during different developmental stages in grapevine tissues?

The expression of psbZ in Vitis vinifera follows tissue-specific and developmental patterns. Using RNA-Seq profiles from different developmental stages, researchers have observed that photosynthetic gene expression, including psbZ, varies significantly during berry development and in response to environmental factors.

Methodological approaches to study psbZ expression regulation include:

  • RNA-Seq analysis across developmental stages

  • Quantitative PCR to measure transcript levels

  • Promoter analysis using reporter gene constructs

  • Weighted Gene Co-expression Network Analysis (WGCNA) to identify co-regulated genes

Analysis should include sampling at multiple time points, such as early morning (6:00), midday (12:00), and afternoon (16:00-18:00), as photosynthetic gene expression shows diurnal variation . When analyzing expression data, normalization against stable reference genes is critical for accurate quantification.

What techniques are most effective for isolating and purifying recombinant psbZ protein from Vitis vinifera?

Isolating recombinant psbZ protein from Vitis vinifera requires specialized techniques due to its hydrophobic nature and association with the thylakoid membrane.

The most effective methodological approach includes:

  • Gene cloning and expression

    • PCR amplification of the psbZ gene from Vitis vinifera genomic DNA

    • Insertion into an appropriate expression vector with a fusion tag (e.g., His-tag)

    • Expression in a prokaryotic (E. coli) or eukaryotic (yeast) system

  • Protein extraction and purification

    • Membrane solubilization using mild detergents (e.g., n-dodecyl β-D-maltoside)

    • Affinity chromatography using the fusion tag

    • Size exclusion chromatography for further purification

  • Quality assessment

    • SDS-PAGE and Western blot analysis using specific antibodies

    • Mass spectrometry to confirm protein identity

    • Functional assays to verify activity

Researchers should pay particular attention to maintaining proper folding and structure throughout the purification process, as membrane proteins like psbZ can easily denature during isolation procedures.

How does photoinhibition affect psbZ protein turnover in Vitis vinifera under field conditions?

Photoinhibition significantly impacts the turnover of photosystem II proteins, including psbZ, in Vitis vinifera under field conditions. Research shows that exposure to high irradiance (1700-1800 μmol m-2 s-1) induces significant changes in PSII protein composition and function.

Methodological approach for studying psbZ turnover during photoinhibition:

  • Experimental design:

    • Field-grown grapevines exposed to natural high irradiance conditions

    • Sampling at different times of day (morning, midday, afternoon)

    • Comparison between short (2h) and extended (4h) high light exposure

  • Analysis methods:

    • Pulse-amplitude modulation (PAM) fluorometry to measure PSII efficiency (Fv/Fm)

    • Thylakoid isolation and protein extraction

    • Western blotting with specific antibodies against psbZ

    • Density gradient ultracentrifugation to isolate PSII complexes

    • Pulse-chase experiments with isotope labeling to track protein synthesis and degradation

  • Data analysis:

    • Quantitative densitometry of Western blots

    • Correlation analysis between Fv/Fm values and protein abundance

    • Statistical analysis of protein turnover rates

The research by Bertamini and Nedunchezhian demonstrated that high irradiance exposure for 4h (HI4) resulted in significantly higher inhibition of PSII activity compared to 2h exposure (HI2), with marked decline in Fv/Fm values and increase in F0 . This suggests accelerated turnover of PSII proteins under extended high light stress, which would affect psbZ stability and function.

What are the molecular differences in psbZ between disease-resistant and susceptible Vitis species?

Molecular differences in psbZ between disease-resistant and susceptible Vitis species can provide insights into potential roles of photosynthetic proteins in plant defense mechanisms.

Methodological framework for comparative analysis:

  • Sample selection:

    • Disease-resistant species (e.g., Vitis rotundifolia)

    • Susceptible species (e.g., Vitis vinifera)

    • Interspecific hybrids with known resistance profiles

    • Backcrossed lines segregating for resistance traits

  • Analytical approaches:

    • Genomic sequence comparison of psbZ loci

    • RNA-Seq analysis to compare expression levels

    • Protein structure modeling and comparison

    • Functional complementation experiments

  • Integration with resistance data:

    • Correlation of psbZ sequence variations with disease resistance phenotypes

    • Analysis of psbZ co-expression with known resistance genes

    • Investigation of potential physical or functional interactions with resistance proteins

Research on V. vinifera × V. rotundifolia hybrids has demonstrated that introgression of resistance genes from V. rotundifolia results in significant transcriptomic changes affecting multiple functional groups, including plant-pathogen interactions . This approach provides a foundation for understanding how photosynthetic proteins like psbZ might differ between resistant and susceptible genotypes or contribute to defense responses.

SpeciesDisease ResistancepsbZ Expression PatternKey Sequence VariationsCo-expressed Resistance Genes
V. viniferaSusceptibleConstitutive, light-regulatedReference sequenceLimited
V. rotundifoliaResistantMay be upregulated during pathogen challengeMultiple polymorphismsMrRUN1/MrRPV1 and related genes
Resistant hybridsVariableOften shows altered regulationCombination of parental allelesIntrogressed resistance gene clusters

How can CRISPR-Cas9 gene editing be optimized for modifying psbZ in Vitis vinifera to enhance photosynthetic efficiency?

Optimizing CRISPR-Cas9 gene editing for modifying psbZ in Vitis vinifera requires careful consideration of targeting strategy, delivery methods, and screening protocols.

Comprehensive methodological approach:

  • Target site selection and gRNA design:

    • Analysis of psbZ sequence for potential editing sites

    • Selection of target sites minimizing off-target effects

    • Design of multiple gRNAs targeting conserved functional domains

    • In silico validation of gRNA specificity

  • Vector construction and delivery:

    • Assembly of CRISPR-Cas9 constructs with appropriate promoters for grapevine

    • Selection of suitable plant selectable markers

    • Optimization of Agrobacterium-mediated transformation for grapevine embryogenic cultures

    • Alternatives: protoplast transformation or biolistic delivery

  • Editing confirmation and plant regeneration:

    • PCR-based screening followed by sequencing

    • T7 endonuclease I assay or restriction enzyme site loss/gain

    • Next-generation sequencing for comprehensive mutation analysis

    • Regeneration of edited plants through somatic embryogenesis

  • Functional validation:

    • Chlorophyll fluorescence measurements (Fv/Fm ratio)

    • Electron transport rate determination

    • Growth analysis under different light conditions

    • Response to photoinhibition and recovery kinetics

Research on photosystem II in grapevines has shown that photochemical efficiency (Fv/Fm) typically ranges from 0.792-0.795 under normal conditions but declines under stress . CRISPR editing of psbZ could target modifications that enhance recovery from photoinhibition or improve efficiency under suboptimal conditions.

What computational approaches are most effective for predicting the impact of psbZ mutations on PSII function in Vitis vinifera?

Predicting the impact of psbZ mutations on PSII function requires sophisticated computational approaches that integrate structural, evolutionary, and functional data.

Advanced methodological framework:

  • Structural analysis:

    • Homology modeling of Vitis vinifera psbZ structure

    • Molecular dynamics simulations to understand protein-protein interactions

    • Assessment of mutation effects on protein stability and complex assembly

    • Binding site and interaction interface analysis

  • Evolutionary approaches:

    • Multiple sequence alignment across plant species

    • Identification of conserved residues as critical functional sites

    • Selection pressure analysis to identify evolutionarily constrained regions

    • Ancestral sequence reconstruction to understand evolutionary trajectory

  • Machine learning integration:

    • Development of predictive models using TabPFN or similar tabular foundation models

    • Training on datasets linking sequence variations to functional outcomes

    • Feature importance analysis to identify critical residues

    • Cross-validation and performance assessment

  • Validation strategy:

    • Comparison of predictions with experimental mutagenesis data

    • Correlation analysis with known functional impacts

    • Testing model predictions with in vitro and in vivo experiments

Recent developments in tabular foundation models like TabPFN demonstrate the potential for accurate predictions from small datasets, which is particularly valuable for specialized proteins like psbZ where large experimental datasets may not be available . TabPFN shows superior performance for datasets with up to 10,000 samples and 500 features, which is sufficient for most protein sequence-function analysis tasks.

How should experiments be designed to study the role of psbZ in grapevine response to high light stress?

Designing experiments to study psbZ's role in grapevine response to high light stress requires careful consideration of environmental conditions, sampling strategies, and analytical methods.

Comprehensive experimental design approach:

  • Plant material and growth conditions:

    • Select multiple Vitis vinifera cultivars with different light sensitivity

    • Include psbZ-silenced or overexpression lines if available

    • Grow plants under controlled conditions before stress treatment

    • Acclimate plants to standard light conditions (400-600 μmol m-2 s-1)

  • High light treatment protocol:

    • Apply high light stress (1700-1800 μmol m-2 s-1) for varying durations (2h, 4h)

    • Include gradual and sudden light transitions

    • Monitor leaf temperature to separate light from heat effects

    • Sample at multiple time points: pre-stress, during stress, recovery phases

  • Physiological measurements:

    • Chlorophyll fluorescence (Fv/Fm, NPQ, ETR)

    • Gas exchange parameters (photosynthetic rate, stomatal conductance)

    • Chlorophyll content and pigment composition

    • ROS detection and antioxidant enzyme activity

  • Molecular analyses:

    • Transcript levels of psbZ and related genes

    • Protein abundance using Western blotting

    • Thylakoid membrane composition

    • Post-translational modifications of PSII proteins

Previous research has established that grapevine leaves exposed to high irradiance (1700-1800 μmol m-2 s-1) show significant decline in Fv/Fm values, with 4h exposure causing greater inhibition than 2h exposure . This experimental framework can be used to determine how psbZ specifically contributes to this response.

What are the best techniques for analyzing psbZ protein interactions with other photosystem components in recombinant systems?

Analyzing psbZ protein interactions requires specialized techniques due to the hydrophobic nature of photosystem components and the complexity of multi-protein complexes.

Methodological framework for interaction studies:

  • In vitro interaction analysis:

    • Yeast two-hybrid with split-ubiquitin system (for membrane proteins)

    • Pull-down assays with recombinant proteins

    • Surface plasmon resonance for binding kinetics

    • Isothermal titration calorimetry for thermodynamic parameters

  • In vivo interaction approaches:

    • Bimolecular fluorescence complementation (BiFC)

    • Förster resonance energy transfer (FRET)

    • Co-immunoprecipitation from thylakoid preparations

    • Chemical crosslinking followed by mass spectrometry

  • Structural analysis:

    • Cryo-electron microscopy of isolated complexes

    • X-ray crystallography (challenging for membrane proteins)

    • Hydrogen-deuterium exchange mass spectrometry

    • Native mass spectrometry of intact complexes

  • Functional validation:

    • Reconstitution of PSII complexes with/without psbZ

    • Measurement of electron transfer rates in reconstituted systems

    • Site-directed mutagenesis of key residues

    • Competition assays with peptide fragments

When designing these experiments, researchers should ensure proper control of detergent concentrations, as excess detergent can disrupt native interactions, while insufficient amounts may lead to protein aggregation and non-specific binding.

How can RNA-Seq data be optimally analyzed to understand psbZ regulation in the context of grapevine development and stress response?

RNA-Seq data analysis for understanding psbZ regulation requires a systematic bioinformatics approach that integrates developmental and stress-responsive gene expression patterns.

Comprehensive RNA-Seq analysis methodology:

  • Experimental design considerations:

    • Multiple developmental stages and tissues

    • Various stress conditions (high light, drought, pathogens)

    • Appropriate biological and technical replicates

    • Time-course sampling for dynamic responses

  • Data processing pipeline:

    • Quality control and trimming of raw reads

    • Alignment to Vitis vinifera reference genome

    • Transcript quantification and normalization

    • Differential expression analysis across conditions

  • Advanced analytical approaches:

    • Weighted Gene Co-expression Network Analysis (WGCNA)

    • Pathway enrichment analysis

    • Cis-regulatory element identification in promoter regions

    • Integration with other -omics data (proteomics, metabolomics)

  • Validation and functional analysis:

    • qRT-PCR validation of key expression changes

    • Comparison with protein abundance data

    • Correlation with physiological measurements

    • Promoter-reporter assays for regulatory element validation

Research has demonstrated the effectiveness of WGCNA in classifying differentially expressed genes in Vitis species into functional modules correlated with specific traits like disease resistance or berry development . This approach can be applied to understand psbZ regulation within the broader context of photosynthetic gene networks and their response to environmental factors.

What are the primary technical challenges in producing functional recombinant psbZ protein, and how can they be overcome?

Producing functional recombinant psbZ protein presents several technical challenges due to its membrane-associated nature and involvement in complex protein assemblies.

Methodological solutions to key challenges:

  • Challenge: Protein insolubility and aggregation
    Solution approaches:

    • Fusion with solubility-enhancing tags (MBP, SUMO, Trx)

    • Codon optimization for expression host

    • Lower induction temperature (16-18°C)

    • Co-expression with molecular chaperones

    • Directed evolution for improved solubility

  • Challenge: Incorrect folding and absence of cofactors
    Solution approaches:

    • Expression in chloroplast-containing organisms (C. reinhardtii)

    • Cell-free expression systems with membrane mimetics

    • Reconstitution with purified chlorophyll and other cofactors

    • Partial denaturation and controlled refolding

  • Challenge: Low yield and difficult purification
    Solution approaches:

    • Scale-up in bioreactors with optimized conditions

    • Detergent screening for optimal solubilization

    • Specialized chromatography techniques for membrane proteins

    • Nanodiscs or amphipols for stabilization during purification

  • Challenge: Functional assessment
    Solution approaches:

    • Reconstitution into liposomes or nanodiscs

    • Spectroscopic assays for cofactor binding

    • Electron transport measurements with artificial electron acceptors/donors

    • Assembly assays with other PSII components

Each approach should be systematically optimized using design of experiments (DoE) methodology to efficiently identify optimal conditions for expression and purification.

How can contradictory results in psbZ function studies between in vitro and in vivo experiments be reconciled?

Contradictory results between in vitro and in vivo psbZ function studies can arise from multiple factors including differences in experimental conditions, protein interactions, and regulatory mechanisms.

Methodological framework for reconciliation:

  • Systematic comparison of experimental conditions:

    • Create detailed documentation of all parameters (pH, temperature, ionic strength)

    • Identify critical differences between in vitro and in vivo environments

    • Establish minimum experimental conditions required for physiological relevance

    • Design experiments that gradually transition from in vitro to in vivo-like conditions

  • Analysis of protein state and interactions:

    • Characterize protein conformation in different experimental settings

    • Identify missing interaction partners in simplified systems

    • Examine post-translational modifications present in vivo but absent in vitro

    • Study temporal dynamics that may be overlooked in endpoint assays

  • Integrative approach to resolve contradictions:

    • Develop mathematical models to explain different behaviors

    • Use genetic approaches to test specific hypotheses

    • Apply complementary techniques to observe the same process

    • Employ systems biology approaches to place observations in broader context

  • Standardization and reporting recommendations:

    • Establish minimum information required for experiment reporting

    • Develop standard assays that bridge in vitro and in vivo conditions

    • Create reference datasets for calibration across laboratories

    • Implement robust statistical analysis to assess significance of differences

When studying photosystem II components like psbZ, researchers must consider that the complex operates differently when isolated compared to its native thylakoid membrane environment, where interactions with antenna complexes, electron transport components, and regulatory proteins create a dynamic functional system .

What statistical approaches are most appropriate for analyzing changes in psbZ expression across different experimental conditions?

Selecting appropriate statistical approaches for analyzing psbZ expression changes requires consideration of experimental design, data types, and biological questions.

Comprehensive statistical methodology:

  • Exploratory data analysis:

    • Assessment of data distribution and variance homogeneity

    • Outlier detection and handling procedures

    • Batch effect identification and correction

    • Visualization techniques to identify patterns and relationships

  • Statistical testing framework:

    • For two-group comparisons: t-tests (parametric) or Mann-Whitney (non-parametric)

    • For multiple groups: ANOVA with appropriate post-hoc tests

    • For time-course data: repeated measures ANOVA or mixed-effect models

    • For high-dimensional data: false discovery rate control methods

  • Advanced analytical approaches:

    • Regression models with relevant covariates

    • Principal component analysis for dimension reduction

    • Multivariate analysis for complex experimental designs

    • Bayesian approaches for integrating prior knowledge

  • Biological interpretation tools:

    • Gene set enrichment analysis for pathway-level insights

    • Network analysis to identify regulatory relationships

    • Meta-analysis across multiple studies

    • Power analysis for experimental design optimization

When analyzing gene expression data from varied experimental conditions, research has shown that foundation models like TabPFN can improve prediction performance on small to medium datasets (up to 10,000 samples) . These models can help identify complex patterns in expression data that might be missed by traditional statistical approaches.

How might synthetic biology approaches be used to modify psbZ for enhanced photosynthetic efficiency in Vitis vinifera?

Synthetic biology offers innovative approaches to modify psbZ for enhanced photosynthetic efficiency in grapevines, potentially improving productivity and stress resilience.

Methodological framework for synthetic biology applications:

  • Rational design strategies:

    • Computational modeling of modified psbZ structures

    • Identification of rate-limiting steps in photosystem II function

    • Design of optimized psbZ variants based on structure-function relationships

    • Creation of synthetic promoters for context-specific expression

  • Directed evolution approaches:

    • Development of high-throughput screening systems for photosynthetic efficiency

    • Creation of psbZ mutant libraries through error-prone PCR or DNA shuffling

    • Selection under varying light conditions and stress parameters

    • Iterative improvement through multiple rounds of selection

  • Integration with other photosynthetic components:

    • Co-engineering of interacting PSII proteins

    • Optimization of antenna size and composition

    • Coordination with carbon fixation machinery

    • Balancing of electron transport chain components

  • Testing and validation pipeline:

    • Chlorophyll fluorescence measurements for functional assessment

    • Field trials under varying environmental conditions

    • Metabolomic analysis to assess downstream effects

    • Long-term stability and inheritance studies

Research on photoinhibition in grapevines has shown that PSII efficiency (Fv/Fm) decreases under high light stress, particularly after extended exposure . Synthetic biology approaches could focus on modifying psbZ to improve recovery from photoinhibition or enhance stability under stress conditions.

What are the potential applications of understanding psbZ variation across Vitis species for climate resilience breeding programs?

Understanding psbZ variation across Vitis species has significant implications for developing climate-resilient grapevine varieties through targeted breeding programs.

Methodological approach for application in breeding:

  • Comparative genomics framework:

    • Sequencing and comparison of psbZ across diverse Vitis germplasm

    • Identification of natural variants associated with stress tolerance

    • Correlation of sequence polymorphisms with photosynthetic performance

    • Integration with genome-wide association studies for climate resilience traits

  • Functional characterization of variants:

    • Assessment of photochemical efficiency under elevated temperature

    • Drought response evaluation in different psbZ variant backgrounds

    • Combined stress tolerance screening (heat+drought, heat+high light)

    • Recovery kinetics following stress events

  • Breeding integration strategies:

    • Development of molecular markers for beneficial psbZ alleles

    • Design of crossing schemes to incorporate optimal variants

    • Marker-assisted selection protocols for segregating populations

    • Evaluation of heterosis effects in hybrid combinations

  • Phenotypic validation pipeline:

    • Field trials in diverse climate conditions

    • Controlled environment testing for specific stress responses

    • Long-term performance assessment (multiple seasons)

    • Integration with other climate resilience traits

Research on Vitis hybrids has demonstrated significant transcriptomic changes resulting from interspecific hybridization, affecting multiple functional pathways including stress responses . This suggests potential for utilizing genetic diversity in psbZ and related genes for developing improved varieties with enhanced climate resilience.

How can multi-omics integration improve our understanding of psbZ function in the context of grapevine photosynthetic adaptation?

Multi-omics integration provides a powerful approach to understand psbZ function within the broader context of photosynthetic adaptation in grapevines.

Comprehensive multi-omics methodology:

  • Data acquisition across platforms:

    • Genomics: Whole genome sequencing, variant identification

    • Transcriptomics: RNA-Seq under various conditions

    • Proteomics: Quantitative proteomics, post-translational modifications

    • Metabolomics: Primary and secondary metabolite profiling

    • Phenomics: High-throughput phenotyping of photosynthetic parameters

  • Integration methods:

    • Multi-layer network analysis

    • Bayesian data integration frameworks

    • Machine learning approaches for pattern recognition

    • Causal inference methods to establish regulatory relationships

  • Functional validation strategies:

    • Genetic manipulation (CRISPR, RNAi) to test hypothesized relationships

    • Metabolic flux analysis to confirm altered pathways

    • Physiological measurements to validate predicted adaptive responses

    • Field trials to assess real-world relevance of findings

  • Computational resources and tools:

    • Development of specialized databases for Vitis multi-omics data

    • Implementation of visualization tools for complex data relationships

    • High-performance computing infrastructure for large-scale analyses

    • Integration with existing plant biology knowledge bases

Research has shown that foundation models like TabPFN can significantly improve predictions from complex tabular data , making them valuable tools for integrating multi-omics datasets to understand complex biological processes like photosynthetic adaptation. These models can help identify non-linear relationships and interaction effects that might be missed by traditional analytical approaches.

Omics LayerData TypeAnalytical ApproachIntegration Point for psbZ Study
GenomicsDNA variantsGWAS, Comparative genomicsIdentification of natural psbZ variants
TranscriptomicsRNA expressionDifferential expression, WGCNACorrelation of psbZ with co-expressed genes
ProteomicsProtein abundance, PTMsQuantitative proteomics, InteractomePsbZ interaction partners and modifications
MetabolomicsMetabolite profilesPathway analysis, Flux balanceDownstream effects of psbZ variation
PhenomicsPhysiological traitsMulti-trait analysis, QTL mappingLinking psbZ to photosynthetic performance

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