YBR126W-A is a 68-amino-acid protein (UniProt ID: Q8TGU7) initially identified through genome-wide homology searches and ribosome profiling . Its recombinant forms are produced for research purposes, typically in E. coli or yeast systems, with His-tag modifications for purification .
YBR126W-A localizes to the ER, as confirmed by GFP and mCherry fusion experiments . While its precise function remains elusive, bioinformatics and interaction studies suggest potential roles:
Partner | Score | Localization | Putative Function |
---|---|---|---|
YAR075W | 0.801 | Cytosol/Nucleus | IMP dehydrogenase-like activity (IMPDH/GMPR) |
YPR098C | 0.765 | Mitochondrial outer membrane | Unknown (mitochondrial membrane protein) |
YBR230W-A | 0.703 | N/A | Paralog of COQ8 (whole-genome duplication) |
YIL077C | 0.697 | Mitochondria | PUP1 family (mitochondrial function) |
These interactions hint at roles in ER-mitochondria communication or membrane-associated processes .
Localization Confirmation: SWAT-GFP and mCherry tagging demonstrated ER localization, resolving earlier doubts about its annotation .
Mass Spectrometry: Identified peptides covering 64.7% of the sequence (44/68 aa) validated its existence .
Recombinant YBR126W-A is used in:
Subcellular Fractionation: Verifying ER localization via GFP-tagged constructs .
Interaction Studies: Co-IP or pull-down assays to map functional partners .
Structural Studies: His-tagged variants enable crystallization and NMR analyses .
Note: While we prioritize shipping the format currently in stock, please specify your format preference in order notes for customized fulfillment.
Note: All proteins are shipped with standard blue ice packs. Dry ice shipping requires prior arrangement and incurs additional charges.
Tag type is determined during production. To request a specific tag, please indicate your preference; we will prioritize fulfilling such requests.
KEGG: sce:YBR126W-A
STRING: 4932.YBR126W-A
YBR126W-A, now named Meo1 (Mini ER ORF1), belongs to the category of small Open Reading Frame (smORF) proteins in Saccharomyces cerevisiae, containing fewer than 110 amino acids. These smORFs were initially omitted from the first yeast genome annotation efforts and were only added in later annotation versions, explaining their historically uncharacterized status . The systematic visualization of this protein was achieved through the SWAT-GFP library approach, which enabled researchers to assign localization to numerous previously unvisualized proteins, including 80% of the smORFs in the library . The protein's small size made it technically challenging to detect and characterize using traditional methods, contributing to its previous obscurity in the research literature.
YBR126W-A (Meo1) has been definitively localized to the endoplasmic reticulum (ER) using multiple complementary approaches. The primary localization was determined using the SWAT-GFP library, where the protein was tagged at its N-terminus with GFP . This localization was subsequently verified through subcellular fractionation experiments using C-terminal epitope tagging (HA or ProtA tags) to ensure that the observed localization was not an artifact of the N-terminal GFP tag . The protein was among 36 previously uncharacterized smORFs found to localize to the ER using this systematic approach, leading to its designation as Meo1 (Mini ER ORF1) .
The amino acid sequence analysis of YBR126W-A (Meo1) requires careful interpretation due to its small size (under 110 amino acids). Researchers should conduct the following sequence-based analyses:
Motif identification for ER retention/retrieval signals (such as KDEL-like sequences)
Transmembrane domain prediction to determine membrane topology
Signal peptide analysis to assess secretory pathway targeting
Conservation analysis across fungal species to identify functionally important residues
Structural prediction to identify potential interaction domains
The protein's ER localization suggests it may function in processes such as protein folding, quality control, lipid metabolism, or ER stress responses. The presence of any conserved domains shared with other ER proteins would provide valuable clues regarding its specific functional role within the ER network.
Research into YBR126W-A (Meo1) expression patterns reveals condition-dependent regulation. The SWAT system studies demonstrated that proteins placed under control of their native promoters versus a constitutive promoter (SpNOP1) showed dramatically different expression levels spanning two orders of magnitude . When investigating YBR126W-A expression specifically, researchers should:
Utilize quantitative PCR to measure transcript levels across various growth conditions
Employ reporter constructs with the native promoter to identify regulatory elements
Analyze the promoter region for transcription factor binding sites
Compare expression patterns with other ER-localized smORFs to identify co-regulated genes
Investigate expression changes under ER stress conditions (tunicamycin, DTT treatment)
The high-throughput data from the SWAT-GFP library suggests that some proteins may only be expressed under specific conditions, making comprehensive condition testing essential for understanding YBR126W-A regulation .
Identifying interaction partners for small proteins like YBR126W-A (Meo1) presents unique challenges that require specialized approaches. Based on its ER localization, researchers should consider the following strategies:
Proximity-dependent labeling approaches:
BioID or TurboID fusions to label proximal proteins in the ER environment
APEX2 tagging for electron microscopy visualization of the precise ER subdomain
Co-immunoprecipitation strategies:
Gentle solubilization conditions optimized for ER membrane proteins
Crosslinking prior to lysis to capture transient interactions
Sequential co-IP from differentially tagged strains to verify interactions
Genetic interaction mapping:
Synthetic genetic array (SGA) analysis with YBR126W-A deletion
Quantitative analysis of genetic interactions under ER stress conditions
Suppressor screens in YBR126W-A mutant backgrounds
Split-reporter systems:
Yeast two-hybrid adaptations for membrane proteins
Split-ubiquitin assays specifically designed for ER-localized proteins
Bimolecular fluorescence complementation (BiFC) with candidate partners
The SWAT library system offers a powerful platform for these interaction studies, as demonstrated by the co-immunoprecipitation experiments that successfully identified interactions between other tagged proteins in the endomembrane system . The co-localization approach used to identify peroxisomal proteins could be adapted to systematically screen for proteins that precisely co-localize with YBR126W-A within ER subdomains .
The SWAp-Tag (SWAT) library system provides a powerful platform for studying YBR126W-A (Meo1) through multiple tag swapping approaches. The system's versatility allows researchers to efficiently create numerous derivatives using a single parental strain . For optimizing this system specifically for YBR126W-A studies:
Tag selection optimization:
Swap the original GFP tag with specialized tags for different applications
Implement proximity labeling tags (BioID, TurboID) for interaction studies
Utilize split tags for complementation assays
Incorporate degron tags for controlled protein depletion studies
Promoter swapping strategies:
Replace the constitutive SpNOP1 promoter with condition-specific promoters
Implement titratable promoter systems for dose-response studies
Create a series of truncated native promoters to map regulatory elements
Develop reporters with the native promoter for regulation studies
Genetic background modifications:
Cross SWAT strains into deletion collection backgrounds
Implement the system in different yeast strain backgrounds
Combine with genome-wide CRISPRi libraries for genetic interaction studies
Create double-tagged strains for co-localization studies
Technical optimization for small proteins:
Optimize linker length and composition for minimal functional interference
Develop specialized immunoprecipitation protocols for small membrane proteins
Fine-tune expression levels to prevent aggregation or mislocalization
Implement sample preparation techniques optimized for small protein detection
The SWAT system is particularly valuable because the homologous recombination efficiency is extremely high (>98% recovery rate with 96% accuracy), enabling rapid creation of strain collections with different tags and regulatory elements . The proven ability to swap tags seamlessly while preserving native regulation makes this an ideal platform for YBR126W-A functional studies.
Detecting and quantifying native levels of small proteins like YBR126W-A (Meo1) presents technical challenges that require specialized approaches. Based on the challenges observed in systematic studies, researchers should consider:
Transcriptional quantification methods:
RNA-seq with optimized library preparation for small transcripts
qRT-PCR with primers specifically validated for small ORFs
Single-molecule FISH for transcript visualization and quantification
Nascent transcript analysis to measure transcription rates
Protein-level detection methods:
Targeted proteomics (SRM/MRM) optimized for small proteins
Custom antibody development against unique epitopes
Epitope tagging at endogenous loci with verification of functionality
Specialized extraction protocols to preserve small membrane proteins
Translational activity measurement:
Ribosome profiling with optimized footprint collection
Polysome profiling to assess translation efficiency
Pulse labeling with amino acid analogs for synthesis rate measurement
In vitro translation assays to confirm coding potential
Single-cell analysis approaches:
Flow cytometry of tagged variants for population heterogeneity assessment
Single-cell RNA-seq for expression heterogeneity analysis
Live-cell imaging of tagged variants for dynamic expression studies
Correlative light and electron microscopy for precise localization
The high-content microscopy approach used in the SWAT library studies provides a valuable model, demonstrating that even with constitutive expression, proteins maintain unique abundance levels spanning two orders of magnitude . This suggests that post-transcriptional mechanisms play a critical role in regulating YBR126W-A levels and should be a focus of quantification studies.
Analyzing expression data for YBR126W-A (Meo1) requires statistical approaches tailored to the challenges of small proteins and condition-specific expression patterns. Based on the observations from the SWAT library studies, researchers should consider:
Normalization strategies:
Size-factor normalization to account for library size differences
Spike-in controls for absolute quantification
Specialized normalization for small proteins often missed in global methods
Considering both fluorescence intensity and cell-to-cell variability metrics
Differential expression analysis:
Employ methods robust to low count numbers (e.g., DESeq2, edgeR)
Account for technical variation specific to small transcripts/proteins
Implement statistical tests appropriate for potentially non-normal distributions
Consider specialized methods for detecting condition-specific expression
Variance analysis:
Quantify both technical and biological sources of variance
Apply generalized linear mixed models to account for batch effects
Implement variance stabilizing transformations appropriate for low-abundance transcripts
Consider Bayesian approaches for improved estimation of small effect sizes
Multivariate approaches:
Cluster analysis to identify co-regulated genes
Principal component analysis to identify major sources of variation
Time-series analysis for temporal expression patterns
Network analysis to place expression in pathway context
The SWAT library studies demonstrated that even with standardized expression from a constitutive promoter, protein abundance varied significantly between different proteins, spanning two orders of magnitude . This suggests post-transcriptional and post-translational regulation significantly impact YBR126W-A levels and should be accounted for in statistical analyses.
Investigating YBR126W-A (Meo1) localization to specific ER subdomains requires specialized approaches that go beyond standard fluorescence microscopy. Given its confirmed ER localization, researchers should implement the following strategies:
Super-resolution microscopy approaches:
Structured illumination microscopy (SIM) to resolve ER tubule structures
Stimulated emission depletion (STED) microscopy for nanoscale resolution
Single-molecule localization microscopy (PALM/STORM) for precise protein clustering analysis
Expansion microscopy to physically magnify subcellular structures
ER subdomain markers co-localization:
Co-localization with ER-mitochondria encounter structure (ERMES) components
Association with ER-plasma membrane contact sites (cortical ER)
Co-distribution with specialized domains like ER exit sites or lipid droplet formation sites
Analysis with ER stress granule markers under stress conditions
Biochemical fractionation approaches:
Density gradient separation of ER subdomains
Detergent resistance membrane fractionation
Immunoisolation of specialized ER regions
Protease protection assays to determine membrane topology
Dynamic analysis methods:
Fluorescence recovery after photobleaching (FRAP) to measure mobility within the ER
Single-particle tracking to analyze diffusion patterns and constraints
Optogenetic approaches to induce relocalization and assess functional consequences
Correlative light and electron microscopy for ultrastructural context
The SWAT-GFP approach used to identify YBR126W-A's ER localization provides a foundation for these more detailed studies . The systematic co-localization approach used for peroxisomal proteins could be adapted to systematically test co-localization with markers of different ER subdomains, potentially revealing more specific localization patterns .
Evolutionary analysis of YBR126W-A (Meo1) across fungal species can provide valuable insights into its function and importance. Given its classification as a small ORF protein that was only later annotated in the yeast genome, investigating its evolutionary conservation is particularly important .
Key evolutionary analyses should include:
Ortholog identification approaches:
Sensitive sequence similarity searches optimized for small proteins
Synteny analysis to identify positionally conserved genes
Profile-based searches using position-specific scoring matrices
Structure-based homology detection for distant relationships
Evolutionary rate analyses:
Calculation of dN/dS ratios to assess selection pressure
Identification of conserved residues suggesting functional importance
Analysis of insertion/deletion patterns across species
Relative evolutionary rate comparison with other ER proteins
Comparative genomics approaches:
Presence/absence patterns across fungal phylogeny
Co-evolution with interacting partners
Association with specific metabolic or stress response pathways
Correlation with lifestyle or environmental adaptations
Functional evolution assessment:
Expression pattern conservation across species
Localization conservation in model organisms
Complementation assays with orthologs from other species
Analysis of species-specific adaptations in sequence or regulation
The identification of YBR126W-A as part of a previously understudied group of smORFs suggests that similar proteins may exist across fungal species but might have been overlooked in genome annotations . Systematic analysis of these evolutionarily related proteins could reveal conserved functions and establish YBR126W-A as part of an ancient functional group of small ER proteins.