UBXN2B Human

What is UBXN2B and which protein family does it belong to?

UBXN2B (UBX domain protein 2B) is a member of the UBX domain containing (UBXN) family of proteins. It specifically belongs to the UBX group within the larger UBXD family (UBXDF). Mammalian cells contain 13 members of the UBXDF, which are divided into two main categories: 8 members in the UBX (ubiquitin regulatory X) group and 5 members in the UBA (ubiquitin-associated)-UBX group . UBXN2B belongs to the UBX group, where the UBX domain is the only ubiquitin-related domain present. This classification is important for understanding its potential functions in cellular processes, particularly those related to protein quality control and degradation pathways.

What are the key structural domains and features of UBXN2B?

UBXN2B is characterized by its UBX domain, which is its primary functional domain. In the UBX group proteins like UBXN2B, the UBX domain stands as the sole ubiquitin-related domain, unlike members of the UBA-UBX group that possess additional domains . The UBX domain enables UBXN2B to interact with p97/VCP (valosin-containing protein), an essential hexameric AAA+ ATPase involved in numerous cellular processes. The protein's structure allows it to participate in various protein interaction networks, influencing cellular functions through the structural constraints it imposes on p97/VCP and its binding partners . The specific amino acid sequence of human UBXN2B corresponds to the accession number NP_001071087, as referenced in antibody development information .

How conserved is UBXN2B across different species?

UBXN2B demonstrates conservation across mammalian species, with documented reactivity in human, mouse, and rat systems . This cross-species conservation suggests evolutionary importance and functional significance. The Harmonizome database indicates that UBXN2B has been studied in both human and mouse tissues, with expression data available from multiple sources including the Allen Brain Atlas for both species . This conservation across mammals provides researchers with valuable model systems for studying UBXN2B function in different experimental contexts and suggests that findings in model organisms may have translational relevance to human biology.

What is the normal tissue distribution pattern of UBXN2B in humans?

UBXN2B shows varying expression levels across different human tissues. According to databases like the Harmonizome, UBXN2B expression has been documented in multiple tissue types, including various brain regions . The protein has been studied across different cell types and tissues through resources such as BioGPS Human Cell Type and Tissue Gene Expression Profiles . In cell lines like U-2-OS, many UBXDF members, potentially including UBXN2B, are predominantly localized to the nucleoplasm . This tissue distribution pattern is important for understanding the protein's normal physiological roles and for interpreting any aberrant expression in disease states.

Is UBXN2B expression developmentally regulated in the human brain?

Evidence suggests developmental regulation of UBXN2B expression in the human brain. The Allen Brain Atlas datasets include information on UBXN2B expression in both developing and adult human brain tissues, including prenatal brain tissue expression profiles . This temporal expression data across brain development suggests potential stage-specific functions for UBXN2B in neural development or maintenance. The presence of UBXN2B expression data in both "Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq" and "Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles" databases indicates scientific interest in its developmental patterns , though specific functional implications of these patterns require further investigation.

How do researchers effectively visualize UBXN2B subcellular localization?

Researchers can visualize UBXN2B subcellular localization using immunohistochemistry techniques with specific antibodies such as the UBXN2B Antibody (OTI1F7) . This monoclonal antibody has been validated for applications including immunohistochemistry on both fresh and paraffin-embedded samples . When conducting localization studies, researchers should expect UBXN2B to potentially show nucleoplasmic localization, as observed for several UBXDF family members in the U-2-OS cell line . For optimal results, antibody dilutions should be experimentally determined for each specific application and cell type . Flow cytometry represents another technique validated for UBXN2B detection and can provide quantitative data on expression levels across cell populations .

What is known about UBXN2B's interaction with p97/VCP?

UBXN2B, like other UBXD family members, interacts with p97/VCP through its UBX domain. Research has shown that p97/VCP is significantly co-expressed with almost all UBXDF members . This interaction is functionally significant as "UBXD regulates p97 through the massive interaction networks they create and the structural constraints they impose on p97 as well as its compounds" . The UBX domain serves as the binding interface to p97/VCP, creating a regulatory network that influences p97/VCP's diverse cellular functions. This interaction positions UBXN2B as a potential modulator of processes including protein degradation, membrane fusion, and stress responses that are mediated by p97/VCP activity.

How does UBXN2B co-expression with other UBXD family members inform its function?

Co-expression analysis reveals relationships between UBXN2B and other UBXD family members that may indicate shared or complementary functions. The correlation network of UBXD family members shows various positive and negative co-expression relationships . While specific correlations for UBXN2B are not detailed in the available data, the patterns seen with other family members (such as the significant positive co-expression between UBXN6 and UBXN1, or between UBXN7 and UBXN2A) suggest that such relationships may exist for UBXN2B as well . These co-expression patterns can help researchers understand functional redundancy, compensation mechanisms, or cooperative functions among UBXD family proteins.

What methods are most effective for studying UBXN2B protein-protein interactions?

For studying UBXN2B protein-protein interactions, researchers should consider multiple complementary approaches. Co-immunoprecipitation using specific antibodies such as the UBXN2B Antibody (OTI1F7) can identify binding partners in cellular contexts . Western blotting can confirm these interactions and provide semi-quantitative data . For more comprehensive interaction mapping, proteomics approaches can be applied following immunoprecipitation. Researchers studying UBXN2B interactions should consider both endogenous protein detection and experiments with recombinant proteins, such as the full-length recombinant human UBXN2B protein that has been produced in HEK293T cells for antibody generation . These approaches can reveal both direct binding partners and components of larger protein complexes.

What are the optimal conditions for Western blot detection of UBXN2B?

For optimal Western blot detection of UBXN2B, researchers should consider several key parameters. The UBXN2B Antibody (OTI1F7) [PerCP] has been validated for Western blot applications, though specific dilutions should be experimentally determined for each laboratory context . The antibody is a monoclonal mouse IgG that reacts with human, mouse, and rat UBXN2B . For optimal results, researchers should consider proper sample preparation techniques, appropriate blocking solutions to minimize background, and optimal primary and secondary antibody incubation times. The antibody is supplied in PBS with 0.05% Sodium Azide as a preservative and should be stored at 4°C in the dark to maintain stability . Careful titration experiments are recommended to determine the minimum antibody concentration that yields specific signal with minimal background.

How can researchers effectively use flow cytometry to study UBXN2B?

Flow cytometry represents a powerful technique for studying UBXN2B in cell populations. The UBXN2B Antibody (OTI1F7) [PerCP] is specifically conjugated with PerCP (Peridinin Chlorophyll Protein Complex), which has an excitation maximum at 490 nm and emission maximum at 675 nm . This spectral characteristic makes it compatible with standard flow cytometers equipped with 488 nm lasers. For optimal results, researchers should:

• Properly fix and permeabilize cells to allow antibody access to intracellular UBXN2B

• Include appropriate negative controls (isotype control, unstained cells)

• Perform compensation if using multiple fluorochromes

• Experimentally determine optimal antibody concentration

• Consider cell type-specific expression levels when interpreting results

This approach allows quantitative assessment of UBXN2B levels across different cell populations or under various experimental conditions .

What control experiments should be included when studying UBXN2B?

When studying UBXN2B, several control experiments should be included to ensure result validity:

• Antibody specificity controls: Include samples where the primary antibody is omitted or replaced with an isotype control. For the UBXN2B Antibody (OTI1F7), the appropriate isotype control would be mouse IgG .

• Positive and negative expression controls: Include cell types or tissues known to express high or low levels of UBXN2B based on databases like the Allen Brain Atlas or BioGPS .

• Knockdown/knockout validation: Where possible, include UBXN2B-depleted samples to confirm signal specificity.

• Cross-reactivity assessment: When working across species, verify that the antibody performs as expected in each species (the UBXN2B Antibody (OTI1F7) is reported to react with human, mouse, and rat UBXN2B) .

• Technical replicates: Include multiple technical replicates to account for experimental variation.

Is UBXN2B expression altered in cancer tissues?

The relationship between UBXN2B expression and cancer remains an area requiring further investigation. While specific data on UBXN2B expression across cancer types is limited in the available research, studies of other UBXD family members have shown variable expression patterns in different cancer types . For instance, UBXN11 shows weak staining or negative results in most cancer cases, with only a subset of breast, prostate, and pancreatic cancers showing moderate staining . Some UBXD family proteins exhibit altered expression in specific cancer types, with UBXN7 showing moderate nuclear positivity in most tumor tissues and strong positivity in certain skin, ovarian, cervical, lung, and testicular cancers . These patterns in related proteins suggest that UBXN2B expression might also be differentially regulated in cancer, making it a potential area for cancer research.

How does altered UBXN2B function potentially contribute to disease mechanisms?

Given UBXN2B's interaction with p97/VCP and its potential role in protein quality control pathways, alterations in its function could contribute to disease processes in several ways. The protein quality control system is crucial for maintaining cellular homeostasis, and disruptions in this system have been linked to various diseases, including neurodegenerative disorders and cancer . While specific disease mechanisms directly linked to UBXN2B dysfunction haven't been fully characterized in the available research, its role in regulating p97/VCP function suggests potential pathogenic mechanisms if this regulation is compromised . Disruptions could affect protein degradation pathways, stress responses, or other p97/VCP-dependent processes. Further research using multi-omics approaches could help elucidate these potential disease mechanisms .

What are the challenges in interpreting UBXN2B expression data in pathological samples?

Interpreting UBXN2B expression data in pathological samples presents several challenges. First, protein expression patterns don't always correspond with mRNA levels, as noted for some UBXD family members: "protein expressions were discordant with mRNA expressions for most tumour types or were unavailable" . Second, the complexity of protein interaction networks involving UBXN2B means that expression levels alone may not reflect functional status. Third, technical variations in antibody performance across different sample types can affect detection sensitivity . Finally, the heterogeneity in patient samples and disease states can lead to variable results that are difficult to interpret without large cohorts. These challenges necessitate careful experimental design, including appropriate controls and multiple detection methods when studying UBXN2B in pathological contexts.

How can multi-omics approaches enhance our understanding of UBXN2B function?

Multi-omics approaches offer powerful strategies for comprehensively studying UBXN2B function. These approaches integrate data from multiple biological levels to provide a more complete picture of protein function and regulation. Tools like DIABLO and NOLAS can integrate genomic, transcriptomic, and proteomic data to identify relationships that wouldn't be apparent from single-omics approaches . For UBXN2B research, multi-omics integration could reveal:

• Correlations between genetic variants and UBXN2B expression or function

• Relationships between UBXN2B expression and broader cellular pathways

• Effects of UBXN2B perturbation across multiple biological layers

• Disease-specific alterations in UBXN2B-related networks

These approaches are particularly valuable for proteins like UBXN2B that function within complex interaction networks, as they can capture the multifaceted effects of alterations in UBXN2B expression or function .

What are the most promising approaches for elucidating UBXN2B's precise role in the p97/VCP interaction network?

To elucidate UBXN2B's precise role in the p97/VCP interaction network, researchers should consider several complementary approaches:

• Structural biology techniques: Determining the three-dimensional structure of UBXN2B-p97/VCP complexes through X-ray crystallography or cryo-electron microscopy.

• Domain mapping and mutagenesis: Creating truncated or point-mutated versions of UBXN2B to identify specific residues critical for p97/VCP binding and functional modulation.

• Functional assays: Developing assays that measure p97/VCP activity in the presence or absence of UBXN2B to determine its regulatory effects.

• Interactome analysis: Using proteomics approaches to map the complete interactome of UBXN2B under different cellular conditions.

• Live-cell imaging: Applying advanced microscopy techniques to visualize UBXN2B-p97/VCP interactions in real-time within cellular contexts.

These approaches would help define UBXN2B's specific contributions to the "massive interaction networks" that UBXD proteins create with p97/VCP and provide insight into how these interactions regulate p97/VCP function .

What computational tools and databases are most valuable for UBXN2B researchers?

UBXN2B researchers benefit from several computational tools and databases:

• Expression databases: Resources like the Allen Brain Atlas and BioGPS provide valuable information on UBXN2B expression across tissues, developmental stages, and species .

• Protein interaction databases: Tools like STRING, BioGRID, and IntAct contain data on protein-protein interactions that may involve UBXN2B.

• Structural prediction tools: In the absence of experimental structures, tools like AlphaFold can predict UBXN2B structure and potential interaction interfaces.

• Multi-omics integration platforms: Tools like DIABLO and NOLAS enable integration of multiple data types to gain comprehensive insights into UBXN2B function .

• The Harmonizome: This resource aggregates information about UBXN2B across multiple datasets, providing a centralized access point to diverse data types .

These computational resources complement experimental approaches and can guide hypothesis generation, experimental design, and data interpretation in UBXN2B research.