DNA Damage Response: Induced by p53 during genotoxic stress, RNF144A suppresses pro-survival signals by degrading DNA-PKcs, tipping the balance toward apoptosis .
Antiviral Immunity: Enhances STING-dependent signaling by promoting its ubiquitination, critical for defense against herpes simplex virus (HSV-1) .
DNA Damage & Apoptosis
Antiviral Activity
Regulatory Mechanisms
KEGG: xtr:100124307
UniGene: Str.35384
RNF144A is an E3 ubiquitin ligase belonging to the RING-between-RING (RBR) family of ubiquitin ligases. These proteins function as RING-HECT hybrid E3 ligases, which play crucial roles in protein ubiquitination and subsequent degradation. RNF144A primarily functions to catalyze the transfer of ubiquitin from E2 conjugating enzymes to specific substrate proteins, targeting them for proteasomal degradation. The enzyme catalyzes ubiquitin linkages specifically at the K6-, K11-, and K48-positions of ubiquitin in vitro .
The biological significance of RNF144A lies in its role in DNA damage response pathways. Research has demonstrated that RNF144A is induced in a p53-dependent manner during DNA damage and targets cytosolic DNA-dependent protein kinase catalytic subunit (DNA-PKcs) for ubiquitination and degradation. This regulation is critical for proper apoptotic response during DNA damage, suggesting RNF144A may function as a tumor suppressor .
The RNF144A protein, particularly its transmembrane domain, shows significant evolutionary conservation across species. This high degree of conservation suggests fundamental importance to its biological function. The TM domain of RNF144A contains the GXXXG motif, which is preserved in five TM-containing RBR E3 ligases, including RNF144A, RNF144B, RNF19A/Dorfin, RNF19B, and RNF217 .
In terms of subfamily relationships, RNF144A is most closely related to RNF144B at the protein level. Together, these two proteins comprise a distinct subdomain within the larger RBR family of proteins. This conservation extends to their functional mechanisms, as studies have shown that RNF144B also self-associates, suggesting a common regulatory principle within this subfamily .
The Xenopus tropicalis RNF144A shares key structural and functional domains with human RNF144A, making the amphibian protein a valuable model for studying the fundamental properties of this E3 ligase. The conservation of critical residues involved in zinc coordination, E2 binding, and self-association suggests mechanistic similarities in their enzymatic functions across vertebrate species.
RNF144A has been identified to target several key proteins for ubiquitination and subsequent degradation, most of which are involved in DNA repair, heat shock/chaperone function, and cellular signaling pathways. The current known substrates include:
The interaction between RNF144A and its substrates is typically mediated by its RING finger domain, which recognizes specific structural features on target proteins. For efficient ubiquitination activity, RNF144A requires both proper membrane localization (via its TM domain) and self-association capability .
The transmembrane (TM) domain of RNF144A serves dual critical functions that significantly impact its enzymatic activity and cellular localization:
Membrane Localization: The TM domain anchors RNF144A to cellular membranes, particularly to endosomal structures. Deletion of the TM domain abolishes membrane localization .
E3 Ligase Activation: The TM domain is required for optimal ubiquitin ligase activity. Experimental evidence shows that deletion of this domain significantly reduces RNF144A's enzymatic function .
Self-Association Mediation: The TM domain facilitates RNF144A self-association through a classic GXXXG interaction motif (specifically G252XXXG256 in human RNF144A). This self-association is critical for its ubiquitin ligase activity .
Mutations affecting the GXXXG motif demonstrate the dual but independent roles of this domain:
RNF144A-G252L/G256L mutant: Preserves membrane localization but is defective in self-association and ubiquitin ligase activity
RNF144A-G252D mutant (found in human cancers): Retains self-association and ligase activity but loses membrane localization and undergoes rapid turnover
These findings underscore the importance of both proper membrane localization and self-association for optimal RNF144A function, suggesting a sophisticated regulatory mechanism that may apply broadly to other RBR family E3 ligases.
For comprehensive investigation of RNF144A enzymatic activity, researchers should consider the following experimental approaches:
Purified recombinant RNF144A can be used in a reconstituted system with E1, E2 enzymes, ubiquitin, ATP, and substrate proteins
Analysis should include immunoblotting for ubiquitinated products and mass spectrometry to identify ubiquitination sites and chain types (K6, K11, K48 linkages)
NMR spectroscopy has proven effective for determining the solution structure of the RING finger domain of RNF144A
Zinc binding stoichiometry can be determined using metallochromic indicators to confirm proper folding and activity
Thermal unfolding curves (measuring tryptophan fluorescence emission) can assess protein stability of wild-type versus mutant proteins
Deletion and point mutation studies of the TM domain (particularly the GXXXG motif) provide insights into the dual roles in membrane localization and catalytic activation
Subcellular fractionation and confocal microscopy to track membrane localization
Co-immunoprecipitation assays to analyze self-association properties
Affinity purification coupled with mass spectrometry (AP-MS)
Proximity-dependent biotin identification (BioID) methods
Validation through direct ubiquitination assays with recombinant substrates
Cell-based degradation assays comparing wild-type RNF144A with catalytically inactive mutants
When working with recombinant Xenopus tropicalis RNF144A specifically, researchers should ensure proper expression systems (typically E. coli for full-length protein with N-terminal His-tag) and appropriate storage conditions (avoiding repeated freeze-thaw cycles). Reconstitution in deionized sterile water to 0.1-1.0 mg/mL with 5-50% glycerol is recommended for long-term storage at -20°C/-80°C .
The GXXXG motif in RNF144A's transmembrane domain represents a classical helix-helix interaction motif that plays a crucial role in protein self-association and functional regulation. Research has revealed several key insights:
The GXXXG motif (specifically G252XXXG256 in human RNF144A) creates a smooth surface on transmembrane helices that facilitates close packing of adjacent helices
This close packing enables van der Waals interactions and potential hydrogen bonding between transmembrane helices, promoting dimerization or higher-order oligomerization
Mutation studies demonstrate that substituting these glycine residues with bulkier amino acids (G252L/G256L) disrupts self-association while preserving membrane localization
Self-association through the GXXXG motif is required for optimal E3 ligase activity
This requirement appears to be independent of membrane localization, as membrane localization-deficient mutants can retain self-association and E3 activity
When both properties are compromised (through combined mutations), enzyme activity is severely impaired
Mutations of GXXXG motifs in RNF144A have been found in human cancers, including a G252D mutation
The G252D mutation preserves self-association and ubiquitin ligase activity but causes loss of membrane localization
This mutant is turned over rapidly, suggesting that proper membrane localization is important for RNF144A stability in cells
This regulatory mechanism may represent a common feature across the RBR E3 ligase family, as all five TM-containing RBR E3 ligases (RNF144A, RNF144B, RNF19A/Dorfin, RNF19B, and RNF217) contain the RBR-TM(GXXXG) superstructure . These findings highlight a sophisticated layer of regulation where both proper subcellular localization and quaternary structure are required for optimal enzymatic function.
Successful expression and purification of functional recombinant RNF144A requires careful consideration of several experimental parameters:
E. coli expression: The full-length Xenopus tropicalis RNF144A has been successfully expressed in E. coli with an N-terminal His-tag
Tagged constructs: N-terminal His-tagging appears to preserve enzymatic function while facilitating purification
Domain-specific considerations: For structural studies of the RING finger domain alone, bacterial expression systems with optimized conditions for zinc incorporation are recommended
Affinity chromatography using Ni-NTA resins for His-tagged proteins
Size exclusion chromatography to ensure monomeric/dimeric state and remove aggregates
Ion exchange chromatography for further purification if needed
Final storage in Tris/PBS-based buffer with 6% Trehalose, pH 8.0
Addition of 5-50% glycerol for long-term storage (50% being optimal)
Lyophilization for extended stability
Avoid repeated freeze-thaw cycles by preparing working aliquots stored at 4°C for up to one week
Brief centrifugation of vial prior to opening
Reconstitution in deionized sterile water to 0.1-1.0 mg/mL
Addition of glycerol to 50% final concentration
In vitro ubiquitination assays to confirm catalytic activity
Thermal stability assessments via fluorescence spectroscopy
Zinc content verification using metallochromic indicators
Structural integrity confirmation via circular dichroism or NMR spectroscopy
For researchers working specifically with transmembrane domain mutants, special attention should be paid to detergent selection during purification to maintain proper folding and self-association properties of the protein.
RNF144A plays a sophisticated role in balancing DNA repair and apoptotic responses following genotoxic stress:
RNF144A expression is induced in a p53-dependent manner following DNA damage
This induction represents part of the cellular DNA damage response (DDR) program
The temporal regulation of RNF144A suggests it functions as a molecular switch between DNA repair and apoptotic pathways
DNA-PKcs (DNA-dependent protein kinase catalytic subunit) is a critical component of the non-homologous end joining (NHEJ) DNA repair pathway
Beyond its nuclear functions, cytosolic DNA-PKcs exhibits pro-survival activity
RNF144A specifically targets cytosolic DNA-PKcs for ubiquitination and degradation
This degradation helps shift cellular responses from survival to apoptosis when DNA damage is extensive
By degrading pro-survival factors like DNA-PKcs, RNF144A promotes apoptotic responses
This function is particularly important for eliminating cells with extensive DNA damage
The process helps maintain genomic integrity at the organismal level by preventing propagation of cells with damaged DNA
RNF144A localizes to endosomal membranes via its transmembrane domain
This localization appears critical for its function in DNA damage response
Cancer-associated mutations that disrupt membrane localization (e.g., G252D) impair RNF144A stability and presumably its tumor suppressor function
The role of RNF144A in promoting appropriate apoptotic responses to DNA damage suggests tumor suppressor functions
Somatic mutations of RNF144A have been cataloged in cancer genetic databases across multiple tumor types, including breast, stomach, lymphoma, glioblastoma, uterine, and lung cancers
These observations position RNF144A as a potentially important regulator of genomic integrity whose dysfunction may contribute to tumorigenesis
Comparing Xenopus tropicalis RNF144A with its human counterpart reveals important insights about evolutionary conservation and species-specific adaptations:
Domain architecture: Both Xenopus and human RNF144A maintain the characteristic RBR (RING1-IBR-RING2) domain arrangement and transmembrane domain
Transmembrane region: The TM domain is highly conserved across species, highlighting its fundamental importance to function
GXXXG motif: This self-association motif within the TM domain is preserved, suggesting conservation of self-association mechanisms
Zinc-binding: Both proteins coordinate two zinc atoms within their RING domains in a cross-braced arrangement
Sequence homology:
The Xenopus tropicalis RNF144A protein (292 amino acids) shares significant sequence homology with human RNF144A, particularly in functional domains. Key residues involved in zinc coordination, E2 binding, and substrate recognition are conserved, suggesting mechanistic similarities in their enzymatic functions.
Xenopus tropicalis RNF144A serves as a valuable model for studying fundamental properties of this E3 ligase
When using recombinant Xenopus RNF144A for studies on human substrates, researchers should consider potential species-specific interaction differences
Complementation studies in human cell lines using Xenopus RNF144A can help determine functional equivalence
Structural studies of Xenopus RNF144A may provide insights applicable to the human protein due to high conservation of key domains
This cross-species conservation makes Xenopus tropicalis RNF144A a valuable research tool, particularly for structural and biochemical studies that require recombinant protein expression. The successful expression of full-length Xenopus tropicalis RNF144A in E. coli systems may offer advantages over human RNF144A for certain experimental applications.
Proper storage and handling of recombinant RNF144A is critical for maintaining protein stability and enzymatic activity. Based on empirical data, the following guidelines should be observed:
Store lyophilized powder at -20°C/-80°C upon receipt
For reconstituted protein, store at -20°C/-80°C with 5-50% glycerol (50% being optimal)
Working aliquots can be stored at 4°C for up to one week
Repeated freeze-thaw cycles should be strictly avoided as they significantly impact protein stability and activity
Briefly centrifuge the vial prior to opening to bring contents to the bottom
Reconstitute in deionized sterile water to a concentration of 0.1-1.0 mg/mL
Add glycerol to a final concentration of 5-50% (50% recommended)
Prepare multiple small aliquots to minimize freeze-thaw cycles
Optimal storage buffer: Tris/PBS-based buffer, 6% Trehalose, pH 8.0
For activity assays, buffers containing divalent cations (particularly zinc) may be necessary to maintain proper folding of the RING domain
Verify protein integrity by SDS-PAGE before experimental use (>90% purity)
Activity can be assessed through in vitro ubiquitination assays
Thermal stability can be monitored through fluorescence-based thermal shift assays
For structural integrity, consider limited trypsin digestion to confirm proper folding
These handling guidelines are particularly important when working with full-length RNF144A containing the transmembrane domain, as this hydrophobic region can contribute to aggregation if improperly handled.
Rigorous experimental design for studying RNF144A activity requires several key controls:
Catalytically inactive mutant: RING domain mutations that disrupt E2 binding or zinc coordination serve as negative enzymatic controls
Transmembrane domain mutants: G252L/G256L mutations (disrupting self-association) provide partial activity controls
Domain deletion constructs: TM domain deletion variants show reduced but not eliminated activity
Known active E3 ligase: Include a well-characterized E3 ligase (e.g., CHIP or Parkin) as positive control
Non-substrate proteins: Include structurally similar proteins not targeted by RNF144A
Binding-deficient substrate mutants: Modify substrate recognition regions to confirm specificity
Competition assays: Use excess untagged substrate to compete with tagged substrate
ATP dependence: Reactions without ATP demonstrate energy requirement
E1/E2 dependence: Omitting either E1 or E2 enzymes confirms the complete ubiquitination cascade
Ubiquitin mutants: Lysine-to-arginine ubiquitin mutants help determine chain type specificity (K6R, K11R, K48R)
Deubiquitinating enzyme: Addition of a DUB confirms reversibility and specificity of ubiquitin linkages
Subcellular fractionation quality controls: Marker proteins for membrane vs. cytosolic fractions
Localization mutants: TM domain mutants that alter membrane association
Membrane disruption: Detergent treatments to disrupt membrane associations
| Control Type | Experimental Condition | Expected Outcome | Purpose |
|---|---|---|---|
| Enzyme activity | Wild-type RNF144A | Full ubiquitination | Baseline activity |
| RING domain mutant | No ubiquitination | Confirm E3 requirement | |
| G252L/G256L mutant | Reduced ubiquitination | Self-association role | |
| TM domain deletion | Reduced ubiquitination | Membrane localization role | |
| Substrate specificity | Known substrate (DNA-PKcs) | Ubiquitination | Positive control |
| Non-substrate protein | No ubiquitination | Specificity control | |
| Reaction components | No ATP | No ubiquitination | Energy requirement |
| No E1 or E2 | No ubiquitination | Complete cascade | |
| K48R ubiquitin | Altered chain formation | Chain specificity |
Implementation of these controls ensures reliable data interpretation and minimizes experimental artifacts when studying this complex E3 ubiquitin ligase.
Working with transmembrane-containing E3 ligases like RNF144A presents unique challenges that require specific experimental strategies:
Solubilization approaches: Use mild detergents (CHAPS, DDM, or digitonin) that preserve native membrane protein structure
Fusion tag strategies: N-terminal solubility-enhancing tags (MBP, SUMO) coupled with C-terminal purification tags can improve expression
Cell-free expression systems: Consider membrane-mimetic environments for direct expression into liposomes or nanodiscs
Insect cell expression: For mammalian proteins, baculovirus expression systems may provide better folding environments than bacterial systems
Nanodisc reconstitution: Incorporate purified protein into defined lipid nanodiscs for activity studies
Liposome-based assays: Assess activity in artificial membrane systems with defined composition
Native membrane isolation: Study the protein in its natural membrane environment through careful subcellular fractionation
Detergent screening: Systematically evaluate detergent effects on self-association and activity
Chemical crosslinking: Membrane-permeable crosslinkers can capture transient interactions
Fluorescence resonance energy transfer (FRET): Tag variants with fluorescent proteins to measure association in live cells
Co-immunoprecipitation from solubilized membranes: Preserve interactions through careful solubilization
Analytical ultracentrifugation: Determine oligomeric states in detergent solutions
Transmembrane domain chimeras: Replace TM domain with alternative TM domains to assess specificity
Targeted GXXXG motif mutations: Distinguish self-association from membrane localization effects
Domain-swapping experiments: Exchange domains between RNF144A and RNF144B to identify family-specific functions
| Challenge | Solution Strategy | Expected Outcome |
|---|---|---|
| Poor solubility | Screen detergent panel | Identify optimal solubilization conditions |
| Use fusion proteins | Enhance solubility while preserving function | |
| Aggregation during purification | Include glycerol and stabilizing agents | Reduce hydrophobic aggregation |
| Optimize protein:detergent ratio | Maintain monomeric/dimeric state | |
| Loss of activity | Reconstitute in lipid environments | Restore native-like membrane context |
| Verify zinc content | Ensure proper RING domain folding | |
| Inconsistent self-association | Standardize membrane isolation | Control lipid environment effects |
| Use crosslinking time courses | Capture dynamic interactions |
These strategies enable researchers to overcome the inherent difficulties of working with membrane-associated E3 ligases, facilitating more comprehensive functional and mechanistic studies of RNF144A.
The current understanding of RNF144A suggests several promising research directions with potential therapeutic implications:
Tumor suppressor validation: Further investigation into RNF144A's proposed tumor suppressor function across different cancer types
Mutation profiling: Comprehensive analysis of RNF144A mutations in cancer genomic databases to identify potential driver mutations
Synthetic lethality approaches: Identification of genes showing synthetic lethality with RNF144A deficiency in cancer cells
Small molecule modulators: Development of compounds that could stabilize or enhance RNF144A activity as potential cancer therapeutics
Pathway mapping: Detailed characterization of how RNF144A integrates with other DNA damage response factors
Resistance mechanisms: Investigation of RNF144A's role in resistance to DNA-damaging chemotherapeutics
Cell fate determination: Further elucidation of how RNF144A influences the balance between DNA repair and apoptosis
Developmental roles: Investigation of RNF144A function during embryonic development in Xenopus
Tissue-specific functions: Analysis of tissue-specific expression patterns and functions in the amphibian model
Evolutionary insights: Comparative studies across vertebrate species to understand conserved and divergent functions
Complete structure determination: Resolution of full-length RNF144A structure including the transmembrane domain
E2-RNF144A interface: Detailed mapping of the interaction interface between RNF144A and its cognate E2 enzymes
Allosteric regulation sites: Identification of potential druggable sites that could modulate RNF144A activity
Structure-based design: Development of peptides or small molecules targeting specific RNF144A functional domains
Proteomics approaches: Global ubiquitinome analysis in cells with RNF144A overexpression or knockout
Substrate recognition motifs: Determination of consensus sequences or structural elements recognized by RNF144A
Substrate network analysis: Systems biology approaches to understand the broader impact of RNF144A activity on cellular proteostasis
These research directions highlight the multifaceted potential of RNF144A as both a fundamental biological regulator and a possible therapeutic target, with Xenopus tropicalis RNF144A serving as a valuable research tool in advancing our understanding of this important E3 ligase.
Cross-species comparative analysis of RNF144A offers powerful insights into its core biological functions and evolutionary significance:
Phylogenetic profiling: Systematic comparison of RNF144A across vertebrate species can reveal selection pressures on specific domains
Domain conservation mapping: Identification of highly conserved vs. variable regions provides clues to functional importance
Species-specific adaptations: Analysis of species-specific sequence variations may reveal specialized functions in different organisms
Cross-species complementation: Testing whether Xenopus tropicalis RNF144A can rescue phenotypes in human cell lines with RNF144A deficiency
Substrate conservation: Determining whether substrates identified in one species (e.g., human DNA-PKcs) are also targeted by RNF144A orthologs from other species
Regulatory mechanism comparison: Analysis of whether the GXXXG-mediated self-association mechanism is conserved across species
Xenopus embryonic expression patterns: Characterization of spatial and temporal expression during development
Functional studies in developing embryos: CRISPR-mediated knockout or morpholino knockdown in Xenopus embryos
Cellular differentiation roles: Investigation of potential roles in cell fate decisions during development
Solution structure comparison: NMR studies comparing the RING domain structures across species
Transmembrane domain analysis: Comparative studies of TM domain properties from different species
Species-specific post-translational modifications: Identification of conserved and variable modification sites
Model system selection guidance: Information on which species most closely resembles human RNF144A function
Conserved regulatory networks: Identification of evolutionarily conserved pathways regulated by RNF144A
Drug target validation: Cross-species conservation of binding sites can inform therapeutic development efforts
This evolutionary perspective not only enhances our fundamental understanding of RNF144A biology but also helps distinguish essential functions from species-specific adaptations, ultimately improving translational research efforts and therapeutic development strategies.
Researchers initiating studies with recombinant RNF144A should consider the following key points to ensure successful experimental outcomes:
Select appropriate expression systems: E. coli works well for Xenopus tropicalis RNF144A with N-terminal His-tagging
Pay careful attention to buffer composition and storage conditions: Tris/PBS-based buffer with 6% Trehalose, pH 8.0, with 50% glycerol for long-term storage
Avoid repeated freeze-thaw cycles by preparing single-use aliquots
Verify protein quality by SDS-PAGE (>90% purity recommended) before experimental use
Include appropriate controls in all ubiquitination assays
Consider both membrane localization and self-association in experimental design
For structure-function studies, incorporate both wild-type and mutant proteins (particularly GXXXG motif mutants)
Validate activity in both in vitro reconstituted systems and cellular contexts
Recognize the challenges associated with the transmembrane domain
Consider detergent effects on protein activity and self-association
Monitor zinc content and protein folding for optimal enzymatic activity
Design experiments that account for RNF144A's dual functions in membrane localization and E3 ligase activity
Consider RNF144A's role in DNA damage response pathways
Explore potential tumor suppressor functions in appropriate experimental systems
Investigate interactions with known substrates (DNA-PKcs, PARP1, HSPA2, BMI1, RAF1)
Design experiments that address both basic mechanisms and disease relevance
By addressing these considerations, researchers can establish robust experimental systems for investigating this fascinating E3 ubiquitin ligase and contribute to our understanding of its biological functions and potential therapeutic applications.
Research on RNF144A provides significant insights into the broader RBR E3 ligase family, illuminating common mechanistic principles and regulatory features:
RNF144A exemplifies the RING-HECT hybrid mechanism characteristic of RBR ligases
Studies on RNF144A's zinc coordination in its RING domain inform structural understanding of other family members
The self-association regulatory mechanism identified in RNF144A may apply to other RBR ligases
Five RBR E3 ligases contain transmembrane domains with GXXXG motifs (RNF144A, RNF144B, RNF19A/Dorfin, RNF19B, and RNF217)
The dual role of this domain in membrane localization and E3 ligase activation likely represents a conserved regulatory principle
This suggests a common evolutionary adaptation for membrane-associated ubiquitination functions
Like RNF144A, other RBR family members have been implicated in human diseases
Parkin (another RBR ligase) is associated with Parkinson's disease
HOIL-1L and HOIP(RNF31) are linked to immunological disorders
This suggests a broader pattern of RBR ligases as critical regulators of cellular homeostasis
Insights from RNF144A substrate targeting may inform understanding of how other RBR ligases select their targets
The combination of RING domain substrate recognition with HECT-like catalytic mechanism represents a unique feature of this enzyme family
Cross-comparison of substrates across the family may reveal shared recognition principles
Strategies developed for targeting or modulating RNF144A may be applicable to other RBR family members
Understanding the regulatory mechanisms of RNF144A provides a conceptual framework for approaching other RBR ligases
The dual membrane localization/self-association paradigm suggests multiple potential intervention points for therapeutic development