Tim50 is a transmembrane protein with a single transmembrane domain (TMD) and a large hydrophilic domain exposed to the intermembrane space (IMS) . It serves as the receptor subunit of the TIM23 complex, recognizing N-terminal presequences of mitochondrial proteins and coordinating their translocation . Key functions include:
Presequence recognition: Binds the N-terminal targeting signal of preproteins.
Translocation coordination: Mediates communication between TOM and TIM23 complexes.
Membrane potential maintenance: Supports the integrity of the inner mitochondrial membrane (IMM) permeability barrier .
Depletion of Tim50 in yeast leads to impaired import of matrix and inner membrane proteins, confirming its essential role in mitochondrial biogenesis .
Tim50 is critical for investigating translocation mechanisms:
Cross-linking assays: Demonstrates interactions with preproteins arrested at TOM or spanning TOM-TIM23 interfaces .
Mutagenesis: Identifies functional regions (e.g., core vs. PBD domains) .
In vitro import assays: Confirms substrate specificity for matrix/inner membrane proteins .
Human TIMM50 mutations are linked to:
| Disease | Symptoms | Mechanism |
|---|---|---|
| Epilepsy | Seizures, intellectual disability | Disrupted mitochondrial protein import |
| 3-Methylglutaconic Aciduria | Metabolic disorder | Impaired IMM permeability barrier |
Core/PBD domains: Essential for TIM23 complex recruitment and presequence binding .
Species-specific TMD: T. brucei Tim50 lacks a strong TMD but retains IMS functionality, suggesting divergent translocation mechanisms in trypanosomatids .
Unlike fungal Tim50, human and T. brucei Tim50 exhibit phosphatase activity, though its role in mitochondrial function remains unclear .
Function: Tim50 is a crucial component of the TIM23 complex, which facilitates the translocation of proteins containing transit peptides across the mitochondrial inner membrane. Its role involves guiding preproteins through the translocation process, directing them to the TIM23 channel protein, and potentially assisting in the transfer of translocating proteins from the TOM complex to the TIM23 complex.
KEGG: spo:SPBC17A3.01c
STRING: 4896.SPBC17A3.01c.1
Tim50 in S. pombe, like its counterparts in other organisms, is a component of the mitochondrial inner membrane translocase (TIM23) complex. It spans the inner mitochondrial membrane with a single transmembrane segment and exposes a large hydrophilic domain in the intermembrane space (IMS) . The protein contains an N-terminal mitochondrial targeting signal that directs it to the mitochondria. The C-terminal domain is exposed to the intermembrane space, where it functions as a receptor for presequence-carrying proteins . Unlike the Tim50 homolog in Saccharomyces cerevisiae which contains only one cysteine residue (C268) in the presequence-binding groove, Tim50 in other organisms including S. pombe contains multiple cysteine residues distributed throughout the protein, though their functional significance remains to be fully determined .
Tim50 serves as a critical receptor component of the TIM23 complex, playing a crucial role in facilitating the transfer of precursor proteins from the translocase of the outer membrane (TOM) complex to the TIM23 complex through the intermembrane space . It recognizes and binds to the presequences of nuclear-encoded mitochondrial proteins as they emerge from the TOM complex into the intermembrane space. This initial recognition is essential for the subsequent translocation of these proteins into the mitochondrial matrix or their insertion into the inner membrane . In cells depleted of Tim50, mitochondria display significantly reduced import kinetics of preproteins using the TIM23 complex, highlighting its essential role in protein import .
Tim50 is essential for viability in various organisms, including yeast . The crucial nature of Tim50 stems from its fundamental role in mitochondrial protein import, a process indispensable for mitochondrial function and consequently cellular survival. When Tim50 is depleted in cells, the import of nuclear-encoded mitochondrial proteins is severely compromised . In zebrafish embryos, downregulation of Tim50 during early development causes neurodegeneration, dysmorphic heart features, and reduced motility due to apoptosis . These observations underscore that the absence of functional Tim50 leads to severe mitochondrial dysfunction, triggering cellular stress responses and ultimately cell death, explaining its essentiality for organismal viability.
To study the effects of Tim50 depletion, researchers typically employ several methodologies:
S. pombe Tim50 shares the fundamental function of mitochondrial protein import with Tim50 homologs in other organisms, but there are notable differences:
Cysteine Content: While Saccharomyces cerevisiae Tim50 (ScTim50) contains only one cysteine residue (C268) located in the presequence-binding groove, S. pombe Tim50, like other Tim50 homologs, contains multiple cysteine residues distributed throughout the protein .
Phosphatase Activity: Similar to human TIMM50 (hTIMM50) but unlike ScTim50, Trypanosoma brucei Tim50 (TbTim50) possesses a dual specificity phosphatase activity with greater affinity for protein tyrosine phosphate than for protein serine/threonine phosphate . This suggests that S. pombe Tim50 might also possess phosphatase activity, though this requires direct experimental verification.
Additional Functions: While the protein import function is conserved, the non-canonical functions of Tim50 vary between species. In humans, TIMM50 is linked to cancer cell growth and apoptosis regulation . In T. brucei, Tim50 is involved in regulating VDAC expression . The specific non-canonical functions of S. pombe Tim50 remain to be fully characterized.
For successful recombinant expression of S. pombe Tim50, researchers should consider the following approaches:
Based on findings that TbTim50 possesses dual specificity phosphatase activity , researchers investigating potential phosphatase activity in S. pombe Tim50 should consider:
Substrate Specificity Assays:
Use synthetic phosphopeptides containing phosphotyrosine, phosphoserine, or phosphothreonine residues
Employ para-nitrophenyl phosphate (pNPP) as a general phosphatase substrate
Compare activity levels against different substrates to determine preference (TbTim50 shows greater affinity for tyrosine phosphate)
Mutational Analysis:
Identification of Physiological Substrates:
Perform pull-down assays using substrate-trapping mutants of Tim50
Use phosphoproteomics approaches to identify changes in the phosphorylation status of proteins in Tim50-depleted or overexpressing cells
Investigate known phosphoproteins of the mitochondrial import machinery as potential substrates
In Vivo Functional Studies:
Complement Tim50-depleted cells with phosphatase-deficient Tim50 mutants to determine if phosphatase activity is essential for viability
Analyze the impact of phosphatase activity on mitochondrial protein import efficiency
Investigate potential connections between phosphatase activity and other cellular functions
To differentiate between Tim50's canonical role in protein import and its non-canonical functions, researchers can employ several strategic approaches:
Domain-Specific Mutations:
Generate mutations that specifically affect either the protein import function or other activities (such as phosphatase activity)
For example, mutations in the presequence-binding region would specifically affect protein import, while mutations in the phosphatase domain would target that function
Complementation assays with these mutants can reveal which functions are essential for viability
Temporal Separation of Functions:
Biochemical Separation of Activities:
Perform in vitro assays that specifically measure protein import (using isolated mitochondria and radiolabeled precursors)
Separately measure phosphatase activity using appropriate substrates
Compare how different mutations or conditions affect these distinct activities
Interaction Partner Analysis:
Identify proteins that interact with Tim50 through co-immunoprecipitation and mass spectrometry
Categorize partners as related to either protein import (e.g., other TIM23 components) or other functions
Use proximity labeling techniques like BioID or APEX to identify transient or context-specific interactions
Human TIMM50 mutations have been linked to severe diseases, including rapidly progressing encephalopathy . S. pombe provides an excellent model to study these mutations due to its genetic tractability and the conservation of mitochondrial import machinery.
Creating Disease-Relevant Models in S. pombe:
Introduce mutations corresponding to human disease mutations into the S. pombe Tim50 gene
For example, mutations analogous to the human S112* (N-terminal truncation) and G190A (in the transmembrane domain) could be created
Use complementation assays to determine if these mutants can rescue Tim50-depleted cells
Functional Characterization of Disease Mutations:
Analyze protein import efficiency using in vitro import assays with isolated mitochondria
Measure effects on membrane potential and ROS production
Assess impacts on respiratory function and ATP production
Determine effects on the stability of other TIM23 complex components
S. pombe-Specific Advantages:
S. pombe has a growth rate of approximately 108 minutes , allowing for relatively rapid experimental cycles
The well-characterized mitotic recombination system in S. pombe enables sophisticated genetic manipulations
S. pombe cells have well-defined mitochondrial networks that can be visualized and quantified
Translating Findings to Human Systems:
Compare phenotypes observed in S. pombe with those in patient-derived cells
Use complementation studies with human TIMM50 in S. pombe tim50 mutants to assess functional conservation
Identify potential therapeutic targets or strategies based on mechanisms elucidated in the S. pombe model
Several advanced methodologies can help researchers study the dynamic interactions and functions of Tim50 in live S. pombe cells:
Live-Cell Imaging Techniques:
Fluorescence Resonance Energy Transfer (FRET) to monitor protein-protein interactions between Tim50 and other TIM23 components
Fluorescence Recovery After Photobleaching (FRAP) to assess the mobility and dynamics of Tim50 within the mitochondrial inner membrane
Split fluorescent protein systems (e.g., split GFP) to visualize specific interactions in living cells
Proximity-Based Labeling Approaches:
BioID or TurboID: Fusion of biotin ligase to Tim50 to identify proximal proteins
APEX2: Peroxidase-based proximity labeling for electron microscopy visualization and proteomic identification of neighbors
These approaches are particularly valuable for capturing transient interactions that might be missed in conventional co-immunoprecipitation experiments
Single-Molecule Tracking:
Use photoactivatable or photoswitchable fluorescent proteins fused to Tim50 to track individual molecules
This approach can reveal the dynamics and heterogeneity of Tim50 behavior in the mitochondrial inner membrane
Cryo-Electron Tomography:
Visualize the TIM23 complex architecture in situ in S. pombe cells
Immunogold labeling of Tim50 can help locate it precisely within the complex
This technique can reveal structural changes associated with different functional states
Optogenetic Tools:
Light-inducible dimerization systems to control Tim50 interactions or localizations
Allows for precise temporal control to study immediate versus long-term effects of Tim50 function disruption
When designing experiments with recombinant S. pombe Tim50, researchers should include the following controls:
Expression Controls:
Empty vector controls to account for effects of the expression system itself
Wild-type Tim50 expression as a positive control alongside any mutant variants
Expression of a known unrelated mitochondrial protein to control for general effects on mitochondrial function
Functionality Controls:
For protein import studies, use well-characterized substrate proteins that depend on the TIM23 pathway
Include substrates that use alternative import pathways (e.g., TIM22-dependent proteins) as negative controls
When studying phosphatase activity, include both positive controls (known phosphatases) and negative controls (phosphatase-dead mutants)
Localization Controls:
Verify correct mitochondrial localization using mitochondrial markers
Ensure proper membrane insertion and topology using protease protection assays
For IMS domain studies, confirm correct submitochondrial localization
Interaction Controls:
When confronted with discrepancies in Tim50 data across different species, researchers should:
Systematic Comparative Analysis:
Create a detailed alignment of Tim50 sequences from multiple species to identify conserved versus divergent regions
Generate a table comparing known functions across species, as shown below:
Direct Experimental Comparison:
Express Tim50 from different species in a single host (e.g., S. pombe tim50Δ cells)
Compare their ability to complement essential functions
Perform side-by-side biochemical assays using recombinant proteins prepared under identical conditions
Domain Swap Experiments:
Create chimeric proteins combining domains from Tim50 of different species
Test which domains confer which specific functions
This approach can help identify the structural basis for functional differences
Consider Evolutionary Context:
Analyze the evolutionary relationships between the species being compared
Consider differences in mitochondrial biology and protein import requirements
Account for potential adaptations to different cellular environments
Crosslinking experiments are valuable for studying Tim50's interactions with preproteins and other components of the protein import machinery . Key optimization parameters include:
Crosslinker Selection:
Choose appropriate crosslinking agents based on the distance between interaction partners:
Short-range crosslinkers (e.g., DSS, BS3) for tight interactions
Longer crosslinkers for more distant interactions
Heterobifunctional crosslinkers (e.g., SMCC) when specific chemistry is needed
Consider photocrosslinking approaches for capturing transient interactions
Reaction Conditions:
Optimize crosslinker concentration (typically 0.1-2 mM) to maximize specific crosslinking while minimizing non-specific reactions
Determine optimal reaction time (usually 15-60 minutes) to capture interactions without excessive non-specific crosslinking
Test various pH conditions, as crosslinking efficiency is often pH-dependent
Control temperature based on the stability of the interaction (4°C for stable complexes, room temperature for transient ones)
Sample Preparation:
For studying interactions with preproteins, generate translocation intermediates by:
For Tim50-Tim23 interactions, use gentle solubilization conditions to preserve the complex
Detection Methods:
Tim50 phosphorylation can significantly impact its function, as demonstrated for ScTim50 where phosphorylation reduces protein import capability . When analyzing Tim50 phosphorylation data, researchers should:
Phosphorylation Site Mapping:
Use mass spectrometry to identify specific phosphorylation sites
Compare identified sites with known functional domains to predict potential effects
Create site-specific phosphomimetic (S/T→D/E) and phospho-null (S/T→A) mutants
Functional Correlation Analysis:
Measure protein import efficiency in relation to phosphorylation status
Assess phosphatase activity (if present) in relation to phosphorylation state
Evaluate how phosphorylation affects interactions with other TIM23 components
Regulatory Mechanism Identification:
Physiological Significance Assessment:
Create a correlation table of phosphorylation status versus various cellular parameters:
| Phosphorylation State | Protein Import Efficiency | Interaction with Tim23 | Cell Growth Rate | Mitochondrial Membrane Potential |
|---|---|---|---|---|
| Hyperphosphorylated | (Measured value) | (Measured value) | (Measured value) | (Measured value) |
| Normal phosphorylation | (Measured value) | (Measured value) | (Measured value) | (Measured value) |
| Hypophosphorylated | (Measured value) | (Measured value) | (Measured value) | (Measured value) |
Computational analyses can provide valuable insights into S. pombe Tim50 structure, function, and evolution:
Sequence Analysis Tools:
Multiple sequence alignment (using CLUSTAL, MUSCLE, T-Coffee) to identify conserved regions
Hidden Markov Models to detect distant homologs and functional domains
Conservation analysis to identify functionally important residues (ConSurf, Evolutionary Trace)
Structural Prediction and Analysis:
AlphaFold2 or RoseTTAFold for predicting Tim50 structure, particularly the IMS domain
Molecular dynamics simulations to study conformational dynamics
Protein-protein docking to model interactions with presequences and other TIM23 components
Electrostatic surface potential analysis to identify potential presequence-binding sites
Systems Biology Approaches:
Network analysis to position Tim50 within the mitochondrial protein import interactome
Gene expression correlation analysis using existing S. pombe transcriptome data
Flux balance analysis to predict metabolic consequences of Tim50 dysfunction
Evolutionary Analysis:
Phylogenetic tree construction to understand Tim50 evolution
Selection pressure analysis (dN/dS ratio) to identify sites under positive or negative selection
Ancestral sequence reconstruction to trace the evolution of specific functions
Accurate quantification of protein import defects is essential for characterizing Tim50 mutants. Researchers should consider:
In Vitro Import Assays:
Use radiolabeled precursor proteins and isolated mitochondria
Quantify import by measuring the appearance of mature (processed) protein or protease-protected protein
Calculate import efficiency as a percentage relative to wild-type mitochondria
Plot import kinetics over time (0-30 minutes) to determine both rate and extent of import
In Vivo Import Measurements:
Use reporter constructs with mitochondrial targeting signals fused to fluorescent proteins
Measure the ratio of mitochondrial to cytosolic fluorescence
Employ flow cytometry for high-throughput quantification of large cell populations
Use pulse-chase experiments with inducible reporters to measure import dynamics
Substrate-Specific Analysis:
Test multiple substrates with different dependencies on the TIM23 pathway
Create a comprehensive table of import efficiencies for different substrates:
| Substrate | Import Pathway | Wild-type Import (%) | Tim50 Mutant Import (%) | Fold Reduction |
|---|---|---|---|---|
| Matrix protein 1 | TIM23 | 100 | (Measured value) | (Calculated) |
| Matrix protein 2 | TIM23 | 100 | (Measured value) | (Calculated) |
| Inner membrane protein | TIM23/Stop-transfer | 100 | (Measured value) | (Calculated) |
| Carrier protein | TIM22 | 100 | (Measured value) | (Calculated) |
Normalization and Controls:
Normalize import data to mitochondrial protein content
Control for changes in mitochondrial membrane potential using potential-independent import substrates
Include positive controls (known import-defective mutants) and negative controls (unrelated mitochondrial protein mutants)
Researchers frequently encounter expression and solubility issues with mitochondrial membrane proteins like Tim50. Effective solutions include:
Expression System Optimization:
Try multiple expression systems (E. coli, S. cerevisiae, S. pombe, insect cells)
For E. coli, use specialized strains designed for membrane proteins (C41, C43) or those with additional tRNAs (Rosetta)
Consider cell-free expression systems which can accommodate detergents during translation
Construct Design Refinement:
Express only the soluble IMS domain (approximately residues 133-476 based on homology)
Use solubility-enhancing fusion partners (MBP, SUMO, TrxA) rather than just affinity tags
Create a panel of constructs with different N- and C-terminal boundaries to identify optimal soluble fragments
Solubilization Optimization:
For full-length Tim50, test different detergents:
Mild detergents: DDM, LMNG, Digitonin
Zwitterionic detergents: CHAPS, LDAO
Novel solubilizing agents: SMALPs, nanodiscs, amphipols
Optimize detergent concentration, temperature, and time for extraction
Refolding Strategies:
Express as inclusion bodies and develop a refolding protocol
Use gradual dialysis with decreasing denaturant concentration
Add lipids or detergents during refolding to stabilize the transmembrane domain
Ensuring that recombinant Tim50 retains its native conformation and activity is crucial. Verification approaches include:
Structural Integrity Assessment:
Circular dichroism (CD) spectroscopy to verify secondary structure content
Thermal shift assays to measure protein stability
Limited proteolysis to probe for well-folded domains resistant to digestion
Dynamic light scattering to check for aggregation
Functional Assays:
Presequence binding assays using synthetic presequence peptides
In vitro reconstitution with other TIM23 components to test complex formation
For phosphatase activity: enzyme kinetics with standard substrates like pNPP
Integration into proteoliposomes to test membrane insertion and orientation
Interaction Validation:
Pull-down assays with known interaction partners (e.g., Tim23)
Surface plasmon resonance to measure binding affinities
Native gel electrophoresis to assess complex formation
Crosslinking experiments to verify specific interactions
In Vivo Complementation:
The ultimate test: Can the recombinant protein complement Tim50 depletion in S. pombe?
Express recombinant Tim50 in Tim50-depleted cells and assess restoration of:
Cell growth and viability
Mitochondrial protein import
Mitochondrial membrane potential
Respiratory function
CRISPR-Cas9 technology offers powerful approaches for manipulating the S. pombe Tim50 gene. Important considerations include:
Guide RNA Design:
Select target sites with minimal off-target potential using S. pombe-specific prediction tools
Consider the GC content (40-60% ideal) and avoid repetitive sequences
Target conserved functional domains for structure-function studies
Design gRNAs for both N- and C-terminal tagging strategies
Repair Template Design:
Include homology arms of appropriate length (40-80 bp typically sufficient in S. pombe)
For tagging, ensure tags do not interfere with critical functional domains
For point mutations, introduce silent mutations near the edit site to prevent re-cutting
Consider including selection markers that can later be removed
Delivery Method Optimization:
Transform CRISPR components as plasmids, RNPs, or a combination
Use appropriate S. pombe-specific promoters for Cas9 and gRNA expression
Consider temperature-sensitive or inducible Cas9 systems for essential genes like Tim50
Validation Strategy:
Design PCR primers outside the homology arms to verify integration
Sequence the entire modified locus to check for unwanted mutations
Verify protein expression levels to ensure they match wild-type levels
Confirm functional integrity through complementation assays
Several cutting-edge technologies hold promise for elucidating new aspects of Tim50 biology:
Cryo-EM Studies:
High-resolution structures of the entire TIM23 complex with bound preproteins
Visualizing conformational changes during protein translocation
Comparative structural biology between Tim50 from different species
Single-Molecule Techniques:
Optical tweezers to measure forces during protein translocation
Single-molecule FRET to track conformational changes during substrate binding
Nanopore recordings to study preprotein translocation in real-time
Spatiotemporal Proteomics:
Proximity labeling combined with quantitative proteomics to map the dynamic Tim50 interactome
Pulse-SILAC to determine protein turnover rates and assembly dynamics
Thermal proteome profiling to identify ligands and interaction partners
Advanced Genome Editing:
Base editing or prime editing for precise manipulation without double-strand breaks
Multiplexed CRISPR screens to identify genetic interactions
CRISPR interference/activation to modulate Tim50 expression levels with temporal control
S. pombe Tim50 research has potential applications for understanding and addressing human diseases:
Neurodegenerative Disorders:
Cardiac Pathologies:
TIM50 has been shown to attenuate pathological cardiac hypertrophy by reducing oxidative stress
S. pombe models could help dissect the molecular mechanisms connecting Tim50 to redox regulation
The relatively fast growth rate of S. pombe (108 minutes ) enables rapid screening of potential therapeutic interventions
Cancer Biology:
Metabolic Disorders:
S. pombe mitochondrial studies can provide insights into fundamental aspects of energy metabolism
Connections between protein import efficiency and metabolic adaptation can be explored
The well-characterized S. pombe system allows for precise genetic manipulations to model metabolic disease states
The multifunctional nature of Tim50, combining protein import and potential phosphatase activities, offers interesting biotechnological opportunities:
Protein Targeting Systems:
Engineer Tim50-based systems for targeted protein delivery to mitochondria
Develop switchable protein import systems controlled by phosphorylation
Create synthetic protein translocation pathways with modified specificity
Biosensors:
Design Tim50-based biosensors that detect changes in mitochondrial function
Develop FRET-based reporters using Tim50's presequence binding to monitor import activity
Create phosphorylation-sensitive reporters based on Tim50's phosphatase domain
Protein Production Platforms:
Optimize mitochondrial import for enhanced production of recombinant proteins in yeast
Engineer Tim50 to improve import efficiency of specific cargo proteins
Develop mitochondrial targeting systems for difficult-to-express proteins
Drug Discovery Platforms:
Use S. pombe Tim50 systems to screen for compounds that modulate protein import
Identify inhibitors or activators of Tim50's phosphatase activity
Develop yeast-based screens for compounds that can rescue disease-associated Tim50 mutations