Recombinant pheT is synthesized using codon-optimized expression systems. For example, the Acinetobacter baylyi pheT gene (UniProt: Q6F873) is cloned into vectors for high-yield production . Critical parameters include:
Expression optimization: Inducible promoters (e.g., T7) in E. coli ensure controlled protein synthesis .
Purification: Affinity chromatography (e.g., His-tag systems) followed by gel filtration achieves >85% purity .
tRNA interactions: Partial pheT variants help map tRNA-binding regions. For instance, truncating the B2 domain reduces editing efficiency but preserves catalytic activity, highlighting modular functionality .
Drug target validation: In Mycobacterium abscessus, CRISPRi-mediated pheT silencing caused growth inhibition, underscoring its essentiality as a therapeutic target .
Antibiotic resistance studies: Mutations in homologous RNA polymerase β-subunits (e.g., rpoB) alter bacterial motility and virulence, providing insights into pheT’s broader regulatory roles .
Enzyme engineering: Recombinant pheT facilitates structure-function analyses to design inhibitors against multidrug-resistant Acinetobacter pathogens .
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KEGG: aci:ACIAD3041
STRING: 62977.ACIAD3041
Phenylalanine-tRNA ligase (PheRS) is a class II aminoacyl-tRNA synthetase that specifically attaches phenylalanine to its cognate tRNA molecules, a critical step in protein synthesis. In most bacteria including Acinetobacter species, PheRS exists as a heterotetramer (α₂β₂) where the beta subunit (encoded by the pheT gene) contains the catalytic domain responsible for aminoacylation activity.
The pheT subunit specifically contributes to:
ATP binding and phenylalanine activation
Transfer of activated phenylalanine to tRNA^Phe
Quality control through editing mechanisms that prevent misacylation
Structural stability of the enzyme complex
In Acinetobacter species, which are increasingly recognized as significant hospital-acquired pathogens, the pheT gene product plays an essential role in protein synthesis and bacterial survival. Recent research has demonstrated that Acinetobacter pittii, a member of this genus, has become an emerging pathogen responsible for outbreaks in healthcare settings worldwide .
For effective recombinant expression of Acinetobacter sp. pheT, several expression systems have been evaluated, with E. coli-based systems demonstrating the highest efficiency. The methodology typically involves:
Gene cloning: The pheT coding sequence is PCR-amplified from Acinetobacter genomic DNA with appropriate restriction sites incorporated into primers.
Vector selection: pET-based expression vectors (particularly pET28a) with N-terminal His-tags facilitate purification and are commonly employed due to their tight regulation under T7 promoter control.
Host selection: E. coli BL21(DE3) and its derivatives are preferred due to reduced protease activity and compatibility with T7-based expression.
Expression optimization protocol:
Cultivation at 16-18°C after induction (rather than 37°C) significantly improves soluble protein yield
Induction with 0.1-0.5 mM IPTG at mid-log phase (OD₆₀₀ = 0.6-0.8)
Addition of 5-10% glycerol to the culture medium enhances protein stability
For genetic modification of the pheT gene itself, recombineering methods utilizing the bacteriophage λ Red system have proven highly effective. This system employs the phage recombination genes gam, bet, and exo, which work together to facilitate precise genetic modifications .
Confirming the functionality of recombinant pheT requires multiple complementary approaches:
Enzymatic activity assay: The aminoacylation activity is measured through ATP-PPi exchange assays or tRNA charging assays. The standard protocol involves:
Incubating purified recombinant pheT with:
ATP (2 mM)
L-phenylalanine (100 μM)
Total or purified tRNA^Phe (10 μM)
Reaction buffer (100 mM HEPES pH 7.5, 10 mM MgCl₂, 50 mM KCl)
After incubation (15-30 minutes at 37°C), reactions are analyzed by:
TCA precipitation for radioactive assays
HPLC analysis for non-radioactive methods
Gel electrophoresis for detection of charged tRNA
Structural verification: Circular dichroism spectroscopy to confirm proper folding, comparing spectra with native protein profiles.
Complementation assays: Introduction of recombinant pheT into conditional pheT mutants to verify rescue of growth phenotypes.
Protein-protein interaction studies: Co-immunoprecipitation or two-hybrid assays to confirm proper interaction with the alpha subunit (pheS) and formation of the functional heterotetramer.
Similar methodological approaches have been successfully applied to other bacterial systems, including validation of genetic variants affecting antimicrobial resistance in H. pylori .
For precise genetic engineering of Acinetobacter sp. pheT, a specialized recombineering approach offers superior results compared to traditional methods. This technique employs the bacteriophage λ Red system consisting of:
λ Red system components:
Optimized protocol for Acinetobacter sp.:
Design parameters for targeting homologies:
Selection strategies:
Positive selection: Integration of antibiotic resistance cassettes
Counterselection: Use of sacB-based systems for scarless modifications
CRISPR-Cas9 screening for markerless mutations
The methodology yields precise modifications with minimal off-target effects, allowing researchers to create specific amino acid substitutions to investigate catalytic mechanisms, antibiotic resistance determinants, or species-specific structural features.
Next-generation sequencing (NGS) provides powerful approaches for investigating pheT evolution and diversity across Acinetobacter species. A comprehensive methodology involves:
Sample collection and preparation:
Clinical isolates from diverse geographical locations
Environmental samples from different ecological niches
Reference strains representing different Acinetobacter species
Custom NGS panel design:
Sequencing protocol:
Library preparation using fragmentation methods that preserve GC-rich regions
Paired-end sequencing (2×150bp) on Illumina platforms
Minimum coverage depth of 100× for reliable variant detection
Bioinformatic analysis pipeline:
Quality control and trimming using FastQC and Trimmomatic
Reference-based alignment using BWA-MEM or Bowtie2
De novo assembly using SPAdes for novel variant discovery
Variant calling using GATK or FreeBayes
Phylogenetic analysis with RAxML or IQ-TREE
Selection pressure analysis with PAML
Data interpretation framework:
Identification of species-specific signatures
Detection of recombination events using ClonalFrameML
Correlation of genetic variants with phenotypic characteristics
This approach has successfully been applied to other bacterial systems, demonstrating the ability to identify both previously reported and novel variants with potential functional significance . For Acinetobacter species, similar approaches would be valuable given the emergence of A. pittii as a significant hospital-acquired pathogen .
Investigating the role of pheT in Acinetobacter pathogenicity and antibiotic resistance requires a multi-faceted experimental approach:
Conditional mutant construction:
CRISPR interference (CRISPRi) system for tunable repression
Antisense RNA expression systems
Degron-tagging for controlled protein degradation
Phenotypic characterization protocols:
Growth curve analysis under varying antibiotic concentrations
Biofilm formation quantification using crystal violet staining
Virulence assessment in infection models:
Galleria mellonella larval infection model
Mouse pulmonary infection model
Human cell line adhesion/invasion assays
Molecular mechanism investigation:
Ribosome profiling to assess translational impacts
Protein-protein interaction network mapping via pull-down assays coupled with mass spectrometry
Structural analysis of pheT-antibiotic interactions using X-ray crystallography or cryo-EM
Resistance mechanism elucidation:
Directed evolution experiments under antibiotic selection pressure
Site-directed mutagenesis of predicted resistance hotspots
Heterologous expression of variant pheT alleles in susceptible backgrounds
Comparative genomics approach:
Analysis of pheT sequence variations in resistant vs. susceptible isolates
Correlation with minimum inhibitory concentration (MIC) values
Identification of co-evolving genes
These approaches have proven effective in studying other bacterial systems, including analyzing antibiotic resistance profiles in clinical isolates of Acinetobacter pittii, which has been identified as responsible for outbreaks in different regions worldwide .
The design of inhibitors targeting Acinetobacter sp. pheT faces several challenges that can be addressed through advanced structure-based approaches:
Key challenges:
Structural conservation across bacterial species may lead to broad-spectrum activity with potential microbiome disruption
The large size of the active site accommodating both ATP and phenylalanine
Conformational changes during catalysis that affect inhibitor binding
Limited structural data specific to Acinetobacter pheT
Methodological solutions:
Homology modeling workflow:
Template selection from closely related species (≥60% sequence identity)
Multiple-template modeling using MODELLER or SWISS-MODEL
Refinement through molecular dynamics simulations (100-500 ns)
Validation through Ramachandran analysis and PROCHECK
Virtual screening protocol:
Receptor preparation using AutoDock Tools
Grid box centered on the ATP-binding pocket
Two-tiered docking approach:
Initial screening with Glide SP or AutoDock Vina
Refinement of top hits with Glide XP or GOLD
Fragment-based design approach:
Thermal shift assays to identify fragment hits
X-ray crystallography or NMR to determine binding modes
Fragment linking or growing strategies
Species-specificity strategies:
Targeting non-conserved residues at the periphery of the active site
Exploiting differences in protein dynamics between species
Development of allosteric inhibitors targeting Acinetobacter-specific regulatory sites
Experimental validation pipeline:
Enzymatic inhibition assays (IC₅₀ and Ki determination)
Crystallography of inhibitor-bound complexes
Cellular penetration assessment
Activity testing against clinical isolates
This methodology has been successfully applied to developing targeted therapeutics for other bacterial pathogens, including personalized approaches for H. pylori eradication treatments , and could be adapted for addressing the emerging threat posed by antibiotic-resistant Acinetobacter species .
Obtaining high-yield, active recombinant Acinetobacter pheT requires a specialized purification protocol designed to maintain the functional integrity of this large, complex protein:
Optimized lysis buffer composition:
50 mM Tris-HCl, pH 8.0
300 mM NaCl
10% glycerol
1 mM DTT
0.1% Triton X-100 (critical for membrane-associated fractions)
Protease inhibitor cocktail (EDTA-free)
Multi-step purification procedure:
Immobilized metal affinity chromatography (IMAC):
Ni-NTA resin for His-tagged constructs
Low imidazole (10 mM) in wash buffers
Step gradient elution (100, 200, 300 mM imidazole)
Ion exchange chromatography:
Q-Sepharose at pH 8.0 (pheT theoretical pI ~5.3)
Linear gradient elution (50-500 mM NaCl)
Size exclusion chromatography:
Superdex 200 column
Running buffer: 25 mM Tris-HCl pH 7.5, 150 mM NaCl, 5% glycerol, 0.5 mM DTT
Critical considerations:
Maintaining temperature at 4°C throughout purification
Addition of 5 mM MgCl₂ to all buffers to stabilize protein structure
Concentration using centrifugal filters with 100 kDa MWCO (larger than theoretical size to prevent aggregation)
Flash-freezing in liquid nitrogen with 10% glycerol for storage
Quality control assessments:
SDS-PAGE analysis (>95% purity)
Dynamic light scattering to confirm monodispersity
Thermal shift assays to verify stability
ATP-PPi exchange assay to confirm activity retention
This protocol typically yields 5-10 mg of pure, active protein per liter of bacterial culture, suitable for structural and functional studies. Similar purification approaches have been successfully applied to other large bacterial proteins involved in translation and antibiotic resistance .
Developing a robust assay system for screening inhibitors of recombinant Acinetobacter pheT requires careful consideration of assay design, controls, and validation steps:
Primary screening assays:
a. ATP-PPi exchange assay:
Principle: Measures the formation of [³²P]ATP from [³²P]PPi and AMP
Assay composition:
100 mM HEPES-KOH (pH 7.5)
10 mM MgCl₂
50 mM KCl
1 mM DTT
2 mM ATP
2 mM [³²P]PPi
1 mM L-phenylalanine
100 nM purified pheT
Quantification: Charcoal filtration and scintillation counting
Z' factor typically >0.7 when optimized
b. Aminoacylation assay (non-radioactive):
Principle: Measures the formation of Phe-tRNAphe using malachite green detection of released phosphate
Assay composition:
100 mM HEPES-KOH (pH 7.5)
10 mM MgCl₂
50 mM KCl
1 mM DTT
2 mM ATP
2 μM tRNAPhe
100 μM L-phenylalanine
50 nM purified pheT
Quantification: Absorbance at 620 nm
Adaptable to 384-well format for high-throughput screening
Counterscreens and validation assays:
Thermal shift assays to confirm direct binding
Surface plasmon resonance for determining binding kinetics
Enzyme panel selectivity screening against other aminoacyl-tRNA synthetases
Cellular penetration assays using Acinetobacter growth inhibition
Assay optimization parameters:
DMSO tolerance (typically stable up to 2% final concentration)
Buffer component optimization (pH 7.2-7.8 range testing)
Enzyme concentration titering to ensure linear response
Incubation time optimization (typically 15-30 minutes)
Data analysis framework:
Percent inhibition calculation: (1 - (signal_inhibitor - signal_negative) / (signal_positive - signal_negative)) × 100
IC₅₀ determination using 4-parameter logistic regression
Structure-activity relationship analysis
This comprehensive assay platform enables efficient screening of compound libraries while minimizing false positives and negatives. Similar methodological approaches have been successfully employed in other antimicrobial development programs targeting essential bacterial enzymes .
Comprehensive structural characterization of recombinant Acinetobacter pheT requires integrating multiple complementary techniques:
X-ray crystallography protocol:
Crystallization optimization:
Initial screening: Commercial sparse matrix screens (400-800 conditions)
Optimization: Varying pH (6.5-8.0), precipitant concentration, and additives
Co-crystallization with substrates: Pre-incubation with 2 mM ATP, 2 mM phenylalanine
Complex formation: Addition of non-hydrolyzable ATP analogs (AMP-PNP)
Crystal improvement: Microseeding, additive screening
Data collection strategy:
Cryoprotection: 20-25% glycerol or ethylene glycol
Resolution target: Better than 2.5 Å
Multiple-wavelength anomalous dispersion (MAD) for phasing
Complete data sets with redundancy >5
Structure determination workflow:
Molecular replacement using homologous structures
Model building with Coot
Refinement with PHENIX or REFMAC5
Validation with MolProbity
Cryo-electron microscopy approach:
Sample preparation:
Protein concentration: 0.5-2 mg/mL
Grid type: Quantifoil R1.2/1.3 with thin carbon support
Vitrification: Vitrobot Mark IV (3-4 second blot time)
Data acquisition parameters:
Magnification: 22,500-36,000×
Defocus range: -0.8 to -2.5 μm
Total dose: 50-60 e-/Ų
Frame count: 40-50
Data processing pipeline:
Motion correction: MotionCor2
CTF estimation: CTFFIND4
Particle picking: crYOLO or Topaz
2D classification: RELION or cryoSPARC
3D reconstruction: Non-uniform refinement in cryoSPARC
Solution NMR for dynamics studies:
Selective isotope labeling (¹⁵N, ¹³C)
TROSY-based experiments for large proteins
Hydrogen-deuterium exchange for conformational studies
Integrative structural biology approach:
Small-angle X-ray scattering (SAXS) for solution conformation
Crosslinking mass spectrometry for interface mapping
Molecular dynamics simulations (100-500 ns) for conformational sampling
This multi-technique approach provides comprehensive structural insights that can inform structure-based drug design efforts against Acinetobacter species, which have been identified as significant emerging pathogens in healthcare settings .
Analysis of pheT sequence variations across clinical isolates requires a comprehensive bioinformatic framework:
Sequence acquisition and quality control:
Whole genome sequencing using Illumina platforms (coverage ≥100×)
Quality filtering (Q-score ≥30, adapter removal)
Assembly verification using multiple algorithms (SPAdes, MEGAHIT)
Alignment and variant calling protocol:
Progressive multiple sequence alignment using MAFFT G-INS-i algorithm
Codon-aware alignment refinement with MACSE
Variant calling parameters:
Minimum read depth: 20×
Minimum variant frequency: 5%
Quality score threshold: ≥20
Classification framework:
| Variant Type | Analysis Method | Significance Assessment |
|---|---|---|
| Synonymous | dN/dS ratio calculation | Potential selection signatures |
| Non-synonymous | PROVEAN, SIFT scoring | Functional impact prediction |
| Indels | Frameshift analysis | Protein truncation assessment |
| Regulatory region | Promoter motif analysis | Expression effect prediction |
Population genetics analysis:
Nucleotide diversity (π) calculation
Tajima's D statistic for selection pressure
FST values for population differentiation
Recombination detection with ClonalFrameML
Correlation with phenotypic data:
Antibiotic susceptibility profiles (MIC values)
Growth rate measurements
Virulence in infection models
Statistical testing using linear mixed models
Visualization and reporting:
Haplotype networks using PopART
Phylogenetic trees with RAxML (GTR+Γ model)
Variant frequency heatmaps
Structure mapping of variants using PyMOL
This methodological framework enables identification of clinically relevant variations and evolutionary patterns in the pheT gene. Similar approaches have been successfully applied to analyze genetic determinants of antibiotic resistance in other bacterial pathogens, as demonstrated in H. pylori studies and could be valuable for understanding the emergence of Acinetobacter pittii as a hospital-acquired pathogen .
For robust analysis of structure-function relationships in mutated pheT variants, specialized statistical approaches are required:
Enzyme kinetics analysis framework:
Parameter estimation methods:
Non-linear regression using least squares
Bayesian inference with MCMC sampling for parameter uncertainty
Global fitting of multiple experiments simultaneously
Statistical comparison of kinetic parameters:
Extra sum-of-squares F-test for nested models
Akaike Information Criterion (AIC) for non-nested models
Bootstrap resampling for confidence interval estimation
Visualization techniques:
Michaelis-Menten plots with confidence bands
Residual analysis plots
Lineweaver-Burk transformations with error propagation
Multivariate analysis of structure-function datasets:
Principal Component Analysis (PCA):
Data preprocessing: Standardization and outlier removal
Component selection: Kaiser criterion or parallel analysis
Interpretation: Variable contribution analysis
Partial Least Squares (PLS) regression:
Cross-validation: Leave-one-out for small datasets
Model evaluation: Q² and R² metrics
Variable importance in projection (VIP) scores
Multiple correspondence analysis for categorical variables
Statistical framework for thermal stability comparisons:
| Method | Parameter | Statistical Test | Visualization |
|---|---|---|---|
| Differential Scanning Fluorimetry | Tm value | One-way ANOVA with Dunnett's post-hoc | Box plots with individual data points |
| Circular Dichroism | Denaturation curve | Non-linear regression comparison | Overlay plots with 95% CI bands |
| Limited proteolysis | Degradation rate | Survival analysis (log-rank) | Kaplan-Meier curves |
Machine learning applications:
Feature selection using random forest importance metrics
Support vector machines for classification of functional impact
Cross-validation strategies: Nested k-fold (k=5)
Performance metrics: Matthews correlation coefficient, precision-recall AUC
These statistical approaches allow for rigorous analysis of how mutations affect pheT structure and function, enabling identification of critical residues and mechanism elucidation. Similar methodological frameworks have been successfully applied to analyze structure-function relationships in other bacterial systems .
Recombinant Acinetobacter pheT research offers several promising avenues for antimicrobial development:
Structure-based inhibitor design:
Fragment-based approach:
Identification of binding hotspots through crystallographic fragment screening
Fragment growing/linking strategies
Optimization of pharmacophore models
Virtual screening workflow:
Pharmacophore-based filtering of compound libraries (>1 million compounds)
Molecular docking using ensemble receptor conformations
Molecular dynamics-based rescoring of top hits
In silico ADMET prediction
Exploitation of species-specific features:
Targeting non-conserved residues unique to Acinetobacter species
Development of narrow-spectrum agents with reduced impact on microbiome
Sequence and structural comparisons between:
Pathogenic Acinetobacter species (A. baumannii, A. pittii)
Non-pathogenic environmental species
Human PheRS
Combination therapy strategies:
Synergistic interactions with existing antibiotics
Targeting multiple tRNA synthetases simultaneously
Experimental design for synergy testing:
Checkerboard assays (8×8 concentration matrix)
Time-kill kinetics
Fractional inhibitory concentration index calculation
Resistance mechanism elucidation and countermeasures:
Directed evolution experiments:
Serial passage under increasing inhibitor concentrations
Whole genome sequencing of resistant mutants
Reconstruction of mutations in clean genetic backgrounds
Pre-emptive inhibitor design:
Multi-target inhibitors to raise resistance barrier
Identification of resistance hotspots through computational prediction
Development of inhibitors targeting conserved catalytic residues
This research direction is particularly relevant given the emergence of Acinetobacter pittii as a significant hospital-acquired pathogen that has been identified as responsible for outbreaks in different regions worldwide . Development of new antimicrobial strategies is crucial for addressing the increasing prevalence of antibiotic-resistant Acinetobacter species.
Several emerging technologies are poised to transform recombinant Acinetobacter pheT research:
Advanced structural biology techniques:
Cryo-electron tomography:
Visualization of pheT in native cellular context
Spatial organization within the translation machinery
Resolution: 10-30 Å for cellular tomograms
Time-resolved crystallography:
X-ray free electron laser (XFEL) studies
Visualization of catalytic intermediates
Temporal resolution: femtosecond to millisecond
Integrative structural modeling:
Combination of cryo-EM, crosslinking-MS, and SAXS data
Enhanced modeling of flexible regions
Improved computational methods for model building
Next-generation protein engineering approaches:
Deep mutational scanning:
Comprehensive mutational landscape analysis
High-throughput functional characterization
Data analysis using machine learning algorithms
Cell-free protein synthesis:
Rapid production of variant libraries
Direct activity screening without purification
Incorporation of non-canonical amino acids
De novo protein design:
AI-driven design of pheT inhibitors
Development of synthetic binding proteins targeting pheT
Computational methods: AlphaFold-based design
Advanced genomic and transcriptomic technologies:
Long-read sequencing:
Complete genome assembly of Acinetobacter clinical isolates
Structural variant detection
Platforms: PacBio HiFi, Nanopore
Spatial transcriptomics:
Localization of pheT expression within bacterial communities
Infection model transcriptional landscape
Resolution: Single-cell level
CRISPR-based technologies:
Base editing for precise mutagenesis
CRISPRi for tunable gene repression
Perturb-seq for high-throughput functional genomics
Computational advances:
AI-driven drug discovery:
Generative models for novel inhibitor design
Binding affinity prediction
Multi-parameter optimization
Enhanced molecular dynamics:
GPU-accelerated simulations
Millisecond-scale simulations
Markov state modeling for rare events
These emerging technologies will significantly enhance our ability to study pheT structure, function, and inhibition, potentially leading to novel antimicrobial strategies against Acinetobacter species, which have been identified as significant emerging pathogens .