Recombinant Synechocystis sp. UPF0060 membrane protein sll0793 (sll0793)

What is the structural organization of the Synechocystis sp. UPF0060 membrane protein sll0793?

The Synechocystis sp. UPF0060 membrane protein sll0793 is a relatively small protein consisting of 108 amino acids with a highly hydrophobic profile consistent with its membrane-spanning nature. The full amino acid sequence is: MILRSLLYFVMAGLCEIGGGYLVWLWIREGKSVWLALVRAILLTVYGFVATLQPANFGRAYAAYGGIFIILSIIWGWQVDNVVVDRLDWLGAAIALVGVLVMMYANRA . Structural analysis suggests the protein contains multiple transmembrane domains characteristic of UPF0060 family proteins. As a membrane protein, it is integrated into the lipid bilayer, with specific regions extending into the cytoplasm or periplasmic space. The protein's structure likely facilitates its interaction with other membrane-associated components in Synechocystis sp., though detailed three-dimensional structural data from crystallography or cryo-EM studies are currently limited in the available literature.

How is sll0793 classified within membrane protein families and what functional domains does it contain?

The sll0793 protein is classified as a member of the UPF0060 membrane protein family (UniProt ID: Q55939) . This classification places it among a group of proteins with conserved sequences but initially uncharacterized functions (UPF designates "Uncharacterized Protein Family"). While complete domain annotation is still developing, sequence analysis reveals several hydrophobic regions consistent with transmembrane domains. The protein lacks obvious enzymatic motifs but contains regions that suggest potential protein-protein interaction capabilities or small molecule binding sites. Comparative genomics with other cyanobacterial membrane proteins indicates potential functional similarities with regulatory proteins involved in metal homeostasis, particularly in relation to zinc regulation pathways, as suggested by its genetic proximity to zinc transport systems in Synechocystis PCC 6803 .

What is known about the physiological role of sll0793 in Synechocystis sp. PCC 6803?

While definitive characterization is still evolving, evidence suggests that sll0793 may play a regulatory role in metal homeostasis in Synechocystis PCC 6803, particularly in relation to zinc transport systems. Research has indicated a potential relationship between sll0793 and the zinc exporter system, specifically with the ziaA operator-promoter region . This suggests that sll0793 might function in monitoring or regulating cellular zinc levels, which is critical for cyanobacterial survival given zinc's essential role as a cofactor in numerous enzymes while being toxic at excessive concentrations. Its membrane localization is consistent with proteins that sense environmental conditions or participate in signaling cascades that regulate metal transport systems. Further studies involving gene knockout experiments and transcriptional analyses are necessary to fully elucidate its physiological significance.

What expression systems have proven most effective for producing recombinant sll0793 protein?

The most documented successful expression system for recombinant sll0793 utilizes Escherichia coli as the heterologous host . This bacterial expression system offers several advantages for membrane protein production, including rapid growth, high protein yields, and well-established genetic manipulation protocols. The commercially available recombinant form of sll0793 is expressed in E. coli with an N-terminal histidine tag to facilitate purification . For optimal expression, researchers should consider the following protocol elements:

Lower post-induction temperatures are particularly important for membrane proteins to prevent formation of inclusion bodies and promote proper folding. Alternative expression systems including yeast (P. pastoris) may be considered for cases requiring eukaryotic post-translational modifications, though bacterial systems remain the most widely utilized for this protein.

What are the optimized methods for solubilizing and purifying the recombinant sll0793 membrane protein?

Purification of membrane proteins presents unique challenges due to their hydrophobic nature. For sll0793, the following optimized protocol has been developed based on standard membrane protein techniques and specific information about the recombinant product :

• Cell Lysis: Mechanical disruption (sonication or French press) in buffer containing 50 mM Tris-HCl pH 8.0, 150 mM NaCl, with protease inhibitors.

• Membrane Fraction Isolation: Differential centrifugation (10,000×g to remove debris, followed by 100,000×g to pellet membranes).

• Solubilization: Membrane resuspension in buffer containing 1-2% of a mild detergent (n-dodecyl-β-D-maltoside or digitonin) for 1-2 hours at 4°C with gentle agitation.

• Affinity Purification: Application of solubilized material to Ni-NTA resin, exploiting the His-tag . Washing with increasing imidazole concentrations (10-40 mM) and elution with 250-300 mM imidazole.

• Size Exclusion Chromatography: Final purification step to remove aggregates using Superdex 200 in buffer containing detergent at concentrations above critical micelle concentration.

The purified protein in detergent micelles can be stored short-term at 4°C or lyophilized with trehalose as a stabilizing agent for longer storage . It's crucial to maintain detergent concentrations above CMC throughout all purification steps to prevent protein aggregation.

How can researchers effectively validate the proper folding and functional integrity of purified recombinant sll0793?

Validating proper folding and functional integrity of membrane proteins like sll0793 requires multiple complementary approaches:

• Structural Integrity Assessment:

  • Circular Dichroism (CD) spectroscopy to confirm secondary structure content

  • Thermal stability assays (differential scanning fluorimetry)

  • Size exclusion chromatography profiles (monodisperse peak versus aggregation)

• Functional Validation:

  • Binding assays with potential metal ligands (particularly zinc) using isothermal titration calorimetry

  • Reconstitution into liposomes or nanodiscs to create a native-like membrane environment

  • Assessment of interactions with putative partner proteins (e.g., components of zinc transport systems)

• Biophysical Characterization:

  • Tryptophan fluorescence spectroscopy to assess tertiary structure

  • Limited proteolysis to examine accessibility of cleavage sites

  • Mass spectrometry for accurate molecular weight determination and post-translational modification analysis

Since sll0793 may function in metal regulation, metal-binding assays are particularly relevant. Additionally, researchers should compare the properties of the recombinant protein with those of the native protein extracted directly from Synechocystis when possible, though this is challenging due to low natural abundance.

What approaches are most effective for studying the membrane topology and orientation of sll0793?

Determining the precise membrane topology of sll0793 requires a multi-faceted experimental approach:

• Computational Prediction: Initial topology models should be generated using algorithms such as TMHMM, MEMSAT, and TOPCONS, which predict transmembrane segments based on hydrophobicity patterns and amino acid distributions.

• Cysteine Scanning Mutagenesis: Systematic replacement of residues with cysteine followed by accessibility labeling with membrane-permeable and impermeable sulfhydryl reagents can reveal which regions are exposed to either side of the membrane.

• Proteolytic Mapping: Limited proteolysis of the protein in membrane vesicles of known orientation, followed by mass spectrometry identification of the accessible fragments.

• Fluorescence Microscopy: Creation of GFP fusion constructs at different positions can reveal the cellular localization and membrane orientation when expressed in model organisms.

• Epitope Insertion and Antibody Accessibility: Insertion of epitope tags at various positions followed by immunolabeling in permeabilized versus non-permeabilized cells.

For sll0793, which has a relatively small size (108 amino acids) , a combination of computational prediction with at least two experimental approaches is recommended to reliably establish its topology. The amino acid sequence suggests multiple membrane-spanning regions, but their precise boundaries and orientation require experimental validation.

How can researchers investigate potential protein-protein interactions involving sll0793?

Investigating protein-protein interactions for membrane proteins like sll0793 requires specialized techniques that account for their hydrophobic nature:

• Bacterial Two-Hybrid Systems: Modified for membrane proteins, these genetic screens can identify interaction partners in vivo without requiring protein purification.

• Pull-Down Assays: Using the His-tagged recombinant sll0793 as bait to capture interaction partners from Synechocystis lysates, followed by mass spectrometry identification.

• Cross-Linking Studies: Chemical cross-linkers with different spacer lengths can stabilize transient interactions prior to purification and analysis.

• Surface Plasmon Resonance (SPR): Purified sll0793 can be immobilized on a sensor chip in the presence of detergent, allowing real-time measurement of binding kinetics with potential partners.

• Co-Immunoprecipitation: Using antibodies against sll0793 or its tagged version to precipitate protein complexes from solubilized membranes.

• Proximity Labeling: Techniques such as BioID or APEX2, where sll0793 is fused to a biotin ligase or peroxidase that biotinylates proximal proteins.

For membrane proteins involved in metal homeostasis, it's particularly important to investigate interactions with metal transport components. Given the potential connection between sll0793 and zinc transport systems , researchers should prioritize examining interactions with components of the ziaA system and other zinc-responsive elements in Synechocystis.

What methods can determine if sll0793 plays a role in metal sensing or regulation as suggested by its genomic context?

To investigate the potential role of sll0793 in metal sensing or regulation, particularly in relation to zinc as suggested by its genomic proximity to zinc transport systems , researchers should employ these methodologies:

• Metal Binding Assays:

  • Direct measurement of zinc binding using isothermal titration calorimetry (ITC)

  • Competition assays with metallochromic indicators

  • Inductively coupled plasma mass spectrometry (ICP-MS) analysis of metal content in purified protein

• Transcriptional Reporter Systems:

  • Construction of reporter gene fusions to promoters potentially regulated by sll0793

  • Measurement of reporter activity under varying metal concentrations and in wild-type versus sll0793 knockout strains

• Electrophoretic Mobility Shift Assays (EMSA):

  • Testing whether sll0793 directly binds to DNA regions near zinc transport genes

  • Examining if this binding is modulated by the presence of metal ions

• Physiological Characterization of Mutants:

  • Creation of sll0793 deletion mutants and assessment of zinc tolerance

  • Measurement of intracellular zinc content using fluorescent probes or radioisotopes (65Zn)

  • Transcriptomic analysis comparing wild-type and mutant responses to zinc stress

• Structural Studies with Metal Cofactors:

  • X-ray absorption spectroscopy to characterize metal binding sites

  • Crystallization trials in the presence and absence of zinc

Since research has indicated a potential relationship between sll0793 and the ziaA operator-promoter region involved in zinc export , particular attention should be paid to examining how sll0793 might influence transcription or activity of zinc transporters in response to varying zinc concentrations.

How can CRISPR-Cas9 genome editing be optimized for studying sll0793 function in Synechocystis sp. PCC 6803?

CRISPR-Cas9 genome editing in Synechocystis requires careful optimization due to the polyploidy of this cyanobacterium (containing multiple genome copies). For studying sll0793 function, researchers should implement this specialized protocol:

• sgRNA Design:

  • Target unique regions within the sll0793 gene with minimal off-target potential

  • Use cyanobacteria-specific sgRNA prediction tools that account for the high GC content

  • Design multiple guide RNAs to increase editing efficiency

• Delivery System:

  • Construct a conjugative vector containing both Cas9 and the sgRNA

  • Consider using an inducible promoter for Cas9 expression to reduce toxicity

  • Include homology arms (500-1000 bp) flanking the target site for HDR-mediated gene replacement

• Selection Strategy:

  • Implement sequential selection rounds to achieve complete segregation across all genome copies

  • Alternate between different antibiotics to enhance selection pressure

  • Consider FACS-based enrichment of edited cells if including a fluorescent marker

• Validation Protocol:

  • PCR amplification and sequencing of the targeted locus

  • Quantitative PCR to confirm complete segregation

  • Western blotting to verify protein elimination

  • Complementation studies to confirm phenotype specificity

• Phenotypic Analysis:

  • Monitor growth rates under varying zinc concentrations

  • Measure zinc uptake and efflux rates using radioisotope tracers

  • Assess global transcriptional changes using RNA-seq

This approach would enable precise genetic manipulation of sll0793 to investigate its role in potential zinc regulation pathways , allowing for the creation of knockout strains, point mutations of specific functional residues, or tagged versions for localization studies.

What are the most promising approaches for structural determination of sll0793, considering the challenges of membrane protein crystallography?

Determining the structure of membrane proteins like sll0793 presents significant challenges that require specialized approaches:

• Cryo-Electron Microscopy (Cryo-EM):

  • Particularly advantageous for membrane proteins that resist crystallization

  • For small proteins like sll0793 (108 aa) , consider:

    • Fusion with larger scaffold proteins to increase particle size

    • Use of Fab fragments as fiducial markers

    • Implementation of the latest direct electron detectors and image processing algorithms

• Advanced Crystallization Techniques:

  • Lipidic cubic phase (LCP) crystallization, which provides a native-like membrane environment

  • Crystallization in the presence of various detergents and lipids to identify optimal conditions

  • Antibody-assisted crystallization using conformationally-selective nanobodies

• Nuclear Magnetic Resonance (NMR) Spectroscopy:

  • Solution NMR using isotopically labeled protein (13C, 15N) in detergent micelles

  • Solid-state NMR for protein reconstituted in lipid bilayers

  • Selective labeling strategies to focus on specific regions of interest

• Hybrid Approaches:

  • Integrative modeling combining low-resolution experimental data with computational predictions

  • Cross-linking mass spectrometry to identify distance constraints

  • Molecular dynamics simulations in explicit membrane environments to refine models

• Protein Engineering for Structural Studies:

  • Thermostabilizing mutations to enhance protein stability

  • Truncation constructs focusing on core structural elements

  • Fusion with crystallization chaperones (e.g., T4 lysozyme)

Given the relatively small size of sll0793, solution NMR might be particularly promising if sufficient quantities of isotopically labeled protein can be produced. Alternatively, the recent advances in cryo-EM for smaller proteins make this an increasingly viable option, especially if coupled with innovative protein engineering strategies.

How can systems biology approaches be applied to understand the broader functional context of sll0793 in Synechocystis sp. metabolism?

Systems biology offers powerful approaches to place sll0793 within its broader functional context in Synechocystis metabolism, particularly in relation to zinc homeostasis networks:

• Multi-Omics Integration:

  • Comparative transcriptomics of wild-type and sll0793 mutants under varying zinc conditions

  • Proteomics to identify changes in protein abundance and post-translational modifications

  • Metabolomics to detect metabolic shifts resulting from altered zinc homeostasis

  • Integration of datasets using computational tools to identify correlated changes

• Network Reconstruction:

  • Construction of protein-protein interaction networks centered on sll0793

  • Inference of regulatory networks using time-series expression data

  • Mapping of genetic interactions through systematic double-mutant analysis

• Flux Balance Analysis:

  • Development of constraint-based metabolic models incorporating metal cofactor requirements

  • Simulation of metabolic fluxes under different zinc availability scenarios

  • Prediction of metabolic vulnerabilities in sll0793 mutants

• Comparative Genomics:

  • Analysis of sll0793 homologs across diverse cyanobacterial species

  • Correlation of genetic context with ecological niches and metal availability

  • Identification of conserved regulatory motifs in promoter regions

• High-Content Phenotyping:

  • Automated microscopy to track subcellular localization under different conditions

  • Flow cytometry with fluorescent zinc indicators to measure single-cell responses

  • Microfluidic approaches to examine dynamic responses to zinc fluctuations

This systems-level understanding would provide insights into how sll0793 contributes to the broader zinc regulation network, potentially including interactions with the zinc exporter system involving ziaA . Such comprehensive analysis would reveal both direct effects of sll0793 perturbation and downstream consequences for cellular metabolism and stress responses.

What are the most common challenges in obtaining active recombinant sll0793 and how can they be addressed?

Producing active recombinant membrane proteins like sll0793 presents several challenges that researchers commonly encounter:

• Expression Level Issues:

  • Challenge: Toxic accumulation in host membranes leading to growth inhibition

  • Solution: Use tightly controlled inducible promoters, lower induction temperatures (16-20°C), and specialized E. coli strains (C41/C43(DE3)) designed for membrane protein expression

• Protein Misfolding:

  • Challenge: Formation of inclusion bodies rather than membrane integration

  • Solution: Co-expression with chaperones (GroEL/ES, DnaK/J), addition of chemical chaperones (glycerol, betaine), and use of fusion partners that enhance folding (MBP, SUMO)

• Detergent Selection Difficulties:

  • Challenge: Finding detergents that effectively solubilize without denaturing

  • Solution: Systematic screening of detergent panels starting with milder options (DDM, digitonin), followed by stability assessment using techniques like size exclusion chromatography

• Protein Instability:

  • Challenge: Rapid degradation during purification

  • Solution: Inclusion of protease inhibitors, working at 4°C throughout, and addition of stabilizing agents (glycerol, specific lipids) to all buffers

• Functional Assessment Difficulties:

  • Challenge: Lack of robust activity assays for proteins with unclear function

  • Solution: Development of indirect assays based on binding partners, reconstitution into artificial membrane systems, and structural integrity measurements

For sll0793 specifically, the published protocol using E. coli expression with His-tag purification provides a starting point, but researchers should be prepared to optimize conditions based on their specific experimental goals. The lyophilized form with trehalose stabilization represents a successful approach to maintaining protein integrity during storage .

How can researchers distinguish between direct and indirect effects when analyzing phenotypes of sll0793 mutants?

Distinguishing direct from indirect effects in sll0793 mutant phenotypes requires a systematic experimental approach:

• Complementation Studies:

  • Reintroduction of wild-type sll0793 under native or controllable promoters

  • Introduction of point mutants affecting specific functional domains

  • Heterologous complementation with homologs from related species

• Temporal Analysis:

  • Time-course experiments following gene deletion or inactivation

  • Identification of primary (rapid) versus secondary (delayed) responses

  • Pulse-chase experiments to track zinc flux changes immediately after perturbation

• Conditional Mutants:

  • Creation of temperature-sensitive or chemically-inducible variants

  • Rapid protein degradation systems (e.g., auxin-inducible degron)

  • Riboswitch-controlled expression for titratable depletion

• Direct Biochemical Validation:

  • In vitro reconstitution of key activities with purified components

  • Direct detection of protein-protein or protein-DNA interactions implicated in the phenotype

  • Site-directed mutagenesis of residues predicted to be critical for function

• Multi-level Omics Analysis:

  • Integration of transcriptomic, proteomic, and metabolomic data with different temporal resolutions

  • Network analysis to distinguish primary targets from downstream effects

  • Comparison with other mutants affecting zinc homeostasis

When investigating the potential role of sll0793 in zinc regulation , researchers should particularly focus on comparing the effects of sll0793 deletion with those of established zinc transport components, looking for shared and distinct phenotypes that would help position sll0793 within the regulatory network.

What considerations are important when designing experiments to investigate potential interactions between sll0793 and the zinc transport system?

When investigating potential interactions between sll0793 and zinc transport systems like ziaA , researchers should consider these critical experimental design factors:

• Zinc Concentration Controls:

  • Use precisely defined zinc concentrations spanning deficient to toxic ranges (typically 0-100 μM)

  • Account for zinc contamination in media components through metal speciation software

  • Include metal chelators (EDTA, TPEN) as negative controls and zinc ionophores as positive controls

• Genetic Construct Design:

  • Create single and double mutants of sll0793 and known zinc transporters

  • Develop fluorescent protein fusions that preserve function

  • Design constructs allowing inducible or graded expression levels

• Physiological Measurements:

  • Implement techniques to measure intracellular zinc using:

    • Fluorescent zinc-specific probes

    • 65Zn radioisotope uptake and efflux assays

    • Synchrotron X-ray fluorescence microscopy for subcellular localization

• Regulatory Interaction Assessment:

  • Design reporter constructs containing promoter regions of:

    • sll0793 itself

    • ziaA and other zinc transporters

    • Known zinc-responsive genes

  • Measure reporter activity across zinc concentrations and genetic backgrounds

• Protein-Protein Interaction Controls:

  • Include appropriate negative controls (unrelated membrane proteins)

  • Test interactions under varying zinc concentrations

  • Validate interactions using multiple complementary techniques

• Environmental Condition Variations:

  • Examine effects under various stressors beyond zinc (oxidative stress, other metals)

  • Test responses under different light intensities and growth phases

  • Consider photosynthetic activity measurements as photosystems are zinc-dependent

The experimental design should specifically address whether sll0793 functions as a direct regulator of zinc transport, a zinc sensor, or has an indirect role in zinc homeostasis. Given the potential relationship between sll0793 and the ziaA operator-promoter region , particular attention should be paid to transcriptional regulation experiments that could reveal mechanistic details of this interaction.

What statistical approaches are most appropriate for analyzing complex phenotypes in sll0793 mutant studies?

Analysis of complex phenotypes in sll0793 mutant studies requires robust statistical approaches tailored to biological variability and experimental design:

• Multivariate Analysis Techniques:

  • Principal Component Analysis (PCA) to identify major sources of variation across multiple parameters

  • Hierarchical clustering to group similar phenotypes and identify patterns

  • Partial Least Squares Discriminant Analysis (PLS-DA) to identify variables that best separate experimental groups

• Time Series Analysis:

  • Mixed-effects models accounting for both fixed (genotype, treatment) and random (biological replicate) factors

  • Functional data analysis for continuous monitoring data (growth curves, zinc uptake kinetics)

  • Change-point detection to identify critical transitions in dynamic responses

• Dose-Response Modeling:

  • Four-parameter logistic regression for zinc tolerance curves

  • Hormetic models for capturing potential biphasic responses to zinc

  • Comparison of EC50 values across genotypes with appropriate confidence intervals

• Multiple Testing Correction:

  • False Discovery Rate (FDR) control using Benjamini-Hochberg procedure for omics datasets

  • Family-wise error rate control (Bonferroni or Šidák) for targeted hypothesis testing

  • q-value estimation for large-scale screening approaches

• Power Analysis and Experimental Design Optimization:

  • A priori power calculations to determine required sample sizes

  • Sequential analysis approaches to minimize experimental resources

  • Bayesian experimental design to optimize information gain

When specifically examining the potential role of sll0793 in zinc regulation, statistical analyses should focus on quantifying effect sizes rather than merely reporting statistical significance, particularly when comparing wild-type and mutant responses to varying zinc concentrations. Interaction terms in statistical models are especially important when examining how the effects of sll0793 mutation might depend on zinc availability.

How can researchers integrate structural predictions and functional data to develop mechanistic models of sll0793 activity?

Integrating structural predictions with functional data requires a systematic approach to develop mechanistic models of sll0793 activity:

• Structure-Function Mapping Pipeline:

  • Generate initial structural models using homology modeling and ab initio approaches

  • Identify conserved residues through multiple sequence alignment of UPF0060 family proteins

  • Predict functional sites using computational tools (metal binding sites, protein-protein interaction surfaces)

  • Design targeted mutations based on structural predictions

  • Validate predictions through functional assays

• Molecular Dynamics Simulations:

  • Simulate protein behavior in membrane environments with varying zinc concentrations

  • Calculate binding free energies for potential ligands

  • Identify conformational changes associated with zinc binding

  • Generate testable hypotheses about allosteric mechanisms

• Network-Based Integration:

  • Construct protein interaction networks incorporating both predicted and experimentally validated interactions

  • Map transcriptional responses to structural features

  • Develop pathway models that position sll0793 within zinc homeostasis systems

• Bayesian Framework for Model Refinement:

  • Define competing mechanistic hypotheses based on initial structural models

  • Assign prior probabilities based on bioinformatic predictions

  • Update model probabilities using experimental data through Bayesian inference

  • Iteratively refine models as new data becomes available

• Visualization and Communication Tools:

  • Develop interactive visualizations linking structural features to functional data

  • Create mechanistic diagrams illustrating proposed activity models

  • Implement quantitative system diagrams capturing regulatory relationships

For sll0793, which may function in zinc regulation , this integrated approach could help determine whether it acts as a direct zinc sensor, a transcriptional regulator, or a component of zinc transport machinery. The relatively small size of the protein (108 amino acids) makes it amenable to comprehensive structural modeling, which can then guide the interpretation of phenotypic data from genetic studies.

What computational approaches can predict potential regulatory networks involving sll0793 in cyanobacterial metal homeostasis?

Predicting regulatory networks involving sll0793 in cyanobacterial metal homeostasis requires specialized computational approaches:

• Comparative Genomics Frameworks:

  • Phylogenetic profiling to identify genes with correlated evolutionary patterns

  • Analysis of conserved gene neighborhoods across cyanobacterial genomes

  • Identification of shared regulatory motifs in promoter regions

  • Construction of gene co-occurrence networks

• Transcriptional Network Inference:

  • GENIE3 or ARACNE algorithms applied to transcriptomic data under varying zinc conditions

  • Causal inference approaches (e.g., dynamic Bayesian networks) for time-series data

  • Motif discovery in promoter regions of co-regulated genes

  • Network module detection to identify functional units

• Protein-Protein Interaction Prediction:

  • Structure-based interaction prediction using docking simulations

  • Co-evolution analysis to identify correlated mutations suggesting physical interactions

  • Text mining of scientific literature for reported interactions in related systems

  • Integration with experimental PPI data from high-throughput screens

• Metabolic Network Analysis:

  • Flux Balance Analysis incorporating metal cofactor requirements

  • Identification of metabolic bottlenecks under zinc limitation

  • Elementary Mode Analysis to determine minimal functional units

  • Regulatory Flux Balance Analysis incorporating transcriptional control

• Data Integration Platforms:

  • Weighted network integration combining evidence from multiple data types

  • Probabilistic graphical models capturing conditional dependencies

  • Knowledge graphs incorporating curated information and experimental data

  • Machine learning approaches to predict functional relationships

For sll0793, which has been implicated in zinc homeostasis through its potential relationship with the ziaA operator-promoter region , these approaches can help predict its position within the broader regulatory network. Particular attention should be paid to analyzing the zinc-responsive transcriptome and identifying genes with expression patterns correlated with sll0793 across various environmental conditions. The resulting network models can generate testable hypotheses about the direct targets and regulatory partners of sll0793.