A Multiscale Modeling Study of Iron Homeostasis in Mycrobacterium Tuberculosis

• Main Author: Ghosh, Soma
• Other Authors: Vishveshwara, Saraswathi
• Language: en_US
• Published: 2018
• Subjects: Mycobacterium Tubercolosis; Mycobacterial Iron Homeostasis; Systems Biology; Host-Pathogen Interaction (HPI) Model; Protein Structure Network; Molecular Dynamics; Tuberculosis Infections; Mycobacterium Tuberculosis Iron Metabolism; Protein Interaction Networks; Iron Dependant Repressor; IdeR-DNA Interactions; Tuberculosis - Iron Homeostasis; IdeR; Molecular Biophysics
• Online Access: http://etd.iisc.ernet.in/2005/3519; http://etd.iisc.ernet.in/abstracts/4386/G26787-Abs.pdf

Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), has remained the largest killer among infectious diseases for over a century. The increasing emergence of drug resistant varieties such as the multidrug resistant (MDR) and extremely drug resistant (XDR) strains are only increasing the global burden of the disease. Available statistics indicate that nearly one-third of the world’s population is infected, where the bacteria remains in the latent state but can reactivate into an actively growing stage to cause disease when the individual is immunocompromised. It is thus immensely important to rethink newer strategies for containing and combating the spread of this disease. Extraction of iron from the host cell is one of the many factors that enable the bacterium to survive in the harsh environments of the host macrophages and promote tuberculosis. Host–pathogen interactions can be interpreted as the battle of two systems, each aiming to overcome the other. From the host’s perspective, iron is essential for diverse processes such as oxygen transport, repression, detoxification and DNA synthesis. Infact, during infection, both the host and the pathogen are known to fight for the available iron, thereby influencing the outcome of the infection. It is of no surprise therefore, that many studies have investigated several components of the iron regulatory machinery of M.tb and the host. However, very few attempts have been made to study the interactions between these components and how such interactions lead to a better adapted phenotype. Such studies require exploration at multiple levels of structural and functional complexity, thereby necessitating the use of a multiscale approach. Systems biology adopts an integrated approach to study and understand the function of biological systems. It involves building large scale models based on individual biochemical interactions, followed by model validation and predictions of the system’s response to perturbations, such as a gene knock-out or exposure to drug. In multiscale modeling, an approach employed in this thesis, a particular biological phenomenon is studied at different spatiotemporal levels. Studying responses at multiple scales provides a broader picture of the communications that occur between a host and pathogen. Moreover, such an analysis also provides valuable insights into how perturbation at a particular level can elicit responses at another level and help in the identification of crucial inter-level communications that can possibly be hindered or activated for a desired physiological outcome. The broad objectives of this thesis was to obtain a comprehensive in silico understanding of mycobacterial iron homeostasis and metabolism, the influence of iron on host-pathogen interactions, identification of key players that mediate such interactions, determination of the molecular consequences of inhibiting the key players and finally the global response of M.tb to altered iron concentration. Perturbation of iron homeostasis holds a strong therapeutic potential, given its essentiality in both the host and the pathogen. Understanding the workings of iron metabolism and regulation in M.tb has been a main objective, so as to ultimately obtain insights about specific therapeutic strategies that capitalize on the criticality of iron concentration. An in-depth study of iron metabolism and regulation is performed at different levels of temporal and spatial scales using diverse methods, each appropriate to investigate biological events associated with the different scales. The specific investigations carried out in the thesis are as follows, a) Reconstruction of a host-pathogen interaction (HPI) model, with focus on iron homeostasis. This study represented the inter-cellular level analysis and was crucial for the identification of key players that mediate communication between the host and pathogen. Additionally, the model also provided a mathematical framework to study the effect of perturbations and gene knock-outs. b) Understanding the influence of iron on IdeR, an iron-responsive transcription factor, also identified as a key player in the HPI model. The study was carried out at the molecular level to identify atomistic details of how IdeR senses iron and the resulting structural modifications, which finally enables IdeR-DNA interaction. The study enabled identification of residues for the functioning of IdeR. c) Genome scale identification of genes that are regulated by IdeR to obtain an overview of the various biological processes affected by changing iron concentrations and IdeR mutation in M.tb. d) To understand the direct and indirect influences of iron and IdeR on the M.tb proteome using large scale protein-protein interaction network. The study enabled identification of highest differentially regulated genes and altered activity of the different biological processes under differing iron concentrations and regulation. e) Systems level analysis of the M.tb metabolome to investigate the metabolic re-adjustments undertaken by M.tb to adapt to altered iron concentration and regulation. The conceptual details and the background of each of the methods used to study the specific aims are provided in the Methodology chapter (Chapter 2). Construction of the host-pathogen interaction (HPI) model and the insights obtained from this study are presented in Chapter 3. A rule based HPI model was built with a focus on the iron regulatory mechanisms in both the host and pathogen. The model consisted of 194 rules, of which 4 rules represented interactions between the host and pathogen. The model not only represented an overview of iron metabolism but also allowed prediction of critical interaction that had the potential to form bottleneck in the system so as to control bacterial proliferation. Infact, model simulation led to the identification of 5 bottlenecks or chokepoints in the system, which if perturbed, could successfully interfere with the host-pathogen dynamics in favour of the host. The model also provided a framework to test perturbation strategies based on the bottlenecks. The study also established the importance of an iron responsive transcription factor, IdeR for regulating iron concentration in the pathogen and mediating host-pathogen interactions. Additionally, the importance of mycobactin and transferrin as key molecular players, involved in host-pathogen dynamics was also determined. The model provided a mathematical framework to test TB pathogenesis and provided significant insights about key molecular players and perturbation strategies that can be used to enhance therapeutic strategies. Given the importance of IdeR in HPI, its molecular mechanism of activation and dimerization was explored in Chapter 4. The main objective of the study was to explore the structural details of IdeR and its iron sensing capacity at the molecular level. A combination of molecular dynamics and protein structure network (PSN) were used to analyse IdeR monomers and dimers in the presence and absence of iron. PSNs used in this thesis are based on non-covalent interactions between sidechain atoms and are quite efficient in identifying iron induced subtle conformational variations. The study distinctly indicated the role of iron in IdeR stability. Further, it was observed that IdeR monomers can take up two major conformations, the ‘open’ and ‘close’ conformation with the iron bound structure preferring the ‘close’ conformation. Major structural changes, such as the N-terminal folding and increased propensity for dimerization were observed upon iron binding. Interestingly, careful analysis of structure suggests a role of these structural modifications towards DNA binding and has been tested in the next chapter. Overall, the results clearly highlight the influence of iron on IdeR activation and dimerization. The predisposition of IdeR to bind to DNA in the presence of metal is clearly visible even when the simulations are performed solely on protein molecules. However, to confirm the conjectures proposed in this chapter and to obtain the atomistic details of IdeR-DNA interactions, the IdeR-DNA complex was investigated. Chapter 5 focuses on the mechanistic details of IdeR-DNA interactions and the influence of iron on the same. IdeR is known to bind to a specific stretch of DNA, known as the ‘iron-box’ motif to form a dimer-of-dimer complex. Molecular dynamics followed by protein-DNA bipartite network analysis was performed on a set of four IdeR-DNA complexes to obtain a molecular level understanding of IdeR-DNA interactions. A striking observation was the dissociation of IdeR-DNA complex in the absence of iron, undoubtedly establishing the importance of iron for IdeR-DNA binding. At the residue level, hydrogen bond and non-covalent interactions clearly established the importance of N-terminal residues for DNA binding, thereby confirming the conjecture put forth in the previous chapter. An important aspect studied in this chapter is the allosteric nature of IdeR-DNA binding. Recent years have witnessed a paradigm shift in the understanding of allostery. Unlike the classical definition of allostery that was based on static structures, the newer definition is based on the conformational ensemble as represented by the shift in the energy landscape of the protein. The allosteric nature of IdeR-DNA complex was probed using simulated trajectories and indeed they suggest iron to be an allosteric regulator of the protein. Finally, based on the known experimental data and observations presented in Chapters 4 and 5, a multi-step model of IdeR activation and DNA binding has been proposed. In chapter 6, a global perspective of IdeR regulation in M.tb was obtained. This was important to gain insights about the influences of iron and its regulation at the M.tb cellular level. A genome scale identification of all possible IdeR targets based on the presence of ‘iron-box’ motif in the promoter region of the genes was carried out. An interesting aspect of this study was the use of energetic information from previous molecular dynamics study as an input for generation of the motif. A total of 255 such IdeR targets were identified and converted into an IdeR target network (IdeRnet). Along with IdeRnet, an unbiased systems level protein-protein interaction network was also generated. To study the response of the pathogen to external perturbations, iron-specific gene expression data was integrated into the network as node weights and edge weights. Analysis of IdeRnet provides interesting associations between fatty acid metabolism and IdeR regulations. Specific genes such as fadD32, DesA3 or lppW have been found to be affected by IdeR mutation. While IdeRnet discusses the direct associations, the global level responses are monitored by analysing pathways for the flow of information in the protein-protein interaction network (PPInet). Comparisons of the PPInets under conditions such as altering iron concentrations and lack of iron homeostasis led to the identification of the ‘top-most’ active paths under the different conditions. The study clearly suggests a halt in the protein synthesis machinery and decreased energy consumption under iron scarcity and an uninhibited consumption of energy when iron homeostasis is perturbed. In the final chapter (Chapter 7), flux balance analyses has been used to investigate the influence of iron on M.tb metabolism. The importance of iron for metabolic enzymes has already been established in the previous chapter. Additionally, M.tb is known to produce siderophores, an important metabolite that requires amino acids as its precursors, for iron extraction. All this, together highlighted the importance of iron and its regulation of M.tb metabolism. Flux balance analysis has been used previously to study the metabolic alterations that occur in an organism under different conditions. For this study, iron specific gene expression data was also incorporated into the model as reaction bounds and the flux values so obtained were compared in different environmental conditions. The study provided valuable insights into the metabolic adjustments taken up by M.tb under iron stress conditions and correlates well with the responses observed from the interactome as well as experimental observations. Most significantly, changes were observed in the energy preferences of the cell. For instance, it was noted that while the wild type strain of M.tb prefers synthesis of ATP via glycolysis, the IdeR mutant strain preferred oxidative phosphorylation. The picture becomes clearer when one accounts for the uncontrolled utilization of energy and rapid activation of protein synthesis machinery in the IdeR mutant strain. Biological systems are inherently multiscale in nature and therefore for a successful drug target regime, analysis of the genome to the phenome, which captures interactions at multiple levels, is essential. In this thesis, a detailed understanding of iron homeostasis and regulation in M.tb at multiple levels has been attempted. More importantly, insights obtained from one level, formed questions in the next level. The study was initiated at the inter-cellular level, where the influence of iron on HPI was modeled and analysed. From this study, IdeR, an iron-responsive transcription factor was identified as a key player that had the potential to alter host-pathogen interactions in the favour of the host. For a complete understanding of how IdeR regulates iron homeostasis, it was imperative to obtain a molecular level insight of its mechanism of action. Finally, the various aspects of IdeR regulation were investigated at the cellular level by analysing direct and indirect influences of IdeR on M.tb proteome and metabolome. The study suggests certain therapeutic interventions, such as 1) reduction in the concentration of free transferrin various, 2) mutations at the N-terminal sites of IdeR, 3) regulation of proteins involved in production of mycolic acids by iron and 4) perturbation of altering energy sources, which capitalize on iron and should be investigated in detail. In summary, the consequences of iron on TB infection were studied by threading different levels. This is based on the belief that most biological functions involve multiple spatio-temporal levels with frequent cross talks between the different levels, thereby making such multiscale approaches very useful.