scholarly journals The glutaredoxin mono- and di-thiol mechanisms for deglutathionylation are functionally equivalent: implications for redox systems biology

2015 ◽  
Vol 35 (1) ◽  
Author(s):  
Lefentse N. Mashamaite ◽  
Johann M. Rohwer ◽  
Ché S. Pillay
Keyword(s):  
Systems Biology ◽  
Active Site ◽  
Redox Regulation ◽  
Computational Models ◽  
Kinetic Modelling ◽  
Side Reaction ◽  
Kinetic Properties ◽  
Computational Systems Biology ◽  
Redox Systems

Glutathionylation plays a central role in cellular redox regulation and anti-oxidative defence. Grx (Glutaredoxins) are primarily responsible for reversing glutathionylation and their activity therefore affects a range of cellular processes, making them prime candidates for computational systems biology studies. However, two distinct kinetic mechanisms involving either one (monothiol) or both (dithiol) active-site cysteines have been proposed for their deglutathionylation activity and initial studies predicted that computational models based on either of these mechanisms will have different structural and kinetic properties. Further, a number of other discrepancies including the relative activity of active-site mutants and contrasting reciprocal plot kinetics have also been reported for these redoxins. Using kinetic modelling, we show that the dithiol and monothiol mechanisms are identical and, we were also able to explain much of the discrepant data found within the literature on Grx activity and kinetics. Moreover, our results have revealed how an apparently futile side-reaction in the monothiol mechanism may play a significant role in regulating Grx activity in vivo.

scholarly journals The Lack of Mitochondrial Thioredoxin TRXo1 Affects In Vivo Alternative Oxidase Activity and Carbon Metabolism under Different Light Conditions

2019 ◽  
Vol 60 (11) ◽  
pp. 2369-2381 ◽  
Author(s):  
Igor Florez-Sarasa ◽  
Toshihiro Obata ◽  
N�stor Fern�ndez Del-Saz ◽  
Jean-Philippe Reichheld ◽  
Etienne H Meyer ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Redox State ◽  
Redox Regulation ◽  
Alternative Oxidase ◽  
Tricarboxylic Acid Cycle ◽  
Reduced Form ◽  
Photosynthetic Parameters ◽  
Primary Metabolism ◽  
Redox Systems

Abstract The alternative oxidase (AOX) constitutes a nonphosphorylating pathway of electron transport in the mitochondrial respiratory chain that provides flexibility to energy and carbon primary metabolism. Its activity is regulated in vitro by the mitochondrial thioredoxin (TRX) system which reduces conserved cysteines residues of AOX. However, in vivo evidence for redox regulation of the AOX activity is still scarce. In the present study, the redox state, protein levels and in vivo activity of the AOX in parallel to photosynthetic parameters were determined in Arabidopsis knockout mutants lacking mitochondrial trxo1 under moderate (ML) and high light (HL) conditions, known to induce in vivo AOX activity. In addition, 13C- and 14C-labeling experiments together with metabolite profiling were performed to better understand the metabolic coordination between energy and carbon metabolism in the trxo1 mutants. Our results show that the in vivo AOX activity is higher in the trxo1 mutants at ML while the AOX redox state is apparently unaltered. These results suggest that mitochondrial thiol redox systems are responsible for maintaining AOX in its reduced form rather than regulating its activity in vivo. Moreover, the negative regulation of the tricarboxylic acid cycle by the TRX system is coordinated with the increased input of electrons into the AOX pathway. Under HL conditions, while AOX and photosynthesis displayed similar patterns in the mutants, photorespiration is restricted at the level of glycine decarboxylation most likely as a consequence of redox imbalance.

scholarly journals Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

2016 ◽  
Vol 13 (117) ◽  
pp. 20151046 ◽  
Author(s):  
Fei He ◽  
Ettore Murabito ◽  
Hans V. Westerhoff
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Regulatory Networks ◽  
Computational Systems Biology ◽  
Control Engineering ◽  
Trade Offs ◽  
Metabolic Systems ◽  
Analytical Approaches

Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo , not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.

6. Simulators

2020 ◽  
pp. 79-107
Author(s):  
Eberhard O. Voit
Keyword(s):  
Metabolic Engineering ◽  
Systems Biology ◽  
Organic Compounds ◽  
Computational Models ◽  
Computational Systems Biology ◽  
Bulk Materials ◽  
Growth Simulation ◽  
Practical Applications ◽  
Crop Development ◽  
Computational Systems

Computational models can serve many purposes, but a particularly powerful application of a model is its use as a system simulator. An emerging branch of computational systems biology strives to develop simulators for complex systems in biology and medicine, the premier example being a disease simulator. ‘Simulators’ discusses the nascent efforts towards the development of simulators for practical applications. Disease simulators will deepen our understanding of the physiology of human diseases and their treatment. Simulators in metabolic engineering have the goal of improving the microbial production of bulk materials and of valuable organic compounds. Relatively simple simulators for the production of biofuels and for crop development, such as the Soybean Growth Simulation Model (SoySim), are already in use.

scholarly journals Insights into the function of NADPH thioredoxin reductase C (NTRC) based on identification of NTRC-interacting proteins in vivo

2019 ◽  
Vol 70 (20) ◽  
pp. 5787-5798 ◽  
Author(s):  
Maricruz González ◽  
Víctor Delgado-Requerey ◽  
Julia Ferrández ◽  
Antonio Serna ◽  
Francisco Javier Cejudo
Keyword(s):  
Redox Regulation ◽  
Fluorescent Protein ◽  
Affinity Purification ◽  
Photosynthetic Apparatus ◽  
Thioredoxin Reductase ◽  
Redox System ◽  
Negative Control ◽  
Bimolecular Fluorescence Complementation ◽  
Redox Systems

Abstract Redox regulation in heterotrophic organisms relies on NADPH, thioredoxins (TRXs), and an NADPH-dependent TRX reductase (NTR). In contrast, chloroplasts harbor two redox systems, one that uses photoreduced ferredoxin (Fd), an Fd-dependent TRX reductase (FTR), and TRXs, which links redox regulation to light, and NTRC, which allows the use of NADPH for redox regulation. It has been shown that NTRC-dependent regulation of 2-Cys peroxiredoxin (PRX) is critical for optimal function of the photosynthetic apparatus. Thus, the objective of the present study was the analysis of the interaction of NTRC and 2-Cys PRX in vivo and the identification of proteins interacting with them with the aim of identifying chloroplast processes regulated by this redox system. To assess this objective, we generated Arabidopsis thaliana plants expressing either an NTRC–tandem affinity purification (TAP)-Tag or a green fluorescent protein (GFP)–TAP-Tag, which served as a negative control. The presence of 2-Cys PRX and NTRC in complexes isolated from NTRC–TAP-Tag-expressing plants confirmed the interaction of these proteins in vivo. The identification of proteins co-purified in these complexes by MS revealed the relevance of the NTRC–2-Cys PRX system in the redox regulation of multiple chloroplast processes. The interaction of NTRC with selected targets was confirmed in vivo by bimolecular fluorescence complementation (BiFC) assays.

Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context

2008 ◽  
Vol 417 (1) ◽  
pp. 269-277 ◽  
Author(s):  
Ché S. Pillay ◽  
Jan-Hendrik S. Hofmeyr ◽  
Brett G. Olivier ◽  
Jacky L. Snoep ◽  
Johann M. Rohwer
Keyword(s):  
Systems Biology ◽  
Redox Regulation ◽  
Systems Approach ◽  
Kinetic Modelling ◽  
Redox Potentials ◽  
Activity Data ◽  
Redox Cycles ◽  
Redox Couples ◽  
Substrate Saturation

Systems biology approaches, such as kinetic modelling, could provide valuable insights into how thioredoxins, glutaredoxins and peroxiredoxins (here collectively called redoxins), and the systems that reduce these molecules are regulated. However, it is not clear whether redoxins should be described as redox couples (with redox potentials) or as enzymes (with Michaelis–Menten parameters) in such approaches. We show that in complete redoxin systems, redoxin substrate saturation and other purported enzymatic behaviours result from limitations in the redoxin redox cycles in these systems. Michaelis–Menten parameters are therefore inappropriate descriptors of redoxin activity; data from redoxin kinetic experiments should rather be interpreted in terms of the complete system of reactions under study. These findings were confirmed by fitting kinetic models of the thioredoxin and glutaredoxin systems to in vitro datasets. This systems approach clarifies the inconsistencies with the descriptions of redoxins and emphasizes the roles of redoxin systems in redox regulation.

scholarly journals Standards and ontologies in computational systems biology

2008 ◽  
Vol 45 ◽  
pp. 211-222 ◽  
Author(s):  
Herbert M. Sauro ◽  
Frank T. Bergmann
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Software Tools ◽  
Computational Systems Biology ◽  
Modelling Languages ◽  
Systems Biology Markup Language ◽  
Visualization Tools ◽  
Computational Systems ◽  
Model Interchange ◽  
Model Annotation

With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced, together with a discussion on the future of modelling languages and visualization tools in systems biology.

scholarly journals New models of atherosclerosis and multi-drug therapeutic interventions

2018 ◽  
Vol 35 (14) ◽  
pp. 2449-2457 ◽  
Author(s):  
Andrew Parton ◽  
Victoria McGilligan ◽  
Melody Chemaly ◽  
Maurice O’Kane ◽  
Steven Watterson
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Laboratory Data ◽  
Therapeutic Interventions ◽  
Supplementary Information ◽  
Pharmaceutical Therapy ◽  
Systems Biology Markup Language ◽  
Supplementary Material

Abstract Motivation Atherosclerosis is amongst the leading causes of death globally. However, it is challenging to study in vivo or in vitro and no detailed, openly-available computational models exist. Clinical studies hint that pharmaceutical therapy may be possible. Here, we develop the first detailed, computational model of atherosclerosis and use it to develop multi-drug therapeutic hypotheses. Results We assembled a network describing atheroma development from the literature. Maps and mathematical models were produced using the Systems Biology Graphical Notation and Systems Biology Markup Language, respectively. The model was constrained against clinical and laboratory data. We identified five drugs that together potentially reverse advanced atheroma formation. Availability and implementation The map is available in the Supplementary Material in SBGN-ML format. The model is available in the Supplementary Material and from BioModels, a repository of SBML models, containing CellDesigner markup. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Systems Biology: The Next Frontier for Bioinformatics

2010 ◽  
Vol 2010 ◽  
pp. 1-10 ◽  
Author(s):  
Vladimir A. Likić ◽  
Malcolm J. McConville ◽  
Trevor Lithgow ◽  
Antony Bacic
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Analytical Techniques ◽  
Reaction Rates ◽  
Data Sets ◽  
Metabolic Reaction ◽  
High Resolution Data ◽  
Biochemical Systems ◽  
Cellular Components

Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i) mathematical and computational modeling; (ii) the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii) the use of near-comprehensive data sets derived from ‘omics platform technologies, in particular “downstream” technologies relative to genome sequencing, including transcriptomics, proteomics and metabolomics. The future progress in understanding biological principles will increasingly depend on the development of temporal and spatial analytical techniques that will provide high-resolution data for systems analyses. To date, particularly successful were strategies involving (a) quantitative measurements of cellular components at the mRNA, protein and metabolite levels, as well as in vivo metabolic reaction rates, (b) development of mathematical models that integrate biochemical knowledge with the information generated by high-throughput experiments, and (c) applications to microbial organisms. The inevitable role bioinformatics plays in modern systems biology puts mathematical and computational sciences as an equal partner to analytical and experimental biology. Furthermore, mathematical and computational models are expected to become increasingly prevalent representations of our knowledge about specific biochemical systems.

Unique substrate specificity of ornithine aminotransferase from Toxoplasma gondii

2017 ◽  
Vol 474 (6) ◽  
pp. 939-955 ◽  
Author(s):  
Alessandra Astegno ◽  
Elena Maresi ◽  
Mariarita Bertoldi ◽  
Valentina La Verde ◽  
Alessandro Paiardini ◽  
...  
Keyword(s):  
Steady State ◽  
Toxoplasma Gondii ◽  
Substrate Specificity ◽  
Active Site ◽  
Structural Features ◽  
Kinetic Properties ◽  
Ornithine Aminotransferase ◽  
Human Homologue

Toxoplasma gondii is a protozoan parasite of medical and veterinary relevance responsible for toxoplasmosis in humans. As an efficacious vaccine remains a challenge, chemotherapy is still the most effective way to combat the disease. In search of novel druggable targets, we performed a thorough characterization of the putative pyridoxal 5′-phosphate (PLP)-dependent enzyme ornithine aminotransferase from T. gondii ME49 (TgOAT). We overexpressed the protein in Escherichia coli and analysed its molecular and kinetic properties by UV-visible absorbance, fluorescence and CD spectroscopy, in addition to kinetic studies of both the steady state and pre-steady state. TgOAT is largely similar to OATs from other species regarding its general transamination mechanism and spectral properties of PLP; however, it does not show a specific ornithine aminotransferase activity like its human homologue, but exhibits both N-acetylornithine and γ-aminobutyric acid (GABA) transaminase activity in vitro, suggesting a role in both arginine and GABA metabolism in vivo. The presence of Val79 in the active site of TgOAT in place of Tyr, as in its human counterpart, provides the necessary room to accommodate N-acetylornithine and GABA, resembling the active site arrangement of GABA transaminases. Moreover, mutation of Val79 to Tyr results in a change of substrate preference between GABA, N-acetylornithine and L-ornithine, suggesting a key role of Val79 in defining substrate specificity. The findings that TgOAT possesses parasite-specific structural features as well as differing substrate specificity from its human homologue make it an attractive target for anti-toxoplasmosis inhibitor design that can be exploited for chemotherapeutic intervention.

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