Constraint-based modeling in microbial food biotechnology

Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype–phenotype relationships. This is essential for the rational improvement of industrial strains, which can further be facilitated through various model-guided strain design approaches. CBM of microbial communities offers a valuable tool for the rational design of defined food cultures, where it can catalyze hypothesis generation and provide unintuitive rationales for the development of enhanced community phenotypes and, consequently, novel or improved food products. In the industrial-scale production of microorganisms for food cultures, CBM may enable a knowledge-driven bioprocess optimization by rationally identifying strategies for growth and stability improvement. Through these applications, we believe that CBM can become a powerful tool for guiding the areas of strain development, culture development and process optimization in the production of food cultures. Nevertheless, in order to make the correct choice of the modeling framework for a particular application and to interpret model predictions in a biologically meaningful manner, one should be aware of the current limitations of CBM.

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The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

Microorganisms ◽

10.3390/microorganisms8122050 ◽

2020 ◽

Vol 8 (12) ◽

pp. 2050

Author(s):

Daniel Craig Zielinski ◽

Arjun Patel ◽

Bernhard O. Palsson

Keyword(s):

Data Science ◽

Strain Engineering ◽

Chemical Production ◽

Protein Structure Analysis ◽

Biological Design ◽

Strain Design ◽

Microbial Strains ◽

Active Research ◽

Constraint Based Modeling ◽

Predictive Design

Microbial strains are being engineered for an increasingly diverse array of applications, from chemical production to human health. While traditional engineering disciplines are driven by predictive design tools, these tools have been difficult to build for biological design due to the complexity of biological systems and many unknowns of their quantitative behavior. However, due to many recent advances, the gap between design in biology and other engineering fields is closing. In this work, we discuss promising areas of development of computational tools for engineering microbial strains. We define five frontiers of active research: (1) Constraint-based modeling and metabolic network reconstruction, (2) Kinetics and thermodynamic modeling, (3) Protein structure analysis, (4) Genome sequence analysis, and (5) Regulatory network analysis. Experimental and machine learning drivers have enabled these methods to improve by leaps and bounds in both scope and accuracy. Modern strain design projects will require these tools to be comprehensively applied to the entire cell and efficiently integrated within a single workflow. We expect that these frontiers, enabled by the ongoing revolution of big data science, will drive forward more advanced and powerful strain engineering strategies.

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Efficient Synthesis of Rare Disaccharides by Engineered β-Glucosidase Based on Hydropathy Index

10.26434/chemrxiv.11942016.v1 ◽

2020 ◽

Author(s):

Kangle Niu ◽

Zhengyao Liu ◽

Yuhui Feng ◽

Tianlong Gao ◽

Zhenzhen Wang ◽

...

Keyword(s):

Amino Acid ◽

Rational Design ◽

Large Scale ◽

Catalytic Site ◽

Scale Production ◽

Total Production ◽

Amino Acid Residues ◽

Hydropathy Index ◽

Reverse Hydrolysis ◽

Hydrolysis Activity

Oligosaccharides have important therapeutic applications. A useful route for oligosaccharides synthesis, especially rare disaccharides, is reverse hydrolysis by β-glucosidase. However, the low conversion efficiency of disaccharides from monosaccharides limits its large-scale production because the equilibrium is biased in the direction of hydrolysis. Based on the analysis of the docking results, we hypothesized that the hydropathy index of key amino acid residues in the catalytic site is closely related with disaccharide synthesis and more hydrophilic residues located in the catalytic site would enhance reverse hydrolysis activity. In this study, positive variants TrCel1bI177S, TrCel1bI177S/I174S, and TrCel1bI177S/I174S/W173H, and one negative variant TrCel1bN240I were designed according to the Hydropathy Index For Enzyme Activity (HIFEA) strategy. The reverse hydrolysis with TrCel1bI177S/I174S/W173H was accelerated and then the maximum total production (<a>195.8 mg/ml/mg enzyme</a>) of the synthesized disaccharides was increased 3.5-fold compared to that of wildtype. On the contrary, <a>TrCel1b</a>N240I lost reverse hydrolysis activity. The results demonstrate that<a> </a><a>the average hydropathy index</a> of <a>the key amino acid residues </a>in the catalytic site of TrCel1b is an important factor for the synthesis of laminaribiose, sophorose, and cellobiose. The HIFEA strategy provides a new perspective for the rational design of β-glucosidases used for the synthesis of oligosaccharides.

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SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

BMC Systems Biology ◽

10.1186/s12918-018-0673-8 ◽

2019 ◽

Vol 13 (1) ◽

Cited By ~ 8

Author(s):

Benjamín J. Sánchez ◽

Feiran Li ◽

Eduard J. Kerkhoven ◽

Jens Nielsen

Keyword(s):

Lipid Metabolism ◽

Modeling Framework ◽

Constraint Based Modeling

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Pharmaceutical Particles Design by Membrane Emulsification: Preparation Methods and Applications in Drug Delivery

Current Pharmaceutical Design ◽

10.2174/1381612823666161117160940 ◽

2017 ◽

Vol 23 (2) ◽

pp. 302-318 ◽

Cited By ~ 12

Author(s):

Emma Piacentini ◽

Marijana Dragosavac ◽

Lidietta Giorno

Keyword(s):

Drug Delivery ◽

Particle Size ◽

Rational Design ◽

Large Scale ◽

Drug Loading ◽

Small Scale ◽

Scale Production ◽

Membrane Emulsification ◽

Preparation Methods ◽

Promising Tool

Nowadays, the rational design of particles is an important issue in the development of pharmaceutical medicaments. Advances in manufacturing methods are required to design new pharmaceutical particles with target properties in terms of particle size, particle size distribution, structure and functional activity. Membrane emulsification is emerging as a promising tool for the production of emulsions and solidified particles with tailored properties in many fields. In this review, the current use of membrane emulsification in the production of pharmaceutical particles is highlighted. Membrane emulsification devices designed for small-scale testing as well as membrane-based methods suitable for large-scale production are discussed. A special emphasis is put on the important factors that contribute to the encapsulation efficiency and drug loading. The most recent studies about the utilization of the membrane emulsification for preparing particles as drug delivery systems for anticancer, proteins/peptide, lipophilic and hydrophilic bioactive drugs are reviewed.

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A novel strategy for efficient disaccharides synthesis from glucose by β-glucosidase

10.21203/rs.3.rs-24804/v1 ◽

2020 ◽

Author(s):

Kangle Niu ◽

Zhengyao Liu ◽

Yuhui Feng ◽

Tianlong Gao ◽

Zhenzhen Wang ◽

...

Keyword(s):

Amino Acid ◽

Rational Design ◽

Large Scale ◽

Catalytic Site ◽

Scale Production ◽

Total Production ◽

Amino Acid Residues ◽

Hydropathy Index ◽

Reverse Hydrolysis ◽

Hydrolysis Activity

Abstract Oligosaccharides have important therapeutic applications. A useful route for oligosaccharides synthesis is reverse hydrolysis by β-glucosidase. However, the low conversion efficiency of disaccharides from monosaccharides limits its large-scale production because the equilibrium is biased in the direction of hydrolysis. Based on the analysis of the docking results, we hypothesized that the hydropathy index of key amino acid residues in the catalytic site is closely related with disaccharide synthesis and more hydrophilic residues located in the catalytic site would enhance reverse hydrolysis activity. In this study, positive variants TrCel1bI177S, TrCel1bI177S/I174S, and TrCel1bI177S/I174S/W173H, and one negative variant TrCel1bN240I were designed according to the Hydropathy Index For Enzyme Activity (HIFEA) strategy. The reverse hydrolysis with TrCel1bI177S/I174S/W173H was accelerated and then the maximum total production (195.8 mg/ml/mg enzyme) of the synthesized disaccharides was increased 3.5-fold compared to that of wildtype. On the contrary, TrCel1bN240I lost reverse hydrolysis activity. The results demonstrate that the average hydropathy index of the key amino acid residues in the catalytic site of TrCel1b is an important factor for the synthesis of laminaribiose, sophorose, and cellobiose. The HIFEA strategy provides a new perspective for the rational design of β-glucosidases used for the synthesis of oligosaccharides.

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Regulatory dynamic enzyme-cost flux balance analysis: A unifying framework for constraint-based modeling

10.1101/802249 ◽

2019 ◽

Author(s):

Lin Liu ◽

Alexander Bockmayr

Keyword(s):

Flux Balance Analysis ◽

Optimization Problem ◽

Linear Optimization ◽

Production Costs ◽

Mixed Integer ◽

Time Interval ◽

Modeling Framework ◽

Flux Balance ◽

Balance Analysis ◽

Constraint Based Modeling

AbstractIntegrated modeling of metabolism and gene regulation continues to be a major challenge in computational biology. While there exist approaches like regulatory flux balance analysis (rFBA), dynamic flux balance analysis (dFBA), resource balance analysis (RBA) or dynamic enzyme-cost flux balance analysis (deFBA) extending classical flux balance analysis (FBA) in various directions, there have been no constraint-based methods so far that allow predicting the dynamics of metabolism taking into account both macromolecule production costs and regulatory events.In this paper, we introduce a new constraint-based modeling framework named regulatory dynamic enzyme-cost flux balance analysis (r-deFBA), which unifies dynamic modeling of metabolism, cellular resource allocation and transcriptional regulation in a hybrid discrete-continuous setting.With r-deFBA, we can predict discrete regulatory states together with the continuous dynamics of reaction fluxes, external substrates, enzymes, and regulatory proteins needed to achieve a cellular objective such as maximizing biomass over a time interval. The dynamic optimization problem underlying r-deFBA can be reformulated as a mixed-integer linear optimization problem, for which there exist efficient solvers.

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Trends in the use of tissue culture, applications and future aspects

International Journal of Plant Biology ◽

10.4081/pb.2020.8385 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 2

Author(s):

Baan Munim Twaij ◽

Zena H. Jazar ◽

Md. Nazmul Hasan

Keyword(s):

Tissue Culture ◽

Secondary Metabolites ◽

Plant Tissue Culture ◽

Plant Tissue ◽

Biological Activities ◽

Significant Advance ◽

Scale Production ◽

Culture Techniques ◽

Plant Culture ◽

Culture Development

Plant tissue culture has developed widely incorporated into biotechnology, the agricultural systems being a key factor to support many pharmaceutical and industrial outcomes. Since 1902 there is vast progress in plant culture and its application has emerged having great diversity in the science filed. Due to development and desire to grow on high scale production in the past few decades, tissue culture techniques were manipulated for improvement of plant growth, biological activities, transformation, and secondary metabolites production. A significant advance in techniques has been sought to deal with problems of low concentrations of secondary metabolites in whole plants. The augmented use of plant culture is due to a superior perceptive of plant oriented compounds and secondary metabolites from economically important plants. Due to development in modern techniques, several particular protocols have been developed for the production of a wide array of secondary metabolites of plants on a commercial scale. Plant tissue culture has to lead to significant contributions in recent times and today they constitute an indispensable tool in the advancement of agricultural sciences and modern agriculture. This review would enable us to have an analysis of plant tissue culture development for agriculture, human health and wellbeing in general.

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Glycosyltransferase engineering for carbohydrate synthesis

Biochemical Society Transactions ◽

10.1042/bst20150200 ◽

2016 ◽

Vol 44 (1) ◽

pp. 129-142 ◽

Cited By ~ 30

Author(s):

John B. McArthur ◽

Xi Chen

Keyword(s):

Directed Evolution ◽

Rational Design ◽

Large Scale ◽

Enzyme Engineering ◽

Lessons Learned ◽

Scale Production ◽

Amino Acid Residues ◽

Large Scale Production ◽

Donor And Acceptor ◽

Substrate Binding Sites

Glycosyltransferases (GTs) are powerful tools for the synthesis of complex and biologically-important carbohydrates. Wild-type GTs may not have all the properties and functions that are desired for large-scale production of carbohydrates that exist in nature and those with non-natural modifications. With the increasing availability of crystal structures of GTs, especially those in the presence of donor and acceptor analogues, crystal structure-guided rational design has been quite successful in obtaining mutants with desired functionalities. With current limited understanding of the structure–activity relationship of GTs, directed evolution continues to be a useful approach for generating additional mutants with functionality that can be screened for in a high-throughput format. Mutating the amino acid residues constituting or close to the substrate-binding sites of GTs by structure-guided directed evolution (SGDE) further explores the biotechnological potential of GTs that can only be realized through enzyme engineering. This mini-review discusses the progress made towards GT engineering and the lessons learned for future engineering efforts and assay development.

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Efficient Synthesis of Rare Disaccharides by Engineered β-Glucosidase Based on Hydropathy Index

10.26434/chemrxiv.11942016 ◽

2020 ◽

Author(s):

Kangle Niu ◽

Zhengyao Liu ◽

Yuhui Feng ◽

Tianlong Gao ◽

Zhenzhen Wang ◽

...

Keyword(s):

Amino Acid ◽

Rational Design ◽

Large Scale ◽

Catalytic Site ◽

Scale Production ◽

Total Production ◽

Amino Acid Residues ◽

Hydropathy Index ◽

Reverse Hydrolysis ◽

Hydrolysis Activity

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SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

10.1101/324863 ◽

2018 ◽

Cited By ~ 3

Author(s):

Benjamín J. Sánchez ◽

Feiran Li ◽

Eduard J. Kerkhoven ◽

Jens Nielsen

Keyword(s):

Experimental Data ◽

Saccharomyces Cerevisiae ◽

Lipid Metabolism ◽

Acyl Chain ◽

Energy Costs ◽

Detailed Data ◽

Modeling Framework ◽

Lipid Species ◽

Constraint Based Modeling ◽

Genome Scale

SummaryA recurrent problem in genome-scale metabolic models (GEMs) is to correctly represent lipids as biomass requirements, due to the numerous of possible combinations of individual lipid species and the corresponding lack of fully detailed data. In this study we present SLIMEr, a formalism for correctly representing lipid requirements in GEMs using commonly available experimental data. SLIMEr enhances a GEM with mathematical constructs where we Split Lipids Into Measurable Entities (SLIME reactions), in addition to constraints on both the lipid classes and the acyl chain distribution. By implementing SLIMEr on the consensus GEM of Saccharomyces cerevisiae, we can predict accurate amounts of lipid species, analyze the flexibility of the resulting distribution, and compute the energy costs of moving from one metabolic state to another. The approach shows potential for better understanding lipid metabolism in yeast under different conditions. SLIMEr is freely available at https://github.com/SysBioChalmers/SLIMEr.

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