On the feasibility of growth-coupled product synthesis in microbial strains

Klamt, Steffen; Mahadevan, Radhakrishnan

doi:10.1016/j.ymben.2015.05.006

Cited by 86 publications

(95 citation statements)

References 39 publications

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“…1a). Thus, the algorithms that design gene deletion strategies to create growth-product coupling (Burgard et al, 2003, Patil et al, 2005, Klamt and Mahadevan, 2015), essentially design network reductions that render an anchor reaction essential for (optimal) growth and that prohibit the utilization of one of the anchor reaction products for biomass synthesis. Due to their direct relevance for biorefining, we here focus on anchor reactions acting on carbon compounds.…”

Section: Resultsmentioning

confidence: 99%

“…Indeed, this strategy has successfully been demonstrated in two industrially important hosts – Escherichia coli and Saccharomyces cerevisiae (Lee et al, 2005, Ng et al, 2012, Otero et al, 2013, Tokuyama et al, 2014). While several algorithms exist to aid the identification of gene deletion strategies to create growth-product coupling (Burgard et al, 2003, Patil et al, 2005, Klamt and Mahadevan, 2015), the biochemical basis of the coupling is yet unresolved. Here, we establish anchor reactions as fundamental biochemical links enabling growth-product coupling.…”

Section: Introductionmentioning

confidence: 99%

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Metabolic anchor reactions for robust biorefining

Jouhten

Huerta-Cepas

Bork

et al. 2017

Metabolic Engineering

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Microbial cell factories based on renewable carbon sources are fundamental to a sustainable bio-economy. The economic feasibility of producer cells requires robust performance balancing growth and production. However, the inherent competition between these two objectives often leads to instability and reduces productivity. While algorithms exist to design metabolic network reduction strategies for aligning these objectives, the biochemical basis of the growth-product coupling has remained unresolved. Here, we reveal key reactions in the cellular biochemical repertoire as universal anchor reactions for aligning cell growth and production. A necessary condition for a reaction to be an anchor is that it splits a substrate into two or more molecules. By searching the currently known biochemical reaction space, we identify 62 C‐C cleaving anchor reactions, such as isocitrate lyase (EC 4.1.3.1) and L-tryptophan indole-lyase (EC 4.1.99.1), which are relevant for biorefining. The here identified anchor reactions mark network nodes for basing growth-coupled metabolic engineering and novel pathway designs.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Metabolic anchor reactions for robust biorefining

Jouhten

Huerta-Cepas

Bork

et al. 2017

Metabolic Engineering

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“…In those cases, all EFVs whose support is a proper superset of any other EFV can be dropped prior to the analysis. This procedure has been used, for example, in [19] to find suitable (support-minimal) EFVs that indicate feasibility of growth-coupled product synthesis.…”

Section: Applications Of Efvsmentioning

confidence: 99%

“…It took several more years until the community started to recognize the potential of EFVs, in particular, that they represent exactly the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. A recent publication demonstrated how EFVs can be used in a realistic application (for metabolic engineering purposes) [19], whereas another paper discussed theoretical properties of elementary vectors in the context of polyhedral geometry [20]. …”

Section: Introductionmentioning

confidence: 99%

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

et al. 2017

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Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated. These additional constraints further restrict the space of feasible flux vectors and turn the flux cone into a general flux polyhedron in which the concept of EFMs is not directly applicable anymore. For this reason, there has been a conceptual gap between EFM-based (pathway) analysis methods and linear optimization (FBA) techniques, as they operate on different geometric objects. One approach to overcome these limitations was proposed ten years ago and is based on the concept of elementary flux vectors (EFVs). Only recently has the community started to recognize the potential of EFVs for metabolic network analysis. In fact, EFVs exactly represent the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. This work aims to present a concise theoretical and practical introduction to EFVs that is accessible to a broad audience. We highlight the close relationship between EFMs and EFVs and demonstrate that almost all applications of EFMs (in flux cones) are possible for EFVs (in flux polyhedra) as well. In fact, certain properties can only be studied with EFVs. Thus, we conclude that EFVs provide a powerful and unifying framework for constraint-based modeling of metabolic networks.

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“…[55][56][57][58][59] Nitrogen is a limiting element in aquatic environments 60,61 and it is available to biological systems either through¯xation (N 2 ), and/or assimilation (NH 4 or NO 3 ). In order to couple a measured rate for the pathways identi¯ed in the EFMs analysis, we used the ecophysiological measurements of N 2¯x ation rates estimated by acetylene reduction assays of microbialites from Pozas Azules II in Cuatro Cienegas, Mexico (published by Beltr an et al 59 ) Using the maximum rate of N 2¯x ation (0.1 mol N 2 gC À1 h À1 ) and the availability of dissolved nitrate (1.5 M) and phosphate (1.3 M) in this system as inhomogeneous equalities to determine the elementary°ux vectors 62,63 in the model. Then we obtained and estimated the rates of CO 2¯x ation for each pathway under this constrained condition (see Fig.…”

Section: Efm Analysis Of Metabolic Networkmentioning

confidence: 99%

Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources

Cerqueda-García

Falcón

2016

J. Bioinform. Comput. Biol.

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Microbialites and microbial mats are complex communities with high phylogenetic diversity. These communities are mostly composed of bacteria and archaea, which are the earliest living forms on Earth and relevant to biogeochemical evolution. In this study, we identified the shared metabolic pathways for uptake of inorganic C and N in microbial mats and microbialites based on metagenomic data sets. An in silico analysis for autotrophic pathways was used to trace the paths of C and N to the system, following an elementary flux modes (EFM) approach, resulting in a stoichiometric model. The fragility was analyzed by the minimal cut sets method. We found four relevant pathways for the incorporation of CO2 (Calvin cycle, reverse tricarboxylic acid cycle, reductive acetyl-CoA pathway, and dicarboxylate/4-hydroxybutyrate cycle), some of them present only in archaea, while nitrogen fixation was the most important source of N to the system. The metabolic potential to incorporate nitrate to biomass was also relevant. The fragility of the network was low, suggesting a high redundancy of the autotrophic pathways due to their broad metabolic diversity, and highlighting the relevance of reducing power source. This analysis suggests that microbial mats and microbialites are "metabolic pumps" for the incorporation of inorganic gases and formation of organic matter.

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On the feasibility of growth-coupled product synthesis in microbial strains

Cited by 86 publications

References 39 publications

Metabolic anchor reactions for robust biorefining

Metabolic anchor reactions for robust biorefining

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

Metabolic potential of microbial mats and microbialites: Autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources

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