Modeling and analysis of flux distribution and bioproduct formation in Synechocystis sp. PCC 6803 using a new genome-scale metabolic reconstruction

Joshi, Chintan; Peebles, Christie A. M.; Prasad, Ashok

doi:10.1016/j.algal.2017.09.013

Cited by 22 publications

(12 citation statements)

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“…In order to evaluate the theoretical ATP/NADPH demand of the three alternative pathways, the number of molecules of ATP and/or NADPH consumed or produced in the stepwise enzyme-catalyzed steps starting from the common intermediate G3P towards sucrose, glycogen and PHB, were calculated using the Synechocystis metabolic model iSynCJ816 [16] as a template (see Additional file 1: Table S2). Although the criteria did not take into account the side reaction pathways (i.e.…”

Section: Resultsmentioning

confidence: 99%

Redirecting photosynthetic electron flux in the cyanobacterium Synechocystis sp. PCC 6803 by the deletion of flavodiiron protein Flv3

Thiel¹,

Patrikainen²,

Nagy³

et al. 2019

Microb Cell Fact

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BackgroundOxygen-evolving photoautotrophic organisms, like cyanobacteria, protect their photosynthetic machinery by a number of regulatory mechanisms, including alternative electron transfer pathways. Despite the importance in modulating the electron flux distribution between the photosystems, alternative electron transfer routes may compete with the solar-driven production of CO2-derived target chemicals in biotechnological systems under development. This work focused on engineered cyanobacterial Synechocystis sp. PCC 6803 strains, to explore possibilities to rescue excited electrons that would normally be lost to molecular oxygen by an alternative acceptor flavodiiron protein Flv1/3—an enzyme that is natively associated with transfer of electrons from PSI to O2, as part of an acclimation strategy towards varying environmental conditions.ResultsThe effects of Flv1/3 inactivation by flv3 deletion were studied in respect to three alternative end-products, sucrose, polyhydroxybutyrate and glycogen, while the photosynthetic gas fluxes were monitored by Membrane Inlet Mass Spectrometry (MIMS) to acquire information on cellular carbon uptake, and the production and consumption of O2. The results demonstrated that a significant proportion of the excited electrons derived from photosynthetic water cleavage was lost to molecular oxygen via Flv1/3 in cells grown under high CO2, especially under high light intensities. In flv3 deletion strains these electrons could be re-routed to increase the relative metabolic flux towards the monitored target products, but the carbon distribution and the overall efficiency were determined by the light conditions and the genetic composition of the respective pathways. At the same time, the total photosynthetic capacity of the Δflv3 strains was systematically reduced, and accompanied by upregulation of oxidative glycolytic metabolism in respect to controls with the native Flv1/3 background.ConclusionsThe observed metabolic changes and respective production profiles were proposedly linked with the lack of Flv1/3-mediated electron transfer, and the associated decrease in the intracellular ATP/NADPH ratio, which is bound to affect the metabolic carbon partitioning in the flv3-deficient cells. While the deletion of flv3 could offer a strategy for enhancing the photosynthetic production of desired chemicals in cyanobacteria under specified conditions, the engineered target pathways have to be carefully selected to align with the intracellular redox balance of the cells.

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Section: Resultsmentioning

confidence: 99%

Redirecting photosynthetic electron flux in the cyanobacterium Synechocystis sp. PCC 6803 by the deletion of flavodiiron protein Flv3

Thiel¹,

Patrikainen²,

Nagy³

et al. 2019

Microb Cell Fact

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“…On the other hand, Qian et al incorporated a light-dependent PSI/PSII electron transport rate algorithm in a GSM of Synechococcus PCC 7002, which allowed simulations of photoautotrophic growth at different light intensities (Qian et al, 2017). In a new GSM of Synechocystis PCC 6803, an unconstrained photo-respiratory reaction and a mechanism to account for changes in energy absorption from light at different wavelengths have been developed (Joshi et al, 2017). To facilitate a better understanding of respiratory and photosynthetic interactions, these authors included features to model known molecular mechanisms of the photosynthetic network around the thylakoid membrane.…”

Section: Predicting and Engineering Cyanobacterial Metabolism Via Genmentioning

confidence: 99%

“…A canonical test useful to benchmark and validate the accuracy of GSMs is to examine their capacity to predict essential genes of the metabolic network (Becker and Palsson, 2008) (Figure 4, central panel).Gene essentiality prediction has been successfully used in several bacteria such as E. coli (Suthers et al, 2009; Orth et al, 2011) and Pseudomonas putida (Nogales et al, 2008, 2017). The quality of two recent cyanobacterial GSMs has been assessing using gene essentiality datasets: i JB785 of S. elongatus PCC 7942 (Broddrick et al, 2016) and i SynCJ816 of Synechocystis PCC 6803 (Joshi et al, 2017). In the first case, 78% of genes were correctly assigned as either essential or non-essential based on data of essentiality in vivo obtained from previous dense-transposon mutagenesis experiments (Rubin et al, 2015).…”

Section: Predicting and Engineering Cyanobacterial Metabolism Via Genmentioning

confidence: 99%

“…In the first case, 78% of genes were correctly assigned as either essential or non-essential based on data of essentiality in vivo obtained from previous dense-transposon mutagenesis experiments (Rubin et al, 2015). In the second case, the new GSM of Synechocystis PCC 6803 was able to predict gene deletions with 77% accuracy, based on a qualitative growth comparison of 167 gene-deletion mutants with experimental studies obtained from online databases and a detailed literature search (Joshi et al, 2017).…”

Section: Predicting and Engineering Cyanobacterial Metabolism Via Genmentioning

confidence: 99%

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New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering

Santos-Merino

Singh

Ducat

2019

Front. Bioeng. Biotechnol.

169

118

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Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.

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“…For example, one strain of cyanobacteria, the Synechocystis sp. PCC6803 has eleven different reconstructed metabolic networks developed by various research groups (Erdrich et al., 2014; Joshi et al., 2017; Knoop et al., 2013; Nogales et al., 2012; Saha et al., 2012; Yu et al., 2013). Unfortunately, the published metabolic networks have been presented inconsistently with substantially different levels of annotations (Swainston et al., 2011).…”

Section: Introductionmentioning

confidence: 99%

iMet: A graphical user interface software tool to merge metabolic networks

Mohammadi

Zahiri

Niroomand

2019

Heliyon

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Nowadays, studying microorganisms has become faster and deeper than the last decades, thanks to the modeling of genome-scale metabolic networks. Completed genome sequencing projects of microorganisms and annotating these sequences have provided a worthwhile platform for reconstructing and modeling genome-scale metabolic networks. The genome-scale metabolic network reconstruction is a laborious and time-consuming task which needs an extensive study and search in different types of databases. Furthermore, it also requires an iterative process of creating and curating the obtained network, particularly with experimental methods. Hence, different types of reconstructions and models of a targeted microorganism can be found with different qualities, as the goal and need of researchers differ. Due to these circumstances, scientists have to continue with only one of the reconstructed metabolic networks of each microorganism and ignore the rest in their in silico works. It is clear that having a tool which merges different metabolic networks of a single organism can be a useful and effective way to study them with minimal cost and time. To meet this need, we have developed iMet , the standalone graphical user interface (GUI) software tool to merge multiple reconstructed metabolic networks of microorganisms. As a case study, we merged three reconstructed metabolic networks of a cyanobacterium using iMet, and then all of them (including the new merged one) became modeled. The results of our evaluations including Flux Balance Analysis (FBA), revealed enhancing metabolic network coverage as well as increasing yield of desired products in the new obtained model.

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Modeling and analysis of flux distribution and bioproduct formation in Synechocystis sp. PCC 6803 using a new genome-scale metabolic reconstruction

Cited by 22 publications

References 83 publications

Redirecting photosynthetic electron flux in the cyanobacterium Synechocystis sp. PCC 6803 by the deletion of flavodiiron protein Flv3

Redirecting photosynthetic electron flux in the cyanobacterium Synechocystis sp. PCC 6803 by the deletion of flavodiiron protein Flv3

New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering

iMet: A graphical user interface software tool to merge metabolic networks

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