Evaluation of central metabolism based on a genomic database ofSynechocystis PCC6803

Hong, Seong-Joo; Lee, Choul‐Gyun

doi:10.1007/bf03028644

Cited by 53 publications

(37 citation statements)

References 32 publications

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“…We identify inconsistencies in the current gene annotation and suggest several genes with putative novel or different enzymatic activity for further experimental validation. Our work significantly improves upon earlier reconstructions, which were either restricted to the primary carbon metabolism (Shastri and Morgan, 2005;Hong and Lee, 2007;Navarro et al, 2009) or incomplete with respect to several metabolic routes (Fu, 2008;Kun et al, 2008). During the reconstruction process, we identified various obstacles that currently hamper the large-scale construction of metabolic models.…”

mentioning

confidence: 79%

“…Carbon uptake was limited to a single transport reaction. The reactions of photophosphorylation and the respiratory chain were adapted from Shastri and Morgan (2005) and Hong and Lee (2007). Finally, a catalase (sll1987) and a thioredoxin-disulfide reductase (slr0600) were added.…”

Section: Metabolic Network Reconstructionmentioning

confidence: 99%

“…PCC 6803 are available. To our knowledge, the first reconstruction was provided by Shastri and Morgan (2005) and subsequently extended by Hong and Lee (2007). Both reconstructions are restricted to the primary metabolism, including glycolysis, the TCA cycle, and the Calvin-Benson cycle.…”

Section: Reconciling Existing Modelsmentioning

confidence: 99%

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The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth

et al. 2010

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and Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN Manchester, United Kingdom (R.S.) Unicellular cyanobacteria have attracted growing attention as potential host organisms for the production of valuable organic products and provide an ideal model to understand oxygenic photosynthesis and phototrophic metabolism. To obtain insight into the functional properties of phototrophic growth, we present a detailed reconstruction of the primary metabolic network of the autotrophic prokaryote Synechocystis sp. PCC 6803. The reconstruction is based on multiple data sources and extensive manual curation and significantly extends currently available repositories of cyanobacterial metabolism. A systematic functional analysis, utilizing the framework of flux-balance analysis, allows the prediction of essential metabolic pathways and reactions and allows the identification of inconsistencies in the current annotation. As a counterintuitive result, our computational model indicates that photorespiration is beneficial to achieve optimal growth rates. The reconstruction process highlights several obstacles currently encountered in the context of large-scale reconstructions of metabolic networks.Cyanobacteria are among the evolutionarily oldest organisms and are the only known prokaryotes capable of plant-like oxygenic photosynthesis. As primary producers in aquatic environments, they play an important role in global CO 2 assimilation and oxygen recycling. Recently, cyanobacteria have also attracted growing attention for economic purposes, including drug discovery and as prolific producers of natural products (Sielaff et al., 2006;Tan, 2007). In particular their ability to directly convert atmospheric CO 2 into biomass and organic compounds, driven by sunlight, offers considerable potential as a novel and renewable resource for bioenergy (Deng and Coleman, 1999;Atsumi et al., 2009;Mascarelli, 2009;Lindberg et al., 2010).Among the diverse cyanobacterial strains, Synechocystis sp. PCC 6803 is one of the most extensively studied model organisms for the analysis of photosynthetic processes. With a rich compendium of genomic, biochemical, and physiological data available, Synechocystis sp. PCC 6803, therefore, offers an ideal starting point to obtain insights into the systemic properties of phototrophic metabolism. The prerequisite for such a systemic description is a detailed reconstruction of the metabolic network of the organism: that is, a reconstruction of the comprehensive set of enzyme-catalyzed reactions required to support cellular growth and maintenance. Once a metabolic reconstruction is available, the vast array of methods developed by computational systems biology over the past decades allows us to dissect the functioning and interplay of possible metabolic routes and biochemical interconversions. In this respect, constraint-based modeling, most notably flux-balance analysis (FBA), has become a quasi-standard in the field. FBA is increasingly utilized to elucidate and characterize largescale network...

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confidence: 79%

Section: Metabolic Network Reconstructionmentioning

confidence: 99%

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The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth

et al. 2010

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“…Some species, such as Chlorella pyrenoidosa and Scenedesmus obliquus, maintain high TCA cycle and mitochondrial oxidative phosphorylation enzymatic activities when grown in illuminated environments, indicating that these pathways are only slightly affected by light in these species (Hong and Lee 2007;Marsh et al 1965;Perez-Garcia et al 2011;Van Baalam and Pulish 1973;Yang et al 2000). Studies by Hiyama et al (1969) found that some eukaryotic microalgae have b-, c-and a-type cytochromes, which are important in the mediation of electron transfer from reduced pyridine nucleotides to oxygen (Hiyama et al 1969;Van Baalam and Pulish 1973).…”

Section: Metabolic Pathwaysmentioning

confidence: 99%

Heterotrophic growth of microalgae: metabolic aspects

Morales‐Sánchez

Martinez-Rodriguez

Kyndt

et al. 2014

World J Microbiol Biotechnol

128

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Microalgae are considered photoautotrophic organisms, however several species have been found living in environments where autotrophic metabolism is not viable. Heterotrophic cultivation, i.e. cell growth and propagation with the use of an external carbon source under dark conditions, can be used to study the metabolic aspects of microalgae that are not strictly related to photoautotrophic growth and to obtain high value products. This manuscript reviews studies related to the metabolic aspects of heterotrophic grow of microalga. From the physiological and metabolic perspective, the screening of microalgal strains in different environments and the development of molecular and metabolic engineering tools, will lead to an increase in the number of known microalgae species that growth under strict heterotrophic conditions and the variety of carbon sources used by these microorganisms.

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“…In general, in cultivations with suitable concentration and type of sugars, the symport system is induced to promote the alkalinization of the culture media by a net movement of protons accompanied by sugar uptake (Figure 1). The rate of the increase in pH fundamentally depends on the concentration and type of sugar used (Hong and Lee, 2007). Additionally, the disaccharides such as sucrose are only used in the pentose phosphate pathway, after a previous hydrolysis that transforms this sugar in monosaccharides, particularly fructose and glucose.…”

Section: Resultsmentioning

confidence: 99%

THIRD GENERATION BIODIESEL PRODUCTION FROM MICROALGAE Phormidium autumnale

Siqueira

Francisco

Queiroz

et al. 2016

Braz. J. Chem. Eng.

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-The aim of this work was to evaluate third generation biodiesel production by the microalgae Phormidium autumnale using sucrose as exogenous carbon source. The study focused on optimization of the different C/N ratios and on the analysis of biofuel quality. The results indicate that a C/N ratio of 40 improved the performance of the system, reaching single-cell oil productivities of 18.9 mg/L in steady-state conditions. This oil has a composition predominantly saturated (45.2%) and monounsaturated (34.7%) suitable for biodiesel synthesis (ester content of 99.8%, cetane number of 58.5%, iodine value of 67.2 gI2/100 g, unsaturation degree of 71.3% and a cold filter plugging point of 6.7 ºC).

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Evaluation of central metabolism based on a genomic database ofSynechocystis PCC6803

Cited by 53 publications

References 32 publications

The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth

The Metabolic Network of Synechocystis sp. PCC 6803: Systemic Properties of Autotrophic Growth

Heterotrophic growth of microalgae: metabolic aspects

THIRD GENERATION BIODIESEL PRODUCTION FROM MICROALGAE Phormidium autumnale

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