Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis

Young, Jamey D.; Shastri, Avantika A.; Stephanopoulos, Gregory; Morgan, John A.

doi:10.1016/j.ymben.2011.08.002

Cited by 315 publications

(385 citation statements)

References 46 publications

(57 reference statements)

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“…In the case of the mutant, the activation of PEP carboxylase under photomixotrophic conditions is unlikely due to (1) the low transcript level, (2) low CO 2 fixation activity, and (3) marked accumulation of malate and fumarate, which could inhibit PEP carboxylase activity (Owttrim and Colman, 1986). Metabolic flux analysis performed by Young et al (2011) suggested that PEP carboxylase and malic enzyme cooperate in Synechocystis sp. PCC 6803 (i.e.…”

Section: Effects Of Addition Of Metabolites On the Dcyabrb2 Mutant Unmentioning

confidence: 99%

Deletion of the Transcriptional Regulator cyAbrB2 Deregulates Primary Carbon Metabolism in Synechocystis sp. PCC 6803

Kaniya¹,

Kizawa²,

Miyagi

et al. 2013

Plant Physiology

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cyAbrB is a transcriptional regulator unique to and highly conserved among cyanobacterial species. A gene-disrupted mutant of cyabrB2 (sll0822) in Synechocystis sp. PCC 6803 exhibited severe growth inhibition and abnormal accumulation of glycogen granules within cells under photomixotrophic conditions. Within 6 h after the shift to photomixotrophic conditions, sodium bicarbonate-dependent oxygen evolution activity markedly declined in the DcyabrB2 mutant, but the decrease in methyl viologen-dependent electron transport activity was much smaller, indicating inhibition in carbon dioxide fixation. Decreases in the transcript levels of several genes related to sugar catabolism, carbon dioxide fixation, and nitrogen metabolism were also observed within 6 h. Metabolome analysis by capillary electrophoresis mass spectrometry revealed that several metabolites accumulated differently in the wild-type and mutant strains. For example, the amounts of pyruvate and 2-oxoglutarate (2OG) were significantly lower in the mutant than in the wild type, irrespective of trophic conditions. The growth rate of the DcyabrB2 mutant was restored to a level comparable to that under photoautotrophic conditions by addition of 2OG to the growth medium under photomixotrophic conditions. Activities of various metabolic processes, including carbon dioxide fixation, respiration, and nitrogen assimilation, seemed to be enhanced by 2OG addition. These observations suggest that cyAbrB2 is essential for the active transcription of genes related to carbon and nitrogen metabolism upon a shift to photomixotrophic conditions. Deletion of cyAbrB2 is likely to deregulate the partition of carbon between storage forms and soluble forms used for biosynthetic purposes. This disorder may cause inactivation of cellular metabolism, excess accumulation of reducing equivalents, and subsequent loss of viability under photomixotrophic conditions.

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Section: Effects Of Addition Of Metabolites On the Dcyabrb2 Mutant Unmentioning

confidence: 99%

Deletion of the Transcriptional Regulator cyAbrB2 Deregulates Primary Carbon Metabolism in Synechocystis sp. PCC 6803

Kaniya¹,

Kizawa²,

Miyagi

et al. 2013

Plant Physiology

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“…Chlorophyll (Chl) fluorescence, which is sensitive to environmental changes and stress conditions that induce alterations in photosynthetic components (Iwai et al, 2008), can monitor the efficiency of linear electron flow (Baker et al, 2007) and has indicated that in N. oceanica (Simionato et al, 2013) and other algae, including C. reinhardtii (Berges et al, 1996;Li et al, 2010;Blaby et al, 2013), photosynthetic efficiency falls after N deprivation. Photosynthetically driven metabolic fluxes can also be probed by supplying 13 C-labeled bicarbonate/CO 2 and quantifying 13 C incorporation into metabolite pools (Shastri and Morgan, 2007;Feng et al, 2010;Young et al, 2011).…”

mentioning

confidence: 99%

The Regulation of Photosynthetic Structure and Function during Nitrogen Deprivation in Chlamydomonas reinhardtii

Juergens

Deshpande²,

Lucker

et al. 2014

Plant Physiology

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The accumulation of carbon storage compounds by many unicellular algae after nutrient deprivation occurs despite declines in their photosynthetic apparatus. To understand the regulation and roles of photosynthesis during this potentially bioenergetically valuable process, we analyzed photosynthetic structure and function after nitrogen deprivation in the model alga Chlamydomonas reinhardtii. Transcriptomic, proteomic, metabolite, and lipid profiling and microscopic time course data were combined with multiple measures of photosynthetic function. Levels of transcripts and proteins of photosystems I and II and most antenna genes fell with differing trajectories; thylakoid membrane lipid levels decreased, while their proportions remained similar and thylakoid membrane organization appeared to be preserved. Cellular chlorophyll (Chl) content decreased more than 2-fold within 24 h, and we conclude from transcript protein and 13 C labeling rates that Chl synthesis was down-regulated both pre-and posttranslationally and that Chl levels fell because of a rapid cessation in synthesis and dilution by cellular growth rather than because of degradation. Photosynthetically driven oxygen production and the efficiency of photosystem II as well as P700 + reduction and electrochromic shift kinetics all decreased over the time course, without evidence of substantial energy overflow. The results also indicate that linear electron flow fell approximately 15% more than cyclic flow over the first 24 h. Comparing Calvin-Benson cycle transcript and enzyme levels with changes in photosynthetic 13 CO 2 incorporation rates also pointed to a coordinated multilevel down-regulation of photosynthetic fluxes during starch synthesis before the induction of high triacylglycerol accumulation rates.

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“…As a first step, modeling will be required at the level of the metabolites themselves and is most probably best supported by the analysis of kinetic labeling data (Arita, 2003;Huege et al, 2007;Young et al, 2011). Collected experimental data may be (1) at metabolic steady state and isotopic steady state, (2) at metabolic steady state but not at isotopic steady state, or (3) at neither metabolic nor isotopic steady state.…”

mentioning

confidence: 99%

“…Dynamic metabolite changes have also been modeled in groundbreaking work on the primary metabolism in E. coli (Yuan et al, 2009). Mathematical methods are also now available to extract information from non-steady-state labeling kinetics and have been applied in studies of plant secondary metabolism (Heinzle et al, 2007) and photosynthesis (Young et al, 2011). The use of stable isotopes to analyze flux is likely to go hand in hand with the further development of mathematical models to extract information from non-steady-state labeling kinetics.…”

mentioning

confidence: 99%

On the Discordance of Metabolomics with Proteomics and Transcriptomics: Coping with Increasing Complexity in Logic, Chemistry, and Network Interactions Scientific Correspondence

2012

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We suspect that many biologists who have been following the development of functional 'omics and systems biology are wondering why, compared with the success in integrating information from large-scale studies of transcripts and, more recently, proteins, there is less success in integrating information about metabolism.Information about thousands of transcripts has been integrated into large databases that are used by thousands of scientists (Zimmermann et al., 2004). Rapid advances will soon allow a similar approach in quantitative proteomics. Strategies also exist to integrate information about the expression of genes, as transcripts, with information about changes in the levels of the encoded proteins. Even when changes in transcript levels do not lead to changes in the levels of the encoded proteins, this apparent discrepancy can often be explained by quantitative analysis of the data sets and information about translational regulation and protein turnover (Piques et al., 2009; Schwanhäusser et al., 2011). Such advances are providing systemslevel information about transcriptional and signaling networks that regulate the transcript and protein abundance. However, another important goal of systems biology is a comprehensive understanding of the functional importance of these changes in transcript and protein abundance. Although there is sometimes an encouragingly simple relationship between changes of transcripts and proteins and changes in downstream biological functions, quite often there is a major discordance. In this scientific correspondence, we will discuss reasons for this apparent disconnect, which lie partly in technical issues and partly in the complexity and structure of metabolic networks, and then propose some priorities in metabolic research to combat these problems.As we climb up what has been described as the "pyramid of life" (Barabási and Oltvai, 2004) from gene through RNA and protein to phenotype (which includes chemical composition), we are confronted with an increasing complexity both at the chemical level and in the logic that is needed to draw inferences from one level to the next. Nucleic acids consist of four bases, joined by the same phosphoester bond and with pairwise interacting side chains. This simple structure allows a near-to-binary storage and transmission of information. Proteins are chemically much more complex, due to the functionalities of 20 different amino acid side chains. This large expansion in chemical complexity lies at the center of the flexibility and complexity of biological systems, as it allows different proteins to perform an enormous range of different functions. Nevertheless, proteins still have a simple primary structure, with amino acids linked via a peptide bond in a fixed sequence that, via the universal genetic code, can be unambiguously linked to the sequence of nucleic acids (Aebersold and Mann, 2003;Fernie et al., 2004; Baerenfaller et al., 2008). This logic breaks down when we consider entities that are generated by the activities of individual pr...

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Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis

Cited by 315 publications

References 46 publications

Deletion of the Transcriptional Regulator cyAbrB2 Deregulates Primary Carbon Metabolism in Synechocystis sp. PCC 6803

Deletion of the Transcriptional Regulator cyAbrB2 Deregulates Primary Carbon Metabolism in Synechocystis sp. PCC 6803

The Regulation of Photosynthetic Structure and Function during Nitrogen Deprivation in Chlamydomonas reinhardtii

On the Discordance of Metabolomics with Proteomics and Transcriptomics: Coping with Increasing Complexity in Logic, Chemistry, and Network Interactions Scientific Correspondence

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