Expression Analysis of Genes Associated with the Induction of the Carbon-Concentrating Mechanism in <i>Chlamydomonas reinhardtii</i>

Yamano, Takashi; Miura, Kenji; Fukuzawa, Hideya

doi:10.1104/pp.107.114652

Cited by 108 publications

(128 citation statements)

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“…When the CCM is expressed and when corresponding enzymes are produced in sufficient amounts, glycolate can be metabolized within the cell and excretion stops. Over a similar time, genes of the Calvin cycle are down-regulated (Yamano et al, 2008).…”

Section: Focus On Differences 3 H After Ccm Inductionmentioning

confidence: 84%

“…4; Supplemental Table S1), we present an attempt to interpret our results in relation to an increased flux through the photorespiratory pathway and closely related primary metabolic pathways. By combining transcriptomic data (Yamano et al, 2008) and physiological/biochemical data (Marek and Spalding, 1991;Bozzo and Colman, 2000) on CCM-inducing cells from the literature and metabolomic data in this work, we propose a model that fits both data sets and therefore may have some relevance (Fig. 5).…”

Section: Focus On Differences 3 H After Ccm Inductionmentioning

confidence: 99%

“…Many genes coding for enzymes of the photorespiratory pathway are up-regulated (Marek and Spalding, 1991;Miura et al, 2002Miura et al, , 2004 within 20 min and show a transient expression pattern (Tural and Moroney, 2005;Yamano et al, 2008). A decline in starch content is also detectable within 30 min after transfer to low CO 2 (Kuchitsu et al, 1988).…”

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confidence: 99%

“…The CCM in C. reinhardtii is typically induced when the concentration of CO 2 in the air bubbled through the cultures is decreased to around 0.5% or lower (Vance and Spalding, 2005). Within the first few hours after starting the induction, numerous genes are either up-or down-regulated (Miura et al, 2004;Yamano et al, 2008;Yamano and Fukuzawa, 2009). However, the change in gene expression is only manifested as rather limited detectable changes in the abundance of proteins (Manuel and Moroney, 1988;Spalding and Jeffrey, 1989).…”

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confidence: 99%

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A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

et al. 2010

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(J.A.R.) Using a gas chromatography-mass spectrometry-time of flight technique, we determined major metabolite changes during induction of the carbon-concentrating mechanism in the unicellular green alga Chlamydomonas reinhardtii. In total, 128 metabolites with significant differences between high-and low-CO 2 -grown cells were detected, of which 82 were wholly or partially identified, including amino acids, lipids, and carbohydrates. In a 24-h time course experiment, we show that the amino acids serine and phenylalanine increase transiently while aspartate and glutamate decrease after transfer to low CO 2 . The biggest differences were typically observed 3 h after transfer to low-CO 2 conditions. Therefore, we made a careful metabolomic examination at the 3-h time point, comparing low-CO 2 treatment to high-CO 2 control. Five metabolites involved in photorespiration, 11 amino acids, and one lipid were increased, while six amino acids and, interestingly, 21 lipids were significantly lower. Our conclusion is that the metabolic pattern during early induction of the carbon-concentrating mechanism fit a model where photorespiration is increasing.

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Section: Focus On Differences 3 H After Ccm Inductionmentioning

confidence: 84%

Section: Focus On Differences 3 H After Ccm Inductionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

et al. 2010

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“…html). At this time, a number of microarrays have been used to interrogate changes in response to environmental factors (Ledford et al, 2004(Ledford et al, , 2007Jamers et al, 2006;Mus et al, 2007;Nguyen et al, 2008;Simon et al, 2008;Yamano et al, 2008;Mustroph et al, 2010). These microarrays could not cover all genes in the genome, but more recently, massively parallel cDNA sequencing approaches were applied to C. reinhardtii, overcoming the shortcomings of microarrays (González-Ballester et al, 2010).…”

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confidence: 99%

Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism

et al. 2010

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Like many microalgae, Chlamydomonas reinhardtii forms lipid droplets rich in triacylglycerols when nutrient deprived. To begin studying the mechanisms underlying this process, nitrogen (N) deprivation was used to induce triacylglycerol accumulation and changes in developmental programs such as gametogenesis. Comparative global analysis of transcripts under induced and noninduced conditions was applied as a first approach to studying molecular changes that promote or accompany triacylglycerol accumulation in cells encountering a new nutrient environment. Towards this goal, high-throughput sequencing technology was employed to generate large numbers of expressed sequence tags of eight biologically independent libraries, four for each condition, N replete and N deprived, allowing a statistically sound comparison of expression levels under the two tested conditions. As expected, N deprivation activated a subset of control genes involved in gametogenesis while down-regulating protein biosynthesis. Genes for components of photosynthesis were also down-regulated, with the exception of the PSBS gene. N deprivation led to a marked redirection of metabolism: the primary carbon source, acetate, was no longer converted to cell building blocks by the glyoxylate cycle and gluconeogenesis but funneled directly into fatty acid biosynthesis. Additional fatty acids may be produced by membrane remodeling, a process that is suggested by the changes observed in transcript abundance of putative lipase genes. Inferences on metabolism based on transcriptional analysis are indirect, but biochemical experiments supported some of these deductions. The data provided here represent a rich source for the exploration of the mechanism of oil accumulation in microalgae.

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In Situ, High‐Resolution Quantification of CO₂ Uptake Rates via Automated Off‐Gas Analysis Illuminates Carbon Uptake Dynamics in Cyanobacterial Cultures

Jones,

Innes,

Holland

et al. 2024

Biotech & Bioengineering

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Quantification of cyanobacterial CO2 fixation rates is vital to determining their potential as industrial strains in a circular bioeconomy. Currently, however, CO2 fixation rates are most often determined through indirect and/or low‐resolution methods, resulting in an incomplete picture of both dynamic behaviors and total carbon fixation potential. To address this, we developed the “Automated Carbon and CO2 Experimental Sampling System” (ACCESS); a low‐cost system for in situ off‐gas analysis that supports the automated acquisition of high‐resolution volumetric CO2 uptake rates from multiple cyanobacterial cultures in parallel. Carbon fixation data obtained via ACCESS were first independently validated by elemental analysis of cultivated biomass. Using ACCESS, we then demonstrate how the volumetric CO2 uptake rate of two model cyanobacteria, Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803, accelerates linearly to a maximum before then decaying monotonically to cessation by stationary phase. Furthermore, consistent with the expected stoichiometry, strong correlations were also found to exist between cell growth and carbon fixation, both in terms of rates as well as total levels. The novel insights made possible via ACCESS will aid other cyanobacterial researchers in diverse fundamental and applied research efforts.

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Expression Analysis of Genes Associated with the Induction of the Carbon-Concentrating Mechanism in Chlamydomonas reinhardtii

Cited by 108 publications

References 78 publications

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism

In Situ, High‐Resolution Quantification of CO₂ Uptake Rates via Automated Off‐Gas Analysis Illuminates Carbon Uptake Dynamics in Cyanobacterial Cultures

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Expression Analysis of Genes Associated with the Induction of the Carbon-Concentrating Mechanism in Chlamydomonas reinhardtii

Cited by 108 publications

References 78 publications

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism

In Situ, High‐Resolution Quantification of CO2 Uptake Rates via Automated Off‐Gas Analysis Illuminates Carbon Uptake Dynamics in Cyanobacterial Cultures

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In Situ, High‐Resolution Quantification of CO₂ Uptake Rates via Automated Off‐Gas Analysis Illuminates Carbon Uptake Dynamics in Cyanobacterial Cultures