Oxidative Carbon Metabolism Research Articles

Transcriptome Profile of Yeast Strain Used for Biological Wine Aging Revealed Dynamic Changes of Gene Expression in Course of Flor Development.

Flor strains of Saccharomyces cerevisiae are principal microbial agents responsible for biological wine aging used for production of sherry-like wines. The flor yeast velum formed on the surface of fortified fermented must is a major adaptive and technological characteristic of flor yeasts that helps them to withstanding stressful winemaking conditions and ensures specific biochemical and sensory oxidative alterations typical for sherry wines. We have applied RNAseq technology for transcriptome analysis of an industrial flor yeast strain at different steps of velum development over 71 days under experimental winemaking conditions. Velum growth and maturation was accompanied by accumulation of aldehydes and acetales. We have identified 1490 differentially expressed genes including 816 genes upregulated and 674 downregulated more than 2-fold at mature biofilm stage as compared to the early biofilm. Distinct expression patterns of genes involved in carbon and nitrogen metabolism, respiration, cell cycle, DNA repair, cell adhesion, response to various stresses were observed. Many genes involved in response to different stresses, oxidative carbon metabolism, high affinity transport of sugars, glycerol utilization, sulfur metabolism, protein quality control and recycling, cell wall biogenesis, apoptosis were induced at the mature biofilm stage. Strong upregulation was observed for FLO11 flocculin while expression of other flocculins remained unaltered or moderately downregulated. Downregulated genes included those for proteins involved in glycolysis, transportation of ions, metals, aminoacids, sugars, indicating repression of some major transport and metabolic process at the mature biofilm stage. Presented results are important for in-depth understanding of cell response elicited by velum formation and sherry wine manufacturing conditions, and for the comprehension of relevant regulatory mechanisms. Such knowledge may help to better understand the molecular mechanisms that flor yeasts use to adapt to winemaking environments, establish the functions of previously uncharacterized genes, improve the technology of sherry- wine production, and find target genes for strain improvement.

Activation of oxidative carbon metabolism by nutritional enrichment by photosynthesis and exogenous organic compounds in the red alga Cyanidioschyzon merolae: evidence for heterotrophic growth

Respiration is an important process in photosynthetic organisms, as it is in other organisms, for the supply of ATP and metabolites required for biosynthesis. Furthermore, individual enzymatic activity is subject to regulation by metabolic intermediates in glycolysis and the citric acid cycle. However, little is known about how glycolysis or catabolism are related to photosynthetic activity or accumulation of photosynthetic products. We previously developed a flat-plate culture apparatus assembled from materials commonly used for gel electrophoresis, which enables high-density culture of the unicellular red alga Cyanidioschyzon merolae. In this study, a stationary dense culture of C. merolae, when re-activated in this culture apparatus, exhibited an accumulation of photosynthetically produced starch. We demonstrated that respiratory activity increased during the culture period, while photosynthetic activity remained constant. Gene expression analysis revealed that the genes involved in cytosolic glycolysis and the citric acid cycle were selectively activated, compared to the genes for the oxidative pentose phosphate pathway and the Calvin–Benson cycle. Measurements of the respiratory rate after addition of various organic substances showed that C. merolae can utilize almost any exogenous organic compound as a respiratory substrate, although the effectiveness of each compound was dependent on the culture time in the flat-plate culture, suggesting that glycolysis was rate-limiting to respiration, and its activity depended on the level of photosynthetic products within the cells. We also demonstrated that organic substances increased the rate of cell growth under dim light and, interestingly, C. merolae could grow heterotrophically in the presence of glycerol. Obligate photoautotrophy should be considered an ecological, rather than physiological, characteristic of C. merolae.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-015-1365-0) contains supplementary material, which is available to authorized users.

Arsenic toxicity: the effects on plant metabolism.

The two forms of inorganic arsenic, arsenate (AsV) and arsenite (AsIII), are easily taken up by the cells of the plant root. Once in the cell, AsV can be readily converted to AsIII, the more toxic of the two forms. AsV and AsIII both disrupt plant metabolism, but through distinct mechanisms. AsV is a chemical analog of phosphate that can disrupt at least some phosphate-dependent aspects of metabolism. AsV can be translocated across cellular membranes by phosphate transport proteins, leading to imbalances in phosphate supply. It can compete with phosphate during phosphorylation reactions, leading to the formation of AsV adducts that are often unstable and short-lived. As an example, the formation and rapid autohydrolysis of AsV-ADP sets in place a futile cycle that uncouples photophosphorylation and oxidative phosphorylation, decreasing the ability of cells to produce ATP and carry out normal metabolism. AsIII is a dithiol reactive compound that binds to and potentially inactivates enzymes containing closely spaced cysteine residues or dithiol co-factors. Arsenic exposure generally induces the production of reactive oxygen species that can lead to the production of antioxidant metabolites and numerous enzymes involved in antioxidant defense. Oxidative carbon metabolism, amino acid and protein relationships, and nitrogen and sulfur assimilation pathways are also impacted by As exposure. Readjustment of several metabolic pathways, such as glutathione production, has been shown to lead to increased arsenic tolerance in plants. Species- and cultivar-dependent variation in arsenic sensitivity and the remodeling of metabolite pools that occurs in response to As exposure gives hope that additional metabolic pathways associated with As tolerance will be identified.

Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions.

DNA microarray analysis was used to profile gene expression in a commercial isolate of Saccharomyces cerevisiae grown in a synthetic grape juice medium under conditions mimicking a natural environment for yeast: High-sugar and variable nitrogen conditions. The high nitrogen condition displayed elevated levels of expression of genes involved in biosynthesis of macromolecular precursors across the time course as compared to low-nitrogen. In contrast, expression of genes involved in translation and oxidative carbon metabolism were increased in the low-nitrogen condition, suggesting that respiration is more nitrogen-conserving than fermentation. Several genes under glucose repression control were induced in low-nitrogen in spite of very high (17%) external glucose concentrations, but there was no general relief of glucose repression. Expression of many stress response genes was elevated in stationary phase. Some of these genes were expressed regardless of the nitrogen concentration while others were found at higher levels only under high nitrogen conditions. A few genes, FSP2, RGS2, AQY1, YFL030W, were expressed more strongly with nitrogen limitation as compared to other conditions.

The yeast UME6 gene product is required for transcriptional repression mediated by the CAR1 URS1 repressor binding site.

URS1 is known to be a repressor binding site in Saccharomyces cerevisiae that negatively regulates expression of many genes including CAR1 (arginase), several required for sporulation, mating type switching, inositol metabolism, and oxidative carbon metabolism. In addition to the proteins previously shown to directly bind to the URS1 site, we show here that the UME6 gene product is required for URS1 to mediate repression of gene expression in the absence of inducer. We also show that mutations in the CAR80 (CARGRI) gene are allelic to those in UME6.

The Mechanism of Hydrogen Evolution by Chlamydomonas moewusii

Using manometric techniques, H(2) evolution in both darkness and light has been studied in the green alga, Chlamydomonas moewusii.Hydrogen evolution in the dark is accompanied by the release of only CO(2) in manometrically detectable amounts. It is depressed by dark starvation and inhibited both by monofluoroacetic acid and by uncouplers of phosphorylation. This evidence suggests that the reaction is dependent on oxidative carbon metabolism for reductant and phosphorylation for energy to raise the reductant to a redox potential capable of reducing H(+).Photoevolution of H(2) is also accompanied by the release of only CO(2). It is depressed by dark starvation and stimulated by acetate or a period of photosynthesis. Monofluoroacetic acid causes complete inhibition, while 3-(3,4-dichlorophenyl)-1,1-dimethylurea causes no or only slight inhibition. These results indicate that oxidative carbon metabolism is the source of reductant for the reaction. Photoevolution of H(2) does not show Emerson enhancement, and it has an action spectrum peaking at a longer wave length than that of photosynthesis. These characteristics, together with the slight effect of 3-(3,4-dichlorophenyl)-1,1-dimethylurea on the reaction, show that only system I of photosynthetic electron transport is involved in the reaction. Photoevolution of H(2) is stimulated by uncouplers; this indicates that the role of light is not to provide energy by phosphorylation. Rather, the results support an electron flow driven directly by light through system I from reductant produced in oxidative carbon metabolism to a redox potential capable of reducing H(+).

Hydrogen evolution by several algae

Out of 33 strains of unicellular algae examined, H2 evolution was observed only in species of Chlamydomonas, Chlorella and Scenedesmus. While the photoevolution of H2 by these algae was generally stimulated both by an organic substrate and by the uncoupler CCCP(1), response to DCMU varied. On the basis of the response to DCMU, it was concluded that the mechanism of photoevolution of H2 differed from one alga to another. The reaction in some algae appeared to be dependent on either the photooxidation of water or oxidative carbon metabolism for reductant; that in other algae was supported by reductant from both these sources.