Requirement of upstream activation sequences for nitrogen catabolite repression of the allantoin system genes in Saccharomyces cerevisiae.

Synthesis of the transport systems and enzymes mediating uptake and catabolism of nitrogenous compounds is sensitive to nitrogen catabolite repression. In spite of the widespread occurrence of the control process, little is known about its mechanism. We have previously demonstrated that growth of cells on repressive nitrogen sources results in a dramatic decrease in the steady-state levels of mRNA encoded by the allantoin and arginine catabolic pathway genes and of the transport systems associated with allantoin metabolism. The present study identified the upstream activation sequences in the 5'-flanking regions of the allantoin system genes as the cis-acting sites through which nitrogen catabolite repression is exerted.     

The URE2 protein regulates nitrogen catabolic gene expression through the GATAA-containing UASNTR element in Saccharomyces cerevisiae.

Many of the gene products that participate in nitrogen metabolism are sensitive to nitrogen catabolite repression (NCR), i.e., their expression is decreased to low levels when readily used nitrogen sources such as asparagine are provided. Previous work has shown this NCR sensitivity requires the cis-acting UASNTR element and trans-acting GLN3. Here, we extend the analysis to include the response of their expression to deletion of the URE2 locus. The expression of these nitrogen catabolic genes becomes, to various degrees, NCR insensitive in the ure2 deletion. This response is shown to be mediated through the GATAA-containing UASNTR element and supports the current idea that the NCR regulatory circuit involves the following steps: environmental signal-->URE2-->GLN3-->UASNTR operation-->NCR-sensitive gene expression. The various responses of the nitrogen catabolic genes' expression to deletion of the URE2 locus also indicate that not all NCR is mediated through URE2.     

Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression

Synthesis of glutamate, the cell's major donor of nitrogen groups and principal anion, occupies a significant fraction of bacterial metabolism. In Bacillus subtilis, the gltAB operon, encoding glutamate synthase, requires a specific positive regulator, GltC, for its expression. In addition, the gltAB operon was shown to be repressed by TnrA, a regulator of several other genes of nitrogen metabolism and active under conditions of ammonium (nitrogen) limitation. TnrA was found to bind directly to a site immediately downstream of the gltAB promoter. As is true for other genes, the activity of TnrA at the gltAB promoter was antagonized by glutamine synthetase under certain growth conditions.     

Concerted changes in gene expression and cell physiology of the cyanobacterium Synechocystis sp. strain PCC 6803 during transitions between nitrogen and light-limited growth

Physiological adaptation and genome-wide expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to gradual transitions between nitrogen-limited and light-limited growth conditions were measured in continuous cultures. Transitions induced changes in pigment composition, light absorption coefficient, photosynthetic electron transport, and specific growth rate. Physiological changes were accompanied by reproducible changes in the expression of several hundred open reading frames, genes with functions in photosynthesis and respiration, carbon and nitrogen assimilation, protein synthesis, phosphorus metabolism, and overall regulation of cell function and proliferation. Cluster analysis of the nearly 1,600 regulated open reading frames identified eight clusters, each showing a different temporal response during the transitions. Two large clusters mirrored each other. One cluster included genes involved in photosynthesis, which were up-regulated during light-limited growth but down-regulated during nitrogen-limited growth. Conversely, genes in the other cluster were down-regulated during light-limited growth but up-regulated during nitrogen-limited growth; this cluster included several genes involved in nitrogen uptake and assimilation. These results demonstrate complementary regulation of gene expression for two major metabolic activities of cyanobacteria. Comparison with batch-culture experiments revealed interesting differences in gene expression between batch and continuous culture and illustrates that continuous-culture experiments can pick up subtle changes in cell physiology and gene expression.     

Regulation of pho regulon gene expression by the carbon control protein A, CcpA, in Bacillus subtilis

Bacterial regulons involved in carbon, nitrogen and phosphorus metabolism must interact for purposes of coordination, but the mechanisms involved are not understood. We here report that the carbon control pro-tein-A (CcpA) of Bacillus subtilis, primarily concerned with carbon metabolism, influences expression of various phosphorus (pho) regulon genes including the two alkaline phosphatase structural genes, phoA and phoB. The directions and magnitudes of the effects of glucose and the loss of CcpA on these two genes depend on growth conditions, but they always correlate inversely. Absolute expression levels of phoA and phoB depend on a rich nitrogen source, and gene activation by a fermentable substrate such as glucose depends on the presence of a respiratory substrate such as succinate. We show that these CcpA-dependent glucose effects can be explained by the effects of glucose and CcpA acting on the phoPR operon. Although a good CcpA-binding site (CRE) is found in the control region of the phoPR operon, direct regulation of phoPR gene expression by CcpA via this CRE could not account for the effects of glucose and CcpA on phoA and phoB gene expression. We conclude that CcpA exerts indirect control over the pho regulon by a mechanism that involves CcpA and PhoRP but does not involve the phoPR operon CRE.     

RNA-editing in trypanosome mitochondria

Sphingosine, the backbone moiety of sphingomyelin, gangliosides and other complex sphingolipids, is a potent inhibitor of protein kinase C in vitro and of cellular events dependent on this enzyme. The systems that have been found, thus far, to be affected by sphingosine encompass various components of host defense system, including the activation of platelets, neutrophils and natural killer cells; the cytolytic activity of pathogens and expression of viral genes; cell growth and differentiation in several cell types, including leukemic and neuronal cells; insulin stimulated hexose transport and metabolism in adipocytes; ion-transport systems in various models; the response of neuronal cells to excitatory compounds; and receptor desensitization. While sphingosine has appeared to be a relatively potent and specific inhibitor of protein kinase C in the systems studied, recent findings with the epidermal growth factor receptor indicate that it may serve as a pleotrophic modulator of cell functions. New strategies for the design of pharmacologically active agents should arise from further studies of the action of long-chain (sphingoid) bases. Furthermore, since free sphingosine is a natural constituent of cells and the levels can be modulated by phorbol esters and other factors, a cycle of complex sphingolipid hydrolysis and resynthesis to regulate the amount of free sphingosine may constitute one mechanism of action of these compounds.     

Transcriptional profiling of wine yeast in fermenting grape juice: regulatory effect of diammonium phosphate

The nitrogen composition of grape musts affects fermentation kinetics and production of aroma and spoilage compounds in wine. It is common practice in wineries to supplement grape musts with diammonium phosphate (DAP) to prevent nitrogen-related fermentation problems. Laboratory strains of Saccharomyces cerevisiae preferentially use rich nitrogen sources, such as ammonia, over poor nitrogen sources. We used global gene expression analysis to monitor the effect of DAP addition on gene expression patterns in wine yeast in fermenting Riesling grape must. The expression of 350 genes in the commercial wine yeast strain VIN13 was affected; 185 genes were down-regulated and 165 genes were up-regulated in response to DAP. Genes that were down-regulated encode small molecule transporters and nitrogen catabolic enzymes, including those linked to the production of urea, a precursor of ethyl carbamate in wine. Genes involved in amino acid metabolism, assimilation of sulfate, de novo purine biosynthesis, tetrahydrofolate one-carbon metabolism, and protein synthesis were up-regulated. The expression level of 86 orphan genes was also affected by DAP.     

Seaweed Oligosaccharides Stimulate Plant Growth by Enhancing Carbon and Nitrogen Assimilation, Basal Metabolism, and Cell Division

It is now well established that plant cell wall oligosaccharides can stimulate or inhibit growth and development in plants. In addition, it has been determined that seaweed (marine algae) cell wall polysaccharides and derived oligosaccharides can enhance growth in plants. In particular, oligo-alginates obtained by depolymerization of alginates from brown seaweeds increase growth of different plants by enhancing nitrogen assimilation and basal metabolism. Interestingly, oligo-alginates also stimulate growth of marine and fresh water green microalgae, increasing the content of fatty acids. On the other hand, oligo-carrageenans obtained by depolymerization of carrageenans from red seaweeds increase growth of tobacco plants by enhancing photosynthesis, nitrogen assimilation, basal metabolism, and cell division. In addition, oligo-carrageenans increase protection against viral, fungal, and bacterial infections in tobacco plants, which is determined, at least in part, by the accumulation of several phenylpropanoid compounds (PPCs) with antimicrobial activity. Moreover, oligo-carrageenans stimulate growth of 3-year-old Eucalyptus globulus trees by increasing photosynthesis, nitrogen assimilation, and basal metabolism. Furthermore, oligo-carrageenans induce an increase in cellulose content and in the level of essential oil and some PPCs with antimicrobial activities, suggesting that defense against pathogens may be also enhanced. Thus, seaweed oligosaccharides induce a dual beneficial effect in plants and trees, enhancing growth, which is determined by the increase in carbon and nitrogen assimilation, basal metabolism, and cell division, and defense against pathogens, which is determined by the accumulation of compounds with antimicrobial activities. In this sense, molecular mechanisms that potentially interconnect activation of plant growth and defense responses are discussed.