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Journal articles on the topic 'Nitrogen catabolite repression'

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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1

Cooper, T. G., R. Rai, and H. S. Yoo. "Requirement of upstream activation sequences for nitrogen catabolite repression of the allantoin system genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 12 (December 1989): 5440–44. http://dx.doi.org/10.1128/mcb.9.12.5440.

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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.

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2

Cooper, T. G., R. Rai, and H. S. Yoo. "Requirement of upstream activation sequences for nitrogen catabolite repression of the allantoin system genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 12 (December 1989): 5440–44. http://dx.doi.org/10.1128/mcb.9.12.5440-5444.1989.

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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.

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3

Scazzocchio, Claudio, Victoria Gavrias, Beatriz Cubero, Cristina Panozzo, Martine Mathieu, and Béatrice Felenbok. "Carbon catabolite repression in Aspergillus nidulans: a review." Canadian Journal of Botany 73, S1 (December 31, 1995): 160–66. http://dx.doi.org/10.1139/b95-240.

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We describe the experimental methodology that led to the discovery of the creA gene in Aspergillus nidulans. This gene codes for a transcriptional repressor mediating carbon catabolite repression in many pathways in this organism. We compare both the mode and the mechanism of action in two pathways subject to CreA-mediated repression. The genes comprising the ethanol regulon are subject to carbon catabolite repression independently of the nitrogen source, while the genes involved in proline utilization are repressed by glucose only when a repressing nitrogen source is also present. In the ethanol regulon, CreA drastically represses the expression of the positive regulatory gene alcR, thus preventing the expression of the structural genes. Direct repression of the structural genes is also existant. In the proline utilization pathway, repression operates directly at the level of the structural genes. In the ethanol regulon, CreA prevents the self-induction of alcR and the induction of the structural genes by competing with the binding of the AlcR protein. In proline gene cluster, CreA does not interfere with induction mediated by PrnA but with the activity of an unknown and more general transcription factor. Key words: carbon catabolite repression, ascomycetes, Zn fingers.

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4

Hofman-Bang, Jacob. "Nitrogen Catabolite Repression in Saccharomyces cerevisiae." Molecular Biotechnology 12, no. 1 (1999): 35–74. http://dx.doi.org/10.1385/mb:12:1:35.

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5

Arst Jr., Herbert N. "Nitrogen metabolite repression in Aspergillus nidulans: an historical perspective." Canadian Journal of Botany 73, S1 (December 31, 1995): 148–52. http://dx.doi.org/10.1139/b95-238.

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The paper of Arst and Cove (Mol. Gen. Genet. 126: 111 – 141, 1973) on "Nitrogen metabolite repression in Aspergillus nidulans" has influenced studies and perceptions of gene regulation in filamentous fungi during the past 21 years. Here I attempt to appraise the contributions of that paper and assess its role in further developments. Nitrogen metabolite repression, carbon catabolite repression, pathway-specific and integrated induction, as-acting regulatory mutations, a useful class of growth inhibitors, and a homologous Neurospora crassa gene are all discussed. Key words: Aspergillus nidulans, carbon catabolite repression, nitrogen metabolite repression.

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6

BELTRAN, G., M. NOVO, N. ROZES, A. MAS, and J. GUILLAMON. "Nitrogen catabolite repression in during wine fermentations." FEMS Yeast Research 4, no. 6 (March 2004): 625–32. http://dx.doi.org/10.1016/j.femsyr.2003.12.004.

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7

Shin, Byung-Sik, Soo-Keun Choi, Issar Smith, and Seung-Hwan Park. "Analysis of tnrA Alleles Which Result in a Glucose-Resistant Sporulation Phenotype in Bacillus subtilis." Journal of Bacteriology 182, no. 17 (September 1, 2000): 5009–12. http://dx.doi.org/10.1128/jb.182.17.5009-5012.2000.

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ABSTRACT Bacillus subtilis cells cannot sporulate in the presence of catabolites such as glucose. During the analysis of Tn10-generated mutants, we found that deletion of the C-terminal region of the tnrA gene, which encodes a global regulator that positively regulates a number of genes in response to nitrogen limitation, results in a catabolite-resistant sporulation phenotype. Analyses of nrg-lacZ and nasB-lacZ, which are activated by TnrA under nitrogen limitation, showed that C-terminally truncated TnrA activates nitrogen-regulated genes constitutively. The relief of catabolite repression of sporulation may result from the uncontrolled expression of the TnrA-regulated genes.

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8

Milhomem Cruz-Leite, Vanessa Rafaela, Silvia Maria Salem-Izacc, Evandro Novaes, Bruno Junior Neves, Wesley de Almeida Brito, Lana O'Hara Souza Silva, Juliano Domiraci Paccez, et al. "Nitrogen Catabolite Repression in members of Paracoccidioides complex." Microbial Pathogenesis 149 (December 2020): 104281. http://dx.doi.org/10.1016/j.micpath.2020.104281.

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9

Palavecino, Marcos D., Susana R. Correa-García, and Mariana Bermúdez-Moretti. "Genes of Different Catabolic Pathways Are Coordinately Regulated by Dal81 in Saccharomyces cerevisiae." Journal of Amino Acids 2015 (September 17, 2015): 1–8. http://dx.doi.org/10.1155/2015/484702.

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Yeast can use a wide variety of nitrogen compounds. However, the ability to synthesize enzymes and permeases for catabolism of poor nitrogen sources is limited in the presence of a rich one. This general mechanism of transcriptional control is called nitrogen catabolite repression. Poor nitrogen sources, such as leucine, γ-aminobutyric acid (GABA), and allantoin, enable growth after the synthesis of pathway-specific catabolic enzymes and permeases. This synthesis occurs only under conditions of nitrogen limitation and in the presence of a pathway-specific signal. In this work we studied the temporal order in the induction of AGP1, BAP2, UGA4, and DAL7, genes that are involved in the catabolism and use of leucine, GABA, and allantoin, three poor nitrogen sources. We found that when these amino acids are available, cells will express AGP1 and BAP2 in the first place, then DAL7, and at last UGA4. Dal81, a general positive regulator of genes involved in nitrogen utilization related to the metabolisms of GABA, leucine, and allantoin, plays a central role in this coordinated regulation.

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10

Pinedo, Catalina Arango, and Daniel J. Gage. "HPrK Regulates Succinate-Mediated Catabolite Repression in the Gram-Negative Symbiont Sinorhizobium meliloti." Journal of Bacteriology 191, no. 1 (October 17, 2008): 298–309. http://dx.doi.org/10.1128/jb.01115-08.

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ABSTRACT The HPrK kinase/phosphatase is a common component of the phosphotransferase system (PTS) of gram-positive bacteria and regulates catabolite repression through phosphorylation/dephosphorylation of its substrate, the PTS protein HPr, at a conserved serine residue. Phosphorylation of HPr by HPrK also affects additional phosphorylation of HPr by the PTS enzyme EI at a conserved histidine residue. Sinorhizobium meliloti can live as symbionts inside legume root nodules or as free-living organisms and is one of the relatively rare gram-negative bacteria known to have a gene encoding HPrK. We have constructed S. meliloti mutants that lack HPrK or that lack key amino acids in HPr that are likely phosphorylated by HPrK and EI. Deletion of hprK in S. meliloti enhanced catabolite repression caused by succinate, as did an S53A substitution in HPr. Introduction of an H22A substitution into HPr alleviated the strong catabolite repression phenotypes of strains carrying ΔhprK or hpr(S53A) mutations, demonstrating that HPr-His22-P is needed for strong catabolite repression. Furthermore, strains with a hpr(H22A) allele exhibited relaxed catabolite repression. These results suggest that HPrK phosphorylates HPr at the serine-53 residue, that HPr-Ser53-P inhibits phosphorylation at the histidine-22 residue, and that HPr-His22-P enhances catabolite repression in the presence of succinate. Additional experiments show that ΔhprK mutants overproduce exopolysaccharides and form nodules that do not fix nitrogen.

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11

Golden, K. J., and R. W. Bernlohr. "Nitrogen catabolite repression of the L-asparaginase of Bacillus licheniformis." Journal of Bacteriology 164, no. 2 (1985): 938–40. http://dx.doi.org/10.1128/jb.164.2.938-940.1985.

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12

Rai, Rajendra, Jennifer J. Tate, Isabelle Georis, Evelyne Dubois, and Terrance G. Cooper. "Constitutive and Nitrogen Catabolite Repression-sensitive Production of Gat1 Isoforms." Journal of Biological Chemistry 289, no. 5 (December 9, 2013): 2918–33. http://dx.doi.org/10.1074/jbc.m113.516740.

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13

Nair, Abhinav, and Saurabh Jyoti Sarma. "The impact of carbon and nitrogen catabolite repression in microorganisms." Microbiological Research 251 (October 2021): 126831. http://dx.doi.org/10.1016/j.micres.2021.126831.

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14

Lorca, Graciela L., Yong Joon Chung, Ravi D. Barabote, Walter Weyler, Christophe H. Schilling, and Milton H. Saier. "Catabolite Repression and Activation in Bacillus subtilis: Dependency on CcpA, HPr, and HprK." Journal of Bacteriology 187, no. 22 (November 15, 2005): 7826–39. http://dx.doi.org/10.1128/jb.187.22.7826-7839.2005.

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ABSTRACT Previous studies have suggested that the transcription factor CcpA, as well as the coeffectors HPr and Crh, both phosphorylated by the HprK kinase/phosphorylase, are primary mediators of catabolite repression and catabolite activation in Bacillus subtilis. We here report whole transcriptome analyses that characterize glucose-dependent gene expression in wild-type cells and in isogenic mutants lacking CcpA, HprK, or the HprK phosphorylatable serine in HPr. Binding site identification revealed which genes are likely to be primarily or secondarily regulated by CcpA. Most genes subject to CcpA-dependent regulation are regulated fully by HprK and partially by serine-phosphorylated HPr [HPr(Ser-P)]. A positive linear correlation was noted between the dependencies of catabolite-repressible gene expression on CcpA and HprK, but no such relationship was observed for catabolite-activated genes, suggesting that large numbers of the latter genes are not regulated by the CcpA-HPr(Ser-P) complex. Many genes that mediate nitrogen or phosphorus metabolism as well as those that function in stress responses proved to be subject to CcpA-dependent glucose control. While nitrogen-metabolic genes may be subject to either glucose repression or activation, depending on the gene, almost all glucose-responsive phosphorus-metabolic genes exhibit activation while almost all glucose-responsive stress genes show repression. These responses are discussed from physiological standpoints. These studies expand our appreciation of CcpA-mediated catabolite control and provide insight into potential interregulon control mechanisms in gram-positive bacteria.

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15

Cunningham, T. S., and T. G. Cooper. "Expression of the DAL80 gene, whose product is homologous to the GATA factors and is a negative regulator of multiple nitrogen catabolic genes in Saccharomyces cerevisiae, is sensitive to nitrogen catabolite repression." Molecular and Cellular Biology 11, no. 12 (December 1991): 6205–15. http://dx.doi.org/10.1128/mcb.11.12.6205.

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We have cloned the negative regulatory gene (DAL80) of the allantoin catabolic pathway, characterized its structure, and determined the physiological conditions that control DAL80 expression and its influence on the expression of nitrogen catabolic genes. Disruption of the DAL80 gene demonstrated that it regulates multiple nitrogen catabolic pathways. Inducer-independent expression was observed for the allantoin pathway genes DAL7 and DUR1,2, as well as the UGA1 gene required for gamma-aminobutyrate catabolism in the disruption mutant. DAL80 transcription was itself highly sensitive to nitrogen catabolite repression (NCR), and its promoter contained 12 sequences homologous to the NCR-sensitive UASNTR. The deduced DAL80 protein structure contains zinc finger and coiled-coil motifs. The DAL80 zinc finger motif possessed high homology to the transcriptional activator proteins required for expression of NCR-sensitive genes in fungi and the yeast GLN3 gene product required for functioning of the NCR-sensitive DAL UASNTR. It was also homologous to the three GATAA-binding proteins reported to be transcriptional activators in avian and mammalian tissues. The latter correlations raise the possibility that both positive and negative regulators of allantoin pathway transcription may bind to similar sequences.

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16

Cunningham, T. S., and T. G. Cooper. "Expression of the DAL80 gene, whose product is homologous to the GATA factors and is a negative regulator of multiple nitrogen catabolic genes in Saccharomyces cerevisiae, is sensitive to nitrogen catabolite repression." Molecular and Cellular Biology 11, no. 12 (December 1991): 6205–15. http://dx.doi.org/10.1128/mcb.11.12.6205-6215.1991.

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We have cloned the negative regulatory gene (DAL80) of the allantoin catabolic pathway, characterized its structure, and determined the physiological conditions that control DAL80 expression and its influence on the expression of nitrogen catabolic genes. Disruption of the DAL80 gene demonstrated that it regulates multiple nitrogen catabolic pathways. Inducer-independent expression was observed for the allantoin pathway genes DAL7 and DUR1,2, as well as the UGA1 gene required for gamma-aminobutyrate catabolism in the disruption mutant. DAL80 transcription was itself highly sensitive to nitrogen catabolite repression (NCR), and its promoter contained 12 sequences homologous to the NCR-sensitive UASNTR. The deduced DAL80 protein structure contains zinc finger and coiled-coil motifs. The DAL80 zinc finger motif possessed high homology to the transcriptional activator proteins required for expression of NCR-sensitive genes in fungi and the yeast GLN3 gene product required for functioning of the NCR-sensitive DAL UASNTR. It was also homologous to the three GATAA-binding proteins reported to be transcriptional activators in avian and mammalian tissues. The latter correlations raise the possibility that both positive and negative regulators of allantoin pathway transcription may bind to similar sequences.

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17

Warner, Jessica B., and Juke S. Lolkema. "CcpA-Dependent Carbon Catabolite Repression in Bacteria." Microbiology and Molecular Biology Reviews 67, no. 4 (December 2003): 475–90. http://dx.doi.org/10.1128/mmbr.67.4.475-490.2003.

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SUMMARY Carbon catabolite repression (CCR) by transcriptional regulators follows different mechanisms in gram-positive and gram-negative bacteria. In gram-positive bacteria, CcpA-dependent CCR is mediated by phosphorylation of the phosphoenolpyruvate:sugar phosphotransferase system intermediate HPr at a serine residue at the expense of ATP. The reaction is catalyzed by HPr kinase, which is activated by glycolytic intermediates. In this review, the distribution of CcpA-dependent CCR among bacteria is investigated by searching the public databases for homologues of HPr kinase and HPr-like proteins throughout the bacterial kingdom and by analyzing their properties. Homologues of HPr kinase are commonly observed in the phylum Firmicutes but are also found in the phyla Proteobacteria, Fusobacteria, Spirochaetes, and Chlorobi, suggesting that CcpA-dependent CCR is not restricted to gram-positive bacteria. In the α and β subdivisions of the Proteobacteria, the presence of HPr kinase appears to be common, while in the γ subdivision it is more of an exception. The genes coding for the HPr kinase homologues of the Proteobacteria are in a gene cluster together with an HPr-like protein, termed XPr, suggesting a functional relationship. Moreover, the XPr proteins contain the serine phosphorylation sequence motif. Remarkably, the analysis suggests a possible relation between CcpA-dependent gene regulation and the nitrogen regulation system (Ntr) found in the γ subdivision of the Proteobacteria. The relation is suggested by the clustering of CCR and Ntr components on the genome of members of the Proteobacteria and by the close phylogenetic relationship between XPr and NPr, the HPr-like protein in the Ntr system. In bacteria in the phylum Proteobacteria that contain HPr kinase and XPr, the latter may be at the center of a complex regulatory network involving both CCR and the Ntr system.

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18

Bringhurst, Ryan M., and Daniel J. Gage. "Control of Inducer Accumulation Plays a Key Role in Succinate-Mediated Catabolite Repression in Sinorhizobiummeliloti." Journal of Bacteriology 184, no. 19 (October 1, 2002): 5385–92. http://dx.doi.org/10.1128/jb.184.19.5385-5392.2002.

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ABSTRACT The symbiotic, nitrogen-fixing bacterium Sinorhizobium meliloti favors succinate and related dicarboxylic acids as carbon sources. As a preferred carbon source, succinate can exert catabolite repression upon genes needed for the utilization of many secondary carbon sources, including the α-galactosides raffinose and stachyose. We isolated lacR mutants in a genetic screen designed to find S. meliloti mutants that had abnormal succinate-mediated catabolite repression of the melA-agp genes, which are required for the utilization of raffinose and other α-galactosides. The loss of catabolite repression in lacR mutants was seen in cells grown in minimal medium containing succinate and raffinose and grown in succinate and lactose. For succinate and lactose, the loss of catabolite repression could be attributed to the constitutive expression of β-galactoside utilization genes in lacR mutants. However, the inactivation of lacR did not cause the constitutive expression of α-galactoside utilization genes but caused the aberrant expression of these genes only when succinate was present. To explain the loss of diauxie in succinate and raffinose, we propose a model in which lacR mutants overproduce β-galactoside transporters, thereby overwhelming the inducer exclusion mechanisms of succinate-mediated catabolite repression. Thus, some raffinose could be transported by the overproduced β-galactoside transporters and cause the induction of α-galactoside utilization genes in the presence of both succinate and raffinose. This model is supported by the restoration of diauxie in a lacF lacR double mutant (lacF encodes a β-galactoside transport protein) grown in medium containing succinate and raffinose. Biochemical support for the idea that succinate-mediated repression operates by preventing inducer accumulation also comes from uptake assays, which showed that cells grown in raffinose and exposed to succinate have a decreased rate of raffinose transport compared to control cells not exposed to succinate.

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19

ter Schure, Eelko G., Natal A. W. van Riel, and C. Theo Verrips. "The role of ammonia metabolism in nitrogen catabolite repression inSaccharomyces cerevisiae." FEMS Microbiology Reviews 24, no. 1 (January 2000): 67–83. http://dx.doi.org/10.1111/j.1574-6976.2000.tb00533.x.

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20

Boczko, E. M., T. G. Cooper, T. Gedeon, K. Mischaikow, D. G. Murdock, S. Pratap, and K. S. Wells. "Structure theorems and the dynamics of nitrogen catabolite repression in yeast." Proceedings of the National Academy of Sciences 102, no. 16 (April 6, 2005): 5647–52. http://dx.doi.org/10.1073/pnas.0501339102.

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21

Sosa, Eduardo, Cristina Aranda, Lina Riego, Lourdes Valenzuela, Alexander DeLuna, José M. Cantú, and Alicia González. "Gcn4 negatively regulates expression of genes subjected to nitrogen catabolite repression." Biochemical and Biophysical Research Communications 310, no. 4 (October 2003): 1175–80. http://dx.doi.org/10.1016/j.bbrc.2003.09.144.

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22

Rai, Rajendra, Jennifer J. Tate, David R. Nelson, and Terrance G. Cooper. "gln3Mutations Dissociate Responses to Nitrogen Limitation (Nitrogen Catabolite Repression) and Rapamycin Inhibition of TorC1." Journal of Biological Chemistry 288, no. 4 (December 5, 2012): 2789–804. http://dx.doi.org/10.1074/jbc.m112.421826.

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23

Choi, Soo-Keun, and Milton H. Saier. "Regulation of sigL Expression by the Catabolite Control Protein CcpA Involves a Roadblock Mechanism in Bacillus subtilis: Potential Connection between Carbon and Nitrogen Metabolism." Journal of Bacteriology 187, no. 19 (October 1, 2005): 6856–61. http://dx.doi.org/10.1128/jb.187.19.6856-6861.2005.

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ABSTRACT A catabolite-responsive element (CRE), a binding site for the CcpA transcription factor, was identified within the sigL structural gene encoding σL in Bacillus subtilis. We show that CcpA binds to this CRE to regulate sigL expression by a “roadblock” mechanism and that this mechanism in part accounts for catabolite repression of σL-directed levD operon expression.

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24

Marzluf, G. A. "Genetic regulation of nitrogen metabolism in the fungi." Microbiology and Molecular Biology Reviews 61, no. 1 (March 1997): 17–32. http://dx.doi.org/10.1128/mmbr.61.1.17-32.1997.

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In the fungi, nitrogen metabolism is controlled by a complex genetic regulatory circuit which ensures the preferential use of primary nitrogen sources and also confers the ability to use many different secondary nitrogen sources when appropriate. Most structural genes encoding nitrogen catabolic enzymes are subject to nitrogen catabolite repression, mediated by positive-acting transcription factors of the GATA family of proteins. However, certain GATA family members, such as the yeast DAL80 factor, act negatively to repress gene expression. Selective expression of the genes which encode enzymes for the metabolism of secondary nitrogen sources is often achieved by induction, mediated by pathway-specific factors, many of which have a GAL4-like C6/Zn2 DNA binding domain. Regulation within the nitrogen circuit also involves specific protein-protein interactions, as exemplified by the specific binding of the negative-acting NMR protein with the positive-acting NIT2 protein of Neurospora crassa. Nitrogen metabolic regulation appears to play a significant role in the pathogenicity of certain animal and plant fungal pathogens.

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25

ZHANG, Weiping, Xinrui ZHAO, Guocheng DU, Huijun ZOU, Jianwei FU, Jingwen ZHOU, and Jian CHEN. "Nitrogen Catabolite Repression inSaccharomyces cerevisiaeand Its Effect on Safety of Fermented Foods." Chinese Journal of Appplied Environmental Biology 18, no. 5 (2012): 862. http://dx.doi.org/10.3724/sp.j.1145.2012.00862.

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26

ter Schure, E. "The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae." FEMS Microbiology Reviews 24, no. 1 (January 2000): 67–83. http://dx.doi.org/10.1016/s0168-6445(99)00030-3.

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27

Huberman, Lori B., Vincent W. Wu, David J. Kowbel, Juna Lee, Chris Daum, Igor V. Grigoriev, Ronan C. O’Malley, and N. Louise Glass. "DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus." Proceedings of the National Academy of Sciences 118, no. 13 (March 22, 2021): e2009501118. http://dx.doi.org/10.1073/pnas.2009501118.

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Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of inorganic and organic nitrogen sources. Nitrogen utilization in N. crassa is regulated by a network of pathway-specific transcription factors that activate genes necessary to utilize specific nitrogen sources in combination with nitrogen catabolite repression regulatory proteins. We identified an uncharacterized pathway-specific transcription factor, amn-1, that is required for utilization of the nonpreferred nitrogen sources proline, branched-chain amino acids, and aromatic amino acids. AMN-1 also plays a role in regulating genes involved in responding to the simple sugar mannose, suggesting an integration of nitrogen and carbon metabolism. The utilization of nonpreferred nitrogen sources, which require metabolic processing before being used as a nitrogen source, is also regulated by the nitrogen catabolite regulator NIT-2. Using RNA sequencing combined with DNA affinity purification sequencing, we performed a survey of the role of NIT-2 and the pathway-specific transcription factors NIT-4 and AMN-1 in directly regulating genes involved in nitrogen utilization. Although previous studies suggested promoter binding by both a pathway-specific transcription factor and NIT-2 may be necessary for activation of nitrogen-responsive genes, our data show that pathway-specific transcription factors regulate genes involved in the catabolism of specific nitrogen sources, while NIT-2 regulates genes involved in utilization of all nonpreferred nitrogen sources, such as nitrogen transporters. Together, these transcription factors form a nutrient sensing network that allows N. crassa cells to regulate nitrogen utilization.

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28

Coffman, J. A., R. Rai, T. Cunningham, V. Svetlov, and T. G. Cooper. "Gat1p, a GATA family protein whose production is sensitive to nitrogen catabolite repression, participates in transcriptional activation of nitrogen-catabolic genes in Saccharomyces cerevisiae." Molecular and Cellular Biology 16, no. 3 (March 1996): 847–58. http://dx.doi.org/10.1128/mcb.16.3.847.

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Saccharomyces cerevisiae cells selectively use nitrogen sources in their environment. Nitrogen catabolite repression (NCR) is the basis of this selectivity. Until recently NCR was thought to be accomplished exclusively through the negative regulation of Gln3p function by Ure2p. The demonstration that NCR-sensitive expression of multiple nitrogen-catabolic genes occurs in a gln3 delta ure2 delta dal80::hisG triple mutant indicated that the prevailing view of the nitrogen regulatory circuit was in need of revision; additional components clearly existed. Here we demonstrate that another positive regulator, designated Gat1p, participates in the transcription of NCR-sensitive genes and is able to weakly activate transcription when tethered upstream of a reporter gene devoid of upstream activation sequence elements. Expression of GAT1 is shown to be NCR sensitive, partially Gln3p dependent, and Dal80p regulated. In agreement with this pattern of regulation, we also demonstrate the existence of Gln3p and Dal80p binding sites upstream of GAT1.

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29

Cajueiro, Danielli Batista Bezerra, Denise Castro Parente, Fernanda Cristina Bezerra Leite, Marcos Antonio de Morais Junior, and Will de Barros Pita. "Glutamine: a major player in nitrogen catabolite repression in the yeast Dekkera bruxellensis." Antonie van Leeuwenhoek 110, no. 9 (June 19, 2017): 1157–68. http://dx.doi.org/10.1007/s10482-017-0888-5.

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30

Ferrer-Pinós, Aroa, Víctor Garrigós, Emilia Matallana, and Agustín Aranda. "Mechanisms of Metabolic Adaptation in Wine Yeasts: Role of Gln3 Transcription Factor." Fermentation 7, no. 3 (September 5, 2021): 181. http://dx.doi.org/10.3390/fermentation7030181.

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Wine strains of Saccharomyces cerevisiae have to adapt their metabolism to the changing conditions during their biotechnological use, from the aerobic growth in sucrose-rich molasses for biomass propagation to the anaerobic fermentation of monosaccharides of grape juice during winemaking. Yeast have molecular mechanisms that favor the use of preferred carbon and nitrogen sources to achieve such adaptation. By using specific inhibitors, it was determined that commercial strains offer a wide variety of glucose repression profiles. Transcription factor Gln3 has been involved in glucose and nitrogen repression. Deletion of GLN3 in two commercial wine strains produced different mutant phenotypes and only one of them displayed higher glucose repression and was unable to grow using a respiratory carbon source. Therefore, the role of this transcription factor contributes to the variety of phenotypic behaviors seen in wine strains. This variability is also reflected in the impact of GLN3 deletion in fermentation, although the mutants are always more tolerant to inhibition of the nutrient signaling complex TORC1 by rapamycin, both in laboratory medium and in grape juice fermentation. Therefore, most aspects of nitrogen catabolite repression controlled by TORC1 are conserved in winemaking conditions.

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31

Georis, Isabelle, André Feller, Fabienne Vierendeels, and Evelyne Dubois. "The Yeast GATA Factor Gat1 Occupies a Central Position in Nitrogen Catabolite Repression-Sensitive Gene Activation." Molecular and Cellular Biology 29, no. 13 (April 20, 2009): 3803–15. http://dx.doi.org/10.1128/mcb.00399-09.

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ABSTRACT Saccharomyces cerevisiae cells are able to adapt their metabolism according to the quality of the nitrogen sources available in the environment. Nitrogen catabolite repression (NCR) restrains the yeast's capacity to use poor nitrogen sources when rich ones are available. NCR-sensitive expression is modulated by the synchronized action of four DNA-binding GATA factors. Although the first identified GATA factor, Gln3, was considered the major activator of NCR-sensitive gene expression, our work positions Gat1 as a key factor for the integrated control of NCR in yeast for the following reasons: (i) Gat1 appeared to be the limiting factor for NCR gene expression, (ii) GAT1 expression was regulated by the four GATA factors in response to nitrogen availability, (iii) the two negative GATA factors Dal80 and Gzf3 interfered with Gat1 binding to DNA, and (iv) Gln3 binding to some NCR promoters required Gat1. Our study also provides mechanistic insights into the mode of action of the two negative GATA factors. Gzf3 interfered with Gat1 by nuclear sequestration and by competition at its own promoter. Dal80-dependent repression of NCR-sensitive gene expression occurred at three possible levels: Dal80 represses GAT1 expression, it competes with Gat1 for binding, and it directly represses NCR gene transcription.

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32

Daugherty, J. R., R. Rai, H. M. el Berry, and T. G. Cooper. "Regulatory circuit for responses of nitrogen catabolic gene expression to the GLN3 and DAL80 proteins and nitrogen catabolite repression in Saccharomyces cerevisiae." Journal of Bacteriology 175, no. 1 (1993): 64–73. http://dx.doi.org/10.1128/jb.175.1.64-73.1993.

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Zomer, Aldert L., Girbe Buist, Rasmus Larsen, Jan Kok, and Oscar P. Kuipers. "Time-Resolved Determination of the CcpA Regulon of Lactococcus lactis subsp. cremoris MG1363." Journal of Bacteriology 189, no. 4 (October 6, 2006): 1366–81. http://dx.doi.org/10.1128/jb.01013-06.

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ABSTRACT Carbon catabolite control protein A (CcpA) is the main regulator involved in carbon catabolite repression in gram-positive bacteria. Time series gene expression analyses of Lactococcus lactis MG1363 and L. lactis MG1363ΔccpA using DNA microarrays were used to define the CcpA regulon of L. lactis. Based on a comparison of the transcriptome data with putative CcpA binding motifs (cre sites) in promoter sequences in the genome of L. lactis, 82 direct targets of CcpA were predicted. The main differences in time-dependent expression of CcpA-regulated genes were differences between the exponential and transition growth phases. Large effects were observed for carbon and nitrogen metabolic genes in the exponential growth phase. Effects on nucleotide metabolism genes were observed primarily in the transition phase. Analysis of the positions of putative cre sites revealed that there is a link between either repression or activation and the location of the cre site within the promoter region. Activation was observed when putative cre sites were located upstream of the hexameric −35 sequence at an average position of −56.5 or further upstream with decrements of 10.5 bp. Repression was observed when the cre site was located in or downstream of putative −35 and −10 sequences. The highest level of repression was observed when the cre site was present at a defined side of the DNA helix relative to the canonical −10 sequence. Gel retardation experiments, Northern blotting, and enzyme assays showed that CcpA represses its own expression and activates the expression of the divergently oriented prolidase-encoding pepQ gene, which constitutes a link between regulation of carbon metabolism and regulation of nitrogen metabolism.

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Coffman, Jonathan A., Rajendra Rai, and Terrance G. Cooper. "Genetic Evidence for Gln3p-Independent, Nitrogen Catabolite Repression-Sensitive Gene Expression in Saccharomyces cerevisiae." jb 178, no. 7 (1996): 2159. http://dx.doi.org/10.1128/.178.7.2159-2159.1996.

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Coffman, J. A., R. Rai, and T. G. Cooper. "Genetic evidence for Gln3p-independent, nitrogen catabolite repression-sensitive gene expression in Saccharomyces cerevisiae." Journal of bacteriology 177, no. 23 (1995): 6910–18. http://dx.doi.org/10.1128/jb.177.23.6910-6918.1995.

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Coffman, Jonathan A., Rajendra Rai, and Terrance G. Cooper. "Genetic Evidence for Gln3p-Independent, Nitrogen Catabolite Repression-Sensitive Gene Expression in Saccharomyces cerevisiae." Journal of Bacteriology 178, no. 7 (April 1996): 2159.2–2159. http://dx.doi.org/10.1128/jb.178.7.2159a.1996.

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Zhao, Xinrui, Huijun Zou, Guocheng Du, Jian Chen, and Jingwen Zhou. "Effects of nitrogen catabolite repression-related amino acids on the flavour of rice wine." Journal of the Institute of Brewing 121, no. 4 (September 16, 2015): 581–88. http://dx.doi.org/10.1002/jib.269.

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38

Fayyad-Kazan, Mohammad, A. Feller, E. Bodo, M. Boeckstaens, A. M. Marini, E. Dubois, and I. Georis. "Yeast nitrogen catabolite repression is sustained by signals distinct from glutamine and glutamate reservoirs." Molecular Microbiology 99, no. 2 (November 13, 2015): 360–79. http://dx.doi.org/10.1111/mmi.13236.

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39

Smart, W. C., J. A. Coffman, and T. G. Cooper. "Combinatorial regulation of the Saccharomyces cerevisiae CAR1 (arginase) promoter in response to multiple environmental signals." Molecular and Cellular Biology 16, no. 10 (October 1996): 5876–87. http://dx.doi.org/10.1128/mcb.16.10.5876.

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CAR1 (arginase) gene expression responds to multiple environmental signals; expression is induced in response to the intracellular accumulation of arginine and repressed when readily transported and catabolized nitrogen sources are available in the environment. Up to 14 cis-acting sites and 9 trans-acting factors have been implicated in regulated CAR1 transcription. In all but one case, the sites are redundant. To test whether these sites actually participate in CAR1 expression, each class of sites was inactivated by substitution mutations that retained the native spacing of the CAR1 cis-acting elements. Three types of sites function independently of the nitrogen source: two clusters of Abflp- and Rap1p-binding sites, and a GC-rich sequence. Two different sets of nitrogen source-dependent sites are also required: the first consists of two GATAA-containing UASNTR sites that mediate nitrogen catabolite repression-sensitive transcription, and the second is arginine dependent and consists of three UAS1 elements that activate transcription only when arginine is present. A single URS1 site mediates repression of CAR1 arginine-independent upstream activator site (UAS) activity in the absence of arginine and the presence of a poor nitrogen source (a condition under which the inducer-independent Gln3p can function in association with the UASNTR sites). When arginine is present, the combined activity of the UAS elements overcomes the negative effects mediated by URS1. Mutation of the classes of sites either singly or in combination markedly alters CAR1 promoter operation and control, supporting the idea that they function synergistically to regulate expression of the gene.

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Park, Heui-Dong, Stephanie Scott, Rajendra Rai, Rosemary Dorrington, and Terrance G. Cooper. "Synergistic Operation of the CAR2(Ornithine Transaminase) Promoter Elements in Saccharomyces cerevisiae." Journal of Bacteriology 181, no. 22 (November 15, 1999): 7052–64. http://dx.doi.org/10.1128/jb.181.22.7052-7064.1999.

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ABSTRACT Dal82p binds to the UIS ALL sites of allophanate-induced genes of the allantoin-degradative pathway and functions synergistically with the GATA family Gln3p and Gat1p transcriptional activators that are responsible for nitrogen catabolite repression-sensitive gene expression. CAR2, which encodes the arginine-degradative enzyme ornithine transaminase, is not nitrogen catabolite repression sensitive, but its expression can be modestly induced by the allantoin pathway inducer. The dominant activators ofCAR2 transcription have been thought to be the ArgR and Mcm1 factors, which mediate arginine-dependent induction. These observations prompted us to investigate the structure of theCAR2 promoter with the objectives of determining whether other transcription factors were required for CAR2expression and, if so, of ascertaining their relative contributions toCAR2’s expression and control. We show that Rap1p binds upstream of CAR2 and plays a central role in its induced expression irrespective of whether the inducer is arginine or the allantoin pathway inducer analogue oxalurate (OXLU). Our data also explain the early report that ornithine transaminase production is induced when cells are grown with urea. OXLU induction derives from the Dal82p binding site, which is immediately downstream of the Rap1p site, and Dal82p functions synergistically with Rap1p. This synergism is unlike all other known instances of Dal82p synergism, namely, that with the GATA family transcription activators Gln3p and Gat1p, which occurs only in the presence of an inducer. The observations reported suggest that CAR2 gene expression results from strong constitutive transcriptional activation mediated by Rap1p and Dal82p being balanced by the down regulation of an equally strong transcriptional repressor, Ume6p. This balance is then tipped in the direction of expression by the presence of the inducer. The formal structure of theCAR2 promoter and its operation closely follow the model proposed for CAR1.

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Beeser, Alexander E., and Terrance G. Cooper. "Control of Nitrogen Catabolite Repression Is Not Affected by the tRNAGln-CUU Mutation, Which Results in Constitutive Pseudohyphal Growth of Saccharomyces cerevisiae." Journal of Bacteriology 181, no. 8 (April 15, 1999): 2472–76. http://dx.doi.org/10.1128/jb.181.8.2472-2476.1999.

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ABSTRACT Saccharomyces cerevisiae responds to nitrogen availability in several ways. (i) The cell is able to distinguish good nitrogen sources from poor ones through a process designated nitrogen catabolite repression (NCR). Good and poor nitrogen sources do not demonstrably affect the cell cycle other than to influence the cell’s doubling time. (ii) Nitrogen starvation promotes the initiation of sporulation and pseudohyphal growth. (iii) Nitrogen starvation strongly affects the cell cycle; nitrogen-starved cells arrest in G1. A specific allele of the SUP70/CDC65tRNAGln gene (sup70-65) has been reported to be defective in nitrogen signaling associated with pseudohyphal formation, sporulation, and NCR. Our data confirm that pseudohyphal growth occurs gratuitously in sup70-65 mutants cultured in nitrogen-rich medium at 30°C. However, we find neither any defect in NCR in thesup70-65 mutant nor any alteration in the control ofYVH1 expression, which has been previously shown to be specifically induced by nitrogen starvation.

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42

Salmon, Jean-Michel, and Pierre Barre. "Improvement of Nitrogen Assimilation and Fermentation Kinetics under Enological Conditions by Derepression of Alternative Nitrogen-Assimilatory Pathways in an Industrial Saccharomyces cerevisiae Strain." Applied and Environmental Microbiology 64, no. 10 (October 1, 1998): 3831–37. http://dx.doi.org/10.1128/aem.64.10.3831-3837.1998.

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ABSTRACT Metabolism of nitrogen compounds by yeasts affects the efficiency of wine fermentation. Ammonium ions, normally present in grape musts, reduce catabolic enzyme levels and transport activities for nonpreferred nitrogen sources. This nitrogen catabolite repression severely impairs the utilization of proline and arginine, both common nitrogen sources in grape juice that require the proline utilization pathway for their assimilation. We attempted to improve fermentation performance by genetic alteration of the regulation of nitrogen-assimilatory pathways in Saccharomyces cerevisiae. One mutant carrying a recessive allele ofure2 was isolated from an industrial S. cerevisiae strain. This mutation strongly deregulated the proline utilization pathway. Fermentation kinetics of this mutant were studied under enological conditions on simulated standard grape juices with various nitrogen levels. Mutant strains produced more biomass and exhibited a higher maximum CO2 production rate than the wild type. These differences were primarily due to the derepression of amino acid utilization pathways. When low amounts of dissolved oxygen were added, the mutants could assimilate proline. Biomass yield and fermentation rate were consequently increased, and the duration of the fermentation was substantially shortened. S. cerevisiae strains lacking URE2 function could improve alcoholic fermentation of natural media where proline and other poorly assimilated amino acids are the major potential nitrogen source, as is the case for most fruit juices and grape musts.

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Godard, Patrice, Antonio Urrestarazu, Stéphan Vissers, Kevin Kontos, Gianluca Bontempi, Jacques van Helden, and Bruno André. "Effect of 21 Different Nitrogen Sources on Global Gene Expression in the Yeast Saccharomyces cerevisiae." Molecular and Cellular Biology 27, no. 8 (February 16, 2007): 3065–86. http://dx.doi.org/10.1128/mcb.01084-06.

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ABSTRACT We compared the transcriptomes of Saccharomyces cerevisiae cells growing under steady-state conditions on 21 unique sources of nitrogen. We found 506 genes differentially regulated by nitrogen and estimated the activation degrees of all identified nitrogen-responding transcriptional controls according to the nitrogen source. One main group of nitrogenous compounds supports fast growth and a highly active nitrogen catabolite repression (NCR) control. Catabolism of these compounds typically yields carbon derivatives directly assimilable by a cell's metabolism. Another group of nitrogen compounds supports slower growth, is associated with excretion by cells of nonmetabolizable carbon compounds such as fusel oils, and is characterized by activation of the general control of amino acid biosynthesis (GAAC). Furthermore, NCR and GAAC appear interlinked, since expression of the GCN4 gene encoding the transcription factor that mediates GAAC is subject to NCR. We also observed that several transcriptional-regulation systems are active under a wider range of nitrogen supply conditions than anticipated. Other transcriptional-regulation systems acting on genes not involved in nitrogen metabolism, e.g., the pleiotropic-drug resistance and the unfolded-protein response systems, also respond to nitrogen. We have completed the lists of target genes of several nitrogen-sensitive regulons and have used sequence comparison tools to propose functions for about 20 orphan genes. Similar studies conducted for other nutrients should provide a more complete view of alternative metabolic pathways in yeast and contribute to the attribution of functions to many other orphan genes.

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Zalieckas, Jill M., Lewis V. Wray, and Susan H. Fisher. "trans-Acting Factors Affecting Carbon Catabolite Repression of the hut Operon inBacillus subtilis." Journal of Bacteriology 181, no. 9 (May 1, 1999): 2883–88. http://dx.doi.org/10.1128/jb.181.9.2883-2888.1999.

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ABSTRACT In Bacillus subtilis, CcpA-dependent carbon catabolite repression (CCR) mediated at several cis-acting carbon repression elements (cre) requires the seryl-phosphorylated form of both the HPr (ptsH) and Crh (crh) proteins. During growth in minimal medium, theptsH1 mutation, which prevents seryl phosphorylation of HPr, partially relieves CCR of several genes regulated by CCR. Examination of the CCR of the histidine utilization (hut) enzymes in cells grown in minimal medium showed that neither theptsH1 nor the crh mutation individually had any affect on hut CCR but that hut CCR was abolished in a ptsH1 crh double mutant. In contrast, theptsH1 mutation completely relieved hut CCR in cells grown in Luria-Bertani medium. The ptsH1 crh double mutant exhibited several growth defects in glucose minimal medium, including reduced rates of growth and growth inhibition by high levels of glycerol or histidine. CCR is partially relieved in B. subtilis mutants which synthesize low levels of active glutamine synthetase (glnA). In addition, these glnAmutants grow more slowly than wild-type cells in glucose minimal medium. The defects in growth and CCR seen in these mutants are suppressed by mutational inactivation of TnrA, a global nitrogen regulatory protein. The inappropriate expression of TnrA-regulated genes in this class of glnA mutants may deplete intracellular pools of carbon metabolites and thereby result in the reduction of the growth rate and partial relief of CCR.

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Rai, Rajendra, Jennifer J. Tate, Karthik Shanmuganatham, Martha M. Howe, David Nelson, and Terrance G. Cooper. "Nuclear Gln3 Import Is Regulated by Nitrogen Catabolite Repression Whereas Export Is Specifically Regulated by Glutamine." Genetics 201, no. 3 (September 2, 2015): 989–1016. http://dx.doi.org/10.1534/genetics.115.177725.

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Cooper, T. G., L. Kovari, R. A. Sumrada, H. D. Park, R. M. Luche, and I. Kovari. "Nitrogen catabolite repression of arginase (CAR1) expression in Saccharomyces cerevisiae is derived from regulated inducer exclusion." Journal of Bacteriology 174, no. 1 (1992): 48–55. http://dx.doi.org/10.1128/jb.174.1.48-55.1992.

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47

Dawson, M. W., I. S. Maddox, and J. D. Brooks. "Evidence for nitrogen catabolite repression during citric acid production byAspergillus niger under phosphate-limited growth conditions." Biotechnology and Bioengineering 33, no. 11 (May 1989): 1500–1504. http://dx.doi.org/10.1002/bit.260331119.

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48

Cunningham, Thomas S., Roopa Andhare, and Terrance G. Cooper. "Nitrogen Catabolite Repression ofDAL80Expression Depends on the Relative Levels of Gat1p and Ure2p Production inSaccharomyces cerevisiae." Journal of Biological Chemistry 275, no. 19 (May 5, 2000): 14408–14. http://dx.doi.org/10.1074/jbc.275.19.14408.

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Tate, Jennifer J., Isabelle Georis, Evelyne Dubois, and Terrance G. Cooper. "Distinct Phosphatase Requirements and GATA Factor Responses to Nitrogen Catabolite Repression and Rapamycin Treatment inSaccharomyces cerevisiae." Journal of Biological Chemistry 285, no. 23 (April 8, 2010): 17880–95. http://dx.doi.org/10.1074/jbc.m109.085712.

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50

Airoldi, Edoardo M., Darach Miller, Rodoniki Athanasiadou, Nathan Brandt, Farah Abdul-Rahman, Benjamin Neymotin, Tatsu Hashimoto, Tayebeh Bahmani, and David Gresham. "Steady-state and dynamic gene expression programs inSaccharomyces cerevisiaein response to variation in environmental nitrogen." Molecular Biology of the Cell 27, no. 8 (April 15, 2016): 1383–96. http://dx.doi.org/10.1091/mbc.e14-05-1013.

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Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate–controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source–specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR-regulated permease genes GAP1, MEP2, DAL5, PUT4, and DIP5. Our results reveal novel aspects of nitrogen-regulated gene expression and highlight the need for a quantitative approach to study how the cell coordinates protein translation and nitrogen assimilation to optimize cell growth in different environments.

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