Nitrogen metabolism in the facultative methylotroph Arthrobacter P1 grown with various amines or ammonia as nitrogen sources

1989 ◽  
Vol 56 (3) ◽  
pp. 221-232 ◽  
Author(s):  
L. De Boer ◽  
J. W. Brouwer ◽  
C. W. Van Hassel ◽  
P. R. Levering ◽  
L. Dijkhuizen
Keyword(s):  
Nitrogen Metabolism ◽  
Nitrogen Sources ◽  
Arthrobacter P1 ◽  
Facultative Methylotroph

Genetic regulation of nitrogen metabolism in the fungi

1997 ◽  
Vol 61 (1) ◽  
pp. 17-32
Author(s):  
G A Marzluf
Keyword(s):  
Nitrogen Metabolism ◽  
Protein Interactions ◽  
Fungal Pathogens ◽  
Metabolic Regulation ◽  
Specific Binding ◽  
Genetic Regulation ◽  
Nitrogen Sources ◽  
Specific Protein ◽  
Genes Encoding ◽  
Gata Family

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.

Complete genome sequence ofParacoccus denitrificansATCC 19367 and its denitrification characteristics

2019 ◽  
Vol 65 (7) ◽  
pp. 486-495 ◽  
Author(s):  
Yuan-yuan Si ◽  
Kai-hang Xu ◽  
Xiang-yong Yu ◽  
Mei-fang Wang ◽  
Xing-han Chen
Keyword(s):  
Nitrogen Metabolism ◽  
Genome Sequence ◽  
Complete Genome ◽  
Paracoccus Denitrificans ◽  
Nitrogen Sources ◽  
Trna Genes ◽  
Protein Coding ◽  
Aerobic Conditions ◽  
Practical Applications ◽  
Protein Coding Genes

Studies show that Paracoccus denitrificans can denitrify nitrogen sources under aerobic conditions. However, the lack of data on its genome sequence has restricted molecular studies and practical applications. In this study, the complete genome of P. denitrificans ATCC 19367 was sequenced and its nitrogen metabolism properties were characterized. The size of the whole genome is 5 242 327 bp, with two chromosomes and one plasmid. The average G + C content is 66.8%, and it contains 5308 protein-coding genes, 54 tRNA genes, and nine rRNA operons. Among the protein-coding genes, 71.35% could be assigned to the Gene Ontology (GO) pathway, 86.66% to the Clusters of Orthologous Groups (COG) pathway, and 50.57% to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Comparative genome analysis between P. denitrificans ATCC 19367 and P. denitrificans PD1222 revealed that there are 428 genes specific to ATCC 19367 and 4738 core genes. Furthermore, the expression of genes related to denitrification, biofilm formation, and nitrogen metabolism (nar, nir, and nor) by P. denitrificans ATCC 19367 under aerobic conditions was affected by incubation time and shaking speed. This study elucidates the genomic background of P. denitrificans ATCC 19367 and suggests the possibility of controlling nitrogen pollution in the environment by using this bacterium.

scholarly journals The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

2015 ◽  
Vol 112 (45) ◽  
pp. E6243-E6252 ◽  
Author(s):  
Stephan Klähn ◽  
Christoph Schaal ◽  
Jens Georg ◽  
Desirée Baumgartner ◽  
Gernot Knippen ◽  
...  
Keyword(s):  
Glutamine Synthetase ◽  
Nitrogen Metabolism ◽  
Nitrogen Assimilation ◽  
Nitrogen Sources ◽  
Transcriptome Profiling ◽  
Site Directed Mutagenesis ◽  
Reporter System ◽  
Available Nitrogen ◽  
Mrna Accumulation

Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress-induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellularSynechocystissp. PCC 6803 and in the filamentous, nitrogen-fixingAnabaenasp. PCC 7120 is stimulated through nitrogen limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling on pulse overexpression, and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5′UTR ofgifAmRNA, which encodes glutamine synthetase inactivating factor (IF)7. InSynechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation ofgifA(IF7) mRNA accumulation influenced the glutamine pool and thusNH4+assimilation via GS. As a second target, we identifiedssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between WT and an ΔnsiR4KO mutant showed that the lack of NsiR4 led to decreased acclimation capabilities ofSynechocystistoward oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is, to our knowledge, the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.

scholarly journals Roles of Glutamate Synthase, gltBD, and gltF in Nitrogen Metabolism of Escherichia coli and Klebsiella aerogenes

2001 ◽  
Vol 183 (22) ◽  
pp. 6607-6619 ◽  
Author(s):  
Thomas J. Goss ◽  
Ana Perez-Matos ◽  
Robert A. Bender
Keyword(s):  
Escherichia Coli ◽  
Nitrogen Metabolism ◽  
Glutamate Synthase ◽  
Nitrogen Sources ◽  
Enteric Bacteria ◽  
The Other ◽  
Klebsiella Aerogenes ◽  
E Coli ◽  
Glutamine Synthesis ◽  
Subsequent Failure

ABSTRACT Mutants of Escherichia coli and Klebsiella aerogenes that are deficient in glutamate synthase (glutamate-oxoglutarate amidotransferase [GOGAT]) activity have difficulty growing with nitrogen sources other than ammonia. Two models have been proposed to account for this inability to grow. One model postulated an imbalance between glutamine synthesis and glutamine degradation that led to a repression of the Ntr system and the subsequent failure to activate transcription of genes required for the use of alternative nitrogen sources. The other model postulated that mutations in gltB or gltD (which encode the subunits of GOGAT) were polar on a downstream gene,gltF, which is necessary for proper activation of gene expression by the Ntr system. The data reported here show that thegltF model is incorrect for three reasons: first, a nonpolar gltB and a polar gltD mutation of K. aerogenes both show the same phenotype; second,K. aerogenes and several other enteric bacteria lack a gene homologous to gltF; and third, mutants of E. coli whose gltF gene has been deleted show no defect in nitrogen metabolism. The argument that accumulated glutamine represses the Ntr system in gltB or gltDmutants is also incorrect, because these mutants can derepress the Ntr system normally so long as sufficient glutamate is supplied. Thus, we conclude that gltB or gltD mutants grow slowly on many poor nitrogen sources because they are starved for glutamate. Much of the glutamate formed by catabolism of alternative nitrogen sources is converted to glutamine, which cannot be efficiently converted to glutamate in the absence of GOGAT activity. Finally, GOGAT-deficient E. coli cells growing with glutamine as the sole nitrogen source increase their synthesis of the other glutamate-forming enzyme, glutamate dehydrogenase, severalfold, but this is still insufficient to allow rapid growth under these conditions.

scholarly journals A mixed nitrogen diet and compartmentalized utilization for Mycobacterium tuberculosis replicating in host cells: results of a systems-based analysis

2019 ◽  
Author(s):  
Khushboo Borah ◽  
Martin Beyss ◽  
Axel Theorell ◽  
Huihai Wu ◽  
Piyali Basu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Mycobacterium Tuberculosis ◽  
Nitrogen Source ◽  
Nitrogen Metabolism ◽  
Nitrogen Sources ◽  
Spectral Ratio ◽  
Host Cells ◽  
Ratio Analysis ◽  
Nitrogen Donor

Nitrogen metabolism of Mycobacterium tuberculosis (Mtb) is crucial for the survival and virulence of this pathogen inside host macrophages but little is known about the nitrogen sources acquired from the host or their route of assimilation. Here we performed a systems-based analysis of nitrogen metabolism in intracellullar Mtb and developed 15N-Flux Spectral Ratio Analysis (FSRA) to probe the metabolic cross-talk between the host cell and Mtb. We demonstrate that intracellular Mtb acquires nitrogen from multiple amino acids in the macrophage including glutamate, glutamine, aspartate, alanine, glycine and valine, with glutamine being the predominant nitrogen donor. Each nitrogen source is uniquely assimilated into specific intracellular pools indicating compartmentalised metabolism. This was not observed for in vitro-grown Mtb indicating that there is a switch in nitrogen metabolism when the pathogen enters the intracellular environment. These results provide clues about the potential metabolic targets for development of innovative anti-tuberculosis therapies.

scholarly journals Isolation and characterization of mutants of the facultative methylotroph Arthrobacter P1 blocked in one-carbon metabolism

1987 ◽  
Vol 146 (4) ◽  
pp. 346-352 ◽  
Author(s):  
P. R. Levering ◽  
L. Tiesma ◽  
J. P. Woldendorp ◽  
M. Steensma ◽  
L. Dijkhuizen
Keyword(s):  
Carbon Metabolism ◽  
Arthrobacter P1 ◽  
Facultative Methylotroph ◽  
Isolation And Characterization ◽  
One Carbon Metabolism

scholarly journals Role of GlnR in Controlling Expression of Nitrogen Metabolism Genes in Listeria monocytogenes

2020 ◽  
Vol 202 (19) ◽  
Author(s):  
Rajesh Biswas ◽  
Abraham L. Sonenshein ◽  
Boris R. Belitsky
Keyword(s):  
Listeria Monocytogenes ◽  
Nitrogen Metabolism ◽  
Transcriptional Regulator ◽  
Nitrogen Sources ◽  
Negative Regulator ◽  
Ammonium Uptake ◽  
Ammonium Transport ◽  
Growth Media ◽  
Content Type

ABSTRACT Listeria monocytogenes is a fastidious bacterial pathogen that can utilize only a limited number of nitrogen sources for growth. Both glutamine and ammonium are common nitrogen sources used in listerial defined growth media, but little is known about the regulation of their uptake or utilization. The functional role of L. monocytogenes GlnR, the transcriptional regulator of nitrogen metabolism genes in low-G+C Gram-positive bacteria, was determined using transcriptome sequencing and real-time reverse transcription-PCR experiments. The GlnR regulon included transcriptional units involved in ammonium transport (amtB glnK) and biosynthesis of glutamine (glnRA) and glutamate (gdhA) from ammonium. As in other bacteria, GlnR proved to be an autoregulatory repressor of the glnRA operon. Unexpectedly, GlnR was most active during growth with ammonium as the nitrogen source and less active in the glutamine medium, apparently because listerial cells perceive growth with glutamine as a nitrogen-limiting condition. Therefore, paradoxically, expression of the glnA gene, encoding glutamine synthetase, was highest in the glutamine medium. For the amtB glnK operon, GlnR served as both a negative regulator in the presence of ammonium and a positive regulator in the glutamine medium. The gdhA gene was subject to a third mode of regulation that apparently required an elevated level of GlnR for repression. Finally, activity of glutamate dehydrogenase encoded by the gdhA gene appeared to correlate inversely with expression of gltAB, the operon that encodes the other major glutamate-synthesizing enzyme, glutamate synthase. Both gdhA and amtB were also regulated, in a negative manner, by the global transcriptional regulator CodY. IMPORTANCE L. monocytogenes is a widespread foodborne pathogen. Nitrogen-containing compounds, such as the glutamate-containing tripeptide, glutathione, and glutamine, have been shown to be important for expression of L. monocytogenes virulence genes. In this work, we showed that a transcriptional regulator, GlnR, controls expression of critical listerial genes of nitrogen metabolism that are involved in ammonium uptake and biosynthesis of glutamine and glutamate. A different mode of GlnR-mediated regulation was found for each of these three pathways.

scholarly journals Expanded Role for the Nitrogen Assimilation Control Protein in the Response of Klebsiella pneumoniae to Nitrogen Stress

2010 ◽  
Vol 192 (19) ◽  
pp. 4812-4820 ◽  
Author(s):  
Ryan L. Frisch ◽  
Robert A. Bender
Keyword(s):  
Growth Rate ◽  
Stress Response ◽  
Klebsiella Pneumoniae ◽  
Nitrogen Metabolism ◽  
Nitrogen Limitation ◽  
Nitrogen Assimilation ◽  
Nitrogen Sources ◽  
Nitrogen Stress ◽  
A Genome ◽  
Regulated Promoters

ABSTRACT Klebsiella pneumoniae is able to utilize many nitrogen sources, and the utilization of some of these nitrogen sources is dependent on the nitrogen assimilation control (NAC) protein. Seven NAC-regulated promoters have been characterized in K. pneumoniae, and nine NAC-regulated promoters have been found by microarray analysis in Escherichia coli. So far, all characterized NAC-regulated promoters have been directly related to nitrogen metabolism. We have used a genome-wide analysis of NAC binding under nitrogen limitation to identify the regions of the chromosome associated with NAC in K. pneumoniae. We found NAC associated with 99 unique regions of the chromosome under nitrogen limitation. In vitro, 84 of the 99 regions associate strongly enough with purified NAC to produce a shifted band by electrophoretic mobility shift assay. Primer extension analysis of the mRNA from genes associated with 17 of the fragments demonstrated that at least one gene associated with each fragment was NAC regulated under nitrogen limitation. The large size of the NAC regulon in K. pneumoniae indicates that NAC plays a larger role in the nitrogen stress response than it does in E. coli. Although a majority of the genes with identifiable functions that associated with NAC under nitrogen limitation are involved in nitrogen metabolism, smaller subsets are associated with carbon and energy acquisition (18 genes), and growth rate control (10 genes). This suggests an expanded role for NAC regulation during the nitrogen stress response, where NAC not only regulates genes involved in nitrogen metabolism but also regulates genes involved in balancing carbon and nitrogen pools and growth rate.

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