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glnK Nitrogen

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https://www.readbyqxmd.com/read/29515895/a-biomolecular-proportional-integral-controller-based-on-feedback-regulations-of-protein-level-and-activity
#1
Francis Mairet
Homeostasis is the capacity of living organisms to keep internal conditions regulated at a constant level, despite environmental fluctuations. Integral feedback control is known to play a key role in this behaviour. Here, I show that a feedback system involving transcriptional and post-translational regulations of the same executor protein acts as a proportional integral (PI) controller, leading to enhanced transient performances in comparison with a classical integral loop. Such a biomolecular controller-which I call a level and activity-PI controller (LA-PI)-is involved in the regulation of ammonium uptake by Escherichia coli through the transporter AmtB...
February 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/28900375/expression-and-purification-of-untagged-glnk-proteins-from-actinobacteria
#2
Edileusa C M Gerhardt, Vivian R Moure, Andrey W Souza, Fabio O Pedrosa, Emanuel M Souza, Lautaro Diacovich, Hugo Gramajo, Luciano F Huergo
The PII protein family constitutes one of the most conserved and well distributed family of signal transduction proteins in nature. These proteins play key roles in nitrogen and carbon metabolism. PII function has been well documented in Gram-negative bacteria. However, there are very few reports describing the in vitro properties and function of PII derived from Gram-positive bacteria. Here we present the heterologous expression and efficient purification protocols for untagged PII from three Actinobacteria of medical and biotechnological interest namely: Mycobacterium tuberculosis, Rhodococcus jostii and Streptomyces coelicolor...
2017: EXCLI journal
https://www.readbyqxmd.com/read/28620026/learning-to-read-and-write-in-evolution-from-static-pseudoenzymes-and-pseudosignalers-to-dynamic-gear-shifters
#3
REVIEW
Abulikemu Abudukelimu, Thierry D G A Mondeel, Matteo Barberis, Hans V Westerhoff
We present a systems biology view on pseudoenzymes that acknowledges that genes are not selfish: the genome is. With network function as the selectable unit, there has been an evolutionary bonus for recombination of functions of and within proteins. Many proteins house a functionality by which they 'read' the cell's state, and one by which they 'write' and thereby change that state. Should the writer domain lose its cognate function, a 'pseudoenzyme' or 'pseudosignaler' arises. GlnK involved in Escherichia coli ammonia assimilation may well be a pseudosignaler, associating 'reading' the nitrogen state of the cell to 'writing' the ammonium uptake activity...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28538158/glnk-facilitates-the-dynamic-regulation-of-bacterial-nitrogen-assimilation
#4
Adam Gosztolai, Jörg Schumacher, Volker Behrends, Jacob G Bundy, Franziska Heydenreich, Mark H Bennett, Martin Buck, Mauricio Barahona
Ammonium assimilation in Escherichia coli is regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins, and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase, the key enzyme for nitrogen assimilation, is poorly understood. We combine experiments and theory to study the dynamic roles of GlnB and GlnK during nitrogen starvation and upshift. We measure time-resolved in vivo concentrations of metabolites, total and posttranslationally modified proteins, and develop a concise biochemical model of GlnB and GlnK that incorporates competition for active and allosteric sites, as well as functional sequestration of GlnK...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28291750/similarities-in-the-structure-of-the-transcriptional-repressor-amtr-in-two-different-space-groups-suggest-a-model-for-the-interaction-with-glnk
#5
Madhumati Sevvana, Kristin Hasselt, Florian C Grau, Andreas Burkovski, Yves A Muller
AmtR belongs to the TetR family of transcription regulators and is a global nitrogen regulator that is induced under nitrogen-starvation conditions in Corynebacterium glutamicum. AmtR regulates the expression of transporters and enzymes for the assimilation of ammonium and alternative nitrogen sources, for example urea, amino acids etc. The recognition of operator DNA by homodimeric AmtR is not regulated by small-molecule effectors as in other TetR-family members but by a trimeric adenylylated PII -type signal transduction protein named GlnK...
March 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27965651/interaction-between-nitrogen-and-phosphate-stress-responses-in-sinorhizobium-meliloti
#6
Kelly L Hagberg, Svetlana N Yurgel, Monika Mulder, Michael L Kahn
Bacteria have developed various stress response pathways to improve their assimilation and allocation of limited nutrients, such as nitrogen and phosphate. While both the nitrogen stress response (NSR) and phosphate stress response (PSR) have been studied individually, there are few experiments reported that characterize effects of multiple stresses on one or more pathways in Sinorhizobium meliloti, a facultatively symbiotic, nitrogen-fixing bacteria. The PII proteins, GlnB and GlnK, regulate the NSR activity, but analysis of global transcription changes in a PII deficient mutant suggest that the S...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27833596/interaction-of-the-nitrogen-regulatory-protein-glnb-p-ii-with-biotin-carboxyl-carrier-protein-bccp-controls-acetyl-coa-levels-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#7
Waldemar Hauf, Katharina Schmid, Edileusa C M Gerhardt, Luciano F Huergo, Karl Forchhammer
The family of PII signal transduction proteins (members GlnB, GlnK, NifI) plays key roles in various cellular processes related to nitrogen metabolism at different functional levels. Recent studies implied that PII proteins may also be involved in the regulation of fatty acid metabolism, since GlnB proteins from Proteobacteria and from Arabidopsis thaliana were shown to interact with biotin carboxyl carrier protein (BCCP) of acetyl-CoA carboxylase (ACC). In case of Escherichia coli ACCase, this interaction reduces the kcat of acetyl-CoA carboxylation, which should have a marked impact on the acetyl-CoA metabolism...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27677556/features-of-gene-expression-of-bacillus-pumilus-metalloendopeptidase
#8
N L Rudakova, A R Sabirova, N P Balaban, A O Tikhonova, M R Sharipova
Features of gene expression of the secreted Bacillus pumilus metalloendopeptidase belonging to the adamalysin/reprolysin family were investigated. In the regulatory region of the gene, we identified hypothetical binding sites for transcription factors CcpA and TnrA. We found that the expression of the metalloendopeptidase gene is controlled by mechanisms of carbon and nitrogen catabolite repression. In experiments involving nitrogen metabolism regulatory protein mutant strains, we found that the control of the metalloendopeptidase gene expression involves proteins of ammonium transport GlnK and AmtB interacting with the TnrA-regulator...
August 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/26744254/structure-of-amtr-the-global-nitrogen-regulator-of-corynebacterium-glutamicum-in-free-and-dna-bound-forms
#9
Carles Palanca, Vicente Rubio
UNLABELLED: Corynebacterium glutamicum is a bacterium used for industrial amino acid production, and understanding its metabolic pathway regulation is of high biotechnological interest. Here, we report crystal structures of AmtR, the global nitrogen regulator of C. glutamicum, in apo (2.25-Å and 2.65-Å resolution) and DNA-bound (3-Å resolution) forms. These structures reveal an all-α homodimeric TetR family regulator composed of a helix-turn-helix-hosting N-terminal DNA-binding domain and a C-terminal dimerization domain...
March 2016: FEBS Journal
https://www.readbyqxmd.com/read/26699934/isotopologue-profiling-of-the-listerial-n-metabolism
#10
Erika Kutzner, Tanja Kern, Angela Felsl, Wolfgang Eisenreich, Thilo M Fuchs
The nitrogen (N-) sources and the relative contribution of a nitrogenous nutrient to the N-pool of the gram-positive pathogen Listeria monocytogenes are largely unknown. Therefore, (15) N-isotopologue profiling was established to study the N-metabolism of L. monocytogenes. The pathogen was grown in a defined minimal medium supplemented with potential (15) N-labeled nutrients. The bacteria were harvested and hydrolysed under acidic conditions, and the resulting amino acids were analysed by GC-MS, revealing (15) N-enrichments and isotopomeric compositions of amino acids...
April 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/26443371/ammonia-transport
#11
Ned S Wingreen
This review reviews the ammonium/methylammonium transport (Amt) proteins of Escherichia coli and Salmonella enterica serovar Typhimurium. The Amt proteins and their homologs, the methylammonium/ammonium permease proteins of Saccharomyces cerevisiae, constitute a distinct class of membrane-associated ammonia transporters. Members of the Amt family are found in archaea, bacteria, fungi, plants, and invertebrate animals. In E. coli and serovar Typhimurium, the Amt proteins are essential to maintain maximal growth at low concentrations of ammonia, the preferred nitrogen source...
December 2004: EcoSal Plus
https://www.readbyqxmd.com/read/26433003/2-oxoglutarate-levels-control-adenosine-nucleotide-binding-by-herbaspirillum-seropedicae-pii-proteins
#12
Marco A S Oliveira, Edileusa C M Gerhardt, Luciano F Huergo, Emanuel M Souza, Fábio O Pedrosa, Leda S Chubatsu
Nitrogen metabolism in Proteobacteria is controlled by the Ntr system, in which PII proteins play a pivotal role, controlling the activity of target proteins in response to the metabolic state of the cell. Characterization of the binding of molecular effectors to these proteins can provide information about their regulation. Here, the binding of ATP, ADP and 2-oxoglutarate (2-OG) to the Herbaspirillum seropedicae PII proteins, GlnB and GlnK, was characterized using isothermal titration calorimetry. Results show that these proteins can bind three molecules of ATP, ADP and 2-OG with homotropic negative cooperativity, and 2-OG binding stabilizes the binding of ATP...
December 2015: FEBS Journal
https://www.readbyqxmd.com/read/26432339/dna-microarray-analysis-of-the-cyanotroph-pseudomonas-pseudoalcaligenes-cect5344-in-response-to-nitrogen-starvation-cyanide-and-a-jewelry-wastewater
#13
V M Luque-Almagro, M P Escribano, I Manso, L P Sáez, P Cabello, C Moreno-Vivián, M D Roldán
Pseudomonas pseudoalcaligenes CECT5344 is an alkaliphilic bacterium that can use cyanide as nitrogen source for growth, becoming a suitable candidate to be applied in biological treatment of cyanide-containing wastewaters. The assessment of the whole genome sequence of the strain CECT5344 has allowed the generation of DNA microarrays to analyze the response to different nitrogen sources. The mRNA of P. pseudoalcaligenes CECT5344 cells grown under nitrogen limiting conditions showed considerable changes when compared against the transcripts from cells grown with ammonium; up-regulated genes were, among others, the glnK gene encoding the nitrogen regulatory protein PII, the two-component ntrBC system involved in global nitrogen regulation, and the ammonium transporter-encoding amtB gene...
November 20, 2015: Journal of Biotechnology
https://www.readbyqxmd.com/read/26176311/effect-of-point-mutations-on-herbaspirillum-seropedicae-nifa-activity
#14
B Aquino, A A Stefanello, M A S Oliveira, F O Pedrosa, E M Souza, R A Monteiro, L S Chubatsu
NifA is the transcriptional activator of the nif genes in Proteobacteria. It is usually regulated by nitrogen and oxygen, allowing biological nitrogen fixation to occur under appropriate conditions. NifA proteins have a typical three-domain structure, including a regulatory N-terminal GAF domain, which is involved in control by fixed nitrogen and not strictly required for activity, a catalytic AAA+ central domain, which catalyzes open complex formation, and a C-terminal domain involved in DNA-binding. In Herbaspirillum seropedicae, a β-proteobacterium capable of colonizing Graminae of agricultural importance, NifA regulation by ammonium involves its N-terminal GAF domain and the signal transduction protein GlnK...
August 2015: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/25691471/structures-of-regulatory-machinery-reveal-novel-molecular-mechanisms-controlling-b-subtilis-nitrogen-homeostasis
#15
Maria A Schumacher, Naga Babu Chinnam, Bonnie Cuthbert, Nam K Tonthat, Travis Whitfill
All cells must sense and adapt to changing nutrient availability. However, detailed molecular mechanisms coordinating such regulatory pathways remain poorly understood. In Bacillus subtilis, nitrogen homeostasis is controlled by a unique circuitry composed of the regulator TnrA, which is deactivated by feedback-inhibited glutamine synthetase (GS) during nitrogen excess and stabilized by GlnK upon nitrogen depletion, and the repressor GlnR. Here we describe a complete molecular dissection of this network. TnrA and GlnR, the global nitrogen homeostatic transcription regulators, are revealed as founders of a new structural family of dimeric DNA-binding proteins with C-terminal, flexible, effector-binding sensors that modulate their dimerization...
February 15, 2015: Genes & Development
https://www.readbyqxmd.com/read/25566239/association-and-dissociation-of-the-glnk-amtb-complex-in-response-to-cellular-nitrogen-status-can-occur-in-the-absence-of-glnk-post-translational-modification
#16
Martha V Radchenko, Jeremy Thornton, Mike Merrick
PII proteins are pivotal players in the control of nitrogen metabolism in bacteria and archaea, and are also found in the plastids of plants. PII proteins control the activities of a diverse range of enzymes, transcription factors and membrane transport proteins, and their regulatory effect is achieved by direct interaction with their target. Many, but by no means all, PII proteins are subject to post-translational modification of a residue within the T-loop of the protein. The protein's modification state is influenced by the cellular nitrogen status and in the past this has been considered to regulate PII activity by controlling interaction with target proteins...
2014: Frontiers in Microbiology
https://www.readbyqxmd.com/read/25557370/the-bacterial-signal-transduction-protein-glnb-regulates-the-committed-step-in-fatty-acid-biosynthesis-by-acting-as-a-dissociable-regulatory-subunit-of-acetyl-coa-carboxylase
#17
Edileusa C M Gerhardt, Thiago E Rodrigues, Marcelo Müller-Santos, Fabio O Pedrosa, Emanuel M Souza, Karl Forchhammer, Luciano F Huergo
Biosynthesis of fatty acids is one of the most fundamental biochemical pathways in nature. In bacteria and plant chloroplasts, the committed and rate-limiting step in fatty acid biosynthesis is catalyzed by a multi-subunit form of the acetyl-CoA carboxylase enzyme (ACC). This enzyme carboxylates acetyl-CoA to produce malonyl-CoA, which in turn acts as the building block for fatty acid elongation. In Escherichia coli, ACC is comprised of three functional modules: the biotin carboxylase (BC), the biotin carboxyl carrier protein (BCCP) and the carboxyl transferase (CT)...
March 2015: Molecular Microbiology
https://www.readbyqxmd.com/read/24846646/structure-and-thermodynamics-of-effector-molecule-binding-to-the-nitrogen-signal-transduction-pii-protein-glnz-from-azospirillum-brasilense
#18
Daphné Truan, Saša Bjelić, Xiao-Dan Li, Fritz K Winkler
The trimeric PII signal transduction proteins regulate the function of a variety of target proteins predominantly involved in nitrogen metabolism. ATP, ADP and 2-oxoglutarate (2-OG) are key effector molecules influencing PII binding to targets. Studies of PII proteins have established that the 20-residue T-loop plays a central role in effector sensing and target binding. However, the specific effects of effector binding on T-loop conformation have remained poorly documented. We present eight crystal structures of the Azospirillum brasilense PII protein GlnZ, six of which are cocrystallized and liganded with ADP or ATP...
July 29, 2014: Journal of Molecular Biology
https://www.readbyqxmd.com/read/24801548/temperature-and-nitrogen-source-dependent-regulation-of-glnr-target-genes-in-listeria-monocytogenes
#19
Daniela Kaspar, Franziska Auer, Jakob Schardt, Franziska Schindele, Alberto Ospina, Claudia Held, Armin Ehrenreich, Siegfried Scherer, Stefanie Müller-Herbst
The ubiquitous pathogen Listeria monocytogenes lives either saprophytically in the environment or within cells in a vertebrate host, thus adapting its lifestyle to its ecological niche. Growth experiments at 24 and 37 °C (environmental and host temperature) with ammonium or glutamine as nitrogen sources revealed that ammonium is the preferred nitrogen source of L. monocytogenes. Reduced growth on glutamine is more obvious at 24 °C. Global transcriptional microarray analyses showed that the most striking difference in temperature-dependent transcription was observed for central nitrogen metabolism genes, glnR (glutamine synthetase repressor GlnR), glnA (glutamine synthetase GlnA), amtB (ammonium transporter AmtB), glnK (PII regulatory protein GlnK), and gdh (glutamate dehydrogenase) when cells were grown on glutamine...
June 2014: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/24610852/nitrogen-utilization-and-metabolism-in-ruminococcus-albus-8
#20
Jong Nam Kim, Emily Decrescenzo Henriksen, Isaac K O Cann, Roderick I Mackie
The model rumen Firmicutes organism Ruminococcus albus 8 was grown using ammonia, urea, or peptides as the sole nitrogen source; growth was not observed with amino acids as the sole nitrogen source. Growth of R. albus 8 on ammonia and urea showed the same growth rate (0.08 h(-1)) and similar maximum cell densities (for ammonia, the optical density at 600 nm [OD600] was 1.01; and for urea, the OD600 was 0.99); however, growth on peptides resulted in a nearly identical growth rate (0.09 h(-1)) and a lower maximum cell density (OD600 = 0...
May 2014: Applied and Environmental Microbiology
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